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    2024-06:
    01 윤미선  
    01 조민아  
    08 이시은  
    08 안세환  
    15 유준기  
    15 임성수  
    22 권호식  
    22 차재현  
    29 최선  
    29 문성희  

    2024-05:
    04 최선  
    04 안세환  
    11 유준기  
    11 문성희  
    18 권호식  
    18 차재현  
    25 전예진  
    25 부은경  

    2024-04:
    06 전예진 Deep learning-based phenotype imputation on population-scale biobank data     
    06 윤미선 A cost-effective sequencing method for genetic studies combining high-depth whole exome and low-depth whole genome    
    13 차재현 Evaluation of Somatic Mutations in Solid Metastatic Pan-Cancer Patients    
    13 최선 Explainable multi-task learning for multimodality biological data analysis    
    20 부은경 Multi-ancestry genome-wide association meta-analysis of Parkinsons disease    
    20 조민아 Uncovering genetic associations in the human diseasome using an endophenotype-augmented disease network    
    27 이시은 Association between glycemic variability and shor    
    27 임성수 Drug ranking using machine learning systematically predicts the efficacy of anti-cancer drugs    

    2024-03:
    02 차재현 Genomic landscape and prognosis of patients with TP53-mutated non-small cell lung cancer    
    02 전예진 Transforming and evaluating the UK Biobank to the OMOP CDM for COVID research    
    09 윤미선 Genome-wide prediction of disease variant effects with a deep protein language model    
    09 조민아 Genomic data in the All of Us Research Program    
    16 부은경 Inferring compound heterozygosity from large-scale exome sequencing data    
    16 유준기 Genome-wide analyses reveal the contribution of somatic variants to the immune landscape of multiple cancer types    
    23 임성수 Gene expression based inference of cancer drug sensitivity    
    23 이시은 Feasibility Study of Federated Learning on the Distributed Research Network of OMOP Common Data Model    
    30 안세환 Empowering personalized pharmacogenomics with generative AI solutions    
    30 권호식 CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server    

    2024-02:
    03 이시은 Federated Medical Learning Framework Based on Blockchain and Homomorphic Encryption    
    03 안세환 Integrating rare genetic variants into DPYD pharmacogenetic testing may help preventing fluoropyrimidine-induced toxicity    
    10 ...  
    10 ...  
    17 권호식 The burden of splice-disrupting variants in inherited heart disease and unexplained sudden cardiac death    
    17 최선 Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps    
    24 유준기 cLD Rare variant linkage disequilibrium between genomic regions identifies novel genomic interactions    
    24 임성수 Disease clusters subsequent to anxiety and stress-related disorders    

    2024-01:
    06 임성수 Synthetic lethality across normal tissues is strongly associated with cancer risk, onset, and tumor suppressor specificity    
    06 차재현 Macrophage-Related SPP1 as a Potential Biomarker for Early Lymph Node Metastasis in Lung Adenocarcinoma 
    13 전예진 the effect of CYP2C19 genotype on proxies of SSRI antidepressant response in the uk biobank    
    13 권호식 DNA Sequencing to Detect Residual Disease in Adults With Acute Myeloid Leukemia Prior to Hematopoietic Cell Transplant    
    20 윤미선 Genome-wide association study on pharmacological outcomes of musculoskeletal pain in UK Biobank    
    20 최선 Development of a human genetics-guided priority score for 19,365 genes and 399 drug indications    
    27 부은경 Network-guided search for genetic heterogeneity between gene pairs     
    27 조민아 The multiplex network of human diseases    

    2023-12:
    02 최선 Clustering of critically ill patients using an individualized learning approach enables dose optimization of mobilization in the ICU    
    02 윤미선 Populational pan-ethnic screening panel enabled by deep whole genome sequencing     
    09 차재현 An integrative analysis of the age-associated multi-omic landscape across cancers    
    09 부은경 Phenotype integration improves power and preserves specificity in biobank-based genetic studies of major depressive disorder    
    16 전예진 Multivariate genome-wide analysis of aging&    
    16 이시은 DNA language models are powerful predictors of genome-wide variant effects    
    23 조민아 Visualizing novel connections and genetic similarities across diseases using a network-medicine based approach    
    23 안세환 Frequencies of pharmacogenomic alleles across biogeographic groups in a large-scale biobank    
    30 배소정 Genome-wide Association Study of Susceptibility to Respiratory Syncytial Virus Hospitalization in Young Children <5 Years of age    
    30 유준기 Identification of Ferroptosis-Related Genes in Alzheimer's Disease Based on Bioinformatic analysis    

    2023-11:
    04 이시은 Medical informatics and digital health multilingual ontology (MIMO): A tool to improve international collaborations     
    04 배소정 Assessment of significance of conditionally independent GWAS signals    
    11 부은경 Age-dependent topic modeling of comorbidities in UK Biobank identifies disease subtypes with differential genetic risk    
    11 조민아 Mexican Biobank advances population and medical genomics of diverse ancestries    
    18 임성수 Mapping the landscape of synthetic lethal interactions in liver cancer    
    18 유준기 Global analysis of suppressor mutations that rescue human genetic defects    
    25 안세환 Deep mutational scanning of CYP2C19 reveals a substrate specificity-abundance tradeoff    
    25 권호식 Systematic pan-cancer analysis of mutation-treatment interactions using large real-world clinicogenomics data    

    2023-10:
    07 이시은 Novel loci for Alzheimers disease identified by a genome-wide association study in Ashkenazi Jews    
    07 안세환 Structural variation of the coding and non-coding human pharmacogenome    
    14 최선 Llama 2: Open Foundation and Fine-Tuned Chat Models    
    14 권호식 Germline rare deleterious variant load alters cancer risk, age of onset and tumor characteristics    
    21 임성수 A pan-cancer analysis of PBAF complex mutations and their association with immunotherapy response    
    21 윤미선 HLA-DQA1*05 and upstream variants of PPARGC1B are associated with infliximab persistence in Japanese Crohns disease patients    
    28 차재현 Detection of somatic structural variants from short-read next-generation sequencing data    
    28 전예진 Drug- Induced Liver Injury with Commonly Used Antibiotics in the All of Us Research Program    

    2023-09:
    02 최선 PhenoScore quantifies phenotypic variation for rare genetic diseases by combining facial analysis with other clinical features using a machine-learning framework    
    02 차재현 Large mosaic cnv confer autism risk    
    09 윤미선 Assessment of clinically actionable pharmacogenetic markers to stratify anti-seizure medications    
    09 배소정 Genome-wide association study identifies new loci associated with risk of HBV infection and disease progression    
    16 부은경 Extremely sparse models of linkage disequilibrium in ancestrally diverse association studies    
    16 조민아 Genetic Structure and Forensic Feature of 38 X-Chromosome InDels in the Henan Han Chinese Population    
    23 유준기 Allelic imbalance of chromatin accessibility in cancer identifies candidate causal risk variants and their mechanisms    
    23 전예진 Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome    
    30 ... ߼ 
    30 ... ߼ 

    2023-08:
    05 부은경 Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases    
    05 차재현 Sex-dependent shared and nonshared Genetic Architecture across mood and psychotic disorders    
    12 안세환 Chracterizing the combined effects of cytochrome P450 missense variation within star allele definitions    
    12 권호식 Single-cell transcriptome profiling of the stepwise progression of head and neck cancer    
    19 조민아 A powerful method for pleiotropic analysis under composite null hypothesis identifies novel shared loci between Type 2 Diabetes and Prostate Cancer    
    19 배소정 Genome-wide study on 72,298 individuals in Korean biobank data for 76 traits     
    26 임성수 Identification of core genes and pathways in melanoma metastasis via bioinformatics analysis    
    26 유준기 An allelic-series rare-variant association test for candidate-gene discovery    

    2023-07:
    01 조민아 From gene to dose: Long-read sequencing and *-allele tools to refine phenotype predictions of CYP2C19    
    01 배소정 A cross-population atlas of genetic associations for 220 human phenotypes    
    08 임성수 Harnessing synthetic lethality to predict the response to cancer treatment    
    08 유준기 Prioritizing autoimmunity risk variants for functional analyses by fine-mapping mutations under natural selection    
    15 안세환 PharmaGScore scores of compound genetic variant burden for psychiatric treatment optimization    
    15 권호식 Cell type prioritization in single-cell data    
    22 최선 Medical Question Understanding and Answering with Knowledge Grounding and Semantic Self-Supervision    
    22 윤미선 The pharmacogenomic landscape of an Indigenous Australian population    
    29 이시은 Improving graph embeddings via entity linking: A case study on Italian clinical notes    
    29 전예진 Genetic validation of neurokinin 3 receptor antagonist for IHD prevention in men    

    2023-06:
    03 최선 biomedgpt 
    03 권호식 STOmicsDB: a database of Spatial Transcriptomic data    
    10 임성수 Synthetic lethality-mediated precision oncology via the tumor transcriptome    
    10 윤미선 Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity     
    17 부은경 Genetic studies of paired metabolomes reveal enzymatic and transport processes at the interface of plasma and urine    
    17 전예진 Assessing Digital Phenotyping to Enhance Genetic Studies of Human Diseases 
    24 이시은 Defining the distance between diseases using SNOMED CT embeddings    
    24 차재현 .    

    2023-05:
    06 배소정 Infectious disease outbreak prediction using machine learning articles with machine learning models    
    06 조민아 Participation bias in the UK Biobank distorts genetic associations and downstream analyses    
    13 부은경 Inference of chronic obstructive pulmonary disease with deep learning on raw spirograms identifies new genetic loci and improves risk models    
    13 안세환 A novel machine learning-based approach for the computational functional assessment of pharmacogenomic variants    
    20 이시은 The Effect of Genotyping on the Number of Pharmacotherapeutic Gene–Drug Interventions in Chronic Kidney Disease Patients    
    20 유준기 The genetic deteriminants of recurrent somatic mutations in 43,693 blood genomes    
    27 ... ó ų 
    27 ... ó ų 

    2023-04:
    01 이시은 Novel Genetic Variants Associated with Chronic Kidney Disease Progression    
    01 조민아 A comparison of the genes and genesets identified by GWAS and EWAS of fifteen complex traits    
    08 안세환 A unifying model to predict variable drug response for personalised medicine.    
    08 유준기 Identifying interpretable gene-biomarker associations with functionally informed kernel-based tests in 190,000 exomes    
    15 임성수 Clinical and bionarker analyses of sintilimab plus gemcitabine and cisplatin as first-line treatment for patients with advanced biliary tract cancer    
    15 권호식 Confronting false discoveries in single-cell differential expression    
    22 전예진 Global Biobank Meta-analysis Initiative_Powering genetic discovery across human disease    
    22 차재현 Single-nucleus gene and gene set expression-based similarity network fusion identifies autism molecular subtypes    
    29 최선 GPT4    
    29 윤미선  

    2023-03:
    04 권호식 Association of Genetic Ancestry and Molecular Signatures with Cancer Survival Disparities: A Pan-Cancer Analysis    
    04 유준기 Germline mutations in mitochondrial complex I reveal genetic and targetable vulnerability in IDH1-mutant acute myeloid leukaemia    
    11 최선 Language Is Not All You Need: Aligning Perception with Language Models    
    11 윤미선 Diffusion Models for Implicit Image Segmentation Ensembles    
    18 전예진 A 12-gene pharmacogenetic panel to prevent adverse drug reactions_an open-label, multicentre, controlled, cluster-randiomised crossover implementation study    
    18 조원일 Utility of long-read sequencing for All of Us    
    25 배소정 Single-cell RNA sequencing reveals a heterogeneous response to Glucocorticoids in breast cancer cells    
    25 부은경 Network expansion of genetic associations defines a pleiotropy map of human cell biology    

    2023-02:
    04 전예진 Association Between Antiepileptic Drugs and Incident Parkinson Disease in the UK Biobank    
    04 김나영 A State-of-the Art Review of SNOMED CT Terminology Binding and Recommendations for Practice and Research    
    11 부은경 Pairwise effects between lipid GWAS genes modulate lipid plasma levels and cellular uptake    
    11 ӿ Mono- and biallelic variant effects on disease at biobank scale    
    18 안세환 Identification and functional validation of novel pharmacogenomic variants using a next-generation sequencing-based approach for clinical pharmacogenomics    
    18 조민아 An Improved Phenotype-Driven Tool for Rare Mendelian Variant Prioritization: Benchmarking Exomiser on Real Patient Whole-Exome Data    
    25 이시은 Impact of SGLT2 inhibitors on old age patients with heart failure and chronic kidney disease    
    25 배소정 Genetic common variants associated with cerebellar volume and their overlap with mental disorders: a study on 33,265 individuals from the UK-Biobank    

    2023-01:
    07 배소정 The landscape of host genetic factors involved in immune response to common viral infections    
    07 조원일 Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants     
    14 유준기 The impact of rare germline variants on human somatic mutation processes    
    14 권호식 Computational comparison of common event based differential splicing tools    
    21 ...  
    21 ...  
    28 최선 Temporal phenotyping using Deep predictive clustering of disease progression    
    28 윤미선 Identification of pathogenic genes associated with CKD: An integrated bioinformatics approach    

    2022-12:
    03 부은경 An integral genomic signature approach for tailored cancer therapy using genome-wide sequencing data    
    03 권호식 Association of altered folylpolyglutamate synthetase pre-mRNA splicing with methotrexate unresponsiveness in early rheumatoid arthritis    
    10 최선 Association of Genome-Wide Polygenic Scores for Multiple Psychiatric and Common Traits in Preadolescent Youths at Risk of Suicide    
    10 김나영 Harvesting metadata in clinical care: a crosswalk between FHIR, OMOP, CDISC and openEHR metadata    
    17 윤미선 EagleImp: fast and accurate genome-wide phasing and imputation in a single tool    
    17 ӿ Genetic risk factors have a substantial impact on healthy life years     
    24 전예진 Loss of function, gain of function and dominant negative mutations have profoundly different effects on protein structure    
    24 조민아 Gene Size Matters: An Analysis of Gene Length in the Human Genome    
    31 안세환 Evaluating the frequency and the impact of pharmacogenetic alleles in an ancestrally diverse Biobank population    
    31 이시은 A pre-trained BERT for Korean medical natural language processing    

    2022-11:
    05 조원일 The genetic landscape of major drug metabolizing cytochrome P450 genes an updated analysis of population scale sequencing data     
    05 ӿ Pan-Cancer Analysis of Potential Synthetic Lethal Drug Targets Specific to Alterations in DNA Damage Response    
    12 정문경 Association of step counts over time with the risk of chronic disease in the All of Us Research Program    
    12 유준기 The mutational signatures of formalin fixation on the human genome    
    19 이시은 Extracting seizure frequency from epilepsy clinic notes: a machine reading approach to natural language processing    
    19 안세환 PharmaKU: A web-based tool aimed at improving outreach and clinical utility of pharmacogenomics    
    26 조민아 Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data    
    26 배소정 Frequency and Phenotype Associations of Rare Variants in 5 Monogenic Cerebral Small Vessel Disease Genes in 200,000 UK Biobank Participants     

    2022-10:
    01 배소정 Ultrafast search of all deposited bacterial and viral genomic data    
    01 안세환 Aldy 4:An efficient genotypes and star-allele caller for pharmacygenomics    
    08 유준기 Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics    
    08 권호식 Identification of differentially expressed genes in lung adenocarcinoma cells using single-cell RNA sequencing not detected using traditional RNA sequencing and microarray    
    15 ̿ Impact of integrating genomic data into the electronic health record on genetics care delivery    
    15 윤미선 Returning individual genomic results to population‑based cohort study participants with BRCA1/2 pathogenic variants    
    22 최선 MolTrans_Molecular Interaction Transformer for DTI prediction    
    22 전예진 Integrating rare genetic variants into pharmacogenetic drug response predictions    
    29 부은경 Integrative analysis of drug response and clinical outcome in acute myeloid leukemia    
    29 김나영 Harmonization and standardization of data for a pan-European cohort on SARS- CoV-2 pandemic    

    2022-09:
    03 김나영 CASIDE: A data model for interoperable cancer survivorship information based on FHIR    
    03 정문경 Recognizing Emotions among Couples Managing Diabetes in Daily Life using Multimodal Real-World Smartwatch Data    
    10 ... 추석 
    10 ... 추석 
    17 조원일 Genomewide pharmacogenetics of antidrug antibody response to bococizumab highlights key residues in HLA DRB1 and DQB1    
    17 이시은 Deep learning-based NLP data pipeline for EHR-scanned document information extraction    
    24 조민아 A Survey of Compound Heterozygous Variants in Pediatric Cancers and Structural Birth Defects    
    24 부은경 Large-scale sequencing identifies multiple genes and rare variants associated with Crohns disease susceptibility    

    2022-08:
    06 배소정 A genome-wide association study in a large community-based cohort identifies multiple loci associated with susceptibility to bacterial and viral infections    
    06 유준기 Rare genetic variability in human drug target genes modulates drug response and can guide precision medicine    
    13 권호식 Copy number variation is highly correlated with differential gene expression: a pan-cancer study    
    13 최선 Integrative multiomics-histopathology analysis for breast cancer classification    
    20 ̿ A pan cancer compendium of chromosomal instability    
    20 윤미선 Development of an extensive workflow for comprehensive clinical pharmacogenomic profiling: lessons from a pilot study on 100 whole exome sequencing data    
    27 전예진 Biobank Scale Pharmacogenomics Informs the Genetic Underpinnings of Simvastatin Use    
    27 ӿ Improved pathogenicity prediction for rare human missense variants    

    2022-07:
    02 이시은 Automatically disambiguating medical acronyms with ontology-aware deep learning 
    02 전예진 Combination of Genome-Wide Polymorphisms and CNVs of Pharmacogenes in Koreans    
    09 ӿ Identification of discriminative gene-level and protein-level features associated with pathogenic gain-of-function and loss-of-function variants     
    09 김나영 Developing an ETL tool for converting the PCORnet CDM into the OMOP CDM to facilitate the COVID-19 data integration    
    16 정문경 Enabling Research and Clinical Use of Patient-Generated HealthData (the mindLAMP Platform): Digital Phenotyping Study    
    16 조민아 Unbiased mosaic variant assessment in sperm: a cohort study to test predictability of transmission    
    23 안세환 Dating genomic variants and shared ancestry in population scale sequencing data    
    23 조원일 Pharmacogenetic genotype and phenotype frequencies in a large Danish population-based case-cohort sample    
    30 이시은 Leveraging clinical data across healthcare institutions for continual learning of predictive risk models    
    30 부은경 A global overview of genetically interpretable multimorbidities among common diseases in the UK Biobank 

    2022-06:
    04 배소정 Loss of Bacitracin Resistance Due to a Large Genomic Deletion among Bacillus anthracis Strains    
    04 최선 Multi-omics prediction of immune-related adverse events during checkpoint immunotherapy    
    11 부은경 Identification of genetic risk loci and prioritization of genes and pathways for myasthenia gravis: a genome-wide association study    
    11 권호식 The frequency of the known mitochondrial variants associated with drug‑induced toxicity in a Korean population    
    18 안세환 Evaluation of population-level pharmacogenetic actionability in Alabama    
    18 유준기 Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity    
    25 ̿ A general framework for identifying oligogenic combinations of rare variants in complex disorders    
    25 윤미선 Building digital twins of the human immune system: toward a roadmap    

    2022-05:
    07 최선 Pre-training graph neural networks for link prediction in biomedical networks    
    07 윤미선 Clinical pharmacogenetic analysis in 5,001 individuals with diagnostic Exome Sequencing data    
    14 전예진 GWAS suggests that variation at the RCOR1 locus is associated with tinnitus in UK Biobank      
    14 김나영 Defining health data elements under the HL7 development framework for metadata management    
    21 ӿ Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes    
    21 정문경 A fusion decision system to identify and grade malnutrition in cancer patients: Machine learning reveals feasible workflow from representative real-world data    
    28 조원일 Comprehensive Allele Genotyping in Critical Pharmacogenes Reduces Residual Clinical Risk in Diverse Populations     
    28 조민아 A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis    

    2022-04:
    02 윤미선 Genetic associations of protein-coding variants in human disease    
    02 최선 DeSIDE_DDI interpretable prediction of drug_drug interactions      
    09 이시은 Developing a Clinical Prediction Rule for Gait Independence at Discharge in Patients with Stroke: A Decision-Tree Algorithm Analysis    
    09 안세환 Pharmacogenomic landscape of Indian population using whole genomes    
    16 조민아 The complete sequence of a human genome     
    16 조원일 Automated Pharmacogenomic Reports for Clinical Genome Sequencing    
    23 부은경 New insights into the genetic etiology of Alzheimers disease and related dementias    
    23 권호식 Mitochondrial DNA variation across 56,434 individuals in gnomAD    
    30 유준기 The individual and global impact of copy-number variants on complex human traits    
    30 ̿ Interpretable prioritization of splice variants in diagnostic next-generation sequencing    

    2022-03:
    05 이시은 ECG‑based machine‑learning algorithms for heartbeat classification    
    05 안세환 Massively parallel characterization of CYP2C9 variant enzyme activity and abundance    
    12 유준기 Analysis of rare genetic variation underlying cardiometabolic diseases and traits among 200,000 individuals in the UK Biobank    
    12 권호식 Changes in Plasma Amyloid and Tau in a Longitudinal Study of Normal Aging, Mild Cognitive Impairment, and Alzheimers Disease    
    19 ̿ Intergrative single cell analysis of allele specific copy number alterations and chromatin accessibility in cancer    
    19 ӿ A pan-cancer landscape of somatic mutations in non-unique regions of the human genome    
    26 김나영 Common Data Elements for Meaningful Stroke Documentation in Routine Care and Clinical Research: Retrospective Data Analysis    
    26 정문경 Design issues in personalized nutrition advice systems    

