Derren Barken

Degree Conferred: Ph.D. Bioinformatics 2007 Spring

Thesis: Temporal encoding and homeostatic control in the IKK-IkB-NF-kB

Advisor(s): Alexander Hoffmann, Shankar Subramaniam

Current Employment: Prometheus (Bioinformatics Scientist)

Ali Bashir

Degree Conferred: Ph.D. Bioinformatics 2009 Winter

Thesis: Computational Methods for Analyzing and Detecting Genomic Structural Variation: Applications to Cancer

Advisor(s): Vineet Bafna, Pavel Pevzner

Current Employment: Pacific Biosciences (Scientist)

Christopher Benner

Degree Conferred: Ph.D. Bioinformatics 2008 Fall

Thesis: Identification of a Conserved Periodic Promoter Structure in Metazoans

Advisor(s): Christopher Glass, Shankar Subramaniam

Current Employment: University of California, San Diego (Glass Lab) (Postdoc)

Kunal Bhutani

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2017 Winter

Thesis: Limiting Biases in Biological Data Analysis by Pooling Information

Advisor(s): Nicholas Schork, Vineet Bafna

Stefano Bonissone

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2015 Fall

Thesis: Deconvolution of immunome and degradome repertoires using computational proteomics

Advisor(s): Pavel Pevzner, Steve Briggs

Kristine Briedis

Degree Conferred: Ph.D. Bioinformatics 2008 Spring

Thesis: The distribution and evolution of protein kinase and phospatase families in the three superkingdoms of life

Advisor(s): Philip Bourne, William Loomis

Current Employment: University of California, San Diego (Bourne Lab) (Postdoc)

Mary Budagyan (Mary Pacold)

Degree Conferred: Ph.D. Bioinformatics 2010 Fall

Thesis: Detecting and Characterizing HIV-1 Intaclade Dual Infection

Advisor(s): Doug Richman, Glenn Tesler

Current Employment: Ion Torrent / Life Technologies (Product Manager, Informatics Applications)

Jason Chan

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2011 Summer

Thesis: Effects of a Highly Repetitive Endogenous Tyl Retrotransposon on Genome Stablility

Advisor(s): Richard Kolodner, Trey Ideker

Roger Chang

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2012 Fall

Thesis: Structural systems biology perspective on the metabolic impact of physicochemical stress

Advisor(s): Bernhard Palsson, Philip Bourne

Current Employment: Harvard Medical School (Postdoctoral Fellow)

Christine Cheng

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2011 Winter

Thesis: Innate immune gene expression programs defined by both regulated mRNA synthesis and decay

Advisor(s): Alexander Hoffmann, Charles Elkan

Current Employment: Broad Institute of MIT and Harvard (Postdoc in Aviv Regev's Lab)

Markus Covert

Degree Conferred: Ph.D. Bioengineering with a specialization in Bioinformatics 2003 Fall

Thesis: Transcriptional Regulation in Escherichia coli: A Systems Biology Approach

Advisor(s): Bernhard Palsson

Current Employment: Stanford (Asst Professor)

Michele Day

Degree Conferred: Ph.D. Bioinformatics 2008 Fall

Thesis: Insights into the functionality and targeting of PKA regulatory subunity Rialpha

Advisor(s): Susan Taylor, Lynn Ten Eyck

Current Employment: University of California, San Diego (Taylor Lab) (Postdoc)

Dinh Diep

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2017 Winter

Thesis: Novel molecular and bioinformatics approaches to investigate DNA methylation in human epigenome

Advisor(s): Kun Zhang, Vineet Bafna

Iman Famili

Degree Conferred: Ph.D. Bioengineering with a specialization in Bioinformatics 2004 Winter

Thesis: Systemic analysis of the stoichiometric matrix and kinetic characterization of metabolic networks.

