Alumni
The list that follows includes graduates of the Designated Emphasis in Computational and Gencomic Biology dating back to the program’s inception in 2004.
Soyeon Ahn (PhD 2009, Statistics)
Postdoctoral Researcher, Seoul National University
Dissertation: Statistical topics in gene regulation
Advisor: Terry Speed
Anil Aswani (PhD 2010, Electrical Engineering)
Dissertation: Systems Theory for Pharmaceutical Drug Discovery
Advisor: Claire Tomlin
Richard Bourgon (PhD 2006, Statistics)
European Bioinformatics Institute
Dissertation: Chromatin immunoprecipitation and high-density tiling microarrays: a generative model, methods for analysis, and methodology assessment in the absence of a “gold standard”
Advisor: Terry Speed
Robert Bradley (PhD 2008, Biophysics)
Postdoctoral Fellow, Massachusets Institute of Technology
Dissertation: Annotation, alignment and reconstruction of non-coding RNA
Advisors: Michael Eisen, Lior Pachter
Duncan Brown (PhD 2006, Bioengineering)
Senior Research Scientist, Merck
Dissertation: Protein subfamily clustering and classification
Advisor: Kimmen Sjolander
James Bullard (PhD 2009, Biostatistics)
Pacific Biosciences
Dissertation: Statistical Methods and Software for High-throughput Gene Expression Experiments.
Advisor: Sandrine Dudoit
Dustin Cartwright (PhD 2010, Mathematics)
Postdoctoral Scholar, Institut Mittag-Leffler
Dissertation: Applications of Non-linear Algebra To Biology
Advisor: Bernd Sturmfels
Anat Caspi (PhD 2007, Bioengineering)
Postdoctoral Researcher, University of Pennsylvania
Dissertation: Comparative genomics of repeat elements
Advisor: Lior Pachter
Lee Chae (PhD 2008, Plant Biology)
Postdoctoral Research Associate, Carnegie Institution, Stanford University
Dissertation: Genomic analysis of the receptor-like kinase superfamily in plants
Advisors: Sheng Luan, Steven Brenner, and Sandrine Dudoit
Jarrod Chapman (PhD 2004, Physics)
DOE Joint Genome Institute
Dissertation: Whole genome shotgun assembly in theory and practice
Advisor: Daniel Rokhsar
Sourav Chatterji (PhD 2006, Computer Science)
Postdoctoral Scholar, UC Davis Genome Center
Dissertation: Computational analyses of eukaryotic gene evolution
Advisors: Richard M. Karp, Lior Pachter
Hua Chen (PhD 2007, Integrative Biology)
Postdoctoral Fellow, Harvard Medical School
Dissertation: Statistical methods for inference of positive selection from genetic polymorphism
Advisor: Montgomery Slatkin
Derek Chiang (PhD 2005, Molecular and Cell Biology)
Faculty, University of North Carolina School of Medicine
Dissertation: Computational and experimental analyses of promoter architecture in yeasts
Advisor: Michael Eisen
Colin Dewey (PhD 2006, Computer Science)
Faculty, University of Wisconsin-Madison
Dissertation: Whole-genome alignments and polytopes for comparative genomics
Advisor: Lior Pachter
Barbara Engelhardt (PhD 2007, Computer Science)
Postdoctoral Fellow, University of Chicago
Dissertation: Predicting protein molecular function
Advisor: Michael Jordan
Nicholas Eriksson (PhD 2006, Mathematics)
Principal Scientist, 23andMe
Dissertation: Algebraic combinatorics for computational biology
Advisor: Bernd Sturmfels
Patrick Flaherty (PhD 2006, Computer Science)
Postdoctoral Research Fellow, Stanford School of Medicine
Dissertation: A kinetic model for G protein-coupled signal transduction in macrophage cells
Advisors: Michael Jordan, Adam Arkin
Hunter Fraser (PhD 2005, Molecular and Cell Biology)
Faculty, Stanford University
Dissertation: Studies of evolution from a geonomic perspective
Advisor: Michael Eisen
Houston Gilbert (PhD 2009, Biostatistics)
Genentech
Dissertation: Multiple Hypothesis Testing: Methodology, Software Implementation, and Applications to Genomics
Advisor: Sandrine Dudoit
Benjamin Goldstein (PhD 2011, Biostatistics)
Instructor – Senior Biostatistician, Quantitative Sciences Unit, Stanford School of Medicine
Dissertation: Finding Genes Related to Disease Using Statistical Learning
Advisors: Alan Hubbard, Lisa Barcellos
Richard Green (PhD 2005, Molecular and Cell Biology)
Faculty, UC Santa Cruz
Dissertation: Gene regulation via alternative splicing and nonsense-mediated mRNA decay
Advisor: Steven Brenner
Kasper Hansen (PhD 2009, Biostatistics)
Postdoctoral Fellow, Johns Hopkins University
Dissertation: Analyses of High-Throughput Gene Expression Data
Advisor: Sandrine Dudoit
Emily Hare (PhD 2008, Molecular and Cell Biology)
Associate Editor, Public Library of Science (PLoS)
Dissertation: Functional conservation of divergent regulatory sequences : lessons from Drosphila, scavenger flies, and the true fruit flies
Advisor: Michael Eisen
Greg Hather (PhD 2008, Statistics)
Biostatistician, Millennium Pharmaceuticals
Dissertation: Statistical analysis of DNA sequence motifs and microarray data
Advisors: Terry Speed, Mary C. Wildermuth
Peter Huggins (PhD 2008, Mathematics)