    2022-02:
    05 조원일 Actionable pharmacogenetic variants in Hong Kong Chinese exome sequencing data and projected prescription impact in the Hong Kong population.pdf    
    05 김나영 PGHD management and quality challenges in remote patient monitoring    
    12
    12 윤미선 Pharmacogenomic analysis of a genetically distinct Indigenous population    
    19 ӿ The Cancer Surfaceome Atlas integrates genomic, functional and drug response data to identify actionable targets    
    19 부은경 Whole-genome sequencing in diverse subjectsidentifies genetic correlates of leukocyte traits:The NHLBI TOPMed program    
    26 정문경 Hybrid Ubiquitous Coaching With a Novel Combination of Mobile and Holographic Conversational Agents Targeting Adherence to Home Exercises: Four Design and Evaluation Studies    
    26 조민아 Germline burden of rare damaging variants negatively affects human healthspan and lifespan    

    2022-01:
    01 ...  
    01 ...  
    08 홍진희 A simple CNN for prediction of enhancer-promoter interactions with DNA seq data    
    08 안세환 Phenotype prediction and characterization of 25 pharmacogenes in Thais from whole genome sequencing for clinical implementation    
    15 조민아 An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci     
    15 권호식 Genetic Background of Mesalamine-induced Fever and Diarrhea in Japanese Patients with Inflammatory Bowel Disease    
    22 유준기 Exome variant discrepancies due to reference-genome differences    
    22 ̿ The context-specific role of germline pathogenicity in tumorigenesis    
    29 이시은 Automatic electrocardiogram detection and classification using bidirectional long short-term memory network improved by Bayesian optimization    
    29 최선 Multi-omic machine learning predictor of breast cancer therapy response    

    2021-12:
    04 김나영 Mapping the Korean National Health Checkup Questionnaire to Standard Terminologies    
    04 ӿ Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology     
    11 정문경 Combined prognostic value of malnutrition using GLIM criteria and renal insufficiency in elderly heart failure    
    11 조원일 Genome-wide Study Identifies Association between HLA-B*55:01 and Self-Reported Penicillin Allergy    
    18 High antibiotic resistance of Helicobacter pylori and its associated novel gene mutations among the mongolian population    
    18 부은경 A polygenic-score-based approach for identification of gene-drug interactions stratifying breast cancer risk    
    25 ... ź 
    25 ... ź 

    2021-11:
    06 조원일 Validation of lipid-related therapeutic targets for coronary heart disease prevention using human genetics     
    06 안세환 Population-scale predictions of DPD and TPMT phenotypes using a quantitative pharmaacogene-specific ensemble classifier    
    13 홍진희 Components of genetic associations across 2,138 phenotype in the UK Biobank highlight adipocyte biology    
    13 이시은 Research on intelligent medical big data system based on Hadoop and blockchain    
    20 ̿ Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer    
    20 최선 MOGONET 
    27 유준기 Calibrated rare variant genetic risk scores for complex disease prediction using large exome sequence repositories    
    27 윤미선 Semi-supervised Contrastive Learning for Label-efficient Medical Image Segmentation    

    2021-10:
    02 최선 The measurement of Cobb angle based on spine X ray    
    02 ӿ Rare variant contribution to human disease in 281,104 UK Biobank exomes    
    09 ... ѱ۳ 
    09 ... ѱ۳ 
    16 윤미선 A RELATIONAL-LEARNING PERSPECTIVE TO MULTI-LABEL CHEST X-RAY CLASSIFICATION     
    16 김나영 Pragmatic MDR: a metadata repository with bottom up standardization of medical metadata through reuse    
    23 조민아 Clinical evolution, genetic landscape and trajectories of clonal hematopoiesis in SAMD9/SAMD9L syndromes    
    23 Position effects at the FGF8 locus are associated with femoral hypoplasia    
    30 정문경 A simulation-based evaluation of machine learning models for clinical decision support: application and analysis using hospital readmission    
    30 부은경 Polygenic basis and biomedical consequences of telomere length variation    

    2021-09:
    04 조원일 Gastroesophageal reflux GWAS identifies risk loci that also associate with subsequent severe esophageal diseases    
    04 이시은 Deep-learning-based automated terminology mapping in OMOP-CDM     
    11 홍진희 scRNA-seq technologies and related computational data analysis 
    11 조동영 Prioritization of candidate causal genes for asthma in susceptibility loci derived from UK Biobank    
    18 권호식 Copy number variation profiling in pharmacogenes using panel-based exome resequencing and correlation to human liver expression    
    18 ̿ Synthetic lethality mediated precision oncology via the tumor transcriptome    
    25 유준기 Set based rare variant expression quantitative trait loci in blood and brain from Alzheimer Disease study participants    
    25 안세환 High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios    

    2021-08:
    07 김나영 Towards achieving semantic interoperability of clinical study data with FHIR    
    07 ӿ Pathogenic missense protein variants affect different functional pathways and proteomic features than healthy population variants    
    14 윤미선 Encoding CT Anatomy Knowledge for Unpaired Chest X-ray Image Decomposition    
    14 Comparison of culture with antibiogram to NGS using bacterial isolates and formalin fixed paraffin embedded gastric biopsies    
    21 ֿ Utilising large electronic medical record datasets to identify novel drug-gene interactions for commonly used drugs    
    21 정문경 Development of a Spanish food exchange list: application of statistical criteria to a rationale procedure    
    28 조민아 The molecular basis, genetic control and pleiotropic effects of local gene co-expression    
    28 부은경 Whole-exome imputation within UK Biobank powers rare coding variant association and fine-mapping analyses    

    2021-07:
    03 조민아 A framework to decipher the genetic architecture of combinations of complex diseases: Applications in cardiovascular medicine    
    03 이시은 A Transparent and Privacy-Preserving Healthcare Platform With Novel Smart Contract for Smart Cities    
    10 홍진희 Estimation of Genetic Correlation via Linkage Disequilibrium Score Regression and Genomic Restricted Maximum Likelihood    
    10 조동영 Genome-wide study identifies association between HLA-B*55:01 and penicillin allergy    
    17 유준기 Association between major depressive disorder and multiple disease outcomes: a phenome-wide Mendelian randomisation study in the UK Biobank    
    17 권호식 Systematic single-variant and gene-based association testing of 3,700 phenotypes in 281,850 UK Biobank exomes    
    24 Combining Ontologies and Open Standards to Derive a Middle Layer Information Model for Interoperability of Personal and Electronic Health Records    
    24 안세환 Haplotype-resolved diverse human genomes and integrated analysis of structural variation    
    31 최선 Medical Transformer: Gated Axial-Attention for Medical Image Segmentation    
    31 ̿ The tumor therapy landscape of synthetic lethality    

    2021-06:
    05 유준기 Transcript expression-aware annotation improves rare variant interpretation    
    05 SMART Markers_ collecting patient-generated health data as a standardized property of health information technology    
    12 High-throughput reclassification of SCN5A variant    
    12 부은경 Genome-wide survival study identifies a novel synaptic locus and polygenic score for cognitive progression in Parkinsons disease    
    19 ֿ Exome-wide evaluation of rare coding variants using electronic health records identifies new gene-phenotype associations    
    19 정문경 Genome-wide gene-diet interaction analysis in the UK Biobank identifies novel effects on Hemoglobin A1c    
    26 조원일 Genome-wide association study of medication-use and associated disease in the UK Biobank    
    26 김나영 One Step Away from Technology but One Step Towards Domain Experts-MDRBridge: A Template-Based ISO 11179-Compliant Metadata Processing Pipeline    

    2021-05:
    01 이시은 An automatic method for lung segmentation and reconstruction in chest X-ray using deep neural networks    
    01 부은경 Genetics of 35 blood and urine biomarkers in the UK Biobank    
    08 안세환 Genetic ancestry plays a central role in population pharmacogenomics    
    08 최선 Genome-wide Modeling of Polygenic Risk Score in Colorectal Cancer Risk    
    15 윤미선 Differential Gene Set Enrichment Analysis: a statistical approach to quantify the relative enrichment of two gene sets    
    15 권호식 A comparison of tools for copy-number variation detection in germline whole exome and whole genome sequencing data    
    22 ̿ Exploiting loss of heterozygosity for allele-selective colorectal cancer chemotherapy    
    22 유경훈 Genetic analyses identify widespread sex-differential participation bias    
    29 조동영 Whole genome sequencing delineates regulatory and novel genic variants in childhood cardiomyopathy    
    29 ӿ Evaluating the molecular diagnostic yield of joint genotyping–based approach for detecting rare germline pathogenic and putative loss-of-function variants 

    2021-04:
    03 ӿ Genome Sequencing as an Alternative to Cytogenetic Analysis in Myeloid Cancers    
    03 유경훈 Identifying loci with different allele frequencies among cases of eight psychiatric disorders using CC-GWAS    
    10 김나영 QL4MDR: a GraphQL query language for ISO 11179-based metadata repositories    
    10 정문경 DIETOS: A dietary recommender system for chronic diseases monitoring and management    
    17 Strong functional data for pathogenicity or neutrality classify BRCA2 DNA-binding-domain variants of uncertain significance    
    17 조원일 Genetic variants associated with cardiometabolic abnormalities during treatment with selective serotonin reuptake inhibitors: a genome-wide association study    
    24 홍진희 Analysis of error profiles in deep next generation sequencing data    
    24 조민아 Cytokines mapping for tissue-specific expression, eQTLs and GWAS traits    

    2021-03:
    06 홍진희 Imputing Amino acid polymorphisms in human leukocyte antigens    
    06 조민아 The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1    
    13 부은경 Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic architecture    
    13 안세환 Systems Pharmacogenomic Landscape of Drug Similarities from LINCS data: Drug Association Networks    
    20 권호식 Analysis of Drug Metabolizing Gene Panel in Osteosarcoma Patients Identifies Association Between Variants in SULT1E1, CYP2B6 and CYP4F8 and Methotrexate Levels and Toxicities    
    20 최선 Learning Transferable Visual Models From Natural Language Supervision    
    27 ̿ Machine Learning of Patient Characteristics to Predict Admission Outcomes in the Undiagnosed Diseases Network    
    27 The HealthChain Blockchain for Electronic Health Records_Development Study    

    2021-02:
    06 ̿ Comprehensive Analysis of Genetic Ancestry and ItsMolecular Correlates in Cancer    
    06 정문경 Statistical Issues in Analyzing 24-Hour Dietary Recall and 24-Hour Urine Collection Data for Sodium and Potassium Intakes    
    13 ...  
    13 ...  
    20 Article Implement an International Interoperable PHR by FHIR—A Taiwan Innovative Application    
    20 유경훈 The mutational constraint spectrum quantified from variation in 141,456 humans    
    27 최선 Insights into the genetic basis of retinal detachment    
    27 De novo and bi-allelic pathogenic variants in NARS1 cause neurodevelopmental delay due to toxic gain-of-function and partial loss-of-function effects    

    2021-01:
    02 ӿ Comprehensive characterization of amino acid positions in protein structures reveals molecular effect of missense variants    
    02 Genomic sequencing for newborn screening: results of the NC NEXUS project    
    09 유경훈 Pharmacogenetic information in Swiss drug labels – a systematic analysis    
    09 정문경 When Chatbots Meet Patients: One-Year Prospective Study of Conversations Between Patients With Breast Cancer and a Chatbot    
    16 홍진희 HLA typing from RNA-Seq sequence reads    
    16 안세환 A systematic comparison of pharmacogene star allele calling bioinformatics algorithm: a focus on CYP2D6 genotyping    
    23 부은경 Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals    
    23 조민아 Exploring the genetic architecture of inflammatory bowel disease by whole-genome sequencing identifies association at ADCY7    
    30 권호식 Real world scenarios in rare variant association analysis: the impact of imbalance and sample size on the power in silico    
    30 ӿ e-MutPath: computational modeling reveals the functional landscape of genetic mutations rewiring interactome networks    

    2020-12:
    05 안세환 A Proteotranscriptomic-Based Computational Drug-Repositioning Method for Alzheimers Disease    
    05 김지헌 Genome analysis and knowledge-driven variant interpretation with TGex    
    12 조민아 Imaging genomics discovery of a new risk variant for Alzheimer    
    12 홍진희 Association between Busulfan Exposure and Outcome in Children Receiving Intravenous Busulfan before Hematologic Stem Cell Transplantation    
    19 권호식 Combining clinical and candidate gene data into a risk score for azathioprine-associated leukopenia in routine clinical practice    
    19 Blockchain for Secure EHRs Sharing of Mobile Cloud based E health Systems    
    26 최선 Comparison of laboratory threshold criteria in drug-induced liver injury detection algorithms for use in pharmacovigilance    
    26 ̿ Advances in germline predisposition to acute leukaemias and myeloid neoplasms    

    2020-11:
    07 최선 Detecting drug-drug interactions using artificial neural networks and classic graph similarity measures    
    07 ӿ Phase and context shape the function of composite oncogenic mutations      
    14 유경훈 Drug Response Pharmacogenetics for 200,000 UK Biobank Participants    
    14 ̿ Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities    
    21 Germline and mosaic variants in PRKACA and PRKACB cause a multiple congenital malformation syndrome    
    21 부은경 Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy    
    28 정문경 Designing for Health Chatbots    
    28 ֿ Population structure and pharmacogenomic risk stratification in the United States    

    2020-10:
    03 ... õ 
    03 ... õ 
    10 ֿ Polygenic architecture informs potential vulnerability to drug-induced liver injury    
    10 조민아 PCSK5 mutation in a patient with the VACTERL association    
    17 안세환 Drug-induced adverse events prediction with the LINCS L1000 data    
    17 홍진희 Vitamin D and IBD: Mendelian randomization analyses in the Copenhagen studies and ukbb    
    24 부은경 Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale    
    24 김지헌 Precision medicine integrating whole-genome sequencing, comprehensive metabolomics, and advanced imaging    
    31 권호식 A novel statistical method for interpreting the pathogenicity of rare variants    
    31 Using HL7 FHIR to achieve interoperability in patient health record    

    2020-09:
    05 김지헌 SWEDEGENE—a Swedish nation-wide DNA sample collection for pharmacogenomic studies of serious adverse drug reactions      
    05 ̿ The repertoire of mutational signatures in human cancer    
    12 ӿ A cancer drug atlas enables synergistic targeting of independent drug vulnerabilities    
    12 An Architecture and Management Platform for Blockchain-Based Personal Health Record Exchange: Development and Usability Study     
    19 정문경 Transparent sharing of digital health data: A call to action    
    19 유경훈 Identification of Neuropsychiatric Copy Number Variants in a Health Care System Population    
    26 최선 Scalable and accurate deep learning with electronic health records    
    26 Biallelic mutations in SORD cause a common and potentially treatable hereditary neuropathy with implications for diabetes    

    2020-08:
    01 정문경 Interaction of DRD2/ANKK1 Taq1A Genotype with in-Store Retail Food Environment Exposures on Diet Quality in a Cohort of Quebec Adults      
    01 De novo variants in SPOP cause two clinically distinct neurodevelopmental disorders    
    08 채정환 Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses    
    08 부은경 High-definition likelihood inference of genetic correlations across human complex traits    
    15 ...  
    15 ...  
    22 조민아 Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden    
    22 안세환 Improving cell-specific drug connectivity mapping with collaborative filtering    
    29 홍진희 .6mp metabolite profiles provide a biochemical explanation for 6mp resistance in patients with inflammatory bowel disease    
    29 권호식 A functional polymorphism in the ATP-Binding Cassette B1 transporter predicts pharmacologic response to combination of nortriptyline and morphine in neuropathic pain patients    

    2020-07:
    04 권호식 Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes    
    04 ̿ Korean Genome Project: 1094 Korean personal genomes with clinical information    
    11 De novo variants in exomes of congenital heart disease patients identify risk genes and pathways    
    11 Development of Comprehensive Personal Health Records Integrating Patient-Generated Health Data Directly From Samsung S-Health and Apple Health Apps    
    18 최선 Comprehensive comparative effectiveness and safety of first-line antihypertensive drug classes: a systematic, multinational, large-scale analysis    
    18 유경훈 Scalable generalized linear mixed model for region-based association tests in large biobanks and cohorts    
    25 ӿ A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer    
    25 ֿ Projected impact of pharmacogenomic testing on medications beyond antiplatelet therapy in percutaneous coronary intervention patients    

    2020-06:
    06 ...  
    06 ...  
    13 Pharmacogenetics at scale: An analysis of the UK Biobank    
    13 안세환 Evaluation of Connectivity Map shows limited reproducibility in drug repositioning    
    20 홍진희 wgs is more poweful than wes for detecting exome variants    
    20 ȿ An ancillary genomics system to support the return of pharmacogenomic results    
    27 조민아 Allele Frequency of Pathogenic Variants Related to Adult-Onset Mendelian Diseases    
    27 김지헌 The emerging landscape of health research based on biobanks linked to electronic health records: Existing resources, statistical challenges, and potential opportunities    

    2020-05:
    02 최선 DeepTox_Toxicity Prediction using Deep Learning    
    02 Toward a Model for Personal Health Record Interoperability    
    09 Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis    
    09 ӿ A reference map of the human binary protein interactome    
    16 정문경 Aggregating multiple real-world data sources using a patient-centered health-data-sharing platform    
    16 ֿ Pharmacogenomic-Based Decision-Support to Predict Adherence to Medications    
    23 채정환 Development of CRISPR as an Antiviral Strategy to Combat SARS-CoV-2 and Influenza    
    23 한봄 Predicted efficacy of a pharmacogenetic passport for inflammatory bowel disease    
    30 SYCP2 translocation-mediated dysregulation and frameshift variants cause human male infertility    
    30 부은경 Complementary genes contribute sex-biased vulnerability in diverse disorders    

    2020-04:
    04 Opposite modulation of RAC1 by mutations in TRIO is associated with distinct, domain-specific neurodevelopmental disorders    
    04 부은경 Excess of singleton loss-of-function variants in Parkinsons disease contributes to genetic risk    
    11 한봄 Whole genome sequencing to identify predictive markers for the risk of drug-induced interstitial lung disease    
    11 Minimal phenotyping yields genome-wide association signals of low specificity for major depression    
    18 안세환 Predict New Therapeutic Drugs for Hepatocellular Carcinoma Based on Gene Mutation and Expression    
    18 ȿ Concepts Driving Pharmacogenomics Implementation Into Everyday Healthcare    
    25 권호식 Genetic and clinical prediction models for the efficacy and hepatotoxicity of methotrexate in patients with rheumatoid arthritis: a multicenter cohort study    
    25 ̿ Interplay between whole-genome doubling and the accumulation of deleterious alterations in cancer evolution     

    2020-03:
    07 Time to Rethink the Genetic Architecture of Long QT Syndrome     
    07 유경훈 A genetics-led approach defines the drug target landscape of 30 immune-related traits    
    14 ӿ Identification of cancer driver genes based on nucleotide context    
    14 최선 A Hybrid Health Journey Recommender System using Electronic Medical Record    
    21 정문경 The mechanisms of pharmacokinetic food_drug interactions_A perspective from the UNGAP group    
    21 ֿ Estimated nationwide impact of implementing a preemptive pharmacogenetic panel approach to guide drug prescribing in primary care in The Netherlands    
    28 국수경 Integrative analysis of multi-omics data identified EGFR and PTGS2 as key nodes in a gene regulatory network related to immune phenotypes in head and neck cancer    
    28 채정환 The complex genetic landscape of familial MDS and AML reveals pathogenic germline variants    

    2020-02:
    01 채정환 Hyperactivation of TORC1 Drives Resistance to the Pan-HER Tyrosine Kina 
    01 한봄 The GenomeAsia 100K Project enables genetic discoveries across Asia    
    08 국수경 Shared genetic and epigenetic mechanisms between chronic periodontitis    
    08 ȿ Harmonizing Clinical Sequencing and Interpretation for the eMERGE III Network     
    15 GeVIR is a continuous gene-level metric that uses variant distribution patterns to prioritize disease candidate genes     
    15 안세환 eVIP2: Expression-based variant impact phenotypic to predict the function of gene variants    
    22 부은경 Genome-wide rare variant analysis for thousands of phenotypes in over 70,000 exomes from two cohorts    
    22 ̿ Discovering the anticancer potential of nononcology drugs by systematic viability profiling    
    29 권호식 Identification of pathogenic variant enriched regions across genes and gene families    
    29 OmniPHR: A distributed architecture model to integrate personal health records    

    2020-01:
    04 ӿ The mutational footprints of cancer therapies    
    04 권호식 Evaluating potential drug targets through human loss-of function genetic variation    
    11 정문경 Multi-trait genome-wide association meta-analysis of dietary intake identifies new loci and genetic and functional links with metabolic traits    
    11 유승원 Inverse similarity and reliable negative samples for drug side-effect prediction    
    18 Gain-of-function MN1 truncation variants cause a recognizable syndrome with craniofacial and brain abnormalities    
    18 ֿ Economic burden of adverse drug reactions and potential for pharmacogenomic testing in Singaporean adults    
    25 ...  
    25 ...  

