Program alumni

Trainee Mentor Years supported by this training grant Terminal Degree(s) Received and Year Topic of Research Project Current position
Fueyo, Joanna L. Ewens, Warren J.
Weiser, Jeffrey N.
2000-2002 PhD 2002 In Silico Discovery of Antimicrobial Targets Visiting Scholar Bioinformatics
Boston University
Buehler, Eugen Unger, Lyle H. 2000-2003 PhD 2003 Statistical Models for the Analysis of Heterogeneous Biological Data Sets Senior Scientist
Data Science
& AI
Schein, Andrew I. Unger, Lyle H. 2000-2004 PhD 2005 Active Learning for Logistic Regression, A -optimality Software Engineer Google
Fingerman, Ethan Sniegowski, Paul 2001-2004 PhD 2004 Sequence evolution of the retrotransposon Ty3 in natural isolates of saccharomyces cerevisiae ad saccharomyces paradozus Associate Director Marketing
Demira, Inc.
Infante, Aniello Kannan, Sampath 2002 None   Unknown
Harb, Boulos Kannan, Sampath
Guha, Sudipto
2003-2005 PhD 2007 Algorithms for Linear and Nonlinear Approximation of Large Data Senior Staff Software Engineer
Suri, Siddharth Kearns, Michael 2003-2005 PhD 2007 The Effects of Network Topology on Strategic Behavior Senior Researcher, Microsoft Research
Sandler, Samuel T. Ungar, Lyle H. 2004-2007 PhD 2010 Regularized learning with feature networks Researcher,
Diskin, Sharon J. Maris, John M.

Ewens, Warren J.

2005-2007 PhD 2008 The Role of Germline and Tumor DNA Copy Number in Neuroblastoma Tumorgenesis Assistant Professor Pediatrics
Perelman School of Medicine, University of Pennsylvania
Imielinski, Marcin B. Rubin, Harvey 2006-2007 PhD 2007
MD 2009
In Silico Analysis of Microbial Biosynthetic Capabilities at the Genome-Scale. Assistant Professor
Pathology and Laboratory Medicine and Computational Genomics
Weill Cornell Medical College
Essien, Kobby Stoeckert, Christian J. 2005-2008 PhD 2009 Computational approaches for studying transcriptional regulation in Plasmodium and other apicomplexan parasites Principal
Launch Center of Excellence
Simola, Daniel F. Kim, Junhyong 2005-2007 PhD 2009 Evolution of Genome-Wide Gene Regulation in the Budding Yeast Cell- Division Cycle GSK Associate Fellow, Scientific Leader, GlaxoSmithKline Pharma GmbH
Hadley, Dexter Kim, Junhyong 2002-2007 PhD 2007

MD 2009

Genome-Scale Annotation of Genetic Factors Underlying Neurotransmission & Neuropsychiatric Disease Assistant Professor Pediatrics
Bochkis, Irina M. Kaestner, Klaus H. 2005-2007 PhD 2008 Hepatic Metabolic Regulatory Networks of Foxa2 Assistant Professor
Pharmacology University of Virginia
Tuteja, Geetu S. Kaestner, Klaus H. 2005-2007 PhD 2009 Illuminating Transcriptional Regulation with Genome-wide Binding Data Assistant Professor and Gregory L. and Kathleen C. Geoffroy Faculty Fellow
Iowa State University
Winter, Cara M. Wagner, Doris 2006-2007 PhD 2011 Genome wide identification of LEAFY target genes reveals novel insights into reproductive development in Arabidopsis thaliana Research Scientist
Duke University
Evans, James P. Ungar, Lyle H. 2007-2010 PhD 2010 Modeling virus-host networks Bioinformatics Scientist
Department of Biomedical and Health Informatics
Children’s Hospital of Philadelphia
Everett, Logan J. Master, Steven
Hannenhalli, Sridhar
2007-2009 PhD 2010 Genomic methods for studying the post-translational regulation of transcription factors Bioinformatics Scientist
Office of Research and Development
National Center for Computational Toxicology
Environmental Protection Agency
Moser, Theresa S. Cherry, Sara 2007-2009 PhD 2011 The role of AMPK in viral infection Medical Writer ETHOS Health Communications
Olarerin-George, Anthony Hogenesch, John B. 2006-2010 PhD 2013 Functional annotation of MicroRNAs in signal Transduction Pathways Postdoctoral Associate
Weill Cornell Medical College
Further Training
Sprouffske, Kathleen M. Maley, Carlo C. 2007-2009 PhD 2011 Modeling the evolutionary and differentiation dynamics of neoplastic progression Postdoctoral Scientist
Oncology Bioinformatics Novartis Institutes for Biomedical Research
Further Training
Coleman, Ryan G. Sharp, Kim A. 2007-2009 PhD 2009 Shortest Geometric paths analysis in structural biology Senior Member of the Technical Staff,

Sandia National Laboratories

Purvis, Jeremy E. Diamond, Scott L.


