Zehwan Kim

(Okgu Kim before 2014.02)

Education:

B.S.: Kyungpook National University College of Engineering,
Department of Electronic Engineering,
Information Communication Major (Digital Communication) (1998.02)

M.S.: Seoul National University College of Natural Sciences,
Interdisciplinary Program in Bioinformatics (2005.08)

M.D.: Kyungpook National University College of Medicine (2012.02)

Ph.D.: Seoul National University College of Medicine,
Interdisciplinary Program in Biomedical Informatics (2019.02)

Research Interests and Current Work:

Bioinformatics

T.A. Brown. GENOMES 2nd Edition. Wiley-Liss, 2002 (studied)
Andres D. Baxevanis, B.F. Francis Ouellette. Bioinformatics. Wiley-Interscience, 2001

Biochemistry, Molecullar Cell Biology, Medicinal Chemistry

David L. Nelson, Michael M. Cox. Lehninger Principles of Biochemistry 3rd Edition. Worth Publisher, 2000 (studied)
Bruce Alberts, et. al. Essential Cell Biology: An introducton to the Molecular Biology of the Cell. Garland Publishing, 1997 (studied)
Graham L. Patrick. An Introduction to Medicinal Chemistry. Oxford University Press, 2001 (studied)

Anatomy, Physiology, Pathology, Clinical Microbiology, Cancer, Pharmacology, and Pharmacogenetics

David Shier, Jackie Butler, Ricki Lewis. Hole's Human Anatomy & Physiology 10th Edition. McGraw-Hill, 2004 (on studying)
Geoffrey M. Cooper. Elements of Human Cancer. Jones and Bartlett, 1992 (studied)
Wendell W. Weber. Pharmacogenetics. Oxford University Press, 1997 (on studying)
Joseph G. Cannon. Pharmacology for Chemists. American Chemical Society, 1999 (studied)

Pharmacoepidemiology (just interest)

Informatics Applicatoin
Epidemiology
Post-Marketing Surveilance (PMS)
Adverse Event Reporting System
Database development for Pharmacoepidemiology

PhactaX: Clinical Trial Process Management System Development
(on development, funded by National Research Laborary Project
of the Ministry of Science and Technology)

PhactaDesigner: eCRF design program
PhactaManager: Clinical Trial Data Management System (XML based, Web based, and for Multicenter)
PhactaForm: Common Data Element and Common eCRF Section Management Website
PhactaDictionary: Standard Coding Dictionary System Management Website (MedDRA 5.0, 5.1, 8.0, COSTART, ICD-10, WHOART)

Publications:

Okgu Kim, Byung Ju Park, Introduction to electronic document standards and guidelines for the management, exchange, and submission of clinical trial data. Journal of Korean Clinical Pharmacology. 2004;12(2)
Okgu Kim, Byung Ju Park. Introduction of electronic adverse event reporting system. Journal of Korean Clinical Pharmacology. 2004;12(1):13-15
Okgu Kim, Seon Ha Kim, Ju Han Kim, Kyun Seop Bae, Hwa Jung Kim, Byung Joo Park. Information technologies for solving the problems of paper based clinical trial. Journal of Korean Clinical Pharmacology. 2003;11(2):75-82

Proceedings:

Okgu Kim, Sun-Ha Kim, Young-Shin Kim, Hee-Jung Ahn, Young Koh, Hyoung-Joo Lim, Jin-Young Jang, Ju Han Kim, Byung Joo Park. PhactaX - a package of data management system and related web sites for conducting medical researches and clinical trials. Journal of Korean Society of Medical Informatics. 2005;11(Suppl 1)
Okgu Kim, Young Shin Kim, Seon Ha Kim, Hwa Jung Kim, Nam-Kyong Choi, Jung-Lim Jung, Ju Han Kim, Byung Joo Park. XML Grammar development for system independent and reusable electronic case report form with online data verification support. Journal of Korean Society of Medical Informatics. 2004;10(Suppl 2)

Professional Experience as M.D. (2012.03 ~ 2018.02):

Intern at Korean Cancer Center Hospital (2012.03~2013.02)
Resident (Laboratory Medicine) at Kyungpook National University Hospital (2013.03~2017.02)
Fellow (Laboratory Medicine) at Samsung Medical Center (2017.03~2018.02)

Work Experience (1998.03 ~ 2005.08):

By Field

Laboratory Medicine:

Genetic Diagnosis
Clinical Chemistry
Genetic Counseling

Principal Database:

Oracle SQL tuning
Oracle Pro*C/C++
Oracle OCI
Oracle PL/SQL

Principal Programming Languages:

Python (main)
C/C++ (for core engine)
MFC (for interface)
x86 Assembly (only for speed and code optimization)

High Performance Computing:

MPI based and native clustering
OpenMP and native multithreading

Distributed Computing:

CORBA on C/C++ and Java

Principal Web Server Script Language:

