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%


Meet our alumni! Graduates are listed by their graduation year:

2019

Alex Amlie-Wolf
Development and Application of Computational Methods for Inferring the Molecular Mechanisms of Noncoding Genetic Variants
Advisor: Li-San Wang
Current Position: Computational Biologist, Arrakis Therapeutics
Publications

Raju Mishra
Genetic insights into Latent Autoimmune Diabetes in Adults
Advisor: Struan Grant
Current position: Statistical Genetics Investigator, GlaxoSmithKline

Katie Siewert
Detecting ancient balancing selection: methods and application to human
Advisor: Ben Voight
Current position: Postdoctoral researcher, Harvard University

Greg Way
Discovering pathway and cell-type signatures in transcriptomic compendia with machine learning
Advisor: Casey Greene
Current position: Postdoctoral associate, The Broad Institute of MIT and Harvard
Publications
 

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2018

Elizabeth Piette
Strategies for improving epistasis detection and replication
Advisor: Jason Moore
Current Position: Data Scientist, Elsevier

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2017

Brett Beaulieu-Jones
Machine Learning Methods to Identify Hidden Phenotypes in the Electronic Health Record
Advisors: Casey Greene and Jason Moore
Current Position: Postdoctoral Research Fellow, Department for Biomedical Informatics, Harvard Medical School
Publications

Erik Clarke
Metagenomic applications in idiopathic and immune diseases
Advisor: Rick Bushman
Current Position: Post-doctoral researcher, University of Pennsylvania
Publications

Jackie Meisel
Metagenomic and Transcriptomic Insights into the Skin Microbiome and Host Response
Advisor: Elizabeth Grice
Current Position: Post-doc, University of Maryland, College Park
Publications

Krishna Vijayendran
Computational approaches for designing protein/inhibitor complexes and membrane protein variants
Advisor: Jeff Saven
Current Position: Postdoctoral Researcher, University of Pennsylvania

Xiao Ji
Essential genes and their role in autism spectrum disorder
Advisor: Maja Bucan
Current Position: Drug Discovery Data Scientist, GlaxoSmithKline
Publications

Yuchao Jiang
Statistical methods for genomic and transcriptomic sequencing
Advisor: Nancy Zhang
Current Position: Assistant Professor, University of North Carolina at Chapel Hill
Publications

Sarah Middleton
Structure-function relationships of RNA and protein in synaptic plasticity
Advisor: Junhyong Kim
Current Position: Computational Biologist, GlaxoSmithKline
Publications
 

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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
Current Position: Bioinformatics Analyst, AncestryDNA
Publications

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

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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: Presidential Management Fellow, National Cancer Institute
Publications

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

Derek Oldridge
Insights into neuroblastoma initiation and disease progression through integrative genomics and epigenomics
Advisors: John Maris and Sharon Diskin
Current Position: Pathology Resident, University of Pennsylvania
Publications

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

Sameer Soi
Characterizing Genome-Wide Patterns of Genetic and Epigenetic Diversity in Sub-Saharan African Populations
Advisors: Junhyong Kim and Sarah Tishkoff
Current Position: Senior Data Scientist, Grand Rounds
Publications

Ray Zhang
Building and Mining an Atlas of the Mamalian Circadian Transcriptome
Advisor: John Hogenesch
Current Position: Fellow, Blood Banking & Transfusion Medicine, Barnes-Jewish Hospital at Washington University Medical Center
Publications

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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

Aleah Caulin
Peto's Paradox and the Evolution of Cancer Suppression
Advisors: Shane Jensen and Carlo Maley
Current Position: Program Director of Preclinical Studies, PEEL Therapeutics
Publications

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2013

Brett Hannigan
Navigating the Extremes of Biological Datasets for Reliable Structural Inference and Design
Advisor: William F. DeGrado
Current Position: Director of Bioinformatics Software and Engineering, Inscripta
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: Staff Data Scientist, Omniome
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: Senior Scientist, Biogen
Publications

Sira Sriswasdi
In-Depth Analysis of Zero-Length Crosslinking for Structural Mass Spectrometry
Advisor: David W. Speicher
Current Position: Lecturer at the Faculty of Medicine, Chulalongkorn University
Publications

Serena Dollive
Dynamics of Microeukaryotes and Archaea in the Mammalian Gut Microbiome
Advisor: Rick Bushman
Current Position: Scientist, Bioinformatics at Homology Medicine, 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

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

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2012

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

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

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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

Kathleen Sprouffske
Modeling the evolutionary and differentiation dynamics of neoplastic progression
Advisor: Carlo Maley
Current Position: Postdoctoral Scholar, Novartis Institutes for Biomedical Research in Basel, Switzerland
Publications

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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: Group Leader, Translational Bioinformatics, Mater Research Institute, University of Queensland
Publications

Logan Everett
Genomic Methods for Studying the Post-Translational Regulation of Transcription Factors
Advisors: Sridhar Hannenhalli and Stephen Master
Current position: Bioinformatics Scientist, Office of Research & Development, Environmental Protection Agency
Publications

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

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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

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

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

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

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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, University of Pennsylvania and the Children's Hospital of Philadelphia
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

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: Associate Professor, Biomedical Sciences at Cornell University
Publications

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

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2007

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

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

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