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:

Joseph Aicher
Improving Molecular Diagnosis of Suspected Mendelian Disorders with RNA Splicing Analysis
Advisors: Yoseph Barash and Elizabeth Bhoj
Current Position: Finishing medical school requirements
Publications

Alexandra Lee
Big Data for Small Organisms: Computational Approaches to Leverage Large-Scale Microbial Transcriptomic Compendia
Advisor: Casey Greene
Current Position: Scientist II, Computational Biology; Rheos Medicine.
Publications

David Nicholson
Unmasking the Language of Science through Textual Analyses on Biomedical Preprints and Published Papers
Advisor: Casey Greene
Current Position: Data Scientist, Digital Science
Publications

Chi-Yun Wu
Multi-omics Integration Through Single-cell Copy Number Analysis in Cancer
Advisor: Nancy Zhang
Current Position: Bioinformatic Postdoctoral Scholar, Gladstone Institutes and UCSF
Publications

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Gregory Chen
Leveraging Systems Immunology to Understand the Molecular Underpinnings of Chimeric Antigen Receptor T-cell Therapy
Advisor: Kai Tan
Current Position: Finishing medical school requirements
Publications

Samantha Klasfeld
Development and Application of Next Generation Sequencing Pipelines in Arabidopsis
Advisor: Doris Wagner
Current Position: Postdoctoral Research Fellow, Pfizer
Publications

David Lee
Insights Into Functional Noncoding RNA Elements through the Analysis of Human Genetic Variation
Advisors: Yoseph Barash, Louis Ghanem
Current Position: Finishing medical school requirements
Publications

Apexa Modi
Characterizing the gene networks associated with non-coding elements in pediatric cancer using integrative genomics
Advisor: Sharon Diskin
Current Position: Bioinformatics Scientist I, AbbVie 

Joseph Park
A genome-first approach to investigating the biological and clinical relevance of exome-wide rare coding variation using electronic health record phenotypes
Advisors: Marylyn Ritchie, Daniel Rader
Current Position: Finishing medical school requirements
Publications

Mengge Shan
The Global Landscape of RNA-Protein Interactions in Physcomitrium Patens ABA Response and in a Model of Mammalian Erythropoesis
Advisor: Brian Gregory
Current Position: Scientist I, Remix Therapeutic
Publications 

Amber Weiner 
Advancing Immunotherapy through Proteogenomics: Identification and Validation of DLK1 as a Target in Neuroblastoma
Advisors: Sharon Diskin, Ben Garcia, John Maris
Current Position: Postdoctoral Fellow, Children's Hospital of Philadelphia

Qin Zhu
Understanding Gene Regulation in Development and Differentiation Using Single Cell Multi-Omics  
Advisors: Junhyong Kim, Kai Tan
Current Position: Postdoctoral Researcher, UCSF
Publications

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Benjamin Emert
Uncovering the Origins of Rare-Cell Phenomena
Advisor: Arjun Raj
Current Position: Postdoctoral Researcher, Caltech
Publications

Binglan Li
Identifying complex trait-related genes via regulation informed gene-based analyses
Advisor: Marylyn Ritchie
Current Position: Postdoctoral research fellow, Stanford University
Publications

Matt Paul
Genomic evolution of breast cancer metastasis
Advisor: Lewis Chodosh
Current Position: Postdoctoral research fellow, University of Cambridge
Publications

Eric Sanford
Gene regulation displays an enrichment of both additive and multiplicative outcomes when combining the effects of two cell signals
Advisor: Arjun Raj
Current Position: Psychiatry Resident, Mount Sinai Hospital
Publications

Blair Zhang
Discovering pleiotropy across circulatory system diseases and nervous system disorders
Advisor: Marylyn Ritchie
Current Position: Senior Statistical Geneticist, Regeneron
Publications

Di Zhang
Sculpting 3D chromatin folding via genome editing​​​​​​​
Advisor: Gerd Blobel
Current Position: Clinical Pathology Resident, Brigham and Women's Hospital
Publications

Linda Zhou
The 3D genome as a new dimension in understanding pathologic short tandem repeat instability
Advisor: Jennifer Phillips-Cremins
Current Position: Dermatology Resident, Penn Medicine
Publications

