Chung, Jaeyoon

(Last updated: Apr **, ****)

Phone: 617-***-**** / E-mail: ac0fqg@r.postjobfree.com or ac0fqg@r.postjobfree.com Bioinformatics and Biomedical Genetics, Boston University 72 East Concord Street E201, Boston, MA 02118

Education

Sep. 2011 – Current PhD, Bioinformatics program at Boston University, Boston, MA Advisor: Lindsay A Farrer PhD

Expected graduation by Sep, 2017

Feb. 2010 ME, Biotechnology and Bioinformatics Engineering, Korea University Joint Research institute Graduate program of

Korea University (KU) and Korea Institute of Science and Technology (KIST) Advisor: Art E. Cho PhD at KU and Jung-Mi Hah PhD at KIST Aug. 2007 BE, Computer Engineering, Inha University, Incheon, South Korea Dissertation

Thesis title: Collapsed Rare Variants Association Study of Multiple Phenotypes Related to Alzheimer disease I developed a statistical method, called versatile gene-based multiphenotype association study (VEMPHAS), to test associations of collapsed rare variants in a gene with pleiotropy effect with multiple endophenotypes related with disease of interest. VEMPHAS was applied to analysis of real genetic data with endophenotypes (or quantitative traits) related with Alzheimer disease (AD) including CSF biomarkers, MRI brain scans, cognitive test measures, or neuropathological traits (neuritic plaque, neurofibrillary tangles, and cerebral amyloid angiopathy).

Project Attendance / Work Experience

Current

Sep, 2014 - Current

Alzheimer Disease Sequencing Project (ADSP; PI: Lindsay A Farrer PhD): Identify new genomic variants contributing to increased risk of developing Late-Onset AD using 500 whole genome sequencing data and 10,000 whole exome sequencing (WES) data.

I participated in the QC procedure for the WES data to generate cleaned genotype (VCF) files. Sep, 2012 - Current

Alzheimer Disease Genetics Consortium (ADGC; PI: Lindsay A Farrer PhD): Identify genetic variants associated with risk for AD using a large scale of GWAS data (more than 30,000 samples of multi-ethnics including European Americans, African American, Hispanics, and Asians from multiple cohorts/centers)

I participated as a main data analyst in the two of ADGC core projects: 1) genome-wide association studies (GWAS) of AD in APOE ε4 carriers and non-carriers and 2) transethnic GWAS of AD including European Americans, African Americans, Japanese, and Israeli-Arabs.

I participated as a main data analyst for the informed conditioning analysis of AD risk for African Americans using various environmental risk factors (diabetes, smoking, education, etc.) for AD.

I proposed and conducted a bivariate analysis of AD-related neuropathological traits (neuritic plaque, neurofibrillary tangles, and cerebral amyloid angiopathy) from about 3,500 autopsy brain samples. I was invited as a speaker to give oral presentation about the novel findings from the bivariate analysis of neuropath data at Alzheimer's Association International Conference 2017 in London.

Recently, I proposed a new study of genetic overlap between breast/ovarian cancers and neurodegenerative disorders. This proposal was accepted in the ADGC and is now under reviewing by Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Jul, 2016 - Current

Chronic Traumatic Encephalopathy (CTE) Genetics; PI: Jesse Mez PhD Identify genetic variants associated with risk for CTE using genetic data from autopsy brain sample

I participated as a main data analyst for this project, which was recently initiated. Past

Jan, 2016 – Jun, 2016

Winter Co-op position at Biogen; Supervisor: Christopher Roberts PhD

I conducted differential expression gene (DEG) and WGCNA network analyses for diseased kidney biopsy RNA profiling data (Affymetrix microarray and RNA-Seq).