    2019-12:
    07 Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations    
    07 안세환 .    
    14 ȿ Genomic Information for Clinicians in the Electronic Health Record: Lessons Learned From the Clinical Genome Resource Project and the Electronic Medical Records and Genomics Network    
    14 최선 Medical device surveillance with electronic health records    
    21 ̿ UK-Biobank Whole Exome Sequence Binary Phenome Analysis with Robust Region-based Rare Variant Test     
    21 유경훈 Towards precision medicine: interrogating the human genome to identify drug pathways associated with potentially functional, population-differentiated polymorphisms    
    28 Secure and Scalable mHealth Data Management Using Blockchain Combined With Client Hashchain: System Design and Validation    
    28 Determining the balance between drug efficacy and safety by the network and biological system profile of its therapeutic target    

    2019-11:
    02 유경훈 Harmonizing Clinical Sequencing and Interpretation for the eMERGE III Network    
    02 Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity    
    09 ӿ Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype    
    09 한봄 HLA and non-HLA genes and familial predisposition to autoimmune diseases in families with a child affected by type 1 diabetes    
    16 유승원 prioritizing target-disease associations with novel safety and efficacy scoring methods    
    16 Diagnostic utility of Next-Generation Sequencing for Disorders of Somatic Mosaicism-a five-year cumulative cohort    
    23 채정환 Low Dose of Paclitaxel Combined with XAV939 Attenuates Metastasis, Angiogenesis and Growth in Breast Cancer by Suppressing Wnt Signaling.    
    23 국수경 A three-gene expression signature associated with positive surgical margins in tongue squamous cell carcinomas: Predicting surgical resectability from tumour biology?    
    30 부은경 Discovering personalized driver mutation profiles of single samples in cancer by network control strategy    
    30 김재환 Recommendations for Clinical CYP2C9 Genotyping Allele Selection    

    2019-10:
    05 안세환 Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures.    
    05 권호식 Exome-wide assessment of the functional impact and pathogenicity of multinucleotide mutations    
    12 ̿ How good are pathogenicity predictors in detecting benign variants?    
    12 최선 BioBERT: a pre-trained biomedical language representation model for biomedical text mining    
    19 Tamper Resistant Mobile Health Using Blockchain Technology    
    19 Genotype-based Treatment With Thiopurine Reduces Incidence of Myelosuppression in Patients With Inflammatory Bowel Diseases    
    26 Genotype-based Treatment With Thiopurine Reduces Incidence of Myelosuppression in Patients With Inflammatory Bowel Diseases     
    26 ֿ Analyzing the Clinical Actionability of Germline Pharmacogenomic Findings in Oncology    

    2019-09:
    07 한봄 Understanding HLA associations from SNP summary association statistics    
    07 국수경 Immune profiles in primary squamous cell carcinoma of the head and neck    
    14 ...  
    14 ...  
    21 김재환 Multi-Gene Panel Testing of 23,179 Individuals for Hereditary Cancer Risk Identifies Pathogenic Variant Carriers Missed by Current Genetic Testing Guidelines    
    21 Massive parallel variant characterization identifies NUDT15 alleles associated with thiopurine toxicity    
    28 부은경 Genetic meta-analysis of diagnosed Alzheimers disease identifies new risk loci and implicates A, tau, immunity and lipid processing    
    28 ȿ The Coriell personalized medicine collaborative pharmacogenomics appraisal, evidence scoring and interpretation system    

    2019-08:
    03 ӿ RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues    
    03 Diagnosis of genetic diseases in seriously ill children by rapid whole-genome sequencing and automated phenotyping and interpretation    
    10 Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome    
    10 유경훈 Impact of pharmacogenomics on clinical outcomes in major depressive disorder in the GUIDED trial: A large, patient- and rater-blinded, randomized, controlled study    
    17 ̿ A longtudinal big data approach for precision health    
    17 κ Noncoding CGG repeat expansions in neuronal intranuclear inclusion disease, oculopharyngodistal myopathy and an overlapping disease    
    24 ֿ Characterizing pharmacogenomic-guided medication use with a clinical data repository    
    24 Paralog studies augment gene discovery:DDX and DHX genes    
    31 유승원 Drug combination sensitivity scoring facilitates the discovery of synergistic and efficacious drug combinations in cancer    
    31 채정환 PPM1D Mutations Drive Clonal Hematopoiesis in Response to Cytotoxic Chemotherapy    

    2019-07:
    06 민유정 TogoGenome/TogoStanza: modularized Semantic Web genome database    
    06 부은경 Expanding Parkinsons disease genetics: novel risk loci, genomic context, causal insights and heritable risk    
    13 김재환 A Model Information Management Plan for Molecular Pathology Sequence Data Using Standards    
    13 Evolutionary coupling analysis identifies the impact ofdisease-associated variants at less-conserved sites    
    20 안세환 L1000 Viewer: A Search Engine and Web Interface for the LINCS Data Repository    
    20 권호식 Pathogenic Germline Variants in 10,389 Adult Cancers    
    27 ȿ A Pharmacogenomics Clinical Decision Support Service Based on FHIR and CDS Hooks     
    27 최선 Cardiologist-level arrhythmia detection and classification in ambulatory electrocardiograms using a deep neural network    

    2019-06:
    01 민유정 .Genomic Common Data Model for Seamless Interoperation of Biomedical Data in Clinical Practice: Retrospective Study    
    01 유경훈 Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program    
    08 ֿ Network, transcriptomic and genomic features differentiate genes relevant for drug response    
    08 κ Biallelic expansion of an intronic repeat in RFC1 is a common cause of late-onset ataxia    
    15 Conditional and interaction gene-set analysis reveals novel functional pathways for blood pressure    
    15 유승원 Systematic discovery of germline cancer predisposition genes through the identification of somatic second hits    
    22 Length of uninterrupted CAG, independent of polyglutamine size, results in increased somatic instability, hastening onset of Huntington Disease    
    22 채정환 Genomic and Transcriptomic Landscape of Triple-Negative Breast Cancers: Subtypes and Treatment Strategies    
    29 한봄 Immune diversity sheds light on missing variation in worldwide genetic diversity panels    
    29 국수경 Tracing Oncogene Rearrangements in the Mutational History of Lung Adenocarcinoma.    

    2019-05:
    04 김재환 Recommendations for interpreting the loss of function PVS1 ACMG/AMP variant criterion    
    04 부은경 Exome sequencing identifies germline variants in DIS3 in familial multiple myeloma    
    11 안세환 New drug candidates for treatment of atypical meningiomas: An integrated approach using gene expression signatures for drug repurposing    
    11 ȿ Pharmacogenomic clinical decision support design and multi-site process outcomes analysis in the eMERGE Network    
    18 권호식 The germline genetic component of drug sensitivity in cancer cell lines    
    18 ̿ Somatic_Mutations_increase_Hepatic_Clonal_Fitness_and_Regeneration_in_Chronic_Liver_Disease    
    25 ӿ Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens    
    25 Interpreting the clinical significance of combined variants in multiple recessive disease genes: systematic investigation of Joubert syndrome yields little support for oligogenicity.    

    2019-04:
    06 채정환 A joint study of whole exome sequencing and structural MRI analysis in major depressive disorder    
    06 Variants of unknown significance in genes associated with heritable thoracic aortic disease can be low penetrant risk variants    
    13 ֿ Analysis of comprehensive pharmacogenomic profiling to impact in-hospital prescribing    
    13 유승원 Discovering the Dark matters in expression data of miRNA based on the miRNA-mRNA and miRNA-lncRNA networks    
    20 한봄 Cross-ethnicity tagging SNPs for HLA alleles associated with adverse drug reaction    
    20 국수경 Whole-exome sequencing and clinical interpretation of FFPE tumor samples to guide precision cancer medicine    
    27 최선 Using RNN to predict heart failure    
    27 Whole exome sequencing and characterization of coding variation in 49,960 individuals in the UK Biobank    

    2019-03:
    02 Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder    
    02 ȿ Toward a normalized clinical drug knowledge base in China—applying the RxNorm model to Chinese clinical drugs    
    09 권호식 Translating genotype data of 44,000 biobank participants into clinical pharmacogenetic recommendations: challenges and solutions    
    09 ̿ Re-identification of individuals in genomic data-sharing beacons via allele inference    
    16 최선 Risk prediction for chronic kidney disease progression using heterogeneous electronic health record data and time series analysis    
    16 Rapid and accurate interpretation of clinical exomes using Phenoxome: a computational phenotype-driven approach    
    23 ӿ Widespread Selection for Oncogenic Mutant Allele Imbalance in Cancer    
    23 유경훈 Improved Pathogenic Variant Localization via a Hierarchical Model of Sub-regional Intolerance    
    30 Pathway Based Analysis of Mutation Data Is Efficient for Scoring Target Cancer Drugs    
    30 κ An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders    

    2019-02:
    02 ֿ Projected impact of a multigene pharmacogenetic test to optimize medication prescribing in cardiovascular patients    
    02 The malaria-protective human glycophorin structural variant DUP4 shows somatic mosaicism and association with hemoglobin levels    
    09 유승원 Predicting protein-protein interactions using high-quality non-interacting pairs 
    09 정문경  
    16 정문경 Patients Know Best: Qualitative Study on How Families Use Patient-Controlled Personal Health Records    
    16 유경훈 Burden Testing of Rare Variants Identified through Exome Sequencing via Publicly Available Control Data    
    23 채정환 Nonsynonymous Variants in PAX4 and GLP1R Are Associated With Type 2 Diabetes in an East Asian Population    
    23 안세환 GenIO: a phenotype-genotype analysis web server for clinical genomics of rare diseases    

    2019-01:
    05 권호식 ClinPred: Prediction Tool to Identify Disease-Relevant Nonsynonymous Single-Nucleotide Variants    
    05 ̿ Forward and reverse mutations in stages of cancer development    
    12 최선 Active Disease Surveillance in an Electronic Health Database Using a Common Data Model Based Tool     
    12 High Yield of Pathogenic Germline Mutations Causative or Likely Causative of the Cancer Phenotype in Selected Children with Cancer    
    19 ӿ A map of constrained coding regions in the human genome    
    19 한봄 Functional annotation of genomic variants in studies of late-onset Alzheimer    
    26 Efficiient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model    
    26 κ Genetic Determinants and Prediction of Antibiotic Resistance Phenotypes in Helicobacter pylori    

    2018-12:
    01 Homozygous mutations in WEE2 cause fertilization failure and female infertility     
    01 유승원 In silico profiling of systemic effects of drugs to predict unexpected interactions    
    08 채정환 Germline Genetic IKZF1 Variation and Predisposition to Childhood Acute Lymphoblastic Leukemia    
    08 한봄 Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data.    
    15 정문경 Advancing Models and Theories for Digital Behavior Change Interventions    
    15 Pathway-Based Drug Repositioning for Cancers: Computational Prediction and Experimental Validation    
    22 Estimating the selective effects of heterozygous protein-truncating variants from human exome data    
    22 안세환 PopViz: a webserver for visualizing minor allele frequencies and damage prediction scores of human genetic variations    
    29 ȿ Accuracy of an automated knowledge base for identifying drug adverse reactions    
    29 권호식 ClinPred: Prediction Tool to Identify Disease-Relevant Nonsynonymous Single-Nucleotide Variants    

    2018-11:
    03 ӿ Network Propagation Predicts Drug Synergy in Cancers    
    03 ̿ The chromatin accessibility landscape of primary human cancers    
    10 최선 MedEx: a medication information extraction system for clinical narratives    
    10 권호식 Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers    
    17 κ Application of next-generation sequencing to characterize novel mutations in clarithromycin-susceptible Helicobacter pylori strains with A2143G of 23S rRNA gene    
    17 ֿ Whole genome sequencing identifies high-impact variants in well-known pharmacogenomic genes    
    24 유경훈 An optimized prediction framework to assess the functional impact of pharmacogenetic variants    
    24 Pathway-structured predictive modeling for multi-level drug response in multiple myeloma    

    2018-10:
    06 유승원 Mapping biological process relationships and disease    
    06 채정환 ANGPTL3 Deficiency and Protection Against Coronary Artery Disease    
    13 Trans effects on gene expression can drive omnigenic inheritance    
    13 정문경 THE IMPACT OF INTERPERSONAL CLOSENESS CUES IN TEXT-BASED HEALTHCARE CHATBOTS ON ATTACHMENT BOND AND THE DESIRE TO CONTINUE INTERACTING: AN EXPERIMENTAL DESIGN      
    20 Synthetic Lethality-based Identifcation of Targets for Anticancer Drugs in the Human Signaling Network    
    20 한봄 MediSyn: uncertainty-aware visualization of multiple biomedical datasets to support drug treatment selection    
    27 안세환 VarCards: an integrated genetic and clinical database for coding variants in the human genome    
    27 ȿ Towards Implementation of OMOP in a German University Hospital Consortium    

    2018-09:
    01 권호식 The landscape of genomic alterations across childhood cancers    
    01 ̿ Evaluation of in silico algorithms for use with ACMG/AMP clinical variant interpretation guidelines    
    08 ӿ Tumor Mutational Burden and Efficacy of Nivolumab Monotherapy and in Combination with Ipilimumab in Small-Cell Lung Cancer    
    08 Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines    
    15 유경훈 Covariate selection for association screening in multiphenotype genetic studies    
    15 κ Risks and Recommendations in Prenatally Detected De Novo Balanced Chromosomal Rearrangements from Assessment of Long-Term Outcomes    
    22 ... ߼    
    22 ... ߼    
    29 ֿ Quantifying the impact of rare and ultra-rare coding variation across the phenotypic spectrum    
    29 A dominantly inherited 5` UTR variant causing methylation-associated silencing of BRCA1 as a cause of breast and ovarian cancer     

    2018-08:
    04 정문경 Histidine catabolism is a major determinant of methotrexate sensitivity      
    04 한봄 Applications of pharmacogenomics in regulatory science: a product life cycle review    
    11 유승원 In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development    
    11 Classifying tumors by supervised network propagation    
    18 Loose ends: almost one in five human genes still have unresolved coding status    
    18 ̼ Analysis of safety reporting requirements during medical device clinical trials in Japan.    
    25 안세환 Gene Graphics: a genomic neighborhood data visualization web application    
    25 ȿ Genomic decision support needs in pediatric primary care    

    2018-07:
    07 ȿ Principles and Recommendations for Standardizing the Use of the Next-Generation Sequencing Variant File in Clinical Settings    
    07 ӿ Systematic analysis of complex genetic interactions    
    14 안세환 Genome U-Plot:a whole genome visualization    
    14 ֿ Impact of germline and somatic missense variations on drug binding sites    
    21 Relationship between Deleterious Variation, Genomic Autozygosity, and Disease Risk: Insights from The 1000 Genomes Project    
    21 κ Germline de novo mutation clusters arise during oocyte aging in genomic regions with high double-strand-break incidence    
    28 Functional assays are essential for interpretation of missense variants associated with variable expressivity    
    28 채정환 Association Between SLC16A5 Genetic Variation and Cisplatin Induced Ototoxic Effects in Adult Patients With Testicular Cancer    

    2018-06:
    02 한봄 Cost-effectiveness of HLA-DQB1/HLA-B pharmacogenetic-guided treatment and blood monitoring in US patients taking clozapine    
    02 정문경 First-Stage Development and Validation of a Web-Based Automated Dietary Modeling Tool: Using Constraint Optimization Techniques to Streamline Food Group and Macronutrient Focused Dietary Prescriptions    
    09 채정환 methylation of l1re1, rarb, and rassf1 function as possible biomarkers for the differential diagnosis of lung cancer.    
    09 Whole Exome Sequencing in 20,197 Persons for Rare Variants in Alzheimer Disease    
    16 Individual specific edge-network analysis for disease prediction    
    16 ̼ Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data    
    23 유경훈 Identification of Misclassified ClinVar Variants via Disease Population Prevalence    
    23 Secure and Trustable Electronic Medical Records Sharing using Blockchain    
    30 권호식 Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes    
    30 ̿ Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome    

    2018-05:
    05 ...  
    05 ...  
    12 유경훈 Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression    
    12 κ Expansions of intronic TTTCA and TTTTA repeats in benign adult familial myoclonic epilepsy    
    19 Antisense therapy for a common corneal dystrophy ameliorates TCF4 repeat expansion-mediated toxicity    
    19 Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation    
    26 ֿ Patient-Centered Precision Health In A Learning Health Care System: Geisingers Genomic Medicine Experience    
    26 유승원 Systematic identification of feature combinations for predicting drug response with Bayesian multi-view task linear regression    

    2018-04:
    07 Lessons learned from additional research analyses of unsolved clinical exome cases    
    07 권호식 Analysis of a gene panel for targeted sequencing of colorectal cancer samples    
    14 ̿ Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls    
    14 MedRec Using Blockchain for Medical Data Access and Permission Management    
    21 ̼ Medication class enrichment analysis: a novel algorithm to analyze multiple pharmacologic exposures simultaneously using electronic health record data    
    21 ӿ Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics     
    28 An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics    
    28 김민정 Pan-cancer analysis of bi-allelic alterations in homologous recombination DNA repair genes    

    2018-03:
    03 Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium    
    03 Identification of protein features encoded by alternative exons using Exon Ontology    
    10 유승원 A framework for the detection of de novo mutations in family-based sequencing data    
    10 채정환 Deep learning improves prediction of CRISPR-Cpf1 guide RNA activity    
    17 한봄 Evaluating somatic tumor mutation detection without matched normal samples    
    17 정문경 Genomic Landscape of Cell-Free DNA in Patients with Colorectal Cancer      
    24 Link synthetic lethality to drug sensitivity of cancer cells    
    24 The Medical Genome Reference Bank: a whole genome data resource of 4,000 healthy elderly individuals. Rationale and cohort design    
    31 ȿ Drug knowledge bases and their applications in biomedical informatics research    
    31 안세환 Visualization portal for genetic variation(VizGVar): a tool for interactive visualization of SNPs and somatic mutations in exons, genes and protein domains    

    2018-02:
    03 Building a semantic web based metadata repository for facilitating detailed clinical modeling in cacer genome studies    
    03 A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles    
    10 Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets    
    10 κ Reccurrent F8 Intronic Deletion Found in Mild Hemophilia A Causes Alu Exonization    
    17 ...  
    17 ...  
    24 김민정 Integrative analysis of genome-wide gene copy number changes and gene expression in non-small cell lung cancer    
    24 ֿ Multisite Investigation of Outcomes With Implementation of CYP2C19 Genotype-Guided Antiplatelet Therapy After Percutaneous Coronary Intervention    

    2018-01:
    06 Hybrid Approach of Relation Network and Localized Graph Convolutional Filtering for Breast Cancer Subtype Classification    
    06 Pharmacogenomics of GPCR Drug Targets    
    13 ȿ A Realism-Based View on Counts in OMOP\'s Common Data Model    
    13 ̿ Network dynamics-based cancer panel stratification for systemic prediction of anticancer drug response    
    20 권호식 Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma    
    20 유경훈 Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes    
    27 Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes    
    27 ӿ Combination Cancer Therapy Can Confer Benefit via Patient-to-Patient Variability without Drug Additivity or Synergy    

    2017-12:
    02 ȣ Risk factors of isoniazid-induced hepatotoxicity in Tunisian tuberculosis patients    
    02 Discovering novel pharmacogenomic biomarkers by imputing drug response in cancer patients from large genomics studies    
    09 Trans-ancestry meta-analyses identify rare and common variants associated with blood pressure and hypertension    
    09 κ Exonic Mosaic Mutations Contribute Risk for Autism Spectrum Disorder    
    16 김민정 Changes in gene expression variability reveal a stable synthetic lethal interaction network in BRCA2- ovarian cancers    
    16 ֿ Pharmacogenomics-Based Point-of-Care Clinical Decision Support Significantly Alters Drug Prescribing    
    23 PGBD5 promotes site-specific oncogenic mutations in human tumors    
    23 Annotation-free quantification of RNA splicing using LeafCutter    
    30 ...     
    30 ...     