Zilu Zhou
Statistical Methods for Multi-Omics Inference from Single Cell Transcriptome
Advisor: Nancy Zhang
Current Position: Senior Data Scientist, Google
Publications

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Divyansh Agarwal
Multivariate Statistical Analysis in Single Cell Transcriptomics
Advisor: Nancy Zhang
Current position: Resident, Surgery, Harvard (MGH)
Publications

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

Casey Bartow-McKenney
Further defining epidermal function through deciphering host-microbe interactions in the skin
Advisor: Elizabeth Grice
Current Position: Senior Data Scientist, CVS Health
Publications

Ian Mellis
Systems biology of gene regulation across scales: from single molecules to cellular identities
Advisor: Arjun Raj
Current position: Resident, Pathology, Columbia
Publications

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

Scott Norton
Methods for robust quantification of RNA alternative splicing in heterogeneous RNA-seq datasets
Advisor: Yoseph Barash
Current position: Bioinformatician, Yale University

Emily Shields
Caste-Specific Expression of Coding and Noncoding Genes in Ant Brains
Advisor: Roberto Bonasio
Current position: Postdoctoral researcher, University of Pennsylvania
Publications

Katie Siewert
Detecting ancient balancing selection: methods and application to human
Advisor: Ben Voight
Current position: Senior Research Scientist, Computational Genomics, Vertex Pharmaceuticals
Publications

Greg Way
Discovering pathway and cell-type signatures in transcriptomic compendia with machine learning
Advisor: Casey Greene
Current position: Assistant Professor, Biochemistry and Molecular Genetics, University of Colorado Anschutz
Publications

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

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Brett Beaulieu-Jones
Machine Learning Methods to Identify Hidden Phenotypes in the Electronic Health Record
Advisors: Casey Greene and Jason Moore
Current Position: Assistant Professor, Biomedical Data Science, University of Chicago
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: Assistant Research Scientist, University of Maryland Institute for Advanced Computer Studies
Publications

Krishna Vijayendran
Computational approaches for designing protein/inhibitor complexes and membrane protein variants
Advisor: Jeff Saven
Current Position: Internal Medicine Resident, University of Connecticut

Xiao Ji
Essential genes and their role in autism spectrum disorder
Advisor: Maja Bucan
Current Position: Associate Director, GlaxoSmithKline
Publications

Yuchao Jiang
Statistical methods for genomic and transcriptomic sequencing
Advisor: Nancy Zhang
Current Position: Assistant Professor, Biostatistics, 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: Associate Director, Computational Biology, GlaxoSmithKline
Publications

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Varun Aggarwala
Human Mutation/Substitution Rate: Variability, Modeling and Applications
Advisor: Ben Voight
Current Position: Postdoctoral Fellow, Icahn School of Medicine at Mount Sinai
Publications

Nate Berkowitz
Genome Wide Approaches for Studying RNA Secondary Structure
Advisor: Brian Gregory
Current Position: Bioinformatics Scientist, Illumina
Publications

Eric Chen
Microbiome and Metagenomics: Statistical Methods, Computation and Application
Advisor: Hongzhe Li
Current Position: Expert Research Scientist, Medical AI, UII America Inc.
Publications

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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: Program Director, Division of Cancer Biology, 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: Principal Scientist, Healthcare Management, DNAnexus
Publications

Derek Oldridge
Insights into neuroblastoma initiation and disease progression through integrative genomics and epigenomics
Advisors: John Maris and Sharon Diskin
Current Position: Assistant Professor, Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania
Publications

Scott Sherrill-Mix
Latency, Expression and Splicing During Infection with HIV
Advisor: Rick Bushman
Current Position: Research Associate, Microbiology, 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 Manager, Data Science, Zymergen
Publications

Ray Zhang
Building and Mining an Atlas of the Mamalian Circadian Transcriptome
Advisor: John Hogenesch
Current Position: Assistant Professor, Pathology, University of Texas Southwestern Medical Center
Publications

