Education

Graduate student in Cancer Biology & Genomics Program, Keck School of Medicine, University of Southern California, 2014-Now

PIBBS program for first year graduate student, Keck School of Medicine, University of Southern California, 2013-2014

M.S. in Health Sciences Informatics, School of Medicine, Johns Hopkins University, 2013

B.S. in Medicinal Chemistry, Arizona State University, 2011

 

Research Area

Develop package in R to profile motifs near double-stranded DNA break

Study aging and aging related DNA repair mechanisms using whole-genome sequencing data analysis

 

Research

SeqApp (Cooperate with Dr. Michael Lieber Lab)

Double-strand breaks (DSB) contribute to genetic instability and cause various diseases. Previously Lieber lab studied ~1900 breakpoints and illustrated a new DSB mechanism, which is marked by a CpG dinucleotide motif in the pro-B/pre-B stage. Now we are developing an R package,enable convenient sequence alignment through local or online BLAST/BLAT,locate target motifs based on breakpoint profiling, calculate the distances from the input sequence breakpoints to known motifs, generate random breakpoints for statistical comparison, and plot the sequence-level breakpoints and frequency diagrams.

SeqApp Work Flow:
SeqApp Workflow

 

 

Aging (Cooperate with Dr. Michael Lieber Lab)

We propose to apply whole genome sequencing analysis to normal human colon crypts to model nuclear and mitochondrial genomic mutations with age. We are interested in all types of genomic mutations including large structural variations, small indels (insertions and deletions, less than 20bps), and single base mutations. In addition to determining the occurrence and frequency of each mutation type during aging, we will study the underlying pathogenetic mechanisms of these mutations, especially whether they are caused by error prone NHEJ (Non-Homologous End Joining) or unsuccessful DNA repair by the high-fidelity pathways (base and nucleotide excision repair, mismatch repair and homologous recombination).

 

Publications

Coughlin, J.M., Wang, Y., Ma, S., Pomper, MG., et. al., "Neuroinflammation and Brain Atrophy in Former NFL Players: An in vivo Multimodal Imaging Study"; Brain; Submitted for review

Coughlin, J.M., Wang, Y., Ma, S, Pomper, MG., et. al., “Regional Brain Distribution of Translocator Protein using [11C]DPA-713 PET in Individuals Infected with HIV”; Journal of NeuroVirology. Jan. 2014

Sawa, A; Coughlin, J; Ma, S; Pomper, MG, et al. “Neuroinflammation In Psychosis: A Multifaceted Study Approach That Includes Imaging The Translocator Protein (TSPO)”. Co-Chair Speak in Society of Biological Psychiatry 2013 Conference.