JUNGHOON WOO PhD Candidate (ABD) Contact Information Department of Biomedical Informatics Columbia University Medical Center New York, NY, USA E-mail: [email protected] Blog (Korean): http://geference.blogspot.com Education PhD MS BS 2010 - Present 2005 - 2007 2001 - 2005 Biomedical Informatics, Columbia University, New York, NY, USA Bioinformatics, Seoul National University, Seoul, South Korea Biochemical Engineering, Seoul National University, Seoul, South Korea Expertise High-throughput genomic data analysis (NGS, microarray) Biomarker Discovery & Validation Programming Language: Python, R, MySQL, MongoDB (NoSQL) Machine Learning, Statistical Analysis Other tools: AWS Cloud Computing Tools, Parallel Computing (Sun Grid Engine), Git Research Experience Researcher Research Advisor Research Engineer Research Assistant 2010 - Present 2010 - 2014 2007 - 2010 2005 - 2007 Columbia University, New York, NY, USA (Academia) Geference Inc., Seoul, South Korea (Industry) Macrogen Inc., Seoul, South Korea (Industry) Seoul National University, Seoul, South Korea (Academia) Selected Publications 1. Woo JH, Shimoni Y, Yang WS, Subramaniam P, Iyer A, Nicoletti P, Martinez MR, Lopez G, Mattioli M, Realubit R, Karan C, Stockwell BR, Bansal M, Califano A (2014) Elucidating Compound Mechanism of Action by Network Dysregulation Analysis in Perturbed Cells (under review) 2. Giorgi FM, Lopez G, Woo JH, Bisikirska B, Califano A, Bansal M (2014) Inferring protein modulation from gene expression data using Conditional Mutual Information PLoS ONE 9(10): e109569 3. Woo JH, Lai AM, Chung W, Weng C. (2011) Knowledge-based Similarity Analysis of Risk Predisposition in Personal Genomes: Proof of Concept AMIA Annu Symp Proc. 2011; 2011: 1524–1531 Accepted as one of the eight finalists in the best student paper competition 4. Han W, Woo JH*, Jeon YK, Ko E, Kim TY, Im SA, Oh DY, Park IA, Hwang KT, Moon HG, Yang KS, Yang SJ, Noh DY (2011) 17p12 deletion in breast cancer predicts resistance to neoadjuvant chemotherapy Eexperimental and Therapeutic Medicine 2: 799-804 * Joint-first author 5. Han W, Woo JH, Yu JH, Lee MJ, Moon HG, Kang D, Noh DY (2011) Common genetic variants associated with breast cancer in Korean women and differential susceptibility according to intrinsic subtype Cancer Epidemiol Biomarkers Prev. 20(5):793-798. 6. Park JH, Woo JH*, Shim SH, Yang SJ, Choi YM, Yang KS, Cha DH (2010) Application of a target array Comparative Genomic Hybridization for Prenatal diagnosis in South Korea BMC Medical Genetics 11:102. * Joint-first author 7. Woo JH, Cho SB, Lee EJ, Kim JH (2010) Identifying regulatory relationships among genomic loci, biological pathways, and disease Artificial Intelligence in Medicine 49(3):161-165. 8. Hur K, Lee HJ, Woo JH, Kim JH, Yang HK (2010) Gene expression profiling of human gastrointestinal stromal tumors according to its malignant potential. Digestive diseases and sciences 55(9):2561-2567. 9. Woo JH, Yang SJ, Shin MJ, Oh EH, Kang HW, Jeong YJ (2010) Replication of the association between copy number variation on 8p23.1 and autism by using ASD-specific BAC array Genomics and Informatics 8(1): 19–27. Professional Experience 09/2010–present Bioinformatics Researcher, Center for Computational Biology and Bioinformatics (C2B2), Irving Cancer Research Center, Columbia University, New York, NY, USA Cancer Genome Sequencing / Next Generation Sequencing (NGS) - Interrogating clonal selection and evolution in a single cancer patient - Predicting true positive somatic mutations using Machine Learning approaches (illumina Exome-seq & Whole genome-seq, Sample size: 30) Systems Biology Research - Developing a method to identify Drug Mechanism-of-Action: DeMAND algorithm - Identifying molecular drivers of cancer subtypes 03/2010–12/2015 Scientific Advisor, Geference