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Joseph Glessner
Biological Role and Disease Impact of Copy Number Variation in Complex Disease
Advisor: Hakon Hakonarson
Current Position: Associate Director, Center for Applied Genomics, Children’s Hospital of Philadelphia
Publications

Nicholas Lahens
The Application and Challenges of RNA-Sequencing to the Study of Circadian Rhythms
Advisor: John Hogenesch
Current Position: Bioinformaticion, Institute for Translational Medicine and Therapeutics, University of Pennsylvania
Publications

Nicholas Stong
Telomere and Proximal Sequence Analysis Using High-Throughput Sequencing Reads
Advisor: Harold C. Riethman
Current Position: Principal Scientist, Bristol-Myers Squibb
Publications

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

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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: CEO, Three Coin Analytics
Publications

Paul Ryvkin
Methods in and applications of the sequencing of short non-coding RNAs
Advisor: Li-San Wang
Current Position: Senior Staff Computational Biologist, 10X Genomics Inc.
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: Associate Director, 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: Senior Scientist II, Oxford Biomedical Solutions
Publications

Najaf Shah
Forward and Reverse Engineering of Cellular Decision-Making
Advisor: Casim Sarkar
Current Position: Partner, The Boston Consulting Group
Publications

Le B Nguyen (Gendo)
An integrative approach identifies predisposition genes in Neuroblastoma
Advisors: Hongzhe Lee and John Maris

Anthony Olarerin-George
Functional Annotation of MicroRNAs in Signal Transduction Pathways
Advisor: John Hogenesch
Current Position: Assistant Professor, Pharmacology, Physiology & Neuroscience, Rutgers University
Publications

Jonathan Toung
Identification of RNA-DNA sequence differences in humans using next-generation sequencing technology
Advisor: Rick Bushman
Current Position: Senior Software Engineer, Robinhood
Publications

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

Rumen Kostadinov
Evolutionary Dynamics of Neoplastic Cell Populations in Barrett's Esophagus
Advisor: Carlo Maley
Current Position: Computational Biologist, GlaxoSmithKline
Publications

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Rithun Mukherjee
Viral Diversity by Deep Sequencing: Approaches to Analyzing Effects of anti-HIV Treatments
Advisor: Rick Bushman
Current Position: Research Scientist, Seattle Children's
Publications

Kathleen Sprouffske
Modeling the evolutionary and differentiation dynamics of neoplastic progression
Advisor: Carlo Maley
Current Position: Investigator, Oncology Data Science, Novartis Institutes for BioMedical Research
Publications

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Perry Evans
Modeling virus-host networks
Advisor: Lyle Ungar
Current Position: Lead Data Scientist, Spark Therapeutics
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, National Center for Computational Toxicology, 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: Associate Professor, Quantitative & Computational Biosciences, 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: Head of Knowledge Management, Sophia Genetics SA
Publications

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Geetu Tuteja
Illuminating Transcriptional Regulation with Genome-wide Binding Data
Advisor: Klaus H Kaestner
Current Position: Associate Professor and Dean's Faculty Fellow in the Department 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, Pharmacology, University of Virginia
Publications

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

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

Daniel Simola
Evolution of Genome-Wide Gene Regulation in the Budding Yeast Cell- Division Cycle
Advisor: Junhyong Kim
Current Position: Director, Computational Biology, GlaxoSmithKline
Publications

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

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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: Associate Professor, Pediatrics, University of Pennsylvania
Publications

Sheng Guo
Computational Analysis and Application of Genotype and Phenotype on Drosophilia Odorant Receptors and RNA
Advisor: Junhyong Kim
Current Positon: Vice President, Data Science & 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: Professor, Biomedical Sciences, Cornell University
Publications

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

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Molly Megraw
Regulation of MicroRNA Transcription
Advisor: Artemis D Hatzigeorgiou
Current Position: Associate Professor, 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
Current Position: Chief of Artificial Intelligence, University of Central Florida College of Medicine
Publications

Marcin Imielinski
In silico analysis of microbial biosynthetic capabilities at the genome scale
Advisor: Harvey Rubin
Current Positions: Associate Professor, Pathology and Laboratory Medicine, Weill Cornell Medical Center
Publications

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