Graduate Group in Genomics and Computational Biology

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GCB Alumni

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Amit Bahl
Machine Learning Engineer and Data Scientist, Facebook

Thesis title and defense date: Design and Application of Multi-functional Microarrays for Toxoplasma gondii, January 2008

Publications


Irina Bochkis
Senior Research Fellow, Broad Institute

Thesis title and defense date: Hepatic Metabolic Regulatory Networks of Foxa2, November 20, 2008.

Publications


Josh Burdick
Post-doctoral researcher, University of Pennsylvania

Thesis title and defense date: Regulation of tissue-specific expression in the C. elegans embryo, November 19, 2015.


Aleah Caulin
Clinical Computational Biology Lead, Driver Group, L. L. C.

Thesis title and defense date: Peto's Paradox and the Evolution of Cancer Suppression, December 13, 2013.

Publications


Jun Chen
Assistant Professor of Biostatistics, Mayo Clinic

Thesis title and defense date: Statistical Methods for Human Microbiome Data Analysis, June 5, 2012.


Zhang (Eric) Chen
Data Scientist, Thomas Jefferson University Hospital

Thesis title and defense date: Microbiome and Metagenomics: Statistical Methods, Computation and Application, April 20, 2016

Publications


ZhongQiang (John) Chen
Staff Bioinformaticist, DuPont

Thesis title and defense date: Identification of proteins associated with specialized (secretory) organelles in apicomplexan parasites, December 10, 2009.


Ryan Coleman
Senior Member of the Technical Staff, Sandia National Laboratories

Thesis title and defense date: Shortest Geometric Paths Analysis in Structural Biology, August 28, 2009.

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Sharon Diskin
Assistant Professor, Children's Hospital of Philadelphia

Thesis title and defense date: The Role of Germline and Tumor DNA Copy Number in Neuroblastoma Tumorgenesis, April 22, 2008.

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Serena Dollive
Scientist, GoodStart Genetics

Thesis title and defense date:Dynamics of Microeukaryotes and Archaea in the Mammalian Gut Microbiome, June 3, 2013.

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Hannah Dueck
Post-doctoral researcher, University of Pennsylvania

Thesis title and defense date: Single-cell gene expression variation as a cell-type-specific trait: a study of mammalian gene expression using single-cell RNA sequencing, October 29, 2015.


Perry Evans
Bioinformatics Scientist, Children's Hospital of Philadelphia

Thesis title and defense date: Modeling virus-host networks, July 29, 2010.

Publications


Logan Everett
Post-doctoral Associate, North Carolina State

Thesis title and defense date: Genomic Methods for Studying the Post-Translational Regulation of Transcription Factors, July 16, 2010.

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Adam Ewing
ARC DECRA fellow, The University of Queensland

Thesis title and defense date: The Role of L1 Retrotransposition in Human Genomic Variability, September 14, 2010.

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Joseph Glessner
Postdoctoral fellow, Massachusetts General Hospital

Thesis title and defense date: Biological Role and Disease Impact of Copy Number Variation in Complex Disease, October 27, 2014.

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Sheng Guo
Director of Bioinformatics, CrownBio

Thesis title and defense date: Computational Analysis and Application of Genotype and Phenotype on Drosophilia Odorant Receptors and RNA, September 26. 2008.


Dexter Hadley
Assistant Professor of Pediatrics, UCSF

Thesis title and defense date: Genome-scale annotation of genetic factors underluying neurotransmission and neuropsychiatric disease, October 2007

Publications


Brett Hannigan
Computational Biology Project Leader, DNAnexus

Thesis title and defense date: Navigating the Extremes of Biological Datasets for Reliable Structural Inference and Design, November 25, 2013.

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Yih-Chii Hwang
Bioinformatician, DNAnexus

Thesis title and defense date: Identification of long-range regulatory elements in the human genome, November 16, 2015.

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Marcin Imielinski
Assistant Professor of Computational Genomics, Pathology and Laboratory Medicine
Assistant Attending Pathologist, New York-Presbyterian Hospital

Thesis title and defense date: In silico analysis of microbial biosynthetic capabilities at the genome scale, December 2005

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Rumen Kostadinov
Research Associate, Johns Hopkins University

Thesis title and defense date: Evolutionary Dynamics of Neoplastic Cell Populations in Barrett's Esophagus, March 26, 2012.

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Nicholas Lahens
Senior Research Coordinator, University of Pennsylvania

Thesis title and defense date: The Application and Challenges of RNA-Seaquencing to the Study of Circadian Rhythms, July 15, 2014.

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Miler Lee
Assistant Professor of Biological Sciences, University of Pittsburgh

Thesis title and defense date: Modular Organization and Composability of RNA, October 9, 2009.

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Fan Li
Senior Bioinformatics Scientist, Children's Hospital Los Angeles

Thesis title and defense date: The Global Landscape of RNA Secondary Structure, November 5, 2013.