By Application

RarePedia

A biomedical knowledgebase well as a web portal service and a command line program
Web query for one variant or gene (HGNC or Ensembl) presents a coherent query result by central dogma scheme
Command line version executes batch analysis of input variants file
For each query, RarePedia presents variant, gene, transcript, protein, pathway, and phenotype section

Assistant Tool (AT), Genomic variant Analysis Assistant Tool (GV-AT), Genomic variant Interpretation Assistant Tool (GI-AT)

Next Generation Sequencing (NGS) data manipulation tool
AT: provides essential functions for GV-AT and GI-AT
GV-AT: NGS-generated BAM to VCF file according to user-specified protocol
GI-AT: VCF file to ACMG/AMP 2015 guideline based variant interpretation, to RarePedia analysis according to user-specified protocol

PhactaX : A package of clinical trial data management programs and websites
(at Seoul National University Hospital Clinical Trial Center)

XML based eCRF description language specified using XML Schema language
Multi-center clinical trial management support
Various Adverse Event Coding Dictionary support using website and Simple Object Access Protocol (SOAP)
Common Data Element (CDE) and Common eCRF Section management website

Asset & Liability Management (ALM) System
(at Samsung Life Insurance Corp., Enterprise Risk Management Team)

Runs on a cluster of three 8-way SMP systems and four 4-way SMP systems
Implements clustering and multi-threading
Implements Risk Management Algorithms (Direct Cashflow, PVDE, MVS)
Handles 1 ~ 20 GB data at one computation cycle (30 min. ~ 4 hours)

Database for Internet Phone Call Log Management
(at Greathuman Corp., Server Development Team and as a Freelancer)

Cache for call logging (hundreds of logs per one second scale)
Large-scale call log traversing (tens of million scale)

High-throughput Message Broker
(at Greathuman Corp., Server Development Team)

Core based on AVL Tree Message Mangement Algorithm
Embedded in Instant Messaging Server
Message delivery between H.323 (VoIP) Gatekeeper and Internet Phone Client

Undergraduate Student Extracurricular Activity (1993.03 ~ 1998.02):

Hanulso Club (the 7th-term member)

Tiny Operating System (1993)

Whole Assembly language in 286 Protected Mode
Basic Keyboard and Screen APIs

Guest Book Program (1993)

With other members
Voice play function
Guest book recording
Presented at Hanulso Software Exhibition '1993

Usenet Data Retriever (1994)

Consists of a client program and a proxy server
Manages concurrent TCP connections for large data transfer
Multi-process management
Network News Transfer Protocol (NNTP) Processing
Automatic uudecode and file assembly

X Window Graphic File Viewer, 'Hanaro'(1994 ~ 1995)

BMP, PCX, GIF, JPEG, TIFF file view
Image Processing (Convex Effect, Sharpening/Smoothing, Boundary Detection in YIQ space,
Discrete Cosine Transform (DCT) Analysis, etc)
Presented at Hanulso Software Exhibition '1994

X Window Text Editor, 'Vada for X Window' (1994 ~ 1995)

Text editor
Embedded C/C++ Compliation
Regular Expression Search
Remote file edit through FTP/TFTP and ZMODEM on Telnet Protocols
Presented at Hanulso Software Exhibition '1994
Won the best prize of Software Exhibition of Department of Electronic Engineering '1995 (1995)

Class Scheduler (1997)

Based on Network Computing Architecture (NCA, 3-tier) of Oracle Corporation
Load balancing among clustered PCs
Won the best prize of Software Exhibition of Department of Electronic Engineering '1997 (1997)

Undergraduate Student Intern:

Telecommunication Lab.(1994~1995)

Ethernet (IEEE 802.3) Protocol Study

Asynchoronous Transfer Mode (ATM) Protocol Study

Other Protocol Studies: FDDI, Token Ring (IEEE 802.5), Logical Link Control (LLC, IEEE 802.2), DQDB

Cryptography Lab.(1996)

RSA, DES, IDEA, Diffie-Hellman Cryptography and MD5 Hashing Implementation using C

Large-number manupulation (addition, multiplication, exponential, residue in Galois Field (GF)) Impelementation using C

Large Prime Number Generation Impelementation using C

Eliptic Curve Cryptography (ECC) Study

Discrete Logarithm Problem, Montgomery Algorithm, Euler and Euclid Theorem Study

Real-time and Embed Lab.(1997)

CORBA Programming using C

Database Programming (Oracle Database)

Software Engineering and Artificial Intelligence Study

Real-time Intrusion Detection Research

Undergraduate Student Research Project:

Legacy-Transparent Crypto-Communication Program (1997)

Funded by Ministry of Information and Communication

Implemented symmetric and assymmetric cryptography algorithms

Transparent to legacy network communication clients and servers
(different to telnet and ftp programs that use SSL with different TCP ports)

Operates in UNIX environment (Linux, AIX(IBM RS6000), Solaris(Sun Sparc20), Digital OS)