Bioinformatics and Systems Biology Alumni

Nassim Ajami

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2018 Spring

Thesis: Identifying Markers and Mechanisms of Atherosclerosis in Endothelial Cells Under Shear Stress Using High-Throughput Sequencing Data

Advisor(s): Shankar Subramaniam, Shu Chien

Karmel Allison

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

Thesis: Enhancers and Transcriptional Regulation in CD4+ T Cell

Advisor(s): Christopher Glass, Stephen Hedrick

 karmelallison [at] ucsd.edu (Email)
website

Sourav Bandyopadhyay

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2010 Spring

Thesis: Integrating Physical and Genetic Interaction Networks for Biological Discovery

Advisor(s): Trey Ideker, Vineet Bafna

Current Employment: Univerity of California, San Francisco (Assistant Professor)

 sourav [at] gmail.com (Email)
website

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)

 dbarken [at] gmail.com (Email)

Leah Barrera

Degree Conferred: Ph.D. Bioinformatics 2007 Spring

Thesis: Genome-wide mapping and analysis of mammalian promoters

Advisor(s): Bing Ren, Philip Bourne

Current Employment: Ambit Biosciences (Scientist)

 leahob [at] gmail.com (Email)

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)

 abashir [at] pacificbiosciences.com (Email)

Gordon Bean

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

Thesis: Development of experimental and computational tools for high-throughput microbial "omics"

Advisor(s): Trey Ideker, Christopher Woelk

 gbean [at] ucsd.edu (Email)

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)

 cbenner [at] ucsd.edu (Email)

Laurence Bernstein

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2018 Spring

Thesis: Penalty-Based Dynamic Programming for the Identification of Post-Translational Modifications in Peptide Mass Spectra

Advisor(s): Nuno Bandeira, Steve Briggs

 lebernstein [at] ucsd.edu (Email)
website

Vipul Bhargava

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

Thesis: Quantitative Transcriptomics From Limiting Amounts of mRNA

Advisor(s): Shankar Subramaniam, Mark Mercola

Current Employment: Janssen Research and Development LLC (Johnson and Johnson company) (Scientist)

 vipul.bhargava [at] gmail.com (Email)

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

 kbhutani [at] ucsd.edu (Email)

Spencer Bliven

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

Thesis: Structure-preserving Rearrangements: Algorithms for Structural Comparison and Protein Analysis

Advisor(s): Philip Bourne, Milton Saier

 sbliven [at] ucsd.edu (Email)

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

 stephano.rb [at] gmail.com (Email)

Olga Botvinnik

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

Thesis: Computational analysis of single-cell alternative splicing

Advisor(s): Gene Yeo, Sheng Zhong

 obotvinn [at] ucsd.edu (Email)
website

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)

 kristinebriedis [at] gmail.com (Email)

Jocelyne Bruand

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

Thesis: Computational Tools for Analysis of Mass spectrometry Imaging Data

Advisor(s): Vineet Bafna, Eduardo Macagno

Current Employment: Illumina (Bioinformatics Scientist)

 jocelyne [at] ucsd.edu (Email)

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)

Mark Chaisson

Degree Conferred: Ph.D. Bioinformatics 2008 Fall

Thesis: Combinatorial Methods for Compuational Genomics: Mammalian Phylogenetics Using Inversions and Fragment Assembly with Short Reads

Advisor(s): Pavel Pevzner, Vineet Bafna

Current Employment: Pacific Biosciences (Senior Algorithms Developer)

 mchaisso [at] gmail.com (Email)

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)

 Roger_Chang [at] hms.harvard.edu (Email)
website

Max Chang

Degree Conferred: Ph.D. Bioinformatics 2008 Summer

Thesis: Computational Structure-Based Methods to Anticipate HIV Drug Resistance Evolution and Accelerate Inhibitor Discovery

Advisor(s): Richard Belew, Lin Chao

Current Employment: TSRI (Postdoc)

 mchang [at] scripps.edu (Email)

Winston Chen

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

Thesis: Deciphering Molecular Mechanism of Adverse Reactions of Drugs

Advisor(s): Ruben Abagyan, Grace Kuo

 yuc023 [at] ucsd.edu (Email)

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)

 c3cheng [at] ucsd.edu (Email)
website

Han-Yu Chuang

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2010 Spring

Thesis: Pathway-based modeling and diagnosis of cancer development and progression

Advisor(s): Trey Ideker, Thomas Kipps

Current Employment: Illumina (Bioinformatics Scientist)

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)

 mcovert [at] stanford.edu (Email)

Jeremy Davis-Turak

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

Thesis: Exploring the Mechanisms of pre-mRNA Splicing Using Mathematical Models of Coupled Transcription and Splicing