I did variant calling with the RNA-Seq data using GATK pipeline (STAR/ PICARD/ HaplotypeCaller). I integrated the expression data with variants called from the same RNA-Seq data sample to conduct eQTL analysis

Aug, 2007 – May, 2011

Research Assistant at KIST in Seoul, South Korea; PIs: Seung Joo Cho PhD and Jung-Mi Hah PhD Science Research Program through the National Research Foundation funded by the Ministry of Education, Science and Technology of Korea

I worked with medicinal chemistry scientists to develop B-Raf and JNK kinase inhibitors via quantitative structure-activity relationship (QSAR), docking simulation, fragment-based drug design, and peptidomimetics.

I developed a pipeline of computer-aided drug design (CADD) techniques including QSAR and docking simulation to design new inhibitors (chemicals).

I developed a protein-ligand docking simulation software (called PythDock) using a machine learning algorithm (particle swarm optimization) with python language. Publication

Submitted to Journals or Manuscript in Preparation

Chung J, Zhang X, Mariet A, et al.

“Bivariate Genome-wide association study of neuropathologic traits related to Alzheimer disease” Submitted to Annals of Neurology

Chung J, Wang X, Maruyama T et al.

“Genome-Wide Association Study of Alzheimer Disease Endophenotypes at Preclinical Stages” Submitted to Alzheimers Dement.

Chung J, Farrer LA, Gyungah Jun

“Post RNA-Seq GUI: graphical browser for allele-specific expressions in isoforms” Manuscript in preparation

Wu1 J, Patel D, Chung J, et al.

“An Efficient Analytic Approach in Genome-wide Identification of Methylation Quantitative Trait Loci Response to Fenofibrate Treatment” Submitted to BMC Genomics

Yonova-Doing E, Zhao W, Igo R, Chung J, et al.

“Genome-wide association meta-analysis identifies novel loci for age-related nuclear cataract” Submitted to Nature Communications

Journal Articles

Jun GR, Chung J, Mez J, et al.

“Transethnic genome-wide scan identifies novel Alzheimer's disease loci” Alzheimers Dement. (2017) accepted (available online).

Mez J, Chung J, Jun G et al.

“Two novel loci, COBL and SLC10A2, for Alzheimer's disease in African Americans” Alzheimers Dement. (2017) 13, 119-129.

Jun G, Ibrahim-Verbaas CA, Vronskaya M, Lambert JC, Chung J, et al.

“A novel Alzheimer disease locus located near the gene encoding tau protein” Mol Psychiatry (2016) 21, 109-117.

Jun G, Asai H, Zeldich E, Drapeau E, Chen C, Chung J, et al.

“PLXNA4 is associated with Alzheimer Disease and modulates Tau phosphorylation” Ann Neurol. (2014) 76, 379-92.

Lacey S, Chung J, Lin H.

“A comparison of whole genome sequencing with exome sequencing for family-based association studies” BMC Proc. (2014) 17:8 (Suppl 1; Genetic Analysis Workshop 18)

Chung J, Cho SJ, Hah J, Cho AE.

“In silico binding free energy predictability with π–π interaction energy-augmented scoring function: Benzimidazole Raf inhibitors as a case study” Bioorg Med Chem Lett. (2012) 22, 3278-83

Chung J, Cho SJ, Hah J

“A python-based docking program utilizing a receptor bound ligand shape: PythDock” Archives of Pharmacal Research (2011) 34, 1451-1458

Chung J, Chung HW, Cho SJ, Hah J, Cho AE

“QM/MM based 3D QSAR Models for Potent B-Raf Inhibitors” Journal of Computer-Aided Molecular Design (2010) 24, 385-397

Lee J, Kim H, Yu H, Chung J, Oh CH, Yoo KH, Sim T, Hah J

“Discovery and initial SAR of pyrimidin-4-yl-1H-imidazole derivatives with antiproliferative activity against melanoma cell lines”

Bioorg Med Chem Lett. (2010) 20, 1573-1577

Chung J, Hah J, Cho AE

“Correlation between Performance of QM/MM Docking and Simple Classification of Binding Sites” Journal of Chemical Information and Modeling (2009) 49, 2382–2387

