Graduate Group in Genomics and Computational Biology

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GCB Alumni


GCB graduates have diverse and interesting career paths. The distribution of career paths is presented here:

Academic: 70%
- Faculty: 26%
- Staff Researchers: 20%
- Post-docs: 20%
- Medical Training: 4%

Industry/Other: 30%

Alumni by Graduation Year (most recent listed first)

2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007

December 2016

Varun Aggarwala
Human Mutation/Substitution Rate: Variability, Modeling and Applications
Advisor: Ben Voight
Current Position: Post-doctoral researcher, University of Pennsylvania
Publications

Nate Berkowitz
Genome Wide Approaches for Studying RNA Secondary Structure
Advisor: Brian Gregory
Publications

May 2016

Eric Chen
Microbiome and Metagenomics: Statistical Methods, Computation and Application
Advisor: Hongzhe Li
Current Position: Data Scientist, Thomas Jefferson University Hospital
Publications

December 2015

Josh Burdick
Regulation of tissue-specific expression in the C. elegans embryo
Advisor: John Murray
Current Position: Computer Analyst, University of Michigan
Publications

Hannah Dueck
Single-cell gene expression variation as a cell-type-specific trait: a study of mammalian gene expression using single-cell RNA sequencing
Advisor: Junhyong Kim
Current Position: Post-doctoral researcher, University of Pennsylvania
Publications

Yih-Chii Hwang

Identification of long-range regulatory elements in the human genome
Advisors: Brian Gregory and Li-San Wang
Current Position: Bioinformatician, DNAnexus
Publications

Derek Oldridge
Insights into neuroblastoma initiation and disease progression through integrative genomics and epigenomics
Advisors: John Maris and Sharon Diskin
Current Position: Finishing Medical School requirements
Publications

August 2015

Scott Sherrill-Mix
Latency, Expression and Splicing During Infection with HIV
Advisor: Rick Bushman
Current Position: Post-doctoral fellow, University of Pennsylvania
Publications

May 2015

Sameer Soi
Characterizing Genome-Wide Patterns of Genetic and Epigenetic Diversity in Sub-Saharan African Populations
Advisors: Junhyong Kim and Sarah Tishkoff
Current Position: Data Scientist, Driver Group, L. L. C.
Publications

Ray Zhang
Building and Mining an Atlas of the Mamalian Circadian Transcriptome
Advisor: John Hogenesch
Current Position: Pathology Resident, Barnes-Jewish Hospital at Washington University Medical Center
Publications

December 2014

Joseph Glessner
Biological Role and Disease Impact of Copy Number Variation in Complex Disease
Advisor: Hakon Hakonarson
Current Position: Postdoctoral fellow, Massachusetts General Hospital
Publications

Nicholas Lahens
The Application and Challenges of RNA-Seaquencing to the Study of Circadian Rhythms
Advisor: John Hogenesch
Current Position: Senior Research Coordinator, University of Pennsylvania
Publications

Nicholas Stong
Telomere and Proximal Seqauence Analysis Using High-Throughput Sequencing Reads
Advisor: Harold C. Riethman
Current Position: UDN Bioinformatician, Columbia University Medical Center Institute for Genome Medicine
Publications

May 2014

Aleah Caulin

Peto's Paradox and the Evolution of Cancer Suppression
Advisors: Shane Jensen and Carlo Maley
Current Position: Clinical Computational Biology Lead, Driver Group, L. L. C.
Publications

December 2013

Brett Hannigan

Navigating the Extremes of Biological Datasets for Reliable Structural Inference and Design
Advisor: William F. DeGrado
Current Position: Computational Biology Project Leader, DNAnexus
Publications

Fan Li
The Global Landscape of RNA Secondary Structure
Advisors: Brian Gregory and Li-San Wang
Current Position: Senior Bioinformatics Scientist, Children's Hospital Los Angeles
Publications

Paul Ryvkin
Methods in and applications of the sequencing of short non-coding RNAs
Advisor: Li-San Wang
Current Position: Data Scientist, 10X Genomics
Publications

Ellen Tsai
Genomic Approaches to Understanding Variable Expressivity in Alagille Syndrome and Genetic Susceptibility to Biliary Atresia

Advisors: Marcella Devoto and Nancy Spinner
Current Position: Sr. Bioinformatician, Partners HealthCare , Research Fellow, Department of Medicine at Harvard Medical School and Channing Division of Network Medicine at Brigham and Women's Hospital
Publications

Sira Sriswasdi
In-Depth Analysis of Zero-Length Crosslinking for Structural Mass Spectrometry
Advisor: David W. Speicher
Current Position: Post-doctoral Fellow, University of Tokyo
Publications

August 2013

Serena Dollive
Dynamics of Microeukaryotes and Archaea in the Mammalian Gut Microbiome
Advisor: Rick Bushman
Current Position: Genomic Scientist, Homology Medicines Inc.
Publications

Najaf Shah

Forward and Reverse Engineering of Cellular Decision-Making
Advisor: Casim Sarkar
Current Postion: Management Consultant, Biopharma and Health Care, The Boston Consulting Group
Publications

May 2013

Le B Nguyen (Gendo)

An integrative approach identifies predisposition genes in Neuroblastoma
Advisors: Hongzhe Lee and John Maris
Current Position: Currently in training to become a Zen Buddhist Monk at ShinKaiRyu Dojo, San Jose, CA

Anthony Olarerin-George
Functional Annotation of MicroRNAs in Signal Transduction Pathways
Advisor: John Hogenesch
Current Position: Post-doctoral Associate, Weill Cornell Medical College
Publications

Jonathan Toung
Identification of RNA-DNA sequence differences in humans using next-generation sequencing technology
Advisor: Rick Bushman
Current Position: Senior Bioinformatics Scientist, GRAIL, Inc
Publications