    2017-11:
    04 Variant Interpretation: Functional Assays to the Rescue    
    04 ȿ Reverse translation of adverse event reports paves the way for de-risking preclinical off-targets    
    11 Genetic variation in human drug-related genes     
    11 ̿ Overexpressed Somatic Alleles are Enriched in Functional Elements in Breast Cancer    
    18 Comparing the Performance of NoSQL Approaches for Managing Archetype Based Electronic Health Record Data    
    18 권호식 Multiregion Whole-Exome Sequencing Uncovers the Genetic Evolution and Mutational Heterogeneity of Early-Stage Metastatic Melanoma    
    25 ӿ Comprehensive Analysis of Hypermutation in Human Cancer    
    25 유경훈 A method to decipher pleiotropy by detecting underlying heterogeneity driven by hidden subgroups applied to autoimmune and neuropsychiatric diseases    

    2017-10:
    07 ...  
    07 ...  
    14 ȣ Sparse whole genome sequencing identifies two loci for major depressive disorder    
    14 ֿ Multidisciplinary model to implement pharmacogenomics at the point of care    
    21 Loss-of-function and gain-of-function mutations in KCNQ5 cause intellectual disability or epileptic encephalopathy    
    21 Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer    
    28 Profiling and leveraging relatedness in a precision medicine cohort of 92,455 exomes    
    28 MR Imaging Radiomics Signatures for Predicting the Risk of Breast Cancer Recurrence as Given by Research Versions of MammaPrint, Oncotype DX, and PAM50 Gene Assays    

    2017-09:
    02 Opening the Duke electronic health record to apps: ImplementingSMART on FHIR    
    02 Common sequence variants affect molecular function more than rare variants?    
    09 ӿ Integrative clinical genomics of metastatic cancer    
    09 유경훈 The druggable genome and support for target identification and validation in drug development    
    16 김민정 Identification of prognostic genes through expression differentiation during metastatic process in lung adenocarcinoma    
    16 Using Clinical Characteristics to Identify Which Patients With Major Depressive Disorder Have a Higher Genetic Load for Three Psychiatric Disorders    
    23 Global profiling of alternative RNA splicing events provides insights into molecular differences between various types of HCC    
    23 κ Evaluation of ACMG-Guideline-Based Variant Classification of Cancer Susceptibility and Non-Cancer- Associated Genes in Families Affected by Breast Cancer    
    30 ... TBC 
    30 ... TBC 

    2017-08:
    05 Genetic diagnosis of Mendelian disorders via RNA sequencing    
    05 RNA splicing is a primary link between genetic variation and disease    
    12 Evaluating the clinical validity of gene-disease associations an evidence-based framework developed by the clinical genome resource    
    12 Measuring intratumor heterogeneity by network entropy using RNA-seq data    
    19 ̿ A Zoom Focus algorithm to locate the optimal testing region for rare variant association tests    
    19 ȿ Signal Detection of Imipenem Compared to Other Drugs from Korea Adverse Event Reporting System Database    
    26 Gene family information facilitates variant interpretation and identification of disease associated genes    
    26 권호식 Burden of Nonsynonymous Mutations among TCGA Cancers and Candidate Immune Checkpoint Inhibitor Responses    

    2017-07:
    01 An Expanded View of Complex Traits: From Polygenic to Omnigenic    
    01 AACR Project GENIE: Powering Precision Medicine Through An International Consortium    
    08 유경훈 Semantic prioritization of novel causative genomic variants    
    08 ӿ A global genetic interaction network maps a wiring diagram of cellular function    
    15 Using large sequencing data sets to refine intragenic disease regions and prioritize clinical variant interpretation    
    15 Automated integration of continuous glucose monitor data in the electronic health record using consumer technology    
    22 ֿ Preemptive Pharmacogenomic Testing for Precision Medicine: A Comprehensive Analysis of Five Actionable Pharmacogenomic Genes Using Next-Generation DNA Sequencing and a Customized CYP2D6 Genotyping Cas    
    22 ȣ Meta-analysis of effects of ABCB1 polymorphisms on clopidogrel response among patients with coronary artery disease    
    29 κ Genetic variants associated with mosaic Y chromosome loss highlight cell cycle genes and overlap with cancer susceptibility    
    29 Disease variants alter transcription factor levels and methylation of their binding sites    

    2017-06:
    03 Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq    
    03 A comprehensive analysis of rare genetic variation in amyotrophic lateral sclerosis in the UK    
    10 Back on Track: A Mobile App Observational Study Using Apple ResearchKit Framework    
    10 Pharmacogenomic variants have larger effect sizes than genetic variants associated with other dichotomous complex traits.    
    17 Supporting precision medicine by data mining across multi-disciplines: an integrative approach for generating comprehensive linkages between single nucleotide variants (SNVs) and drug-binding sites    
    17 ̿ Mutational landscape of matastatic cancer revealed from prospective clinical sequencing of 10,000 patients    
    24 Electronic health record phenotype in subjects with genetic variants associated with arrhythmogenic right ventricular cardiomyopathy: a study of 30,716 subjects with exome sequencing     
    24 ȿ The Drug Data to Knowledge Pipeline: Large-Scale Claims Data Classification for Pharmacologic Insight    

    2017-05:
    06 unknown  
    06 unknown  
    13 ȣ Genetic Polymorphisms Contribute to the Individual Variations of Imatinib Plasma Levels and ADR in Chinese GIST    
    13 Pathway-Structured Predictive Model for Cancer Survival Prediction: A Two-Stage Approach    
    20 RNA sequence context effects measured in vitro predict in vivo protein binding and regulation    
    20 κ Tumor-suppressor genes that escape from X-inactivation contribute to cancer sex bias    
    27 ֿ Creating a scalable clinical pharmacogenomics service with automated interpretation and medical record result integration-experience from a pediatric tertiary care facility    
    27 A common variant at the 14q32 endometrial cancer risk locus activates AKT1 through YY1 binding    

    2017-04:
    01 Successful weight reduction and maintenance by using a smartphone application in those with overweight and obesity    
    01 Network perturbation by recurrent regulatory variants in cancer    
    08 Rare and low-frequency coding variants alter human adult height    
    08 ̰ȭ A systematic approach to the reporting of medically relevant findings from whole genome sequencing    
    15 ȿ The other side of the coin: Harm due to the non-use of health-related data    
    15 ̿ Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data    
    22 SPATIAL: A System-level PAThway Impact AnaLysis approach    
    22 C3-PRO. Connecting ResearchKit to the Health System Using i2b2 and FHIR    
    29 유경훈 Whole-genome sequencing identifies common-to-rare variants associated with human blood metabolites    
    29 ӿ Reassessment of Genomic Sequence Variation to Harmonize Interpretation for Personalized Medicine    

    2017-03:
    04 WT U2AF1 Antagonizes the Splicing Program Characteristic of U2AF1 mutant tumors    
    04 κ InterVar: Clinical Interpretation of Genetic Variants by the 2015 ACMG-AMP Guidelines    
    11 ֿ Clinical impact of pharmacogenetic profiling with a clinical decision support tool in polypharmacy home health patients: A prospective pilot randomized controlled trial    
    11 Mutations in three genes encoding proteins involved in hair shaft formation cause uncombable hair syndrome    
    18 Comprehensive analyses of tumor immunity: implications for cancer immunotherapy    
    18 Mutation Detection of Fibroblast Growth Factor Receptor 3 for Infiltrative Hepatocellular Carcinoma by Whole-Exome Sequencing    
    25 Prospective participant selection and ranking to maximize actionable pharmacogenetic variants and discovery in the eMERGE Network    
    25 Characterization of ADME gene variation in 21 populations by exome sequencing    

    2017-02:
    04 ̼ Evaluating common data models for use with a longitudinal community registry    
    04 ̿ Massive interstitial copy-neutral loss of heterozygosity as evidence for cancer being a disease of the DNA-damage response    
    11 ȿ Patients, care partners, and shared access to the patient portal: online practices at an integrated health system    
    11 Metadata Repository for Improved Data Sharing and Reuse Based on HL7 FHIR    
    18 Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets    
    18 ӿ Somatic Mutation Patterns in Hemizygous Genomic Regions Unveil Purifying Selection during Tumor Evolution    
    25 Pathway-based gene signatures predicting clinical outcome of lung adenocarcinoma    
    25 ȣ Circular RNAs and their associations with breast cancer subtypes    

    2017-01:
    07 Opening the Duke electronic health record to apps: Implementing SMART on FHIR    
    07 ̰ȭ Comparison of Approaches for Heart Failure Case Identification From Electronic Health Record Data    
    14 The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes    
    14 Molecular analysis of urothelial cancer cell lines for modeling tumor biology and drug response    
    21 Distribution and clinical impact of functional variants in 50,726 whole-exome sequences from the DiscovEHR study    
    21 ȫֿ A novel algorithm for analyzing drug-drug interactions from MEDLINE literature    

    2016-12:
    03 ̼ Electronic Health Record Based Algorithm to Identify Patients with Autism Spectrum Disorder    
    03 Cancer associated SF3B1 mutatnts recognize otherwise inaccessible cryptic 3 splice sites within RNA secondary structures    
    10 κ Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant    
    10 ֿ Identification of causal genes for complex traits    
    17 Sequencing the GRHL3 coding region reveals rare truncating mutations and a common susceptibility variant for nonsyndromic cleft palate    
    17 The prognostic potential of alternative transcript isoforms across human tumors     
    24 Increased burden of deleterious variants in essential genes in autism spectrum disorder    
    24 The global spectrum of protein-coding pharmacogenomic diversity    
    31 ü Ʈ 
    31 ü Ʈ 

    2016-11:
    05 ȿ Clinical reasoning in the context of active decision support during medication prescribing     
    05 ̰ȭ Development of clinical decision support alerts for pharmacogenomic incidental findings from exome sequencing     
    12 ̿ Genome-wide significance testing of variation from single case exomes    
    12 A pathway-centric approach to rare variant association analysis    
    19 SMART on FHIR implemented over i2b2    
    19 ȣ Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study    
    26 ӿ Exploring genetic suppression interactions on a global scale    
    26 A new correlation clustering method for cancer mutation analysis    

    2016-10:
    01 Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer     
    01 Family-based association analyses of imputed genotypes reveal genome-wide significant association of Alzheimer    
    08 REVEL: an Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants    
    08 ȫֿ How Informative Are Drug-Drug Interactions of Gene-Drug Interactions?    
    22 Genetic Variation Among 82 Pharmacogenes: The PGRNseq Data From the eMERGE Network     
    22 Detecting Unplanned Care From Clinician Notes in Electronic Health Records    
    29 ENCAPP: elastic-net-based prognosis prediction and biomarker discovery for human cancers    
    29 The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes     

    2016-09:
    03 ӿ A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy    
    03 ODMedit_ uniform semantic annotation for data integration in medicine based on a public metadata repository    
    10 Analysis of protein-coding genetic variation in 60,706 humans    
    10 κ Determinants of Power in Gene-Based Burden Testing for Monogenic Disorders    
    24 ֿ The effect of pharmacogenetic profiling with a clinical decision support tool on healthcare resource utilization and estimated costs in the elderly exposed to polypharmacy    
    24 Parent-of-origin-specific signatures of de novo mutations    

    2016-08:
    06 Developing a data element repository to support EHR-driven phenotype algorithm authoring and execution    
    06 A Landscape of Pharmacogenomic Interactions in Cancer    
    13 ȿ User-driven prioritization of features for a prospective InterPersonal Health Record: Perceptions from the Italian context    
    13 ̿ Protein-structure-guided discovery of functional mutations across 19 cancer types    
    20 ̼ Design considerations, architecture, and use of the Mini-Sentinel distributed data system    
    20 ȣ Natural Selection and Functional Potentials of Human Noncoding Elements Revealed by Analysis of Next Generation Sequencing Data    
    27 Identifying overlapping mutated driver pathways by constructing gene networks in cancer.    
    27 Determination of a Comprehensive Alternative Splicing Regulatory Network and Combinatorial Regulation by Key Factors during EMT    

    2016-07:
    02 An integrative somatic mutation analysis to identify pathways linked with survival outcomes across 19 cancer types    
    02 SURVIV for survival analysis of mRNA isoform variation     
    09 κ Frequency and Complexity of De Novo Structural Mutation in Autism    
    09 ֿ Computational discovery of transcription factors associated with drug response    
    16 Identification of important lncRNAs and highly recurrent aberrant alternative splicing events in HCC through integrative analysis of multiple RNA Seq datasets    
    16 Somatic activating mutations in GNAQ and GNA11 are associated with congenital hemangioma    
    23 Metabolic Network Prediction of Drug Side Effects    
    23 Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes.    
    30 The human gene damage index as a gene-level approach to prioritizing exome variants    
    30 ̰ȭ The genetic architecture of type 2 diabetes    

    2016-06:
    04 ȿ Considering complexity in healthcare systems    
    04 Network-based in silico drug efficacy screening     
    11 ̼ Detecting Drug Interactions From Adverse-Event Reports: Interaction Between Paroxetine and Pravastatin Increases Blood Glucose Levels    
    11 Rare genetic variants in cellular transporters, metabolic enzymes, and nuclear receptors can be important determinants of interindividual differences in drug response.    
    18 SMART precision cancer medicine a FHIR-based app to provide genomic information at the point of care    
    18 ̿ Modeling local gene networks increases power to detect trans-acting genetic effects on gene expression    
    25 ӿ Characterizing genomic alterations in cancer by complementary functional associations    
    25 ȣ genome-wide association study identifies multiple loci for variation in human ear morphology    

    2016-05:
    07 Genetic Variation among 82 Pharmacogenes: the PGRN-Seq data from the eMERGE Network     
    07 DIDA: A curated and annotated digenic diseases database     
    21 Harnessing person-generated health data to accelerate patient-centered outcomes research: the Crohns and Colitis Foundation of America PCORnet Patient Powered Research Network    
    21 Integrated Drug Expression Analysis for leukemia: an integrated in silico and in vivo approach to drug discovery    
    28 Genetic risk for autism spectrum disorders and neuropsychiatric variation in the general population    
    28 ̰ȭ Comparison and integration of deleteriousness prediction methods for non synonymous SNVs in whole exome sequencing studies    

    2016-04:
    02 Polymorphisms and phenotypic analysis of Cytochrome P450 3A4 in the Uygur population in northwest China    
    02 Portal of medical data models information infrastructure for medical research and healthcare    
    09 An Ensemble Based Top Performing Approach for NCI-DREAM Drug Sensitivity Prediction Challenge    
    09 ӿ Identification of neutral tumor evolution across cancer types    
    16 Cancer type-dependent genetic interactions between cancer driver alterations indicate plasticity of epistasis across cell types    
    16 ȣ Effect of malignancy rates on cost-effectiveness of routine gene expression classifier testing for indeterminate thyroid    
    23 Intron retention is a widespread mechanism of tumor-suppressor inactivation    
    23 κ Germline Mutations in Predisposition Genes in Pediatric Cancer    
    30 A network-based analysis of colon cancer splicing changes reveals a tumorigenesis-favoring regulatory pathway emanating from ELK1    
    30 De novo loss-of-function mutations in USP9X cause a female-specific recognizable syndrome with developmental delay and congenital malformations    

    2016-03:
    05 Quantifying prion disease penetrance using large population control cohorts     
    05 SMART on FHIR: a standards-based, interoperable apps platform for electronic health records    
    12 An exploratory study using an openEHR 2-level modeling approach to represent common data elements    
    12 Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories    
    19 Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics    
    19 ̰ȭ Polygenic overlap between schizophrenia risk and antipsychotic response: a genomic medicine approach    
    26 ȿ Development, implementation and evaluation of an information model for archetype based user responsive medical data visualization    
    26 ̿ Patterns and functional implications of rare germline variants across 12 cancer types    

    2016-02:
    06 Polymorphic Cytochrome P450 Enzymes (CYPs) and Their Role in Personalized Therapy    
    06 ȣ Association of peroxisome proliferator-activated receptor-gamma gene polymorphisms and gene-gene interaction with asthma risk    
    13 Identifying adverse drug reactions and drug-induced diseases using network-based drug mapping    
    13 κ Timing, rates and spectra of human germline mutation    
    20 ֿ A prognostic model based on readily available clinical data enriched a pre-emptive pharmacogenetic testing program    
    20 SRSF1-Regulated Alternative Splicing in Breast Cancer    
    27 Mutations in the transcriptional repressor REST predispose to Wilms tumor    
    27 Prediction of drugs having opposite effects on disease genes in a directed network     

    2016-01:
    02 unknown غ . 
    02 unknown Happy New Year 
    09 ̰ȭ The contribution of rare variation to prostate cancer heritability    
    09 ӿ A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing    
    16 unknown NCRC & ǥȸ 
    16 unknown NCRC & ǥȸ 
    23 Use of the Blue Button Online Tool for Sharing Health Information: Qualitative Interviews With Patients and Providers    
    23 ̿ Systematic discovery of complex insertions and deletions in human cancers    
    30 A system to build distributed multivariate models and manage disparate data sharing policies    
    30 Leveraging ancestry to improve causal variant identification in exome sequencing for monogenic disorders    

    2015-12:
    05 κ Post-zygotic Point Mutations Are an Underrecognized Source of De Novo Genomic Variation    
    05 RNA-Seq of Tumor-Educated Platelets Enables Blood-Based Pan-Cancer, Multiclass, and Molecular Pathway Cancer Diagnostics    
    12 ֿ Making pharmacogenomic-based prescribing alerts more effective: A scenario-based pilot study with physicians    
    12 Germline heterozygous variants in SEC23B are associated with Cowden Syndrome and enriched in apparently sporadic thyroid cancer    
    19 Pan-cancer analysis of the extent and consequences of intratumor heterogeneity    
    19 BOOGIE: Predicting Blood Groups from High Throughput Sequencing Data     
    26 Systematic comparison of variant calling pipelines using gold standard personal exome variants    
    26 A comparison of two Detailed Clinical Model representations: FHIR and CDA    

    2015-11:
    07 unknown TBC 2015 
    07 unknown TBC 2015 
    14 ӿ An Evolutionary Approach for Identifying Driver Mutations in Colorectal Cancer    
    14 Cost-Effectiveness of Combinatorial Pharmacogenomic Testing for Treatment-Resistant Major Depressive Disorder Patients    
    21 Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data    
    21 SMART on FHIR Genomics: Facilitating standardized clinico-genomic apps    
    28 ȣ efficient genotype compression and analysis of large genetic-variation data sets    
    28 DGIdb 2.0: mining clinically relevant drug-gene interactions    

    2015-10:
    10 GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations    
    10 Standardizing data exchange for clinical research protocols and case report forms: An assessment of the suitability of the CDISC ODM    
    17 Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles    
    17 Using electronic health record data to develop inpatient mortality predictive model: Acute Laboratory Risk of Mortality Score (ALaRMS)    
    24 Comprehensive genetic exploration of skeletal dysplasia using targeted exome sequencing    
    24 ̼ Feasibility and utility of applications of the common data model to multiple, disparate observational health databases    
    31 ̰ȭ The UK10K project identifies rare variants in health and disease     
    31 ̿ Age-related mutations associated with colnal hemtopoietic expansion and malignancies    

    2015-09:
    05 ȣ Single-cell messenger RNA sequencing reveals rare intestinal cell types    
    05 Achieving high-sensitivity for clinical applications using augmented exome sequencing    
    12 κ Mutations in DDX3X Are a Common Cause of Unexplained Intellectual Disability with Gender-Specific Effects on Wnt Signaling    
    12 ֿ Electronic health record design and implementation for pharmacogenomics: a local perspective    
    19 Germline HABP2 Mutation Causing Familial Nonmedullary Thyroid Cancer    
    19 The support of human genetic evidence for approved drug indications     

    2015-08:
    01 ȿ Associations between healthcare quality and use of electronic health record functions in ambulatory care    
    01 ̿ Recurrent somatic mutations in regulatory regions of human cancer genomes    
    08 ̼ Similarity-Based Modeling Applied to Signal Detection in Pharmacovigilance    
    08 Cost-effectiveness of one-time genetic testing to minimize lifetime adverse drug reactions    
    22 Semantic enrichment of clinical models towards semantic interoperability The heart failure summary use case.    
    22 Human symptoms-disease network    
    29 ӿ Co-occurring Genomic Alterations Define Major Subsets of KRAS-Mutant Lung Adenocarcinoma with Distinct Biology, Immune Profiles, and Therapeutic Vulnerabilities    
    29 Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas    

    2015-07:
    11 Integration of somatic mutation, expression, and functional data reveals potential driver genes predictive of breast cancer survival    
    11 Development, implementation, and initial evaluation of a foundational open interoperability standard for oncology treatment planning and summarization    
    18 Genome-wide patterns and properties of de novo mutations in humans     
    18 Clinical decision support for atypical orders: detection and warning of atypical medication orders submitted to a computerized provider order entry system    
    25 Whole-genome sequence variation, population structure and demographic history of the Dutch population    
    25 ̰ȭ Factors influencing success of clinical genome sequencing across a broad spectrum of disorders    

    2015-06:
    13 Somatic mutations in arachidonic acid metabolism pathway genes enhance oral cancer post-treatment disease-free survival     
    13 ֿ Adoption of a clinical PGx implementation program during outpatient care--initial results of the University of Chicago 1,200 Patients Project    
    20 κ Cancer genomics: one cell at a time    
    20 DSigDB: Drug Signatures Database for Gene Set Analysis    
    27 Copy-Number Variation of the Glucose Transporter Gene SLC2A3 and Congenital Heart Defects in the 22q11.2 Deletion Syndrome    
    27 Ranking Adverse Drug Reactions With Crowdsourcing    

    2015-05:
    02 Genetic Diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data    
    02 Transformation of standardized clinical models based on OWL technologies: from CEM to OpenEHR archetypes    
    09 Improved data analysis for the MinION nanopore sequencer    
    09 ̼S Disease Risk Factors Identified Through Shared Genetic Architecture and Electronic Medical Records    
    16 ̰ȭ Analysis of loss-of-function variants and 20 risk factor phenotypes in 8,554 individuals identifies loci influencing chronic disease    
    16 ӿ Assessing the clinical utility of cancer genomic and proteomic data across tumor types    
    23 Large scale exploration and analysis of drug combinations    
    23 Lessons learned in detailed clinical modeling at Intermountain Healthcare    
    30 ̼ Systems Pharmacology Augments DrugSafety Surveillance    
    30 ̿ Characterization and identification of hidden rare variants in the human genome    

    2015-04:
    04 Uncovering disease-disease relationships through the incomplete interactome    
    04 SFINX - a drug-drug interaction database designed for clinical decision support systems    
    11 κ Germline loss-of-function mutations in LZTR1 predispose to an inherited disorder of multiple schwannomas    
    11 ֿ Economic evaluation of a pharmacogenetic dosing algorithm for coumarin anticoagulants in The Netherlands     
    18 A recurrent mutation in PARK2 is associated with familial lung cancer    
    18 Development of a broad-based ADME panel for use in pharmacogenomic studies     
    25 Drug2Gene: an exhaustive resource to explore effectively the drug-target relation network.    
    25 A methodology for a minimum data set for rare diseases to support national centers of excellence for healthcare and research    