Cho AE, Chung J, Kim M, Park K

“Quantum mechanical scoring for protein docking”

The Journal of Chemical Physics (2009) 131, 134***-******

Chung J, Cho AE, Hah J

“Hologram and Receptor-Guided 3D QSAR Analysis of Anilinobipyridine JNK3 Inhibitors” Bulletin of the Korean Chemical Society (2009) 30, 2739-2748

Chung J, Pasha FA, Cho SJ, Won M, Lee JJ, Lee K

“Pharmacophore-based 3D-QSAR of HIF-1 Inhibitors Archives of Pharmacal Research” Archives of Pharmacal Research (2009) 32, 317-323

Chung J, Pasha FA, Chung HW, Yang BS, Lee CJ, Oh JS, Moon MW, Cho SJ, Cho AE

“Topomer-CoMFA Study of Tricyclic Azepine Derivative-EGFR Inhibitors” Molecular & Cellular Toxicity (2008) 4, 78-84

Oral Presentation

Jul, 2017 “Bivariate Genome-wide association study of neuropathologic traits related to Alzheimer

(Scheduled) disease”

at the Alzheimer’s Association International Conference (AAIC), London, UK Feb, 2017 “Bivariate Genome-wide association study of AD-related neuropathological features including neuritic plaque, neurofibrillary tangles, and cerebral amyloid angiopathy” at Annual Meeting of Alzheimer Disease Genetic Consortium, Cleveland, OH Jun, 2016 “Genome-wide Association Study of Alzheimer Disease at Different Clinical Stages” at Boston University ARC Meeting, Boston, MA

Apr, 2016 “WGCNA Network Analysis of Chronic Kidney Disease” at Biogen Fibrosis Consortium, Cambridge, MA

Oct, 2016 “Genome-wide Association Study for Alzheimer Disease Adjusted for APOE Influence” at Boston University ARC Symposium, Boston, MA

Posters

Oct, 2016 Chung J, Jung GR, and Farrer LA

“Post RNA-Seq Analysis Graphic User Interface”

Poster at the American Society of Human Genetics (ASHG) Annual Meeting, Vancouver, Canada

Jul, 2016 Chung J, Ma Y, Lunetta KL, Mez J, Jung GR, and Farrer LA

“Multivariate phenotypes association study of neuropathological features of Alzheimer’s disease and related dementias”

Poster at the AAIC Meeting, Toronto, Canada

Aug, 2015 Chung J, Farrer LA, and Jun G.

“Genome-wide Association Study in Different Clinical Stages of Alzheimer Disease” Poster at the AAIC Meeting, Washington, DC

Oct, 2014 Chung J, Farrer LA, and Jun G.

“Genome-Wide Association Study in Different Stages of Clinical Progression of Alzheimer Disease”

Poster at the ASHG Annual Meeting, San Diego, CA.

Aug, 2014 Chung J, Farrer LA, and Jun G.

“Bivariate genome-wide association study of Alzheimer disease endophenotypes identifies novel loci”

Poster at the AAIC Meeting, Copenhagen, Denmark.

Aug, 2013 Chung J, Lohsen M, Sherva R, Koesterer R, Mayeux R, and Farrer LA

“Interaction Analysis Identifies Susceptibility Loci Associated with the Rate of Cognitive Decline”

Poster at the AAIC Meeting, Boston MA

Aug, 2009 Chung J, Hah J, Cho AE

“Correlation between Performance of QM/MM Docking and Simple Classification of Binding Sites”

Poster at the Fall American Chemical Society National Meeting, Washington DC Software Development

2017 Chung J., Jun RG, Farrer, LA

“Post RNA-Seq GUI”

Python/R program with graphic user interface for integrating genetic association results, expression data (e.g. RNA-Seq) with protein structural information

- https://youtu.be/3uwKt13jkRU (combine genetic data and expression data for conducting eQTL tests)

- https://youtu.be/3SUtyyjzTUY (locate amino acids in a protein structure encoded by exonic variants)

- https://youtu.be/4UZaGpwqJ3s (locate genomic coordinates corresponding for AAs of interest) 2017 Chung J.