Advisor(s): Bernhard Palsson, Shankar Subramaniam

Current Employment: GT Life Sciences, Inc. (Research Director)

Merril Gersten

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2011 Fall

Thesis: Systems Analysis of Model Organisms in the Study of Human disease

Advisor(s): Shankar Subramaniam, Gabriel Haddad

Current Employment: UCSD Dept Bioengineering (Postdoc)

Nitin Gupta

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2009 Fall

Thesis: Computational and Comparative Proteogenomics: Annotating Genomes and Proteomes using Tandem Mass Spectrometry

Advisor(s): Pavel Pevzner, Steve Briggs

Current Employment: University of California, San Diego (Aron Lab) (Postdoc)

Markus Herrgard

Degree Conferred: Ph.D. Bioengineering with a specialization in Bioinformatics 2004 Fall

Thesis: Reconstruction and Systems Analysis of Genome-Scale Metabolic and Regulatory Networks inSaccharomyces cerevisiae

Advisor(s): Bernhard Palsson, Shankar Subramaniam

Current Employment: synthetic genomics (Senior Bioinformatics Scientist)

Albert Hsiao

Degree Conferred: Ph.D. Bioengineering with a specialization in Bioinformatics 2005 Spring

Thesis: Comparative functional genomics of energy metabolism and insulin resistance in mammalian systems

Advisor(s): Shankar Subramaniam, Jerrold Olefsky

Current Employment: UCSD (Assistant Professor of Radiology, In-Residence)

Kasey Hutt

Degree Conferred: Ph.D. Bioinformatics 2008 Fall

Thesis: High-throughput genomic assays: Applications and analysis of DSL technology and next-generation sequencing

Advisor(s): Michael Rosenfeld, Terry Gaasterland

Current Employment: University of California, San Diego (Rosenfeld Lab) (Postdoc)

Andrew Joyce

Degree Conferred: Ph.D. Bioinformatics 2007 Summer

Thesis: Modeling and analysis of the e. coli transcriptional regulatory network: an assessment of its properties, plasticity and role in adaptive evolution

Advisor(s): Bernhard Palsson, Bing Ren

Current Employment: Philip Morris (Post Doc)

Eugene Ke

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2012 Spring

Thesis: Insights from reconstructing cellular networks in transcription, stress and cancer

Advisor(s): Shankar Subramaniam, Inder Verma

Current Employment: Salk Institute (Research Associate (Postdoc))

Marcus Kinsella

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2013 Spring

Thesis: Computational Techniques to Investigate Structural Variation

Advisor(s): Vineet Bafna, Kelly Frazer

Current Employment: Pacific Biosciences (Senior Engineer (Bioinformatics))

Joanne Liu

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2017 Summer

Thesis: Predicting Growth Optimization Strategies with Metabolic/Expression Models

Advisor(s): Karsten Zengler, Nathan E. Lewis

Qi Ma

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2015 Winter

Thesis: Understanding the Functional Properties of Enhancers

Advisor(s): Michael Rosenfeld, Gene Yeo

Current Employment: UCSD (Postdoctoral Fellow in Rosenfeld Lab)

John Mongan

Degree Conferred: Ph.D. Bioinformatics 2006 Winter

Thesis: Implicit Solvent Method Development and Application: Fast Molecular Surfaces, Constant pH and Accelerated Dynamics, and Rational Drug Design

Advisor(s): Andrew McCammon, Gary Huber

Current Employment: Stanford (Radiology residency)

Coleman Mosley

Degree Conferred: Ph.D. Bioinformatics 2006 Summer

Thesis: Global Views of Human Genetic Variation: Single Nucleotide Polumorphises (SNPs) Effects and their Random Nature

Advisor(s): Nicholas Schork, Daniel O'Connor

Current Employment: Magellan Health-National Imaging Associates (Physician Clinical Reviewer)

Harish Nagarajan

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2012 Fall

Thesis: Electromicrobiiology: A Systems Perspective

Advisor(s): Bernhard Palsson, Milton Saier

Current Employment: Genomatica Inc. (Research Scientist I, Computational Technologies)

Jason Papin

Degree Conferred: Ph.D. Bioengineering with a specialization in Bioinformatics 2005 Winter

