Graduate Group in Genomics and Computational Biology

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GCB Alumni

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Amit Bahl
Research Associate, Merck and Company

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

Publications


Irina Bochkis
Post-doctoral Fellow, Regev Lab, Broad Institute

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

Publications


Aleah Caulin
Bioinformatics Analyst, Cancer Therapeutics Innovation Group

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

Publications


Jun Chen
Post-doctoral Fellow, Lin Lab, Harvard University

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


ZhongQiang (John) Chen
Post-doctoral Fellow, Roos Lab, University of Pennsylvania

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


Ryan Coleman
Post-doctoral fellow, Shoichet Lab, University of California-San Francisco

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

Publications


Serena Dollive
Scientist, GoodStart Genetics

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

Publications


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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Perry Evans
Post-doctoral fellow, Krauthammer Lab, Yale University

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

Publications


Logan Everett
Post-doctoral fellow, Lazar Lab, University of Pennsylvania

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

Publications


Adam Ewing
Post-doctoral fellow, University of California, Santa Cruz

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

Publications


Sheng Guo
Statistical Geneticist, Syngenta Biotechnology, Inc.

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


Dexter Hadley
Lead Clinical Data Analysis, Center for Applied Genomics, Children's Hospital of Philadelphia

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, DNA Nexus

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

Publications


Marcin Imielinski
Postdoctoral Fellow, Meyerson Lab, Broad Institute of MIT and Harvard
Clinical Fellow, Pathology, Massachusetts General Hospital

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

Publications


Rumen Kostadinov
Post-doctoral Associate, Irizarry Lab, Johns Hopkins University

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

Publications


Miler Lee
Post-doctoral Associate, Department of Genetics, Yale School of Medicine

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

Publications


Fan Li
Postdoctoral Associate, Gregory Lab, University of Pennsylvania

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


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.

Publications


Molly Megraw
Uwe Ohler Lab, Duke 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


Anthony Olarerin-George
Post-doctoral fellow, Hogenesch Lab, University of Pennsylvania

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

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Thomas Petty
Post-doctoral fellow, Swiss Institute of Bioinformatics

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
Post-doctoral Fellow, Galit Lahav Laboratory, Department of Systems Biology, Harvard University

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

Publications


Paul Ryvkin
Statistician/Software Engineer, Ariosa Diagnostics

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
Senior Scientist, Merck and Company

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

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Daniel Simola
Post-doctoral Fellow, Berger Lab, University of Pennsylvania

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

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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.

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Jonathan Toung
Student, Harvard Business School

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

Publications


Geetu Tuteja
Post-doctoral Fellow, Stanford University

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

Publications


Zhi Wei
Assistant 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

Publications