Inc. Seoul, Korea Big Data Analysis using a Mobile Weight Loss Coach App User Database - Subgroup identification and Yoyo user predictions (Sample size: 48,095) Worked with Sang Youl Rhee at the Department of Endocrinology and Metabolism, Kyung Hee University School of Medicine Breast Cancer Sequencing using Exome-seq & RNA-seq (Sample size: 120) Worked with Won-Sik Han at the Department of Breast Surgery, Seoul National University College of Medicine Book Translations - Translating ‘$1000 Genome by Kevin Davis’ from English to Korean 03/2007–03/2010 Research Engineer, MACROGEN Inc. Seoul, Korea Translational genomics research (Biomarker Discovery) - Identifying markers of response to neo-adjuvant chemotherapy in breast cancer patients Worked with Won-Sik Han at the Department of Surgery, Seoul National University College of Medicine - Constructing DNA copy number-based breast cancer recurrence prognostic model Worked with Ki-Tae Hwang at the Department of Surgery, Seoul National University Boramae Hospital - Constructing SNP-based acute Graft Versus Host Disease (GVHD) prognostic model Worked with Seon Yang Park, M.D. at the Department of Internal Medicine, Seoul National University College of Medicine In-house staff development seminars 01/2008–03/2010 (Regular) Seminar for Genomic Analysis (average enrollment 20) 04/2007–03/2010 (Occasional) Review of current issues in Genomics (average enrollment 10) : Applications of Next Generation Sequencing Technology 03/2005–07/2010 Research Assistant, Seoul National University, Seoul National University, Seoul, Korea High-dimensional microarray data analysis - Identifying differentially expressed genes across benign, borderline, and malignant gastrointestinal stromal tumors - Discovering genomic differences between rheumatoid arthritis and osteoarthritis - Characteristics and predictors of drug-eluting stent thrombosis Patents Woo JH, Keum C, Park J: Method and System estimating resemblance between subject using single nucleotide polymorphism Korean patent No. 10-2013-0006489 (pending) Woo JH, Yang SJ, Shin MJ, Han WS, Noh DY, Yang KS, Seo JS, Kim JW: Prediction of drug-responsibility against breast cancer through chromosomal aberration detection Korean patent No. 10-0925337 Woo JH, Yang SJ, Yang KS, Seo JS, Kang JH, Han WS, Kwak GB: Method, Composition, and Kit for Predicting the Risk of Developing Breast Cancer, Korea Patent No. 10-1012601 Talks 10/2014 “Interrogating drug mechanism of action using network dysregulation” Department of Biomedical Informatics Student Seminar, Columbia University Medical Center, New York, NY, USA 04/2014 “Machine learning based somatic mutation calling in whole genome sequencing data from Formalin-fixed, paraffin-embedded (FFPE) tumor samples” Department of Biomedical Informatics Student Seminar, Columbia University Medical Center, New York, NY, USA 09/2013 A systems biology approach for interrogating the footprint of a drug in a cell. Department of Statistics Student Seminar, Columbia University, New York, NY, USA 10/2012 “D-MAND: Identifying Drug Mode of Action using Network Dysregulation” Department of Biomedical Informatics Student Seminar, Columbia University Medical Center, New York, NY, USA 05/2010 Invited by Kiwon Kim M.D., Department of Rehabilitation Medicine, Seoul National University College of Medicine, Korea “A snap shot of integrative genomics” & “NGS & its application” Teaching Spring 2013 Teaching Assistant for Biological Sequence Analysis (BINF-G4013), Dept. of Biomedical Informatics, Columbia University, New York, NY10032, USA Spring 2014 Teaching Assistant for Computational Aspects of Infectious Diseases (BINF-G4016), Dept. of Biomedical Informatics, Columbia University, New York, NY10032, USA
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