    2015-03:
    07 ̼S How common are drug and gene interactions? Prevalence in a sample of 1143 patients with CYP2C9, CYP2C19 and CYP2D6 genotyping    
    07 Ethnic specific associations of rare and low frequency DNA sequence variants with asthma    
    14 ̰ȭ Actionable exomic incidental findings in 6503 participants: challenges of variant classification.    
    14 ̿ DNA methylation age of human tissues and cell types    
    21 ̼ Medication-wide association studies    
    21 Ontology-Based Data Integration between Clinical and Research Systems    
    28 Human Genome Variation and the Concept of Genotype Networks    
    28 ӿ A method for calculating probabilities of fitness consequences for point mutations across the human genome    

    2015-02:
    07 ֿ PG4KDS: A Model for the Clinical Implementation of Pre-Emptive Pharmacogenetics    
    07 The CYP2D6 Activity Score: Translating Genotype Information into a Qualitative Measure of Phenotype    
    14 Whole-genome sequencing of quartet families with autism spectrum disorder    
    14 Sharing behavioral data through a grid infrastructure using data standards    
    28 Multi-source development of an integrated model for family health history    
    28 Identification of mutated core cancer modules by integrating somatic mutation, copy number variation, and gene expression data    

    2015-01:
    03 ̼ Automatic identification of methotrexate-induced liver toxicity in patients with rheumatoid arthritis from the electronic medical record    
    03 Multilingual Medical Data Models in ODM Format    
    10 ̰ȭ Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence     
    10 The role of the interactome in the maintenance of deleterious variability in human populations    
    17 Trait-Associated SNPs Are More Likely to Be eQTLs. Annotation to Enhance Discovery from GWAS    
    17 In silico comparative characterization of pharmacogenomic missense variants    
    24 ӿ Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complex     
    24 Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss    
    31 κ Inactivating Mutations in NPC1L1 and Protection from Coronary Heart Disease    
    31 TBX6 Null Variants and a Common Hypomorphic Allele in Congenital Scoliosis    

    2014-12:
    06 ȼ Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types    
    06 Activating germline mutations in STAT3 cause early-onset multi-organ autoimmune disease    
    13 ֿ Development and use of active clinical decision support for preemptive pharmacogenomics    
    13 HTSeq-a Python framework to work with high-throughput sequencing data    
    20 A multi-technique approach to bridge electronic case report form design    
    20 Are Meaningful Use Stage 2 certified EHRs ready for interoperability? Findings from the SMART C-CDA Collaborative    
    27 Somatic mutations identify a subgroup of aplastic anemia patients who progress to myelodysplastic syndrome    
    27 ̿ Mutational heterogeneity in cancer and the search for new cancer-associated genes    

    2014-11:
    01 Personalized pharmacogenomics profiling using whole-genome sequencing    
    01 Korean, Japanese, and Chinese populations featured similar genes encoding drug-metabolizing enzymes and transporters: a DMET Plus microarray assessment    
    08 Distribution and medical impact of loss-of-function variants in the Finnish founder population    
    08 ӿ Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene    
    15 Molecular Findings Among Patients Referred for Clinical Whole-Exome Sequencing    
    15 An empirical estimate of carrier frequencies for 400+ causal Mendelian variants: results from an ethnically diverse clinical sample of 23,453 individuals    
    22 Interpretation of Genomic Variants Using a Unified Biological Network Approach    
    22 ̰ȭ Uncovering the Hidden Risk Architecture of the Schizophrenias: Confirmation in Three Independent Genome-Wide Association Studies    
    29 Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin    
    29 κ Refining analyses of copy number variation identifies specific genes associated with developmental delay    

    2014-10:
    04 A systematic review of cancer GWAS and candidate gene meta-analyses reveals limited overlap but similar effect sizes.    
    04 Breast Cancer Risk in Families with Mutations in PALB2    
    11 ̼S Pharmacogenomic characterization of gemcitabine response – a framework for data integration to enable personalized medicine    
    11 ̿ Genome-wide analysis of noncoding regulatory mutations in cancer    
    18 ̼ The U.S. Food and Drug Administrations Mini-Sentinel program: status and direction    
    18 Procurement of shared data instruments for Research Electronic Data Capture (REDCap)    

    2014-09:
    06 ӿ Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality    
    06 Integrative and comparative genomic analysis of HPV-positive and HPV-negative head and neck squamous cell carcinomas    
    13 κ Molecular defects in the factor X gene caused by novel heterozygous mutations    
    13 A common missense variant in NUDT15 confers susceptibility to thiopurine-induced leukopenia    
    20 ֿ Design and Anticipated Outcomes of the eMERGE-PGx Project: A Multicenter Pilot for Preemptive Pharmacogenomics in Electronic Health Record Systems    
    20 Increased genetic diversity of ADME genes in African Americans compared with their putative ancestral source populations and implications for Pharmacogenomics     
    27 Modular design, application architecture, and usage of a self-service model for enterprise data delivery: The Duke Enterprise Data Unified Content Explorer (DEDUCE)    
    27 Computing Health Quality Measures Using Informatics for Integrating Biology and the Bedside    

    2014-08:
    02 Multi-Institutional Sharing of Electronic Health Record Data to Assess Childhood Obesity    
    02 The implications of familial incidental findings from exome sequencing: the NIH Undiagnosed Diseases Program experience    
    09 Automated UMLS-Based Comparison of Medical Forms 
    09 Network Characteristic Analysis of ADR-related Proteins and Identification of ADR-ADR Associations    
    16 Whole-exome sequencing identifies rare pathogenic variants in new predisposition genes for familial colorectal cancer    
    16 ֿ Preemptive genotyping for personalized medicine: design of the right drug, right dose, right time-using genomic data to individualize treatment protocol    
    23 ̿ Deep RNA sequencing Reveals dynamic regulation of myocardial noncoding rnas in failing human heart and remodeling with mechanical circulatory support 
    23 ̼S Quantifying rare, deleterious variation in 12 human cytochrome P450 drug-metabolism genes in a large-scale exome dataset     
    30 Epistatic Selection between Coding and Regulatory Variation in Human Evolution and Disease 
    30 ̰ȭ Comprehensive molecular characterization of gastric adenocarcinoma 

    2014-07:
    05 μ Personal health records: a randomized trial of effects on elder medication safety    
    05 Network-based stratification of tumor mutations    
    12 κ Whole-genome DNA methylation profiling using MethylCap-seq    
    12 ȼ Integrated RNA and DNA sequencing improves mutation detection in low purity tumors    
    19 Using Multiplexed Assays of Oncogenic Drivers in Lung Cancers to Select Targeted Drugs 
    19 Diagnosis of copy number variation by Illumina next generation sequencing is comparable in performance to oligonucleotide array comparative genomic hybridisation    
    26 ֿ Computational Drug Repositioning: From Data to Therapeutics    
    26 ISMB_Review: MicroRNA-Gene Association As a Prognostic Biomarker in Cancer Exposes Disease Mechanisms    
    26 ISMB review : Simultaneously identification of multiple driver pathways in cancer 
    26 ISMB review : A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes    
    26 Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures 
    26 ӿ ISMB review: Dissecting cancer heterogeneity with a probabilistic genotype-phenotype model    

    2014-06:
    07 Toward Enhanced Pharmacovigilance using Patient-Generated Data on the Internet  
    07 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy    
    14 Integrating Systems Biology Sources Illuminates Drug Action    
    14 Heritability and genomics of gene expression in peripheral blood 
    21 ̼S Clinical Interpretation and Implications of Whole-Genome Sequencing  
    21 ̿ Association Between BRAF V600E Mutation and Mortality in Patients With Papillary Thyroid Cancer 
    28 ̰ȭ Prioritizing Diesase-Linked Variants, Genes, and Pathways with an Integrative Whole-Genome Analysis Pipeline    
    28 ӿ A general framework for estimating the relative pathogenicity of human genetic variants.    

    2014-05:
    03 Integrative and Comparative Genomic Analysis of Lung Squamous Cell Carcinomas in East Asian Patients    
    03 κ A SWI/SNF-related autism syndrome caused by de novo mutations in ADNP    
    10 ȼ Technical Variations in Low-Input RNA-seq Methodologies    
    10 Loss-of-function mutations in SLC30A8 protect against type 2 diabetes    
    17 Allelic expression of deleterious protein-coding variants across human tissues  
    17 ֿ Optimizing Drug Outcomes through Pharmacogenetics: a Case for Preemptive genotyping    
    24 Personalized genomic disease risk of volunteers    
    24 Presentation of clinical laboratory results 

    2014-04:
    05 Using ontology-based annotation to profile disease research    
    05 ̼S Inconsistency in large pharmacogenomic studies    
    12 ̼ Dose-specific adverse drug reaction identification in electronic patient records: temporal data mining in an inpatient psychiatric population.    
    12 Systematic identification of genomic markers of drug sensitivity in cancer cells    
    19 Understanding mechanisms underlying human gene expression variation with RNA sequencing    
    19 ̰ȭ Identification of potential synthetic lethal genes to p53 using a computational biology approach    
    26 ӿ Identification of synthetic lethal pairs in biological systems through network information centrality    
    26 μ Cross-domain targeted ontology subsets for annotation: The case of SNOMED CORE and RxNorm    

    2014-03:
    08 μ Automated Mapping of Pharmacy Orders from Two Electronic Health Record Systems to RxNorm within the STRIDE Clinical Data Warehouse    
    08 Comprehensive identification of mutational cancer driver genes across 12 tumor types    
    15 κ A Higher Mutational Burden in Females Supports a Female Protective Model in Neurodevelopmental Disorders    
    15 ȼ A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis    
    22 Using Whole-Exome Sequencing to Identify Inherited Causes of Autism    
    22 Clinically Actionable Genotypes Among 10,000 Patients With Preemptive Pharmacogenomic Testing 
    29 ֿ DGIdb: mining the druggable genome    
    29 Rare coding variants in the phospholipase D3 gene confer risk for Alzheimers disease    

    2014-02:
    15 ̰ȭ InSiGHT    
    15 ӿ Discovery and saturation analysis of cancer genes across 21 tumour types    

    2014-01:
    04 ̼S Chemotherapeutic drug susceptibility associated SNPs are enriched in expression quantitative trait loci    
    04 Development and evaluation of an ensemble resource linking medications to their indications    
    18 Genetic variants associated with warfarin dose in African-American individuals: a genome-wide association study    
    18 ̼ Phenotyping for patient safety: algorithm development for electronic health record based automated adverse event and medical error detection in neonatal intensive care    
    25 A Structure-Based Approach for Mapping Adverse Drug Reactions to the Perturbation of Underlying Biological Pathways    
    25 Incorporating personalized gene sequence variants, molecular genetics knowledge, and health knowledge into an EHR prototype based on the Continuity of Care Record standard 

    2013-12:
    07 ̰ȭ Tracking the clonal origin of lethal prostate cancer    
    07 ӿ Integrative annotation of variants from 1092 humans: application to cancer genomics.    
    14 μ Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium    
    14 ȼ Finding the active genes in deep RNA-seq gene expression studies    
    21 κ Diagnostic Exome Sequencing in Persons with Severe Intellectual Disability    
    21 Mutational landscape and significance across 12 major cancer types 
    28 Assessing the phenotypic effects in the general population of rare variants in genes for a dominant Mendelian form of diabetes    
    28 PubChem BioAssay : 2014 update    

    2013-11:
    02 A new subtype of bone sarcoma defined by BCOR-CCNB3 gene fusion    
    02 κ Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders    
    09 ȼ Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data    
    09 Systematic Pharmacogenomics Analysis of Malay Whole Genome : Proof of Concept for Personalized Medicine    
    16 ̼S Pathway analysis of genome-wide data improves warfarin dose prediction    
    16 A method for inferring medical diagnoses from patient similarities    
    23 Altering physiological networks using drugs: steps towards personalized physiology 
    23 ̼ Harvest: an open platform for developing web-based biomedical data discovery and reporting applications    
    30 The Coriell personalized medicine collaborative pharmacogenomics appraisal, evidence scoring and interpretation system    
    30 canSAR: an integrated cancer public translational research and drug discovery resource    

    2013-10:
    05 ̼ Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text. 
    05 ̼S Analytical and simulation methods for estimating the potential predictive ability of genetic profiling: a comparison of methods and results    
    12 Predicting Adverse Drug Reactions Using Publicly Available PubChem BioAssay Data    
    12 Transcriptome and genome sequencing uncovers functional variation in humans  
    19 ӿ Discovery Analysis of TCGA Data Reveals Association between Germline Genotype and Survival in Ovarian Cancer Patients 
    19 ̰ȭ Deleterious- and disease-allele prevalence in healthy individuals insights from current predictions, mutation databases, and population-scale resequencing.    
    26 μ Utilizing RxNorm to support practical computing applications: Capturing medication history in live electronic health records    
    26 Germline variation in TP53 regulatory network genes associates with breast cancer survival and treatment outcome 

    2013-09:
    07 μ Evaluating standard terminologies for encoding allergy information    
    07 DrGaP: A Powerful Tool for Identifying Driver Genes and Pathways in Cancer Sequencing Studies    
    14 Mutations in NOTCH2 cause Hajdu-Cheney syndrome, a disorder of severe and progressive bone loss    
    14 κ Detection of Clinically Relevant Genetic Variants in Autism Spectrum Disorder by Whole-Genome Sequencing    
    28 Signatures of mutational processes in human cancer    
    28 Normalized names for clinical drugs: RxNorm at 6 years    

    2013-08:
    03 ̿  
    03 Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas    
    10 The feasibility of QR-code prescription in Taiwan    
    10 ̼S Variations in predicted risks in personal genome testing for common complex diseases    
    17 ̼ Effect of Direct-to-Consumer Genomewide Profiling to Assess Disease Risk    
    17 Structure of Protein Interaction Networks and Their implications on Drug Design 
    24 The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology    
    24 Using SIFT and PolyPhen to Predict Loss-of-Function and Gain-of-Function Mutations    
    31 ̰ȭ MI-ONCOSEQ_1    
    31 ӿ  

    2013-07:
    06 ̰ȭ Total and Regional Adiposity and cognitive change in older adults -The Health, aging and body composition(ABC) study    
    06 ӿ CpG island shore methylation regulates caveolin-1 expression in breast cancer      
    20 μ Mapping Partners Master Drug Dictionary to RxNorm using an NLP-based approach 
    20 Comprehensive molecular characterization of clear cell renal cell carcinoma 
    27 Target Essentiality and Centrality Characterize Drug Side Effects 
    27 κ Frequent somatic mutations in MAP3K5 and MAP3K9 in metastatic melanoma identified by exome sequencing    

    2013-06:
    01 ̿ Evolution of the cancer genome 
    01 integrated genomic characterization of endometrial carcinoma 
    08 Mutations in NMNAT1 cause Leber congenital amaurosis and identify a new disease pathway for retinal degeneration    
    08 κ Exome sequencing supports a de novo mutational paradigm for schizophrenia    
    15 Discovery of Stress Responsive DNA Regulatory Motifs in Arabidopsis    
    15 A corpus-based approach for automated LOINC mapping 
    22 ̼S Annotation of functional variation in personal genomes using RegulomeDB.     
    22 ̼ Performance of pharmacovigilance signal-detection algorithms for the FDA adverse event reporting system.    
    29 Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score, Condel    
    29 ̿ The Life History of 21 Breast Cancers    

    2013-05:
    04 Literature Based Drug Interaction Prediction with Clinical Assessment Using Electronic Medical Records: Novel Myopathy Associated Drug Interactions     
    04 An Integrated Approach to Uncover Drivers of Cancer 
    11 ӿ DNA co-methylation analysis suggests novel functional associations between gene pairs in breast cancer samples    
    11 Comprehensive genomic characterization defines human glioblastoma genes and core pathways    
    25 μ The ISO/IEC 11179 norm for metadata registries: Does it cover healthcare standards in empirical research?    
    25 ̰ȭ Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia 

    2013-04:
    06 ̿ Risk Prediction of Complex Diseases from Family History and Known Susceptibility Loci, with Applications for Cancer Screening    
    06  
    13 Mosaic overgrowth with fibroadipose hyperplasia is caused by somatic activating mutations in PIK3CA     
    13 κ Germline BAP1 mutations predispose to malignant mesothelioma     
    20 Personalized Pathway Enrichment Map of Putative Cancer Genes from Next Generation Sequencing Data    
    20 SHRINE: Enabling Nationally Scalable Multi-Site Disease Studies    
    27 ̼S Cancer GAMAdb: database of cancer genetic associations from meta-analyses and genome-wide association studies    
    27 ̼ Pharmacovigilance Using Clinical Notes.    

    2013-03:
    02 Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants    
    02 Lifelog Data Model and Management: Study on Research Challenges    
    09 ̼S SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS.    
    09 ̼ Enhancing Adverse Drug Event Detection in Electronic Health Records Using Molecular Structure Similarity:Application to Pancreatitis  
    16 SNAP: predict effect of non-synonymous polymorphisms on function    
    16 Genomic Variation landscape of the human gut microbiome     
    23 ̰ȭ A method for identifying biomarkers of aging and constructing an index of biological age in humans    
    23 Functional characterization of motif sequences under purifying selection    
    30 ӿ Identification of markers associated with global changes in DNA methylation regulation in cancers      
    30 μ The effect of electronic medical record system sophistication on preventive healthcare for women 

    2013-02:
    02 Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances    
    02 Alexander A gene ontology inferred from molecular networks      
    09 GenePING : secure, scalable management of personal genomic data 
    09 ATHENA A tool for meta-dimensional analysis applied to genotypes and gene expression data to predict HDL cholesterol levels    
    23 Disease-related mutations predicted to impact protein function 
    23 PASTE: patient-centered SMS text tagging in a medication management system    

    2013-01:
    05 Contribution of Transcription Factor Binding Site Motif Variants to Condition-Specific Gene Expression Patterns in Budding Yeast    
    05 Performance comparison of whole-genome sequencing platforms    
    12 ̼S DARNED: a DAtabase of RNa EDiting in humans    
    12 CAERUS: Predicting CAncER oUtcomeS Using Relationship between Protein Structural Information, Protein Networks, Gene Expression Data, and Mutation Data    
    19 ̼ The EU-ADR Web Platform: delivering advanced pharmacovigilance tools.     
    19 Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference    
    26 lincRNA Disease association 
    26 ̰ȭ Clonal evolution in relapsed acute myeloid leukemia revealed by whole genome sequencing    

    2012-12:
    01 ̰ȭ A novel, privacy-preserving cryptographic approach for sharing sequencing data.    
    01 ̼ Comparative analysis of pharmacovigilance methods in the detection of adverse drug reactions using electronic medical records    
    08 Integration of External signaling Pathways with the Core Transctriptional Network in Embryonic Stem Cells 
    08 Federated ontology-based queries over cancer data 
    15 հ Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns    
    15 Alexander Associating Genes and Protein Complexes with Disease via Network Propagation      
    22 Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing    
    22 Atlas2 Cloud: a framework for personal genome analysis in the cloud    
    29 A pragmatic method for electronic medical record-based observational studies - developing an electronic medical records retrieval system for clinical research    
    29 PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations    

    2012-11:
    03 PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis    
    03 The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research    
    10 In silico blood genotyping from exome sequencing data    
    10 Clinical documentation: composition or synthesis?    
    17 ̼S Subnetwork-based analysis of chronic lymphocytic leukemia identi&    
    17 An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people    
    24 Alternative isoform regulation in human tissue transcriptomes    
    24 Large-scale prediction and testing of drug activity on side-effect targets    

    2012-10:
    06 the genetic landscape of a cell    
    06 Encode(2) : Landscape of transcription in human cells     
    13 ü TBC 
    13 ü TBC 
    20 ̰ȭ A framework for evaluating the appropriateness of clinical decision support alerts and reponses    
    20 հ Comparative analysis of somatic copy-number alterations across different human cancer types reveals two distinct classes of breakpoint hotspots 
    27 Analysis and design of RNA sequencing experiments for identifying isoform regulation(MISO)    
    27 Linking disease associations with regulatory information in the human genome    

    2012-09:
    01 Comprehensivemolecular characterization of human colon and rectal cancer    
    01 Chromatin organization is a major influence on regional mutation rates in human cancer cells     
    08 Portability of an algorithm to identify rheumatoid arthritis in electronic health records    
    08 ̼S How accurate can genetic predictions be?    
    15 Patterns and rates of exonic de novo mutations in autism spectrum disorders    
    15 ̼ Development and evaluation of a common data model enabling active drug safety surveillance using disparate healthcare databases    
    22 Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers.    
    22 Construction of regulatory networks using expression time-series data of a genotyped population    

    2012-08:
    04 Emerging Patient-Driven Health Care Models: An Examination of Health Social Networks, Consumer Personalized Medicine and Quantified Self-Tracking    
    04 The CancerCell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity    
    11 ISMB Review 
    11 ISMB Review 
    18 Highly interconnected genes in disease-specific networks are enriched for disease-associated polymorphisms    
    18 Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics    
    25 Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes    
    25 The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups    

    2012-07:
    07 An i2b2-based, generalizable, open source, self-scaling chronic disease registry    
    07 ̼S REGENT: a risk assessment and classi&    
    21 Personalized Pathway Enrichment Map of Putative Cancer Genes from Next Generation Sequencing Data    
    21 ̼ Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs    
    28 ranking of multidimensional drug profiling data by fractional adjusted bi-partitional scores    
    28 ̰ȭ Variation in Patient-Sharing Networks of Physicians Across the United States    

    2012-06:
    02 ȭ Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states    
    02 Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses     
    09 Transcriptomic analysis of autistic brain reveals convergent molecular pathology    
    09 ̰ȭ Operational implementation of Prospective Genotyping for Personalized Medicine: The Design of the Vanderbilt PREDICT Project    
    16 Clustering of DNA Sequences in Human Promoters    
    16 A pharmacogenomic method for individualized prediction of drug sensitivity    
    23 Differential expression in RNA-seq:A matter of depth    
    23 A Mathematical Methodology for Determining the Temporal Order of Pathway Alterations Arising during Gliomagenesis    
    30 Automated discovery of drug treatment patterns for endocrine therapy of breast cancer within an electronic medical record    
    30 A high-resolution map of human evolutionary constraint using 29 mammals    

    2012-05:
    12 ̼S Microarray meta-analysis database (M2DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database    
    12 Transcriptomic landscape of breast cancers through mRNA sequencing    
    19 ̼ High-priority drug-drug interactions for use in electronic health records    
    19 Interpretome: A Freely available, modular, and secure personal genome interpretation engine     

    2012-04:
    07 Mutual exclusivity analysis identifies oncogenic network modules    
    07 The SMART Platform: early experience enabling substitutable applications for electronic health records    
    14 PSB Review 
    14 AMIA Review 
    21 Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes    
    21 Serving the enterprise and beyond with informatics for integrating biology and the bedside    
    28 Quality evaluation of value sets from cancer study common data elements using the UMLS semantic groups    
    28 Detecting and annotating genetic variations using the HugeSeq pipeline.    