2008-2009 PhD 2009 A system approach to cellular signal transduction Assistant Professor Genetics
University of North Carolina, Chapel Hill
Ryvkin, Paul Wang, Li-San 2009-2010 PhD 2013 Methods in and applications of the sequencing of short non-coding RNAs Staff Data Scientist
Omniome Inc.
Lahens, Nicholas F. Hogenesch, John B. 2009-2010 PhD 2014 RNA Splicing and the Circadian Clock Bioinformatics Researcher
Institute for Translational Medicine and Therapeutics Researcher
Perelman School of Medicine, University of Pennsylvania
Barendt, Pamela


Sarkar, Casim A.


2009-2010 PhD 2011 Broad-Specificity mRNA–rRNA Complementarity in Efficient Protein Translation Associate
Equity Research Cowen and Company
Tsai, Ellen A. Devoto, Marcella
Spinner, Nancy B.
02011-2012 PhD 2013 Genomic approaches to understanding variable expressivity in alagille syndrome and genetic susceptibility to biliary atresia Computational Scientist
Burdick, Joshua T. Murray, John I. 2010-2012 PhD 2015 Location of gene expression in developing C. elegans Computer Analyst
Life Sciences Institute
University of Michigan
Li, Fan Gregory, Brian D.
Wang, Li-San
2011-2013 PhD 2013 The global landscape of RNA secondary structure Senior Statistician
UCLA Health
Sherrill-Mix, Scott Bushman, Frederic D. 2011-2013 PhD 2015 Developing methods to investigate alternative splicing in HIV and other lentiviruses Post-Doctoral Researcher Microbiology University of Pennsylvania
Further Training
Rupp, Levi J. Bassing, Craig H. 2011-2013 PhD 2014 The role of the RNA processing enzyme Dicer in regulating silencing of the co-receptors CD4 and CD8 during T cell development CAR-T Group Leader
Discovery/Preclinical Research
Janssen Inc.
Hannigan, Brett T. DeGrado, William F. 2012-2013 PhD 2013 Navigating the extremes of biological datasets for reliable structural inference and design Senior Director of Science
Richards, Allison Cheung, Vivian G. 2012-2013 PhD 2015 –mentor moved to University of Michigan The Role of RNA Editing in Organelle Function Computational Biologist II, Memorial Sloan Kettering Cancer Center
Kraya (Akl), Adam Speicher, David W. 2012-2014 PhD 2015 Identification and validation of autophagy biomarkers in genetically related melanoma cell lines with high or low levels of basal autophagy Computational Biologist
Vijayendran, Krishna G Saven, Jeffrey L. 2013-2016 PhD 2017
MD 2019
Computationally design a water-soluble variant of the GPCR Smoothened (SMO), area of therapeutic drug resistance Post-doctoral researcher
University of Pennsylvania
Further Training


Zhang, Ray Hogenesch, John B. 2012-2013 PhD 2014
MD 2016
Profiling the Circadian transciptomes from a variety of mouse organs Resident
Clinical Pathology Washington University Medical Center
Further Training
Oldridge, Derek A. Diskin, Sharon J.
Maris, John M.
2013-2014 PhD 2015
MD 2017
Non-coding mechanisms of functional dysregulation in neuroblastoma Clinical Pathology Chief Resident
Clinical Pathology Program
University of Pennsylvania
Further Training
Rosario, Jean Kim, Junhyong 2014-2018 In Training Identifying species specific differences in the dendritic transcriptomes of rodents  
Meisel, Jacqueline S. Grice, Elizabeth A. 2014-2016 PhD 2017 Characterizing the community composition, metabolic potential, and temporal stability of the healthy human skin metagenome and its impact on the host Postdoctoral Associate
Center for Bioinformatics & Computational Biology
University of Maryland, College Park
Further Training
Tian, Kevin Kannan, Sampath 2015-2016 PhD 2016 Detecting Character Dependencies in Phylogenies  
Slaff, Barry Wang, Li-San 2015-2017 None Computational analysis of Alzheimer’s disease Graduate Student, Computer Science
University of Pennsylvania
Further Training



Siewert, Katherine M. Voight, Benjamin F. 2015-2017 PhD 2019 Population genetics

approach to complex disease genetics

Post-doctoral fellow Harvard School of Public Health
Further Training





Berry, Alexander Brisson, Dustin 2014-2016 PhD 2018 Comparative analysis of biogeographic distribution of

T. cruzi

Postdoctoral Researcher
University of Pennsylvania
Further Training


Mellis, Ian Raj, Arjun 2016-2017 In Training Experimental and computational analysis of RNA editing

in mammalian cells.

Way, Gregory P. Greene, Casey S. 2017-2019 PhD
Obtaining knowledge from gene expression data across different cancer-types. Postdoctoral Research
Biomedical Imaging, Genomics Associate
Broad Institute of MIT and Harvard
Further Training