“Versatile gene-based multiphenotype association study (VEMPHAS)” An R script for multivariate gene-based association test correcting for correlation between phenotypes

Sep, 2010 Chung J, Hah J

“PythDock”

Python program for predicting the binding position of small chemical (drug candidate) with protein structures in 3D space

*Reg. No.160574, Reg. ID 2010-01-121- 005451

Oct, 2008 Chung HW, Oh SJ, Cho SJ, Chung J

“TozongDOCK: Stochastic Optimization based Molecular Docking” C/C++ program for predicting the binding position of small chemical (drug candidate) with protein structures in 3D space

*Reg. No.139909, Reg. ID 2008-01-121-005352

Authors are ordered by major contributor first.

*The above simulation programs are registered in Korean SORS (Software Online Registration System, www.sors.or.k) Computer (programming) Languages and Software

1. Computer languages

• Python (matplotlib, PyQT4, sqlite3, pandas, rpy2, SciPy/NumPy, etc)

• R (knitr/Markdown, Shiny, biomaRt, etc.)

• Unix or Linux shell script in high performance computing (HPC) cluster (job submitting/scheduling)

• Database SQLite

• C/C++

• Perl and SAS (not professional level)

2. Statistical methods/library/packages for analysis of genetic/genomic data

• PLINK, EPACTS and R/GENESIS

• SHAPEIT/IMPUTE2 and HRC for imputation of GWAS data

• METAL, METASOFT, and MANTRA for meta-analysis of genetic association summary data

• SMR and PrediXcan for analysis of gene-based association test with eQTL

• R/WGCNA for network analysis using expression data

• FASTQC, STAR, GATK, and RSEM for sequencing data

• R/DESeq2 for RNA-Seq expression data

3. Protein Structure Modeling software

• PyMol, Schrodinger (MAESTRO), SYBYL, and OPENEYE packages Awards

Apr, 2017 Travel funding award in Bioinformatics Program at Boston University, Boston, MA for AAIC 2017 at London

Jul, 2012 Scholarship for Summer Institute in Statistical Genetics (SISG) in University of Washington, Seattle, WA

Feb. 11, 2010 Academic Excellence Award (magna cum laude) in KIST Oct. 10, 2009 Best poster announcement

in the 9th KIAS-SNU Conference on Protein Structure and Function Dec. 24, 2009 Oral Presentation Award in the 8th KIAS Protein Folding Winter School Spring, 2007 Honor scholarships in Inha University Fall, 2006 Honor scholarships in Inha University

Spring, 1999 Honor scholarships in Inha University Research Interests

- Genetic association testing in Genome-wide association study (GWAS) or Whole Genome/Exome Sequencing (WGS/WES) data

- Statistical methods in multiple phenotypes data (i.e. pleiotropy effects)

- Analysis of sequencing data with expression profiling data (eQTL/DEG)

- Genetic annotation data by mapping/prioritizing genetic variants in 3D protein structures

Other Activities

Jul, 2014 – Aug, 2014

Mentorship in Research Internship in Science & Engineering (RISE) Program at Boston University

- Instructed a high school student on analyzing genetic data and querying public genetic databases. Jan, 2014 – Apr, 2014

Teaching Assistant in the class, Computational Systems Biology of Human Disease (BE568) at Boston University

- Assisted the professor (Simon Kasif PhD) in preparing class materials, graded biweekly homework and tutored students with assignments and concepts in TA hours (2 hours a week). Jan, 2014 – May, 2014

Cambridge School Volunteers (CSV) at Cambridge Street Upper School; NetPals program Executive Director: Lance Hartford in Massachusetts Biotechnology Education Foundation

- Participated in NetPals program as a volunteer for one semester. Every month, volunteers met students in Cambridge Street Upper School as tutor/mentor.

Contact this candidate