August 2012

Jun Chen
Statistical Methods for Human Microbiome Data Analysis
Advisor: Hongzhe Lee
Current Position: Assistant Professor of Biostatistics, Mayo Clinic
Publications

May 2012

Rumen Kostadinov
Evolutionary Dynamics of Neoplastic Cell Populations in Barrett's Esophagus
Advisor: Carlo Maley
Current Position: Research Associate, Johns Hopkins University
Publications

December 2011

Rithun Mukherjee

Viral Diversity by Deep Sequencing: Approaches to Analyzing Effects of anti-HIV Treatments
Advisor: Rick Bushman
Current Position: Post-doctoral fellow, Fred Hutchinson Cancer Research Center
Publications

May 2011

Kathleen Sprouffske
Modeling the evolutionary and differentiation dynamics of neoplastic progression
Advisor: Carlo Maley
Current Position: Post-doctoral Fellow, University of Zurich
Publications

December 2010

Perry Evans
Modeling virus-host networks
Advisor: Lyle Ungar
Current Position: Bioinformatics Scientist, Children's Hospital of Philadelphia
Publications

Adam Ewing
The Role of L1 Retrotransposition in Human Genomic Variability
Advisor: Haig H. Kazazian
Current Position: ARC DECRA fellow, The University of Queensland
Publications

August 2010

Logan Everett
Genomic Methods for Studying the Post-Translational Regulation of Transcription Factors
Advisors: Sridhar Hannenhalli and Stephen Master
Current position: Post-doctoral Associate, North Carolina State
Publications

May 2010

ZhongQiang (John) Chen
Identification of proteins associated with specialized (secretory) organelles in apicomplexan parasites
Advisor: David Roos
Current position: Staff Bioinformaticist, DuPont
Publications

Zhandong Liu
The Quantative Prediction of Signal Pathway Activity through Genome-wide Gene Expression Data
Advisor: Lewis Chodosh
Current Position: Assistant Professor, Department of Pediatrics, Baylor College of Medicine
Publications

Thomas Petty
The Structure of a Multidomain P53 Oligomer Bound to DNA; Applications of Probabilistic Protein Design
Advisor: Thanos Halazonetis
Current Position: Bioinformatics Specialist, Sophia Genetics SA
Publications

May 2009

Geetu Tuteja
Illuminating Transcriptional Regulation with Genome-wide Binding Data
Advisor: Klaus H Kaestner
Current Position: Assistant Professor and Gregory L. and Kathleen C. Geoffroy Faculty Fellow of Genetics, Development and Cell Biology, Iowa State University
Publications

December 2009

Irina Bochkis
Hepatic Metabolic Regulatory Networks of Foxa2
Advisor: Klaus H Kaestner
Current Position: Assistant Professor of Pharmacology, University of Virginia
Publications

Ryan Coleman
Shortest Geometric Paths Analysis in Structural Biology
Advisor: Kim Sharp
Current Position: Senior Member of the Technical Staff, Sandia National Laboratories
Publications

Sheng Guo

Computational Analysis and Application of Genotype and Phenotype on Drosophilia Odorant Receptors and RNA
Advisor: Junhyong Kim
Current Positon: Director of Bioinformatics, CrownBio

Miler Lee
Modular Organization and Composability of RNA
Advisor:
Junhyong Kim
Current Position: Assistant Professor of Biological Sciences, University of Pittsburgh
Publications

Daniel Simola
Evolution of Genome-Wide Gene Regulation in the Budding Yeast Cell- Division Cycle
Advisor: Junhyong Kim
Current Position: Scientific Investigator, Computational Biology, GSK Pharma R&D, King of Prussia, PA
Publications

August 2009

Jeremy Purvis
A Systems Approach to Cellular Signal Transduction
Advisor: Scott Diamond and Ravi Radhakrishnan
Current Position: Assistant Professor, Department of Genetics, University of North Carolina-Chapel Hill
Publications

May 2008

Amit Bahl
Design and Application of Multi-functional Microarrays for Toxoplasma gondii
Advisor: David Roos
Current Position: Machine Learning Engineer and Data Scientist, Facebook
Publications

Sharon Diskin
The Role of Germline and Tumor DNA Copy Number in Neuroblastoma Tumorgenesis
Advisor: John Maris and Warren Ewens
Current Position: Assistant Professor, Children's Hospital of Philadelphia
Publications

Praveen Sethupathy
Analysis on the Role of Gene Regulatory Elements in Human Health and Evolution
Advisors: Sridhar Hannenhalli, Artemis D Hatzigeorgiou, Stephen A Liebhaber
Current Position: Assistant Professor of Genetics, University of North Carolina-Chapel Hill
Publications

Zhi Wei
Statistics Methods for Network-Based Analysis on Genomic Data
Advisor: Hongzhe Lee
Current Position: Associate Professor, Computer Science Department, New Jersey Institute of Technology
Publications

August 2007

Molly Megraw

Regulation of MicroRNA Transcription
Advisor: Artemis D Hatzigeorgiou
Current Position: Assistant Professor, Department of Botany and Plant Pathology, Oregon State University
Publications

May 2007

Dexter Hadley
Genome-scale annotation of genetic factors underluying neurotransmission and neuropsychiatric disease
Advisors: Maja Bucan, Junhyong Kim, Lyle Ungar
Assistant Professor of Pediatrics, UCSF
Publications

Marcin Imielinski
In silico analysis of microbial biosynthetic capabilities at the genome scale
Advisor: Harvey Rubin
Current Positions: Assistant Professor of Computational Genomics, Pathology and Laboratory Medicine, Assistant Attending Pathologist, New York-Presbyterian Hospital
Publications