Advisor(s): Alexander Hoffmann, Gene Yeo

 jdavistu [at] ucsd.edu (Email)

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)

 meday2001 [at] gmail.com (Email)

Christopher DeBoever

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2016 Spring

Thesis: Genetic regulation of RNA splicing and expression in cancer and stem cells

Advisor(s): Kelly Frazer, Trey Ideker

 cdeboeve [at] ucsd.edu (Email)
website

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

 ddiep [at] ucsd.edu (Email)
website

Kuan-Fu Ding

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

Thesis: Quantifying and Accommodating Heterogeneity in High Throughput Drug Response Studies

Advisor(s): Nicholas Schork, Bing Ren

 kuding [at] ucsd.edu (Email)
website

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)

 ifamili [at] gtlifesciences.com (Email)

Stephen Federowicz

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

Thesis: Elucidating mechanisms of transcriptional regulation at the genome-scale

Advisor(s): Bernhard Palsson, Wei Wang

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)

 mgersten [at] ucsd.edu (Email)

Andrew Gross

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2016 Winter

Thesis: Understanding disease through data driven biology

Advisor(s): Trey Ideker, Kelly Frazer

Current Employment: Illumina (Bioinformatics Scientist)

 the.andrew.gross [at] gmail.com (Email)
website

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)

 ngupta [at] ucsd.edu (Email)

Yupeng He

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

Thesis: Beyond DNA sequence : Exploring and Exploiting Mammalian DNA Methylation

Advisor(s): Joseph Ecker, Wei Wang

 yuh026 [at] ucsd.edu (Email)
website

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)

 markus.herrgard [at] gmail.com (Email)
website

Gary Hon

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

Thesis: Understanding the global architecture of gene regulation in human cells through analysis of chromatin signatures

Advisor(s): Bing Ren, Wei Wang

Current Employment: Ludwig Institute for Cancer Research (Postdoc)

 garyhon1 [at] gmail.com (Email)

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)

 alhsiao [at] stanford.edu (Email)

Justin Huang

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2018 Spring

Thesis: Applications of Network Propagation for the Discovery of Candidate Genes in Human Disease

Advisor(s): Trey Ideker

 jkh013 [at] ucsd.edu (Email)
website

Stephanie Huelga

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

Thesis: Comprehensive discovery and analysis of RNA binding protein-dependent post-transcriptional events in mammalian systems

Advisor(s): Gene Yeo, Christopher Woelk

Current Employment: NuGEN (Data Analysis Scientist)

 shuelga [at] gmail.com (Email)
website

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)

 khutt [at] ucsd.edu (Email)

Leen Jamal

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2018 Winter

Thesis: A Journey Through the Brain & Heart and Into The Machine

Advisor(s): Gene Yeo

 ljamal [at] eng.ucsd.edu (Email)
website

James Jensen

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2018 Winter

Thesis: Toward precision medulloblastoma treatment through integrated functional and genomic analysis of realistic preclinical models

Advisor(s): Jill Mesirov, Pablo Tamayo

 jdjensen [at] eng.ucsd.edu (Email)
website

Suchit Jhunjhunwala

Degree Conferred: Ph.D. Biology with a specialization in Bioinformatics 2009 Summer

Thesis: The 3-D Structure of the Immunoglobulin Heavy Chain Locus:Implications for Long-Range Genomic Interactions

Advisor(s): Cornelis Murre, Maho Niwa

Current Employment: Synthetic Genomics, Inc. (Senior Bioinformatics Scientist)

 jsuchit [at] ucsd.edu (Email)

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)

 arjoyce26 [at] gmail.com (Email)

Boyko Kakaradov

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

Thesis: Statistical models for RNA biology: from single nucleotides to single cells

Advisor(s): Gene Yeo, Charles Elkan

Current Employment: Deep Genomics (Senior Scientist)

 boyko [at] ucsd.edu (Email)

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))

 Email

Ryan M. Kelley

Degree Conferred: Ph.D. Bioinformatics 2009 Winter

Thesis: Analysis and integration of high-throughput biological data for pathway discovery

Advisor(s): Trey Ideker, Vineet Bafna

Current Employment: Illumina (Bioinformatics Scienist 1)

 kelleyRyanM [at] gmail.com (Email)

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))

 mckinsel [at] ucsd.edu (Email)

Joshua Lerman

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

Thesis: Genome-scale Models of Metabolism and Gene Expression: Construction and Use for Growth Phenotype Prediction

Advisor(s): Bernhard Palsson, Milton Saier

Current Employment: Total New Energies USA, Inc. (seconded to Amyris Amyris, Inc.) (Computational Biology Post-Doctoral Scientist)

 jlerman44 [at] gmail.com (Email)
website

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

 jkl055 [at] ucsd.edu (Email)