    2012-03:
    03 An Environment-Wide Association Study (EWAS) on Type 2 diabetes    
    03 Social but safe? Quality and safety of diabetes-related online social networks    
    10 A Combination of Dopamine Genes Predicts Success by Professional Wall Street Traders    
    10 A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes    
    17 Impact of data fragmentation across healthcare centers on the accuracy of a high-throughput clinical phenotyping algorithm for specifying subjects with type 2 diabetes mellitus    
    17 ̼S Content-based microarray search using differential expression profiles    
    24 ̼ Data-Driven Prediction of Drug Effects and Interactions    
    24 Systematic Drug Repositioning Based on Clinical Side-Effects    
    31 ȭ Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing    
    31 A comparison of cataloged variation between International HapMap Consortium and 1000 Genomes Project data    

    2012-02:
    04 CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge    
    04 FusionMap : detecting fusion genes from next-generation sequencing data at base-pair resolution    
    18 ̼ Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing    
    18 Using text to build semantic networks for pharmacogenomics    
    25 Exome Sequencing Reveals DNAJB6 Mutations in Dominantly Inherited Myopathy    
    25 Association of BRCA1 and BRCA2 mutations with survival, chemotherapy sensitivity, and gene mutator phenotype in patients with ovarian cancer    

    2012-01:
    07 Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease    
    07 Integrative network analysis to identify aberrant pathway networks in ovarian cancer    
    14 Incorporating personalized gene sequence variants, molecular genetics knowledge, and health knowledge into an EHR prototype based on the CCR standard    
    14 ̼ Predicting Adverse Drug Events Using Pharmacological Network Models     
    20 A Network-Based Approach to Prioritize Results from Genome-Wide Association Studies     
    20 Use of diverse electronic medical record systems to identify genetic risk for type 2 diabetes within a genome-wide association study    
    28 ̼S Web-Based Genome-Wide Association Study Identifies Two Novel Loci and a Substantial Genetic Component for Parkinson Disease     
    28 Defining the Role of Essential Genes in Human Disease    

    2011-12:
    03 BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications    
    03 ̼S Modelling schizophrenia using human induced pluripotent stem cells    
    10 Protein localization as a principal feature of the etiology and comorbidity of genetic diseases    
    10 Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence    
    17 Assessing Vaccination Sentiments with Online Social Media: Implications for Infectious Disease Dynamics and Control    
    17 Network neighbors of drug targets contribute to drug side-effect similarity    
    24 PROMISCUOUS: a database for network-based drug-repositioning    
    24 SNPedia: a wiki supporting personal genome annotation, interpretation and analysis    
    31 ̼ SeqGene a comprehensive software solution for mining exome- and transcriptome- sequencing data    
    31 Validation of a common data model for active safety surveillance research    

    2011-11:
    05 Integrating clinical research with the Healthcare Enterprise: From the RE-USE 3 project to the EHR4CR platform    
    05 Prioritizing candidate disease genes by network-based boosting of genome-wide association data    
    19 Time to recurrence and survival in serous ovarian tumors predicted from integrated genomic profiles    
    19 Evaluating Relevance Ranking Strategies for MEDLINE Retrieval    
    26 Predicting phenotypic variation in yeast from individual genome sequences    
    26 Disease-associated epigenetic changes in monozygotic twins discordant for schizophrenia and bipolar disorder    

    2011-10:
    01 Using machine learning for concept extraction on clinical documents from multiple data sources    
    01 ̼S Utility of genetic and non-genetic risk factors in prediction of type 2 diabetes: Whitehall II prospective cohort study.    
    08 Methyl-Analyzer—whole genome DNA methylation profiling    
    08 ̼ Comparison of a basic and an advanced pharmacotherapy-related clinical decision support system in a hospital care setting in the Netherlands     
    22 Generating Genome-Scale Candidate Gene Lists for Pharmacogenomics     
    22 Discovery of drug mode of action and drug repositioning from transcriptional responses    
    29 PREDICT: a method for inferring novel drug indications with application to personalized medicine.    
    29 Correlated genotypes in friendship networks    

    2011-09:
    03 Quality Evaluation of Cancer Study Common Data Elements Using the UMLS Semantic Network    
    03 Exome Sequencing and Unrelated Findings in the Context of Complex Disease Research: Ethical and Clinical Implications    
    17 A development taxonomy of GBM defined and maintained by microRNAs    
    17 Genotype Score in addition to common risk factors for prediction of type 2 diabetes    
    24 S tructural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly.    
    24 The implications of relationships between human diseases and metabolic subpathways    

    2011-08:
    06 A ten-microRNA expression signature predicts survival in glioblastoma    
    06 Sharing Data for Public Health Research by Members of an International Online Diabetes Social Network    
    13 Mapping clinical phenotype data elements to standardized metadata repositories and controlled terminologies: the eMERGE Network experience    
    13 ̼ Use of primary care electronic medical record database in drug efficacy research on cardiovascular outcomes: comparison of database and randomised controlled trial findings    
    20 A DNA methylation fingerprint of 1,628 human samples    
    20 ̼S Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals    
    27 Automated validation of genetic variants from large databases ensuring that variant references refer to the same genomic locations    
    27 Discovery and preclinical validation of drug indications using compendia of public gene expression data     

    2011-07:
    02 ̼ A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports    
    02 The use of VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency    
    16 Gene-Disease Network Analysis Reveals Functional Modules in Mendelian, Complex and Environmental Diseases    
    16 ̼ MU2A - reconciling the genome and transcriptome to determine the effects of base substitutions    
    23 Exploring the Genetic Basis of Variation in Gene Predictions with a Synthetic Association Study    
    23 Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis    
    30 Obesity related methylation changes in DNA of peripheral blood leukocytes    
    30 A knowledge discovery and reuse pipeline for information extraction in clinical notes    

    2011-06:
    04 A Novel Adaptive Method for the Analysis of Next-Generation Sequencing Data to Detect Complex Trait Associations with Rare Variants Due to Gene Main Effects and Interactions    
    04 Effect of Direct-to-Consumer Genomewide Profiling to Assess Disease Risk    
    11 Whole-Exome Re-Sequencing in a Family Quartet Identifies POP1 Mutations As the Cause of a Novel Skeletal Dysplasia    
    11 Data Integration Workflow for Search of Disease Driving Genes and Genetic Variants    
    18 Data standards for clinical research data collection forms: current status and challenges    
    18 Leukocyte DNA methylation signature differentiates pancreatic cancer patients from healthy controls    
    25 Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival    
    25 ̼S Widespread RNA and DNA Sequence Differences in the Human Transcriptome    

    2011-05:
    07 The ClinicalTrials.gov Results Database Update and Key Issues    
    07 ̼S DSGeo: Software tools for cross-platform analysis of gene expression data in GEO     
    14 ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments    
    14 ̼ A web-based quantitative signal detection system on adverse drug reaction in china    
    21 Global analysis of disease-related DNA sequence variation in 10 healthy individuals: implications for whole genome-based clinical diagnostics    
    21 ̼ miRGator v2.0 : an integrated system for functional investigation of microRNAs    
    28 CCancer a birds eye view on gene lists reported in cancer-related studies     
    28 AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services    

    2011-04:
    02 PathLocdb: a comprehensive database for the subcellular localization of metabolic pathways and its application to multiple localization analysis    
    02 Improving disease gene prioritization using the semantic similarity of Gene Ontology terms      
    09 ̼ Towards computational prediction of microRNA function and activity    
    09 The military health system`s personal health record pilot with Microsoft HealthVault and Google Health    
    16 A map of human genome variation from population-scale sequencing    
    16 Detecting Cancer Gene Networks Characterized by Recurrent Genomic Alterations in a Population    
    23 ۿ Targeted next-generation sequencing detects point mutations, insertions, deletions and balanced chromosomal rearrangements as well as identifies novel leukemia-specific fusion genes in a single proced    
    23 Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions    
    30 Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level.     
    30 Metabolic Robustness and Network Modularity: A Model Study    

    2011-03:
    05 ̼S A global map of human gene expression    
    05 Future Developments of Medical Informatics from the Viewpoint of Networked Clinical Research    
    12 ۿ Cancer Therapy Design Based on Pathway Logic    
    12 A sub-pathway-based approach for identifying drug response principal network    
    19 Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak    
    19 Discovery of common Asian copy number variants using integrated high-resolution arrayCGH and massively parallel DNA sequencing     
    26 ̼ Comorbidity and repeat admission to hospital for adverse drug reactions in older adults: retrospective cohort study    
    26 Measuring the Evolutionary Rewiring of Biological Networks    

    2011-02:
    12 ̼ a method for encoding clinical datasets with SNOMED-CT     
    12 Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation    
    19 ̼ Using GOstats to test gene lists for GO term association    
    19 NINDS common data element project: a long-awaited breakthrough in streamlining trials.    
    26 Clinical assessment incorporating a personal genome    
    26 CNAmet_an R package for integrating copy number, methylation and expression data    

    2011-01:
    08 Approaching semantic interoperability in Health Level Seven    
    08 A basic study design for expedited safety signal evaluation based on electronic healthcare data    
    15 Biological Process Linkage Networks    
    15 The UMLS-CORE project: a study of the problem list terminologies used in large healthcare institutions     
    22 ۿ Association of tissue lineage and gene expression: conservatively and differentially expressed genes define common and special functions of tissues    
    22 ̼S BioPortal: ontologies and integrated data resources at the click of a mouse    
    29 Large scale data integration framework provides a comprehensive view on glioblastoma multiforme    
    29 Combining Network Modeling and Gene Expression Microarray Analysis to Explore the Dynamics of Th1 and Th2 Cell Regulation 

    2010-12:
    11 Mutated genes, pathways and processes in tumours    
    11 ̼ miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature    
    18 Computational identification of tissue-specific alternative splicing elements in mouse genes from RNA-Seq    
    18 Rocky Single-nucleotide polymorphisms inside microRNA target sites influence tumor susceptibility    

    2010-11:
    06 Rocky MicroSNiPer : A Web Tool for Prediction of SNP Effects on Putative microRNA Targets    
    06 permGPU: Using graphics processing units in RNA microarray association studies    
    13 ۿ The Human Phenotype Ontology    
    13 FMM: a web server for metabolic pathway reconstruction and comparative analysis.    
    20 Epigenetic Epidemiology of Common Complex Disease: Prospects for Prediction, Prevention, and Treatment    
    27 ̼S Microarray retriever: a web-based tool for searching    
    27 ̼ Adverse Drug Reactions in Hospital In-Patients: A Prospective Analysis of 3695 Patient-Episodes    

    2010-10:
    02 Heterogeneity prevails: the state of clinical trial data management in Europe - results of a survey of ECRIN centres    
    02 ̼S ArrArrayExpress update from an archive of functional genomics experiments to the atlas of gene expression    
    09 ̼ The Application of an Institutional Clinical Data Warehouse to the Assessment of Adverse Drug Reactions (ADRs)    
    09 Scaling the walls of discovery: using semantic metadata for integrative problem solving    
    16 ̼ High-Throughput SuperSAGE for Digital Gene Expression Analysis of Multiple Samples Using Next Generation Sequencing    
    16 Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information    
    30 CNAseg - a novel framework for identification of copy number changes in cancer from second-generation sequencing data    
    30 An integrative mutidimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer    

    2010-09:
    04 ̼ RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays    
    04 Exome sequencing identifies the cause of a mendelian disorder    
    11 Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis    
    11 Rocky A Catalog of Polymorphisms Falling in MicroRNA-Binding Regions of Cancer Genes    
    18 A standard variation file format for human genome sequences    
    18 ۿ HyBrow: a prototype system for computer-aided hypothesis evaluation    
    25 Extending pathways based on gene lists using InterPro domain signatures    
    25 Identification and evaluation of a possible signal of exacerbation of colitis during rofecoxib treatment, using Prescription-Event Monitoring data    

    2010-08:
    07 The FDA Critical Path Initiative and Its Influence on New Drug Development    
    07 GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms    
    14 Mining consequence events in temporal health data    
    14 ۿ Symbolic rule-based classification of lung cancer stages from free-text pathology reports    
    21 ̼S Recent developments in StemBase: a tool to study gene expression in human and murine stem cells.    
    21 ̼ Computerized Surveillance for Adverse Drug Events in a Pediatric Hospital    
    28 PathText: a text mining integrator for biological pathway visualizations    
    28 Supporting Ontology-Based Dynamic Property and Classification in WebSphere Metadata Server    

    2010-07:
    03 Applications in Detecting Adverse Drug Reactions : Applications in Detecting Adverse Drug Reactions    
    03 Toward an ontology-based framework for clinical research databases    
    10 Semantic web data warehousing for caGrid    
    10 ̼ DSAP : deep-sequencing small RNA analysis    
    17 MADNet: microarray database network web server    
    17 ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data    
    24 Improved Microarray-Based Decision Support with Graph Encoded Interactome Data    
    24 Pandora, a PAthway and Network DiscOveRy Approach based on common biological evidence    
    31 Rocky Human polymorphism at microRNAs and microRNA target sites    
    31 Uniformly curated signaling pathways reveal tissue-specific cross-talks and support drug target discovery    

    2010-06:
    05 Harmonization of health data at national level: A pilot study in China    
    05 Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma    
    12 International network of cancer genome projects    
    12 Fault Tolerance in Protein Interaction Networks: Stable Bipartite Subgraphs and Redundant Pathways    
    19 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets    
    19 Rocky Genome-Wide Analysis of Small RNA and Novel MicroRNA Discovery in Human Acute Lymphoblastic Leukemia Based on Extensive Sequencing Approach    
    26 ۿ caTIES: a grid based system for coding and retrieval of surgical pathology reports and tissue specimens in support of translational research    
    26 PhenoFam-gene set enrichment analysis through protein structural information    

    2010-05:
    01 LookSeq: A browser-based viewer for deep sequencing data    
    01 IntOGen: integration and data mining of multidimensional oncogenomic data    
    08 Rare Variants Create Synthetic Genome-Wide Associations    
    08 Rocky Discovery of Novel MicroRNAs in Female Reproductive Tract Using Next Generation Sequencing    
    15 Deciphering the splicing code    
    15 ۿ Formulation of a model for automating infection surveillance: algorithmic detection of central-line associated bloodstream infection    
    22 HAMSTER: visualizing microarray experiments as a set of minimum spanning trees    
    22 A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery    
    29 A Pathway-Based View of Human Diseases and Disease Relationships    
    29 ̼ Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms    

    2010-04:
    03 The gputools package enables GPU computing in R    
    03 ۿ Statistical search on the Semantic Web    
    17 NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways    
    17 HPD: an online integrated human pathway database enabling systems biology studies    
    24 ̼ Cepred: Predicting the Co-Expression Patterns of the Human Intronic microRNAs with Their Host Genes    
    24 A metadata approach for clinical data management in translational genomics studies in breast cancer.    

    2010-03:
    06 ConceptGen: a gene set enrichment and gene set relation mapping tool    
    06 PID: the Pathway Interaction Database    
    13 ̼ MTar: a computational microRNA target prediction architecture for human transcriptome    
    13 The Enterprise Data Trust at Mayo Clinic: a semantically integrated warehouse of biomedical data    
    20 Repertoire of microRNAs in Epithelial Ovarian Cancer as Determined by Next Generation Sequencing of Small RNA cDNA Libraries    
    20 Rocky Ontology-driven indexing of public datasets for translational bioinformatics    
    27 Integration of clinical and microarray data with kernel methods    
    27 Large-scale prediction of protein-protein interactions from structures    

    2010-02:
    06 MIRAGAA-a methodology for finding coordinated effects of microRNA expression changes and genome aberrations in cancer    
    06 Incorporating functional inter-relationships into protein function prediction algorithms    
    20 Prediction of Human Functional Genetic Networks from Heterogeneous Data Using RVM-Based Ensemble Learning    
    20 Rocky An Analysis of Human MicroRNA and Disease Associations    
    27 Multifactor Dimensionality Reduction for Graphics Processing Units Enables Genome-wide Testing of Epistasis in Sporadic ALS    
    27 ۿ An ontological modeling approach to cerebrovascular disease studies: The NEUROWEB case    

    2010-01:
    09 A methodology for the analysis of differential coexpression across the human lifespan    
    09 Human gene expression sensitivity according to large scale meta-analysis    
    16 A statistical framework for genomic data fusion    
    16 Rocky In silico method for systematic analysis of feature importance in microRNA-mRNA interactions    
    23 ۿ Relations in biomedical ontologies    
    23 Automated Database Mediation Using Ontological metadata mappings    
    30 ̼ Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts    
    30 PathCase: pathways database system 

    2009-12:
    05 Exome sequencing identifies the cause of a mendelian disorder    
    05 Gene set internal coherence in the context of functional profiling    
    12 Rocky Computational Challenges in miRNA Target Predictions: To Be or Not to Be a True Target?    
    12 An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer    
    19 ۿ Standards to Support Information Systems Integration in Anatomic Pathology    
    19 Drug target identification using side-effect similarity    
    26 ̼ Genome-Wide Transcriptional Profiling Reveals MicroRNA-Correlated Genes and Biological Processes in Human Lymphoblastoid Cell Lines    
    26 mimiRNA: a microRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their target    

    2009-11:
    07 A kernel based integration of genome wide data for clinical decision support    
    07 Rocky ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization    
    14 ۿ Application and evaluation of automated semantic annotation of gene expression experiments    
    14 WhichGenes: a web-based tools for gathering, building, storing and exporting gene sets with application in gene set enrichment analysis    
    21 Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists    
    21 Genomic signatures to guide the use of chemotherapeutics    
    28 ̼ Tissue and Process Specific microRNA-mRNA Co-Expression in Mammalian Development and Malignancy    
    28 Identification of microRNA activity by Targets Reverse EXpression    

    2009-10:
    10 Rocky mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer    
    10 The effects of probe binding affinity differences on gene expression measurements and how to deal with them    
    17 ۿ The Stanford Tissue Microarray Database    
    17 Gene expression signatures, clinicopathological features, and individualized therapy in breast cancer    
    24 KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database    
    24 Conserved Expression Patterns Predict microRNA Targets    
    31 ̼ Decoding global gene expression programs in liver cancer by noninvasive imaging    
    31 Integrating protein-protein interactions and text mining for protein function prediction    

    2009-09:
    05 Validation of Biomarker-Based Risk Prediction Models    
    05 Corpus-based and Knowledge-based Measures of Text Semantic Similarity    
    12 A semantic web approach to biological pathwa data reasoning and integration    
    12 ̼ TargetMiner: MicroRNA target prediction with systematic identification of tissue specific negative example    
    19 Metadata-Driven Software for Clinical Trials    
    19 microPred: effective classification of pre-miRNAs for human miRNA gene prediction    
    26 Pharmacogenomics 2009 Review 
    26 Semantic Similarity in Biomedical Ontologies    

    2009-08:
    01 Rocky DIANA-microT web server: elucidating microRNA functions through target prediction    
    01 GEFERENCE: Reference Database for Construing Personal Genome Expression. (BIOCOMP`09 presentation)    
    08 Improved detection of overrepresentation of Gene-Ontology annotations with parent-child analysis    
    08 ۿ Non-genetic heterogeneity - a mutation-independent driving force for the somatic evolution of tumours    
    22 Intrinsic variability of gene expression encoded in nucleosome positioning sequences    
    22 Instrumenting the health care enterprise for discovery research in the genomic era    
    29 CRONOS: the cross-reference navigation server      
    29 Bridging real world semantics to model world semantics for taxonomy based knowledge representation system    