Publications


Zhandong Liu
Assistant Professor, Department of Pediatrics, Baylor College of Medicine

Thesis title and defense date: The Quantative Prediction of Signal Pathway Activity through Genome-wide Gene Expression Data, April 15, 2010.

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Molly Megraw
Assistant Professor, Department of Botany and Plant Pathology, Oregon State University

Thesis title and defense date: Regulation of MicroRNA Transcription, June 2007

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Rithun Mukherjee
Post-doctoral fellow, Fred Hutchinson Cancer Research Center

Thesis title and defense date: Viral Diversity by Deep Sequencing: Approaches to Analyzing Effects of anti-HIV Treatments, September 30, 2011.

Publications


Le B Nguyen (Gendo)
Currently in training to become a Zen Buddhist Monk at ShinKaiRyu Dojo, San Jose, CA

Thesis title and defense date: An integrative approach identifies predisposition genes in Neuroblastoma, April 2013

Publications


Anthony Olarerin-George
Post-doctoral Associate, Weill Cornell Medical College

Thesis title and defense date: Functional Annotation of MicroRNAs in Signal Transduction Pathways, February 26, 2013.

Publications


Derek Oldridge

Thesis title and defense date: Insights into neuroblastoma initiation and disease progression through integrative genomics and epigenomics, November 20, 2015.


Thomas Petty
Bioinformatics Specialist, Sophia Genetics SA

Thesis title and defense date: The Structure of a Multidomain P53 Oligomer Bound to DNA; Applications of Probabilistic Protein Design, January 4, 2010.

Publications


Jeremy Purvis
Assistant Professor, Department of Genetics, University of North Carolina-Chapel Hill

Thesis title and defense date: A Systems Approach to Cellular Signal Transduction, June 2009

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Paul Ryvkin
Data Scientist, 10X Genomics

Thesis title and defense date: Methods in andapplications of the sequencing of short non-coding RNAs, August 21, 2013.

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Praveen Sethupathy
Assistant Professor of Genetics, University of North Carolina-Chapel Hill

Thesis title and defense date: Analysis on the Role of Gene Regulatory Elements in Human Health and Evolution, March 2008

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Najaf Shah
Management Consultant, Biopharma and Health Care, The Boston Consulting Group

Thesis title and defense date: Forward and Reverse Engineering of Cellular Decision-Making, May 21, 2013

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Scott Sherrill-Mix
Post-doctoral fellow, University of Pennsylvania

Thesis title and defense date: Latency, Expression and Splicing During Infection with HIV, June 4, 2015

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Daniel Simola
Scientific Investigator, Computational Biology, GSK Pharma R&D, King of Prussia, PA

Thesis title and defense date: Evolution of Genome-Wide Gene Regulation in the Budding Yeast Cell- Division Cycle, September 3, 2009.

Publications


Sameer Soi
Data Scientist, Driver Group, L. L. C.

Thesis title and defense date: Characterizing Genome-Wide Patterns of Genetic and Epigenetic Diversity in Sub-Saharan African Populations, April 10, 2015.

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Kathleen Sprouffske
Post-doctoral Fellow, University of Zurich

Thesis title and defense date: Modeling the evolutionary and differentiation dynamics of neoplastic progression, January 21, 2011.

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Sira Sriswasdi
Post-doctoral Fellow, University of Tokyo

Thesis title and defense date: In-Depth Analysis of Zero-Length Crosslinking for Structural Mass Spectrometry, September 12, 2013.

Publications


Nicholas Stong
UDN Bioinformatician, Columbia University Medical Center Institute for Genome Medicine

Thesis title and defense date: Telomere and Proximal Seqauence Analysis Using High-Throughput Sequencing Reads, November 24, 2014.

Publications


Jonathan Toung
Bioinformatics Scientist, Illumina

Thesis title and defense date: Identification of RNA-DNA sequence differences in humans using next-generation sequencing technology, February 26, 2013.

Publications


Ellen Tsai
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

Thesis title and defense date: Genomic Approaches to Understanding Variable Expressivity in Alagille Syndrome and Genetic Susceptibility to Biliary Atresia, October 18, 2013.

Publications


Geetu Tuteja
Assistant Professor and Gregory L. and Kathleen C. Geoffroy Faculty Fellow of Genetics, Development and Cell Biology, Iowa State University

Thesis title and defense date: Illuminating Transcriptional Regulation with Genome-wide Binding Data, December 15, 2008.

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Zhi Wei
Associate Professor, Computer Science Department, New Jersey Institute of Technology

Thesis title and defense date: Statistics Methods for Network-Based Analysis on Genomic Data, March 2008

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Ray Zhang
Pathology Resident, Barnes-Jewish Hospital at Washington University Medical Center

Thesis title and defense date: Building and Mining an Atlas of the Mamalian Circadian Transcriptome, December 2, 2014.

Publications