Paul Loriaux

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

Thesis: Steady State Control of the Cellular Response to Stress

Advisor(s): Alexander Hoffmann, Pavel Pevzner

 ploriaux [at] ucsd.edu (Email)
website

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)

 maqiwinner [at] gmail.com (Email)
website

Rachel Marty

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2018 Fall

Thesis: The Role of MHC Variation in Tumor Progression

Advisor(s): Hannah Carter

 ramarty [at] ucsd.edu (Email)
website

Daria Merkurjev

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

Thesis: Understanding Enhancer Role in the Transcriptional Response

Advisor(s): Michael Rosenfeld, Wei Wang

 dariamerkurjev [at] gmail.com (Email)

Nathan Mih

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2018 Spring

Thesis: Understanding genetic variation in the proteome: a multi-scale structural systems biology toolkit

Advisor(s): Bernhard Palsson, Philip Bourne

Current Employment: Lygos, Inc (Software Engineer)

 nmih [at] ucsd.edu (Email)
website

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)

 jtm [at] stanfordalumni.org (Email)

Ann Thuy Mongan (Thuy Vo)

Degree Conferred: Ph.D. Bioinformatics 2007 Winter

Thesis: Systems Analysis of Engergy Metabolism Elucidates the Roles of Mitochondria in Human Health and Disease

Advisor(s): Bernhard Palsson, Andrew McCulloch

Current Employment: BioInformative (Founder and CEO)

 ann.mongan [at] bioinformative.com (Email)
website

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)

 cmosley [at] ucsd.edu (Email)

Kavitha Mukund

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2016 Spring

Thesis: Systems Biology Approaches to Discerning Striated Muscle Pathologies

Advisor(s): Shankar Subramaniam

 k1mukund [at] ucsd.edu (Email)

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)

 nagarajan.harish [at] gmail.com (Email)
website

Julio Ng

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

Thesis: Computational Mass Spectrometry: Algorithms for Identification of Peptides not present in Protein Databases

Advisor(s): Pavel Pevzner, Pieter Dorrestein

 website

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)

 papin [at] virginia.edu (Email)
website

Anand Patel

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

Thesis: Genome Rearrangements in Cancer and Human Genomes

Advisor(s): Vineet Bafna, Yu-Tsueng Liu

 adp002 [at] ucsd.edu (Email)

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)

 samuel.payne [at] gmail.com (Email)

Josué Pérez-Santiago

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

Thesis: The Human Gut Microbiome: Characterization Challenges and HIV Disease Association

Advisor(s): Doug Richman, Kun Zhang

Current Employment: UCSD (Postdoctoral Fellow)

 joperez [at] ucsd.edu (Email)
website

Gabriel Pratt

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2018 Winter

Thesis: Methods for Integrative Analysis of RNA Binding Proteins

Advisor(s): Gene Yeo, Sheng Zhong

 gpratt [at] ucsd.edu (Email)
website

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)

 ndprice [at] illinois.edu (Email)

Nisha Rajagopal

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

Thesis: Navigating the Human Epigenome through Random Forests

Advisor(s): Bing Ren, Wei Wang

 nirajago [at] ucsd.edu (Email)

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)

 jlrflores [at] gmail.com (Email)

Roy Ronen

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

Thesis: Identifying and Characterizing the Genomic Signatures of Natural Selection

Advisor(s): Vineet Bafna, Gabriel Haddad

 rronen [at] ucsd.edu (Email)
website

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

 psamayoa [at] gmail.com (Email)

Jan Schellenberger

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2010 Summer

Thesis: Monte Carlo Sampling in Systems Biology

Advisor(s): Bernhard Palsson, Vineet Bafna

Current Employment: ID Analytics (Scientist)

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)

 schultzmattd [at] gmail.com (Email)
website

Eric Scott

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

Thesis: Genomic structural characterization of the Greater Middle East to assist in the identification of disease variation

Advisor(s): Joseph Gleeson, Vineet Bafna

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

 sselvaraj [at] ucsd.edu (Email)

Maxim Shokhirev

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

Thesis: Developing a multi-scale understanding of the B cell immune response

Advisor(s): Alexander Hoffmann, Andrew McCulloch

 maxshok [at] gmail.com (Email)
website

Dylan Skola

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2019 Spring

Thesis: Understanding the Influence of Genetic Variation on Transcriptional Regulation in Humans and Other Metazoans

Advisor(s): Christopher Glass, Wei Wang

Current Employment: Illumina (Bioinformatics Scientist)

 ucsd [at] phageghost.net (Email)
website

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

 msmith [at] ucsd.edu (Email)