    2009-07:
    04 MIMAS 3.0 is a Multiomics Information Management and Annotation System    
    04 Gene Ontology term overlap as a measure of gene functional similarity    
    11 Rocky Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application    
    11 ISMBECCB2009 Conference report 
    18 ۿ The First RSBI (ISA-TAB) Workshop: Can a Simple Format Work for Complex Studies?    
    18 Decision support methods for the detection of adverse events in post-marketing data    
    25 ConsensusPathDB - a database for integraing human functional interaction networks    
    25 ̼ MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression    

    2009-06:
    13 ۿ Integration of Prostate Cancer Clinical Data Using an Ontology    
    13 Novel integration of hospital electronic medical records and gene expression measurements to identify genetic markers of maturation    
    20 Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation    
    20 ̼ GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists    
    27 The clinical document architecture and the continuity of care record: a critical analysis    
    27 UTGB Toolkit for Personalized Genome Browsers    

    2009-05:
    09 Medusa: a simple tool for interaction graph analysis and STRING database    
    09 ̼ Quality Assessment and Data Analysis for microRNA expression Arrays    
    16 HL7 RIM: An Incoherent Standard    
    16 A combinatorial approach to determine the context-dependent role in transcriptional and posttranscriptional regulation in Arabidopsis thaliana    
    23 In Vitro Analysis of Integrated Global High-Resolution DNA Methylation Profiling with Genomic Imbalance and Gene Expression in Osteosarcoma    
    23 A relation based measure of semantic similarity for Gene Ontology annotations.    
    30 Rocky RNAdba comprehensive mammalian noncoding RNA database    
    30 Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues    

    2009-04:
    04 GS2: An efficiently computable measure of GO-based similarity of gene sets    
    04 Identification of microRNAs with regulatory potential using a matched microRNA-mRNA time-course data    
    11 Clinical Research Informatics: Challenges, Opportunities and Definition for an Emerging Domain [Clinical Research]   
    11 GraphWeb: mining heterogeneous biological networks for gene modules with functional significance    
    18 Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome    
    18 Rocky Argonaute database for gene regulation by mammalian miRNAs    
    25 ۿ Cruella Developing a Scalable Tissue Microarray Data Management System    
    25 Changing course in ageing research- The Healthy Ageing Phenotype    

    2009-03:
    07 Filtering of false positive microRNA candidates by a clustering-based approach    
    07 GenomeGraphs: integrated genomic data visualization with R    
    14 Information theory applied to the sparse gene ontology annotation network to predict novel gene function    
    14 ۿ Bio2RDF: Towards a mashup to build bioinformatics knowledge systems    
    21 aging from molecules to populations    
    21 Gene expression trends and protein features effectively complement each other in gene function prediction    
    28 PathExpress: a web-based tool to identify relevant pathways in gene expression data      
    28 ̼ Comparison of normalization methods with microRNA microarray    

    2009-02:
    07 SIGMA2: A system for the integrative genomic multi-dimensilnal analysis of cancer genomes, epigenomes, and transcriptomes    
    07 Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data    
    14 ۿ Ontology driven integration platform for clinical and translational research    
    14 Meta-analysis of age-related gene expression profiles identifies common signatures of aging    
    21 Human microRNAs co-silence in well-separated groups and have different predicted essentialities    
    21 An integrative approach for biological data mining and visualization    
    28 ̼ MicroRNA target prediction by expression analysis of host genes    
    28 Metadata mapping and reuse in caBIG    

    2009-01:
    03 Systematic reconstruction of TRANSPATH data into cell system markup language      
    03 ۿ A system for sharing routine surgical pathology specimens across institutions: the Shared Pathology Informatics Network    
    10 A method for identifying biomarkers of agings and constructing an index of biological age in humans    
    10 Identification of transcription factor and microRNA binding sites in responsible to fetal alcohol syndrome    
    17 KEGG spider: interpretation of genomics data in the context of the global gene metabolic network      
    17 ̼ Genomic Profiling of MicroRNA and Messenger RNA Reveals Deregulated MicroRNA Expression in Prostate Cancer    
    31 The Common Data Elements for cancer research: remarks on functions and structure.    
    31 Finding microRNA regulatory modules in human genome using rule induction    

    2008-12:
    06 Further evaluation of the basic nature of the human biological aging process based on a factor analysis of age-related physiological variables    
    06 Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma    
    13 Genome-wide screening of copy nuber alterations and LOH events in renal cell carcinomas and integration with gene expression profile    
    13 ̼ Global correlation analysis for micro-RNA and mRNA expression profiles in human cell lines    
    20 Research electronic data capture (REDCap)-A metadata-driven methodology and workflow process for providing translational research informatics support.    
    20 Identification of MicroRNA Regulatory Modules in Arabidopsis via A Probabilistic Graphical Model    
    27 Correlation between Gene Expression and GO Semantic Similarity    

    2008-11:
    01 ۿ Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHE)    
    01 A new approach to the concept and computation of biological age    
    08 Network-based global inference of human disease genes    
    08 A global pathway crosstalk network    
    15 ̼ An Integrative Analysis of microRNA and mRNA Expression - A Case Study    
    15 Auditing the Semantic Completeness of SNOMED CT Using Formal Concept Analysis    
    22 Analysis of regulatory network topology reveals functionally distinct classes of microRNAs    
    22 MD-SeeGH: a platform for integrative analysis of multi-dimensional genomic data    
    29 An ontology-driven semantic mashup of gene and biological pathway    
    29 ۿ Synoptic tool for reporting of hematological and lymphoid neoplasms based on World Health Organization classification and College of American Pathologists checklist.    

    2008-10:
    04 ECCB 2008 review 
    04 Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways    
    04 SIRENE: supervised inference of regulatory networks    
    04 Clinically driven semi-supervised class discovery in gene expression data    
    11 ̼ The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression    
    11 Translational Bioinformatics: Coming of Age 
    18 Removal of AU Bias from Microarray mRNA Expression Data Enhances Computational Identification of Active MicroRNAs    
    18 Metrics for GO based protein semantic similarity: a systematic evaluation    
    25 RNA-seq Review 
    25 Integrative Genomic Analysis 

    2008-09:
    06 Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma    
    06 Gene Vector Analysis (Geneva): A unified method to detect differentially-regulated gene sets and similar microarray experiments    
    20 ۿ Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project    
    20 Disentangling the Genetic Determinants of Human Aging:Biological Age as an Alternative to the Use of Survival Measures    
    27 Unraveling transcriptional regulatory programs by integrative analysis of microarray and transcription factor binding data    
    27 Reconstructing networks of pathways via significance analysis of their intersections.      

    2008-08:
    02 Exploring the functional landscape of gene expression: directed search of large microarray compendia      
    09 Novel MicroRNA Candidates and miRNA-mRNA Pairs in Embryonic Stem (ES) Cells    
    09 ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses    
    16 ۿ Integrative mathematical oncology    
    16 ̼ mRNA/microRNA gene expression profile in microsatellite unstable colorectal cancer    
    23 A gene recommender algorithm to identify coexpressed genes in C. elegans      
    23 SIRENE: supervised inference of regulatory networks    
    30 semCDI: A Query Formulation for Semantic Data Integration in caBIG      
    30 MicroRNA regulation and the variability of human cortical gene expression    

    2008-07:
    05 A semantic grid infrastructure enabling integrated access and analysis of multilevel biomedical data in support of postgenomic clinical trials on cancer.    
    05 Proliferating cells express mRNAs with shorted 3-untranslated regions and fewer microRNA target sites    
    12 SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levels 
    12 GEPAS, a web-based tool for microarray data analysis and interpretation    
    19 ۿ Differential variability analysis of gene expression and its application to human diseases    
    19 Nucleosome positioning from tiling microarray data    
    26 The Primary Care Research Object Model (PCROM): A Computable Information Model for Practice-Based Primary Care Research    
    26 ̼ Prediction of both conserved and nonconserved microRNA    

    2008-06:
    07 Metadata review    
    07 Individual mRNA expression profiles reveal the effects of specific microRNAs    
    14 SNP@Promoter: a database of human SNPs (Single Nucleotide    
    14 Identification of differentially expressed gene categories in microarray studies using nonparametric multivariate analysis    
    21 ۿ Ontology-based, Tissue MicroArray oriented, image centered tissue bank    
    21 Computational epigenetics    
    28 Use and miuse of the gene ontology annotations    
    28 ̼ Genomic and epigenetic alterations deregulate microRNA expression in human epithelial ovarian cancer    

    2008-05:
    03 The OBO Foundry: coordinated evulution of ontologies to support biomedical data integration    
    03 ̼ Computational analysis of biological functions and pathways    
    10 HealthMap: Global Infectious Disease Monitoring through Automated Classification and Visualization of Internet Media Reports    
    10 Inferring MicroRNA Activities by Combining Gene Expression with MicroRNA Target Prediction    
    17 The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge    
    17 Data Mining for Chinese Materia Medica and Pharmacological Research    
    24 ۿ Expression of MicroRNAs and Protein-Coding Genes Associated With Perineural Invasion in Prostate Cancer    
    24 Predicting cancer involvement of genes from heterogeneous data    
    31 The Mouse Tumor Biology database    
    31 ̼ The microRNA.org resource:targets and expression    

    2008-04:
    05 SPIKE - a databse, visulization and analysis tool of cellular signaling pathways    
    05 ̼ MicroRNA acuurately identify cancer tissue origin    
    12 Epoch: an Ontological Framework to Support Clinical Trials Management    
    12 Dissecting microregulation of a master regulatory network      
    19 The complete genome of an individual by massively parallel DNA sequencing    
    19 SNPLims: a data management system for genome wide association studies    
    26 Using formal concept analysis for microarray data comparison 
    26 WilcoxCV: an R package for fast variable selection in cross validation      
    26 ۿ  

    2008-03:
    08 Sharing Data and Analytical Resources Securely in a Biomedical Research Grid Environment    
    08 Systematic functional characterization of cis-regulatory motifs in human core promoters    
    15 Predicting expression patterns from regulatory sequence in Drosophila segmentation.      
    15 Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene    
    22 A method of microarray data storage using array data type    
    22 ҿ DNA repair gene XRCC3 polymorphisms and cancer risk_ a meta analysis of 48 case control study    
    29 NetworkBLAST: Comparative analysis of protein networks    
    29 Merging microarray data from separate breast cancer studies provides a robust prognostic test    

    2008-02:
    02 CancerGenes: a gene selection resource for cancer genome projects    
    02 PathExpress: a web-based tool to identify relevant pathways in gene expression data    
    16 Successful anti-cancer drug targets able to pass FDA review demonstrate the identifiable signature distince from the signatures of random genes and initially proposed targets    
    16 KEGGanim: pathway animations for high-throughput data    
    23 ̼ A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments    
    23 α A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans    

    2008-01:
    05 From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis      
    05 Towards zoomable multidimensional maps of the cell 
    12 ̼ Mining co-regulated gene profiles for the detection of functional associations in gene expression data    
    12 The BRIDG Project: A Technical Report    
    19 α Novel Integration of Hospital Electronic Medical Records and Gene Expression Measurements to Identify Genetic Markers of Maturation    
    19 Global and Local Architecture of the Mammalian microRNA-Transcription Factor Regulatory Network    
    26 Cis- and Trans- Loci Influence Expression of the Schizophrenia Susceptibility Gene DTNBP1.      
    26 LOCATE: a mammalian protein subcellular localization database      

    2007-12:
    01 Network-Based Analysis of Affected Biological Processes in Type 2 Diabetes Models      
    01 Use of SNOMED CT to Represent Clinical Research Data: A Semantic Characterization of Data Items on Case Report Forms in Vasculitis Research    
    08 A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers      
    08 Genomic analysis of human microRNA transcripts      
    15 ̼ Cancer immunomics: Using autoantibody signatures in the early detection of prostate cancer    
    15 AILUN: reannotating gene expression data automatically    
    22 BNDB-The Biochemical Network Database    
    22 Evaluation of high-throughput functional categorization of human disease genes      

    2007-11:
    03 BioCLASS : A semantic comparison of microarray gene expression data 
    03 Network-based discovery of functional differences between intronic and intergenic miRNAs 
    03 α Sample selection in RiPeter 
    03 An architecture for biomedical semantic map: an integrated map from biology to clinical 
    03 An integrated system for heterogeneous data management and analysis 
    17 DNA, diseases and databases:disastrously deficient    
    17 Strategy for encoding and comparison of gene expression signatures      
    24 PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation      
    24 α Functional Specificity among Ribosomal Proteins Regulates Gene Expression [RiPeter]   

    2007-10:
    06 Identifying Genomic Regulators of Set-Wise Co-Expression (presentation for BIBE 2007 ) 
    06 ̼ Feature Selection and Molecular Classification of Cancer Using Genetic Programming    
    13 Advancing translational research with the Semantic Web 
    13 α A systems biology approach for pathway level analysis    
    20 Estimating the annotation error rate of curated GO database sequence annotations.    
    20 Bayesian modelling of shared gene function      
    27 MicroRNA regulation of human protein-protein interaction network      
    27 Annotation and query of tissue microarray data using the NCI Thesaurus      

    2007-09:
    01 ̼ GPDTI A Genetic Programming Decision Tree Induction method to find epistatic effects in common complex diseases    
    01 Research Talk 
    08 Challenges and standards in integrating surveys of structural variation [CNVreview]     
    08 α A full Bayesian hierarchical mixture model for the variance of gene differential expression    
    15 Detection of a MicroRNA Signal in an In Vivo Expression Set of mRNAs      
    15 Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution.    
    29 Identification of aberrant chromosomal regions from gene expression microarray studies applied to human breast cancer      
    29 Quantitative assessment of relationship between sequence similarity and function similarity    

    2007-08:
    04 Increasing the Power to Detect Causal Associations by Combining Genotypic and Expression Data in Segregating Populations    
    04 Status of text-mining techniques applied to biomedical text [Text miningbiomedical field]   
    11 Cancer Genomics Object Model : An Object Model for Cancer Research using Multiple Functional Genomics Data 
    11 A New Method to Measure the Semantic Similarity of GO terms    
    18 Matrix formalism to describe functional state of trasncriptional regulatory systems    
    18 Semantic Search among Heterogeneous Biological Databases Based on Gene Ontology [Semantic integration]   

    2007-07:
    07 ̼ maSigPro: a Method to Identify Significantly Differential Expression Profiles in Time-Course Microarray Experiments    
    07 Developing a similarity measure in biological function space      
    14 A genomic code for nucleosome positioning    
    14 The Gene Set Builder: collation, curation, and distribution of sets of genes [gene set]     
    21 Evidence of spatially bound gene regulation in Mus musculus: decreased gene expression proximal to microRNA genomic location      
    21 Design aspects of a distributed clinical trials information system      
    28 α Integrative molecular concept modeling of prostate cancer progression    
    28 Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide    

    2007-06:
    02 FatiGO and GAzer 
    02 MicroGen: a MIAME compliant web system for microarray experiment information and workflow management [MIAMEmicroarrayrepository]     
    09 AffyMiner: mining differentially expressed genes and biological knowledge in GeneChip microarray data    
    09 BioGuideSRS: querying multiple sources with a user-centric perspective    
    16 ̼ Significance analysis of mcroarray transcript levels in time series experiments    
    16 Global clinical data interchange standards are here    
    23 α Improving identification of differentially expressed genes in microarray studies using information from public databases    
    23 microRNA Modulation of Circadian-Clock Period and Entrainment      
    30 The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics.      
    30 A UMLS-based spell checker for natural language processing in vaccine safety    

    2007-05:
    12 Dynamic Tables: An Architecture for Managing Evolving, Heterogeneous Biomedical Data in Relational Database Management Systems    
    12 MicroRNA expression alterations are linked to tumorigenesis and non-neoplastic processes in pancreatic ductal adenocarcinoma      
    19 α A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription      
    19 Bayesian meta-analysis models for microarray data: a comparative study    
    26 Completing the map of human genetic variation [CNVstructural variation]     
    26 ¼ Discovery of principles of nature from mathematical modeling of DNA microarray data    

    2007-04:
    07 Weighted Cohesiveness for Identification of Functional Modules and their Interconnectivity    
    07 ArrayQuest: a web resource for the analysis of DNA microarray data [Microarray data analysis system]   
    14 cPath    
    14 A tutorial on statistical methods for population association studies      
    21 ܺƯ BIG-round 
    28 ̼ Modeling Nonlinearity in Dilution Design Microarray Data [microarraydilution]     
    28 Heritability and tissue specificity of expression quantitative trait loci.      

    2007-03:
    03 Integrating domain knowledge with statistical and data mining methods for high density genomic SNP disease association analysis    
    03 High-Throughput Multi-dimensional Scaling (HiT-MDS) for cDNA-Array Expression Data      
    10 ̼ A Five-Gene Signature and Clinical Outcome in Non-Small-Cell Lung Cancer      
    10 Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos      
    17 α Large-scale identification of novel transcripts in the human genome      
    17 A general temporal data model and the structured population event history register [Temporal modelMetadata]   
    24 High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping.      
    24 Relative impact of nucleotide and copy number variation on gene expression phenotypes [CNV SNP expression]     
    31 Predicting the prognosis of breast cancer by integrating clinical and microarray data with Bayesian network    
    31 ¼ Not All Scale Free Networks are Born Equal    

    2007-02:
    03 Integrating genetic and network analysis to characterize genes related to mouse weight.      
    03 Combination of text-mining algorithms increases the performance [Text miningcombination]     
    10 Copy number variation: New insights in genome diversity [CNVcopy number variants]     
    10 ¼ Estimating p-values in small microarray experiments [p-valuet-test]     
    24 Identifying clusters of functionally related genes in genome      
    24 Microarray data analysis: from disarray to consolidation and consensus    

    2007-01:
    06 ¼ How Scale-Free Are Biological Networks    
    06 Combining functional and topological properties to identify core modules in protein interaction networks      
    13 Discovering implicit associations between genes and hereditary diseases    
    13 GenMAPP2.1 
    20 ChromoScan: a scan statistic application for identifying chromosomal regions in genomic studies [scan statisticsSNP]     
    20 The CAP cancer protocols--a case study of caCORE based data standards implementation to integrate with the Cancer Biomedical Informatics Grid. [caCORECAP cancer protocol]     
    27 α Common genetic variants account for differences in gene expression among ethnic groups      
    27 Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray      

    2006-12:
    02 Microdeletion encompassing MAPT at chromosome 17q21.3 is associated with developmental delay and learning disability      
    02 Group testing for pathway analysis improves comparability of different microarray datasets    
    09  
    09 SNiPer-HD: Improved Genotype Calling Accuracy by an Expectation-Maximization Algorithm for High-Density SNP Arrays      
    16 Finding function: evaluation methods for functional genomic data.      
    16 α Large scale data mining approach for gene-specific standardization of microarray gene expression data    
    23 Strategies to determine the biological function of microRNAs      
    23 Integrative genetic analysis of transcription modules: towards filling the gap between genetic loci and inherited traits      
    30 Automatic document classification of biological literature [Information RetrievalPhrase-based Document ClusteringSupport Vector Machine]   
    30 Global variation in copy number in the human genome [CNV]

    2006-11:
    04 α Predicting rules on organization of cis-regulatory elements, taking the order of elements into account      
    04 A new measure for functional similarity of gene products based on Gene Ontology [semantic map]     
    11 ¼ Singular value decomposition of genome-scale mRNA length distribution reveals saymmetry in RNA gel electrophoresis band broadening [SVDasymmetric gaussian]   
    11 Design of a combinatorial DNA microarray for protein-DNA [PBM]   
    25 AMIA 2006 Review Paper [AMIAHMMText ClassificationOntology]
    25 AMIA 2006 review [AMIAconference review]

    2006-10:
    14 Discovering disease genes by topological features in human protein-protein interaction network    
    14 BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.    
    28 To permute or not permute [permutation]     
    28 Normalization procedures and detection of linkage signal in genetical-genomics experiments.      

