Skills

python

R

Data Science

Problem Solving

Experience

 
 
 
 
 
September 2015 – Present
Houston

Postdoctoral Associate

Baylor College of Medicine

Focusing on the development of quantification algorithm and pipeline construction for next-generation sequencing data for the neurological disorder.
 
 
 
 
 
March 2014 – August 2015
Suwon, South Korea

Research Associate

Ajou University

Participated in GenomicSelf - Translational Bioinformatics for Genomic Health and Personalized Medicine. project. Developed tools for Integrative omics data analysis using clinical outcome-guided mutual information network.

Selected Publications

Aging and neurodegenerative disease are characterized by genomic instability in neurons, including aberrant activation and mobilization of transposable elements (TEs). Integrating studies of human postmortem brain tissue and Drosophila melanogaster models, we investigate TE activation in association with Tau pathology in Alzheimer’s disease (AD). Leveraging RNA sequencing from 636 human brains, we discover differential expression for several retrotransposons in association with neurofibrillary tangle burden and highlight evidence for global TE transcriptional activation among the long interspersed nuclear element 1 and endogenous retrovirus clades. In addition, we detect Tau-associated, active chromatin signatures at multiple HERV-Fc1 genomic loci. To determine whether Tau is sufficient to induce TE activation, we profile retrotransposons in Drosophila expressing human wild-type or mutant Tau throughout the brain. We discover heterogeneous response profiles, including both age- and genotype-dependent activation of TE expression by Tau. Our results implicate TE activation and associated genomic instability in Tau-mediated AD mechanisms.
Cell Reports, 2018

bioRxiv, 2018

We present a user-friendly, cloud-based, data analysis pipeline for the deconvolution of pooled screening data. This tool, CRISPRcloud, serves a dual purpose of extracting, clustering and analyzing raw next generation sequencing files derived from pooled screening experiments while at the same time presenting them in a user-friendly way on a secure web-based platform. Moreover, CRISPRcloud serves as a useful web-based analysis pipeline for reanalysis of pooled CRISPR screening datasets. Taken together, the framework described in this study is expected to accelerate development of web-based bioinformatics tool for handling all studies which include next generation sequencing data.
Bioinformatics, 2017

Recent Publications

. A druggable genome screen identifies modifiers of α-synuclein levels via a tiered cross-species validation approach. Journal of Neuroscience, 2018.

DOI

. Tau activates transposable elements in Alzheimer’s disease. Cell Reports, 2018.

PDF DOI

. CRISPRCloud2: A cloud-based platform for deconvoluting CRISPR screen data. bioRxiv, 2018.

PDF DOI

. An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data. Biocomputing 2018, 2018.

PDF DOI

. CRISPRcloud: a secure cloud-based pipeline for CRISPR pooled screen deconvolution. Bioinformatics, 2017.

PDF DOI

Recent & Upcoming Talks

Targeted genome editing, CRISPR
Sep 21, 2018 12:00 PM

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