Postdoctoral Research Fellow, Carnegie Mellon University
Dissertation: Polytopes in computational biology
Advisors: Lior Pachter, Bernd Sturmfels
Venky Iyer (PhD 2007, Molecular and Cell Biology)
Data Scientist, Facebook
Dissertation: Comparative genomics in Drosophila
Advisor: Michael Eisen
Philip Johnson (PhD 2009, Biophysics)
Postdoctoral Fellow, Emory University
Dissertation: Unbiased population genetic inference from high-throughput sequencing data
Advisor: Montgomery Slatkin
Sunduz Keles (PhD 2003, Biostatistics)
Faculty, University of Wisconsin-Madison
Dissertation: Statistical methods for cis-regulatory motif detection in DNA sequences and two censored data problems
Advisor: Mark van der Laan
Alex Lancaster (PhD 2006, Integrative Biology)
Postdoctoral Research Associate, University of Arizona
Dissertation: Identifying associations between natural selection and molecular function in human MHC genes
Advisor: Glenys J. Thomson
Liana Lareau (PhD 2008, Molecular and Cell Biology)
Postdoctoral Scholar, Stanford School of Medicine
Dissertation: Unproductive mRNA splicing and ultraconserved DNA elements
Advisor: Steven Brenner
Richard Lusk (PhD 2010, Molecular and Cell Biology)
Postdoctoral Researcher, UC Berkeley
Dissertation: Models to Mechanisms: Leveraging Functional and Evolutionary Information to Describe Regulatory Sequences
Advisor: Michael Eisen
Jon McAuliffe (PhD 2005, Statistics)
Adjunct Faculty, UC Berkeley
Dissertation: Statistical methods for comparing genomes
Advisor: Michael Jordan
Annette Molinaro (PhD 2004, Biostatistics)
Faculty, Yale University
Dissertation: Novel approaches to prediction of survival in cancer research : focus on genomics
Advisor: Mark van der Laan
Alan Moses (PhD 2005, Biophysics)
Faculty, University of Toronto
Dissertation: Molecular evolution of transcriptional regulation
Advisor: Michael Eisen
Manikandan Narayanan (PhD 2007, Computer Science)
Senior Research Scientist, National Institutes of Health
Dissertation: Comparative and evolutionary analysis of cellular pathways
Advisor: Richard M. Karp
John Novembre (PhD 2006, Integrative Biology)
Faculty, UCLA
Dissertation: Statistical methods for neutral and adaptive genetic variation in continuous isolation-by-distance models
Advisor: Montgomery Slatkin
Daniel Pollard (PhD 2007, Biophysics)
Postdoctoral Fellow, UCSD
Dissertation: Evoluation of cis-regulatory sequences in Drosophila : a systematic approach
Advisor: Michael Eisen
Sriram Sankararaman (PhD 2010, Computer Science)
Postdoctoral Fellow, Harvard Medical School
Dissertation: Statistical models for analyzing human genetic variation
Advisors: Michael Jordan, Kimmen Sjolander
Anne Shiu (PhD 2010, Mathematics)
Postdoctoral Fellow, Duke University
Dissertation: Algebraic methods for biochemical reaction network theory
Advisors: Lior Pachter, Bernd Sturmfels
Amoolya Singh (PhD 2006, Computer Science)
Scientist, Amyris
Dissertation: Evolution, modularity, and dynamics of gene regulatory networks
Advisors: Richard Karp, Adam Arkin
David Soergel (PhD 2010, Biophysics)
Postdoctoral Researcher, UC Berkeley
Dissertation: Computational Methods for Evaluating Microbial Diversity
Advisor: Steven Brenner
Owen Solberg (PhD 2008, Integrative Biology)
Programmer Analyst , Woodruff Lab, UCSF
Dissertation: Population genetic diversity of two pathogens and the role of balancing selection in HLA immunogenetics
Advisor: Montgomery Slatkin
Margaret Taub (PhD 2009, Statistics)
Postdoctoral Fellow, Johns Hopkins Bloomberg School of Public Health
Dissertation: Analysis of high-throughput biological data: some statistical problems in RNA-seq and mouse genotyping
Advisor: Terry Speed
Lenny Teytelman (PhD 2009, Molecular and Cell Biology)
Postdoctoral Research Associate, Massachusets Institute of Technology
Dissertation: Evolution of silencers and silenced DNA in budding yeasts
Advisors: Jasper Rine, Michael Eisen
Nancy Wang (PhD 2009, Statistics)
Scientist, Exponent Engineering and Scientific Consulting
Dissertation: Statistical problems in DNA microarray data analysis
Advisor: Terry Speed
Leor Weinberger (PhD 2004, Biophysics)
Faculty, UCSD
Dissertation: Elucidating a novel stochastic mechanism in HIV-1 Tat tranactivation and harnessing it for AIDS therapy
Advisor: Adam Arkin
Na Xu (PhD 2008, Statistics)
Senior Biostatistican, Genentech
Dissertation: Transcriptome detection by multiple RNA tiling array analysis and identifying functional conserved non-coding elements by statistical testing
Advisors: Peter Bickel, Haiyan Huang
Weiwei Zhai (PhD 2008, Integrative Biology)
Research Associate, Beijing Institute of Genomics
Dissertation: Explorations in studying natural selection
Advisor: Montgomery Slatkin
Xiaoyue Zhao (PhD 2005, Statistics)
Senior Computational Biologist, Celgene
Dissertation: Statistical methods for elucidating DNA motifs and modules
Advisor: Terry Speed