Silpa Suthram

Degree Conferred: Ph.D. Bioinformatics 2008 Winter

Thesis: Understanding Cellular Function through the Analysis of Protein Interaction Networks

Advisor(s): Trey Ideker, Philip Bourne

Current Employment: Stanford working w/ Dr. Atul Butte (Postdoc)

 silpasuthram [at] yahoo.com (Email)

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)

Stephen Tanner

Degree Conferred: Ph.D. Bioinformatics 2007 Spring

Thesis: Efficient and Accurate Bioinformatics Algorithms for Peptide Mass Spectrometry

Advisor(s): Vineet Bafna, Julian Schroeder

Current Employment: Illumina (Bioinformatics Scientist)

 stanner [at] illumina.com (Email)
website

Jenhan Tao

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2018 Fall

Thesis: Machine learning approaches for relating genomic sequence to enhancer activity and function

Advisor(s): Christopher Glass, Christopher Benner

 jenhantao [at] gmail.com (Email)
website

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)

 ines.thiele [at] googlemail.com (Email)
website

Alex Thomas

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

Thesis: Moving Towards Interpretable Mechanisms in Human Systems Biology

Advisor(s): Nathan E. Lewis, Dorothy Sears

 a1xt06 [at] gmail.com (Email)

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)

 elainet [at] mccammin.ucsd.edu (Email)

Brian Yik Tak Tsui

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2019 Winter

Thesis: Building bioinformatic tools for massive repurposing of multi-omic data in the Sequence Read Archive

Advisor(s): Hannah Carter, Jill Mesirov

Current Employment: Illumina (Bioinformatics scientist)

 btsui [at] eng.ucsd.edu (Email)
website

Nitin Udpa

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

Thesis: The Genetic Basis of Hypoxia Tolerance

Advisor(s): Vineet Bafna, Kelly Frazer

Current Employment: Illumina (Bioinformatics Scientist)

 nudpa [at] ucsd.edu (Email)

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)

Jian Wang

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

Thesis: Expanding the toolbox of tandem mass spectrometry with algorithms to identify mass spectra from more than one peptide

Advisor(s): Philip Bourne, Pieter Dorrestein

 bugouzhi [at] gmail.com (Email)

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

 yiwen [at] ucsd.edu (Email)

Cory White

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2016 Summer

Thesis: Investigations of HIV Latency Through Transcriptomic and Proteomic Profiling

Advisor(s): Doug Richman, David Smith

 cwhite [at] ucsd.edu (Email)

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

 chia.yi.wu.tw [at] gmail.com (Email)

Jason Yao

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

Thesis: Modeling and Measuring Dynamic Cellular Signaling States

Advisor(s): Roy Wollman, Shankar Subramaniam

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

 yostshawn [at] gmail.com (Email)
website

Michael Yu

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

Thesis: Hierarchical Models of Biological Systems

Advisor(s): Trey Ideker, Christopher Glass

 mkyu003 [at] ucsd.edu (Email)

Jeffrey Yuan

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2019 Winter

Thesis: Genome Assembly of Long Error-Prone Reads Using De Bruijn Graphs and Repeat Graphs

Advisor(s): Pavel Pevzner, Bing Ren

 jeyuan [at] eng.ucsd.edu (Email)

James Yurkovich

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2018 Winter

Thesis: The Systems Biology of Red Cell Metabolism: Physiology under Storage Conditions

Advisor(s): Bernhard Palsson, Jeff Hasty

Current Employment: Institute for Systems Biology (Translational Research Fellow)

 james.yurkovich [at] systemsbiology.org (Email)
website

Noah Zaitlen

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

Thesis: Methods for the Analysis of Human Genetic Variation in the Search for the Genetic Basis of Human Disease

Advisor(s): Vineet Bafna, Eleazar Eskin

Current Employment: Harvard School of Public Health (Postdoc)

 noahaz [at] gmail.com (Email)

Kai Zhang

Degree Conferred: Ph.D. Bioinformatics and Systems Biology 2018 Summer

Thesis: Novel Network-Based Integrated Analyses of Multi-Omics Data Reveal New Insights into CD8+ T Cell Differentiation and Mouse Embryogenesis

Advisor(s): Wei Wang, Pavel Pevzner

 kaz007 [at] ucsd.edu (Email)
website

Degui Zhi

Degree Conferred: Ph.D. Bioinformatics 2006 Winter

Thesis: Discovery and Analysis of mosaic arrangements in biological squesces and structures

Advisor(s): Pavel Pevzner, William Loomis

Current Employment: University of Alabama (Asst Professor)

 zhidegui [at] gmail.com (Email)
website