Thesis: Systems Analysis of Cellular Signaling Networks

Advisor(s): Bernhard Palsson, Jerrold Olefsky

Current Employment: University of Virginia (Assistant Professor)

Samuel Payne

Degree Conferred: Ph.D. Bioinformatics 2008 Summer

Thesis: Advances in Computational Mass Spectrometry: Phosphoprteomics and Proteogenomics

Advisor(s): Vineet Bafna, William Loomis

Current Employment: J. Craig Venter Institute (Bioinformatics Engineer)

Nathan Price

Degree Conferred: Ph.D. Bioengineering with a specialization in Bioinformatics 2005 Summer

Thesis: Unbiased Assessment of Genome-Scale Metabolic Network States

Advisor(s): Bernhard Palsson, Shankar Subramaniam

Current Employment: University of Illinois, Urbana-Champaign (Assistant Professor)

Juan Lorenzo Rodriguez Flores

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2009 Spring

Thesis: In Silico In Vitro In Vivo and In Populo Regulatory Single Nucleotide Polymorphisms in the Phenylethanolamine N-Methyltransferase Promoter

Advisor(s): Daniel O'Connor, Shankar Subramaniam

Current Employment: Ludwig Institute for Cancer Research (Postdoc)

Philip Samayoa

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2014 Spring

Thesis: Applications of synthetic biology inspired by natural bacterial functionality

Advisor(s): Jeff Hasty, Ruth Williams

Matthew Schultz

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2014 Winter

Thesis: What Your Genome Doesn't Tell You: Population-level and Genome-wide Epigenomic Surveys of Plants and People

Advisor(s): Joseph Ecker, Vineet Bafna

Current Employment: Human Longevity, Inc. (Bioinformatics Scientist)

Siddarth Selvaraj

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2014 Spring

Thesis: Analysis of 3D genome organization and gene regulation in mammalian cells

Advisor(s): Bing Ren, Vineet Bafna

Martin Smith

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2015 Winter

Thesis: Increasing Biological Realism in Models of Sequence Evolution for Improved Statistical and Computational Performance

Advisor(s): Sergei L. Kosakovsky Pond, Doug Richman

Lukasz Szpankowski

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2011 Spring

Thesis: Coordination of Axonal Transport Revealed by Particle Tracking and Quantitative Immunogluorescence

Advisor(s): Lawrence Goldstein, Shankar Subramaniam

Current Employment: Fluidigm (Scientist - R&D, New Technologies)

Ines Thiele

Degree Conferred: Ph.D. Bioinformatics 2009 Spring

Thesis: A Stoichiometric Model of E. Coli's Macromolecular Synthesis Machinery and its Integration with Metablism

Advisor(s): Bernhard Palsson, Steve Briggs

Current Employment: University of Iceland (Asst Professor)

Elaine Thompson

Degree Conferred: Ph.D. Bioinformatics 2008 Summer

Thesis: Characterizing Protein Structures by Surface Mapping

Advisor(s): Lynn Ten Eyck, Vineet Bafna

Current Employment: University of California, San Diego (Susan Taylor Lab) (Postdoc)

Ruben Valas

Degree Conferred: Ph.D. Bioinformatics 2010 Summer

Thesis: The Gospel According to LUCA (the last universal common ancestor)

Advisor(s): Philip Bourne, William Loomis

Current Employment: University of California, San Diego (Bourne Lab) (Postdoc)

Yi Wen

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2013 Summer

Thesis: Serial Post-Transcriptional Splicing Establishes Negative Feedback Regulation in HIV-1 Expression

Advisor(s): Leor Weinberger, Doug Richman

Chia-Yi Allison Wu

Degree Conferred: Ph.D. 2016 Winter

Thesis: Dissecting the Worn Intestinal Genetic Network with Quantitative Measurement and Modeling

Advisor(s): Scott Rifkin, Jeff Hasty

Shawn Yost

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2013 Summer

Thesis: Accurate Identification of Somatic Mutations in Clinical Tumor Specimens

Advisor(s): Kelly Frazer, Vineet Bafna