    2006-09:
    23 MGED9 review [MGED]
    23 Creation and implications of a phenome-genome network      
    30 ¼ Network motif identification in stochastic networks [network motifstochastic network motifmixture model]     
    30 Assessing semantic similarity measures for the characterization of human regulatory pathways [Semantic distance]     

    2006-07:
    01 High-resolution ChIP-chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome    
    01 CoPub Mapper: mining MEDLINE based on search term co-publication    
    08 A model diagram layout extension for SBML 
    08 A Systems Approach to Mapping DNA Damage Response Pathways [DNA damage response pathway]     
    15 α Identification of biochemical networks by S-tree based genetic programming      
    15 A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies      

    2006-06:
    03 Genome-wide analysis of mammalian promoter architecture and evolution 
    03 α Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae [cca]     
    09 An integrative genomics approach to infer causal associations between gene expression and disease [genetical genomics]     
    10 The model organism as a system:integrating omics data sets      
    17 From XML to RDF: how semantic web technologies will change the design of omic standards [XML RDF]     
    17 A System for Automated Lexical Mapping [LOINC mappingtext mining]     
    24 A text-mining analysis of the human phenome [phenometext miningphenotype-genotype relations]     
    24 ¼ Reconstructing the pathways of a cellular system from genome-scale signals by using matrix and tensor computations [pathwayEVD]     

    2006-05:
    06 Ab initio genotype–phenotype association reveals intrinsic modularity in genetic networks      
    06 Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. [genetical genomics]     
    13 Oncogenic pathway signatures in human cancers as a guide to targeted therapies      
    13 Data integration and genomic medicine [genomicmedicinedata integration]     
    20 ¼ Pathway recognition and augmentation by computational analysis of microarray expression data [PathPlus]     
    20 A System Based Approach to Interpret Dose and Time-dependent Microarray Data: Quantitative Integration of GO Ontology Analysis for Risk Assessment [microarray]     
    27 Lung cancer genome analysis with SNP arrays    
    27 Graph-based analysis and visulization of experimental results with ONDEX    

    2006-04:
    01 Genetic regulators of large-scale transcriptional signatures in cancer.      
    01 An XML-based System for Synthesis of Data from Disparate Databases    
    08 DrugBank: a comprehensive resource for in silico drug discovery and exploration      
    08 Integrated analysis of gene expression by Association Rules Discovery      
    15 Genome-wide association study in esophageal cancer using GeneChip mapping 10k array    
    15 CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks    
    22 Different methods of calculating gene expression from short oligonucleotide array data will give different results      
    22 Uncovering the overlapping community structure of complex networks in nature and society      
    29 RxNorm: Prescription for electronic drug information exchange      
    29 α Contributions of low molecule number and chromosomal positioning to stochastic gene expression    

    2006-03:
    04 Instance-based concept learning from multiclass DNA microarray data      
    04 Epistasis analysis with global transcriptional phenotypes      
    11 α Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer      
    18 ¼ A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae      
    18 Proteome survey reveals modularity of the yeast cell machinery      
    25 WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data      
    25 Functional annotation and network reconstruction through cross-platform integration of microarray data      

    2006-02:
    04 Finding biological process modifications in cancer tissues by mining gene expression correlations      
    04 α Shifting and scaling patterns from gene expression data      
    11 Chemical Effects in Biological Systems (CEBS) object model for toxicology data, SysTox-OM: design and application.      
    11 A statistical approach to scanning the biomedical literature for pharmacogenetics knowledge.      
    18 Multi-way clustering of microarray data using probabilistic sparse matrix factorization      
    25 Creation and implications of a phenome-genome network      
    25 ¼ Standardizing global gene expression analysis between laboratories and acroos platforms      

    2006-01:
    07 Comparison of normalization methods for CodeLink Bioarray data      
    07 A protocol for building and evaluting predictors of disease state based on microarray data      
    14 A haplotype map of the human genome      
    21 Biological profiling of gene groups utilizing gene ontology      

    2005-12:
    24 α Differential coexpression analysis using microarray data and its application to human cancer      
    31 Overview of BioCreAtIvE: critical assessment of information extraction for biology      

    2005-11:
    05 Statistical methods for ranking differentially expressed genes.      
    05 An expression index for Affymetrix GeneChips based on the generalized logarithm      
    12 α Assessing the limits of genomic data integration for predicting protein networks      
    12 Improving molecular cancer class discovery through sparse non-negative matrix factorization      
    26 Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed genes in lung cancer tissues      
    26 A new algorithm for comparing and visulaizing relationships beween hierarchical and flat gene expression data clusterings      

    2005-10:
    01 Mining Ratio Rules Via Principal Sparse Non-Negative Matrix Factorization      
    01 Study of coordinative gene expression at the biological process level      
    08 A Theoretical Analysis of Gene Selection      
    08 Validation and refinement of gene-regulatory pathways on a network of physical interactions    
    15 PAGE: Parametric Analysis of Gene Set Enrichment      
    22 Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data      
    22 Mining coherent dense subgraphs across massive biological networks for functional discovery      
    29 A network-based analysis of systemic inflammation in humans      

    2005-09:
    03 Ontological analysis of gene expression data current tools, limitations, and open problems      
    03 Generalized biological database platform based on cross-referenced tables(XRT)    
    10 Intergrative analysis of cancer transcriptome    
    10 α Local modeling of global interactome networks      
    24 ¼ Biomarker discovery in microarray gene expression data with Gaussian processes      
    24 Ensemble dependence model for classification and prediction of cancer and normal gene expression data      

    2005-08:
    06 Healthcare IT Collaboration in Massachusetts: The Experience of Creating Regional Connectivity      
    06 Visualizing information across multidimensional post-genomic structured and textual databases    
    13 Use of extreme patient samples for outcome prediction from gene expression data      
    13 Prediction of Nephrotoxicant Action and Identification of Candidate Toxicity-Related Biomarkers      
    20 Metagenes and molecular pattern discovery using matrix factorization      
    20 ¼ Alignment of metabolic pathways      
    27 Using process diagrams for the graphical representation of biological networks      
    27 PhD: a web database application for phenotype data management      

    2005-07:
    02 ¼ Supervised enzyme network inference from the integration of genomic data and chemical information [vertkernel]     
    02 α A procedure for assessing GO annotation consistency      
    09 LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts.      
    09 ѹ̷ The Interactive Online SKY/M-FISH & CGH Database and the Entrez Cancer Chromosomes Search Database: Linkage of Chromosomal Aberrations with the Genome Sequence      
    16 GoPubMed: exploring PubMed with the Gene Ontology      
    16 An oncogenic KRAS2 expression signature identified by cross-species gene-expression anlaysis    
    23 Comparison of computational methods for the identification of cell cycle-regulated genes      
    23 Peeling the yeast protein network.      
    30 ѹ̷ Visualization-based discovery and analysis of genomic aberrations in microarray data      
    30 Automated Detection of Adverse Events Using Natural Language Processing of Discharge Summaries      

    2005-06:
    04 Pattern Robustness of Diagnostic Gene expression Signatures in Leukemia      
    04 α Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments.      
    11 Standardization initiatives in the (eco)toxicogenomics domain: a review      
    11 Validation of a Discharge Summary Term Search Method to Detect Adverse Events      
    18 Application of Revised Version of Neural Independent Component Analysis to Classification Problems of Confiscated Methaphetamine      
    25 Integration of text- and data-mining using ontologies successfully selects disease gene candidates      
    25 Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information      

    2005-05:
    07 Diagnostic plots for detecting outlying slides in a cDNA microarray experiment      
    07 Modularized learning of genetic interaction networks from biological annotations and mRNA expression data      
    14 ¼ NETWORK BIOLOGY: UNDERSTANDING THE CELLS FUNCTIONAL ORGANIZATION      
    21 RNA expression microarrays (REMs), a high-throughput method to measure differences in gene expression in diverse biological samples      
    28 GeneWays: a system for extracting, analyzing, visualizing,and integrating molecular pathway data      

    2005-04:
    02 GECKO: a complete large-scale gene expression analysis platform      
    16 α Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae      
    30 ѹ̷ Use of Targeted Array-Based CGH for the Clinical Diagnosis of Chromosomal Imbalance: Is Less More?      
    30 Genomic Messaging System and DNA Mark-Up Language for Information-Based Personalized Medicine with Clinical and Proteome Research Applications      

    2005-03:
    07 Generating XML schemas for DICOM structured reporting templates.      
    07 Can gene expression profiling predict survival for patients with squamous cell carcinoma of the lung?      
    14 A statistical method for identifying differential gene–gene co-expression patterns      
    14 ¼ Inferring quantitative models of regulatory networks from expression data      
    26 ¼ Quick & simple: quality control of microarray data.    
    26 CLOE Identification of putative functional relationships among genes by comparison of expression profiles between two species      

    2005-02:
    14 ̼ A comparison of normalization methods for high density oligonucleotide array data based on variance and bias      
    14 Hierarchical clustering analysis of tissue microarray immunostaining data identifies prognostically significant groups of breast carcinoma.      
    21 α Modular organization of cellular networks      
    21 Molecular decomposition of complex clinical phenotypes using biological structured analysis of microarray data      
    28 ѹ̷ A method for calling gains and losses in array CGH data      
    28 A High Productivity/Low Maintenance Approach to High-performance Computation for Biomedicine: Four Case Studies      

    2005-01:
    03 Achieving Evolvable Web-Database Bioscience Applications Using the EAV/CR Framework: Recent Advances      
    10 A function-based framework for understanding biological systems    
    10 ȭ The Development of MML (Medical Markup Language) Version 3.0 as a Medical Document Exchange Format for HL7 Messages      
    17 ¼ GenRate: A Generative Model That Finds and Scores New Genes and Exons in Genomic Microarray Data [PSB]   
    17 ¼ Sparse Factorizations of Gene Expression Guided by Binding Data [PSB]   
    24 ¼ Hidden Markov Models Approach to the Analysis of Array CGH Data    

    2004-12:
    04 ȭ Clinical Document Architecture Enables Electronic Medical Records to Wireless Mobile Computing      
    11 ¼ Systematic benchmarking of microarray data classification: assessing the role of non-linearity and dimensionality reduction      
    18 α Mining Gene Expression Data for Positive and Negative Co-regulated Gene Clusters      
    27 The ArrayExpress Gene Expression Database: a Software Engineering and implementation Perspective      
    27 ѹ̷ Detection of low level genomic alterations by comparative genomic hybridization based on cDNA micro-arrays      

    2004-11:
    06 ¼ Analysis of array CGH data: from signal ratio to gain and loss of DNA regions      
    06 Exploring the Portability of Informatics Capabilities from a Clinical Application to a Bioscience Application      
    13 Local correlation of expression profiles with gene annotation - proof of concept for a general conciliatory method      
    13 ѹ̷ Genome-wide array comparative genomic hybridization analysis reveals distinct amplifications in osteosarcoma      
    20 Transcriptional regulatory code of a eukaryotic genome      
    20 Independent component analysis of microarray data in the study of endometrial cancer      
    27 QIS: A framework for biomedical database federation.      

    2004-10:
    02 Statistical significance for hierarchical in genetic association and microarray expression studies      
    09 ̼ȣ arrayMagic : two-colour cDNA microarray quality control and preporcessing    
    09 ѹ̷     
    16 α Discovering Local Structure in Gene Expression Data: The Order-Preserving Submatrix Problem      
    16 Using the gene ontology for microarray data mining      
    23 ȭ A standard XML Schema for computerised anaesthetic records      
    30 CEBS object model for systems biology data, SysBio-OM      

    2004-09:
    04 TRANSFAC, TRANSPATH and CYTOMER as starting points for an ontology of regulatory networks    
    04 The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource.      
    11 ¼ Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph      

    2004-08:
    07 Predicting Gene Expression from Sequence      
    07 ̼ȣ PCA disjoint models for multiclass cancer analysis using gene expression data      
    14 affy-analysis of Affymetrix GeneChip data at the probe level      
    14 ȭ XML-based application interface services - a method to enhance integrability of disease specific systems      
    21 α Finding disease specific alterations in the co-expression of genes      
    21 The male specific region of human Y chromosome is a mosaic of discrete sequence classes      
    28 An object model and database for functional genomics.      
    28 ѹ̷ Prediction of prognosis of estrogen receptor-positive breast cancer with combination of selected estrogen-regulated genes.      
    31 Statistical modeling of sequencing errors in SAGE libraries
     
        
    31 Predicting genetic regulatory response using classification      
    31 α     
    31 Filling gaps in a metabolic network using expression information [ISMB2004]   
    31     

    2004-07:
    03 Methods for automated concept mapping between medical databases      
    10 The aMAZE LightBench: a web interface to a relational database of cellular processes      
    10 How (not) to protect genomic data privacy in a distributed network: using trail re-identification to evaluate and design anonymity protection systems.      
    24 ¼ TopNet: a tool for comapring biological subnetworks, correlating protein properties with topological statistics      
    24 The Genome Knowledgebase: A Resource for Biologists and Bioinformaticists      

    2004-06:
    05 ArrayTrack.Supporting Toxicogenomic Research at the U.S. Food and Drug Administration National Center for Toxicological Research      
    12 ȭ XML as standard for communicating in a document-based electronic patient record: a 3 years experiment.      
    12 α Transcriptional regultory networks in Saccharomyces cerevisiae      
    26 TRMP: A Dataqbase of Therapeutically Relevant Multiple-Pathways      

    2004-05:
    01 ѹ̷ Expression profiling to predict postoperative prognosis for estrogen receptor-negative breast cancers by analysis of 25,344 genes on a cDNA microarray      
    01 Development of common data elements: the experience of and recommendations from the early detection research network      
    08 Discovering modes of action for therapeutic compounds using a genome-wide screen of yeast heterozygotes      
    08 (H) Gene selection and clustering for time-course and dose-response microarray experiments using order-restricted inference.      
    15 Quantifying the relationship between co-expression, co-regulation and gene function      
    15 GoMiner: a resource for biological interpretation of genomic and proteomic data      
    22 ¼ Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data [segal]     
    22 An Architecture for Biological Information Extraction and Representation      
    29 PubMatrix: a tool for multiplex literature mining.      

    2004-04:
    03 Biological detection of low radiation doses by combining results of two microarray analysis methods      
    03 Inferring transcriptional regulation relationship from microarray time series data      
    10 ȭ UML-XML-RDB Model Mapping Solution for Facilitating Information Standardization and Sharing in Construction Industry      
    10 Selective automated indexing of findings and diagnoses in radiology reports      
    17 ¼ Discovering molecular pathways from protein interaction and gene expression data [segal]     
    17 (H) Differential amplification of gene expression in lens cell lines conditioned to survive peroxide stress      
    24 Common structural patterns in human genes.      
    24 α Network-based approach for the comprehensive mapping between biological identifiers      

    2004-03:
    06 Molecular profiling of mouse lung tumors: association with tumor progression, lung development, and human lung adenocarcinomas      
    06 α Meta-databases providing collection of hyperlinks      
    13 ѹ̷ Gene expression predictors of breast cancer outcomes      
    13 Ontology Versioning as an Element of an Ontology-Management Framework      
    20 Chipping away at the chip bias: RNA degradation in microarray analysis      
    20 The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface      
    27 A new distributed data mining model based on similarity      
    27 Pharmacogenetics: potential for individualized drug therapy through genetics      

    2004-02:
    07 Statistical resynchronization and Bayesian detection of periodically expressed genes      
    07 Automatic extraction of mutations from Medline and cross-validation with OMIM      
    14 A Mapping Schema and Interface for XML Stores      
    14 ȭ Presenting XML-based medical discharge letters according to CDA      
    21 CloseGraph: Mining Closed Frequent Graph Patterns      
    21 Towards linking patients and clinical information: detecting UMLS concepts in e-mail      
    28 ¼ ESPD: a pattern detection model underlying gene expression profiles      
    28 Computational knowledge integration in biopharmaceutical research      

    2004-01:
    03 ȭ XPERANTO: Publishing Object-Relational Data as XML      
    03 GenePublisher: Automated analysis of DNA microarray data      
    10 Gene expression profile of normal lungs predicts genetic predisposition to lung cancer in mice      
    10 α A protein interaction map of Drosophila melanogaster      
    17 ѹ̷ Differentiation of lobular versus ductal breast carcinomas by expression microarray analysis      
    17 caCORE: A common infrastructure for cancer informatics      
    31 Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data      
    31 (H) EVALUATION AND COMPARISON OF CLUSTERING ALGORITHMS IN ANGLYZING ES CELL GENE EXPRESSION DATA      

    2003-12:
    06 (H) Statistical tests for identifying differentially expressed genes in time-course microarray experiments      
    13 Computational discovery of gene modules and regulatory networks      
    13 Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in Humans      
    20 A New Inlining Algorithm for Mapping XML DTDs to Relational Schemas      
    20 ¼ Scoring clustering solutions by their biological relevance      
    27 Deriving phylogenetic trees from the similarity analysis of metabolic pathways      
    27 A Study of Biomedical Concept Identification: MetaMap vs. People      

    2003-11:
    08 ¼ Using Bayesian Networks to Analyze Expression Data      
    08 Artificial gene networks for objective comparison of analysis algorithms      
    15 Information extraction from full text scientific articles: where are the keywords?      
    15 ȭ Discharge and referral data exchange using global standards--the SCIPHOX project in Germany      
    22 PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis      
    22 A training-testing approach to the molecular classification of resected non-small cell lung cancer      
    29 α Genome-wide pathway analysis and visualization using gene expression data      
    29 ѹ̷ Molecular classification of familial non-BRCA1/BRCA2 breast cancer      

    2003-10:
    04 Pathways database system: an integrated system for biological pathways      
    04 α Comparing protein abundance and mRNA expression levels on a genomic scale      
    11 ѹ̷ Gene expression profiles of human breast cancer progression      
    11 Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies      
    18 (H) Power of multifactor dimensionality reduction for detecting gene-gene interactions in the presence of genotyping error, missing data, phenocopy, and genetic heterogeneity      
    18 Phase-independent rhythmic analysis of genome-wide expression patterns      
    25 Personalized and Automated dbSNP Surveillance System      
    25 A Generic Load/Extract Utility for Data Transfer between XML Documents and Relational Databases      

    2003-09:
    06 ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis      
    06 The Design and Performance Evaluation of Alternative XML Storage Strategies      
    08 Expression deconvolution: A reinterpretation of DNA microarray data reveals dynamic changes in cell populations      
    08 Molecular Profiling of Non-Small Cell Lung Cancer and Correlation with Disease-free Survival      
    08 ȭ Using the eXtensible Markup Language (XML) in a regional electronic patient record for patients with malignant diseases      
    20 ¼ The topology of the transcription regulatory network in the yeast, Saccharomyces cerevisiae      
    20 A Pilot Study of Contextual UMLS(R) Indexing to Improve the Precision of Concept-Based Representation in XML-Structured Clinical Radiology Reports      
    27 Improving Information Extraction through Biological Correlation      
    27 Association of genes to genetically inherited diseases using data mining      

    2003-08:
    09 The creation of an ontology of clinical document names      
    09 ¼ Subnetwork hierarchies of biochemical pathways      
    16 (H) Clustering of housekeeping genes provides a unified model of gene order in the human genome      
    16 Global functional profiling of gene expression      
    23 α Meta-Analysis of Microarrays: Interstudy Validation of Gene Expression Profiles Reveals Pathway Dysregulation in Prostate Cancer      

    2003-07:
    03 An approach to object-relational mapping in bioscience domains      
    10 Gene interaction in DNA microarray data is decomposed by information geometric measure      
    24 Active Learning with Strong and Weak Views: A Case Study on Wrapper Induction      
    31 ȭ Using the XML-Based Clinical Document Architecture for Exchange of Structured Discharge Summaries      

    2003-06:
    05 The Role of Domain Knowledge in Automating Medical Text Report Classification      
    19 (H) Genetics of gene expression surveyed in maize, mouse and man      

    2003-05:
    16 Analysis of cell-cycle-specific gene expression in human cells as determined by microarrays and double-thymidine block synchronization      
    22 ȭ Data extraction and ad hoc query of an entity-attribute-value database      
    26 The application of the unified modeling language in object-oriented analysis of healthcare information systems      

    2003-04:
    03 Gene Functional classification by Semi-supervised Learning from Heterogeneous Data      
    10 A literature-based method for assessing the functional coherence of a gene group      
    14 ȭ Designing and implementing special-purpose databases: lessons from the pharmacogenetic network      
    24 (H) Diagnosis of multiple cancer types by shrunken centroids of gene expression      

    2003-03:
    06 (H) Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer      
    13 A multivariate approach applied to microarray data for identification of genes with cell cycle-coupled transcription      
    20 Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO)      
    27 A database on alternative splice forms on the Integrated Genetic Map Service (IGMS)    

    2003-02:
    06 MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data      
    13 ȭ A user-centered model for web site design: needs assessment, user interface design, and rapid prototyping      
    20 Mining gene expression databases for association rules      
    27 Associating Genes with Gene Ontology Codes Using a Maximum Entropy Analysis of Biomedical Literature      

    2003-01:
    09 (H) Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors      
    16 Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level      
    23 SNPper: retrieval and analysis of human SNPs      

    2002-12:
    05 XML for electronic clinical communications in Scotland      
    12 ȭ Integrating medical information and knowledge in the HL7 RIM      
    26 Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees      

    2002-11:
    07 Binary analysis and optimization-based normalization of gene expression data      
    14 Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis      
    21 The meaning of it all: web-based resources for large-scale functional annotation and visualization of DNA microarray data      

    2002-10:
    10 A bioinformatic strategy to rapidly characterize cDNA libraries      
    17 ȭ Plug-and-play XML: a health care perspective      
    24 Handling Very Large Numbers of Association Rules in the Analysis of Microarray Data      
    31 (H) Variance stabilization applied to microarray data calibration and to the quantification of differential expression      

    2002-09:
    05 (H) Large-scale prediction of Saccharomyces cerevisize gene function using overlapping transcriptional clusters      
    12 A motif-based profile scanning approach for genome-wide prediction of signaling pathways      
    16 Identification of regulatory elements using a feature selection method      
    26 The Binding Database: data management and interface design      

    2002-08:
    22 Discrimination between paralogs using microarray analysis: Application to the Yap1p and Yap2p transcriptional networks      

    2002-07:
    04 Automating data acquisition into ontologies from pharmacogenetics relational data sources using declarative object definitions and XML      
    11 Active + Semi-Supervised Learning = Robust Multi-View Learning      

    2002-06:
    20 Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm      
    25 A cluster validity framework for genome expression data      

    2002-05:
    02 Argus--a new database system for Web-based analysis of multiple microarray data sets      
    09 XML documentation of biopathways and their simulations in Genomic Object Net      
    16 ȭ Standard method for describing an electronic patient record template: application of XML to share domain knowledge      
    23 Systematic determination of genetic network architecture      
    30 (H) Missing value estimation methods for DNA microarrays      

    2002-04:
    02 Gene expression analysis with universal n-mer arrays      
    09 (H) Significance analysis of microarrays applied to the ionizing radition response      
    16 Re-annotation of genome microbial coding-sequence: finding new genes and inaccurately annotated genes      
    23 Prediction of probable genes by Fourier analysis of genomic sequences      

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