Alumni
The UC San Diego Libraries provide access to official copies of all UC San Diego dissertations. Search the UC San Diego Libraries Catalog for UC San Diego Bioinformatics dissertations.

Jason Hyun
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Comparative Pangenomics: Finding structure in the endless diversity of microbial life
Advisor(s): Bernhard Palsson, Terry Gaasterland

Rick Li
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Deciphering genomic grammar in regulatory sequences
Advisor(s): Christopher Glass, Christopher Benner
Yue Qin
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Towards an in silico cell
Advisor(s): Trey Ideker, Jill Mesirov
Next Position: Broad Institute of MIT and Harvard, Eric and Wendy Schmidt Center Fellow

James Sorrentino
Degree Conferred: Bioinformatics and Systems Biology
Advisor(s): Nathan E. Lewis, Jeffrey Esko

Jingtian Zhou
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Analysis of 3D Genome Structure in Single Cells
Advisor(s): Joseph Ecker, Eran Mukamel

George Armstrong
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Rob Knight, Pieter Dorrestein

Kanishk Asthana
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Fast Single Cell RNA-Seq measurements using Chrono-seq

Metin Balaban
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Distance-aware Algorithms for Scalable Evolutionary and Ecological Analyses
Advisor(s): Siavash Mirarab, Vineet Bafna

Bokan Bao
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Using emerging data analysis technics to improve pediatric disease diagnosis
Advisor(s): Nathan E. Lewis, Eric Courchesne

Andrey Bzikadze
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Human centromeres: from initial assemblies to structural and evolutionary analysis
Advisor(s): Pavel Pevzner, Melissa Gymrek

Andrea Castro
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical Informatics
Thesis: Determinants for Effective Neoantigen Based Anti-Tumor Immune Response
Advisor(s): Hannah Carter, Ludmil Alexandrov

Nathaniel Delos Santos
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical Informatics
Advisor(s): Christopher Benner, Melissa Gymrek

Edahí González-Avalos
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Integrative Analysis of 5-Hydroxymethylcytosine Signal in the Context of Gene Regulation
Advisor(s): Anjana Rao, Ferhat Ay

Miin Lin
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Decoding Phenotypes via Transcriptomics and Proteomics: Cancer and beyond
Advisor(s): Vineet Bafna, David J. Gonzalez

Cameron Martino
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Tracking Microbial Communities Across Human Development in Response to Disturbance and Restoration
Advisor(s): Rob Knight, Pieter Dorrestein

Robert Morey
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Understanding trophoblast development using human embryonic stem cells
Advisor(s): Louise Laurent, Melissa Gymrek
Next Position: University of California, San Diego, Computational and Data Science Research Specialist

Daniela Nachmanson
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Profiling archival samples to examine the molecular underpinnings of early carcinogenesis
Advisor(s): Olivier Harismendy, Ludmil Alexandrov

Kivilicim Ozturk
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Hannah Carter, Prashant Mali

Timofey Prodanov
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Read mapping, variant calling, and copy number variation detection in segmental duplications
Advisor(s): Vikas Bansal, Melissa Gymrek

Michelle Franc Ragsac
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Decoding the genomic regulatory syntax driving notochord development
Advisor(s): Emma Farley, Terry Gaasterland
Next Position: Empirico, Senior Data Scientist

Isaac Shamie
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Nathan E. Lewis, Christopher Benner

Chao Zhang
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Scalable Algorithms for Inference and Simulation under Complex Phylogenetic Models
Advisor(s): Siavash Mirarab, Pavel Pevzner

Lina Zheng
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: New insights into 3D chromatin organization and function

Anthony Aylward
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Statistical strategies and resources for deciphering mechanisms of diabetes risk loci
Advisor(s): Kyle Gaulton, Dorothy Sears


Patrick Fiaux
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Discovery of novel sequences through the analysis of tiling CRISPR screens
Advisor(s): Graham McVicker, Bing Ren

Jens Luebeck
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Reconstructing and Profiling Extrachromosomal DNA
Advisor(s): Vineet Bafna, Julie Law
Next Position: Bafna Lab, Postdoctoral Scholar


Patrick Phaneuf
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data
Advisor(s): Bernhard Palsson, Nathan E. Lewis

Samuel Roth
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Identification and Characterization of Systems with Defects in Transcription Termination
Advisor(s): Christopher Benner, Sven Heinz

Argus Athanas-Crannell
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Leveraging Longitudinal Data for Predictive Modeling in Clinical and Mental Health Settings
Advisor(s): Nicholas Schork, Lucila Ohno-Machado

Bahar Behsaz
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Scalable Computational Methods for Discovering Novel Natural Products
Advisor(s): Pavel Pevzner, Rob Knight

Arjun Chandrasekhar
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Derivation and Analysis of Distributed Computing Algorithms in Biological Systems
Advisor(s): Saket Navlakha, Glenn Tesler

Michelle Dow
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical Informatics
Thesis: Integrative Multi-omics Analysis to Understand Cancer and Anticancer Therapy
Advisor(s): Hannah Carter

Yingxiang Huang
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical Informatics
Thesis: Preservation of Patient Level Privacy : Federated Classification and Calibration Models
Advisor(s): Lucila Ohno-Machado

Benjamin Kellman
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Nathan E. Lewis, Hannah Carter

Jamison McCorrison
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Exploitation of Metadata in Molecular Genomics Studies
Advisor(s): Nicholas Schork, Vikas Bansal

Margaret Donovan
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical Informatics
Advisor(s): Kelly Frazer

Rongxin Fang
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Single Cell Analysis of Chromatin Accessibility
Advisor(s): Bing Ren, Vineet Bafna

Robert Foreman
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Cell States Explain Calcium Signaling Heterogeneity in MCF10a Cells in Response to ATP Stimulation
Advisor(s): Scott Rifkin, Roy Wollman

William Greenwald
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Exploring the Regulatory Genome and Functional Genetic Variation
Advisor(s): Kelly Frazer
Next Position: Monoceros Biosystems, Bioinformatics Scientist

Nicolaus Lance Hepler
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Sergei L. Kosakovsky Pond, Doug Richman
Next Position: 10X Genomics, Staff Computational Biologist

Isaac Lopez Moyado
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Association of TET loss of function with heterochromatin DNA hypomethylation and genome instability
Advisor(s): Anjana Rao, Vineet Bafna

Jia Lu
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Understanding cis-Regulatory Activities with Evolutionary Epigenomic Analyses
Advisor(s): Sheng Zhong, Bing Ren

Shamim Mollah
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Integrative Approaches to Targeting Chromatin Remodeling in Breast Cancer Therapy
Advisor(s): Shankar Subramaniam, Vineet Bafna
Next Position: Washington University School of Medicine in St. Louis, Assistant Professor

Niema Moshiri
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Mathematical Modeling of Viral Evolution and Epidemiology
Advisor(s): Siavash Mirarab, Pavel Pevzner
Next Position: UC San Diego Department of Computer Science & Engineering, Assistant Teaching Professor

Vu Ngo
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Interplays between DNA motifs and epigenetic elements
Advisor(s): Wei Wang
Next Position: Cradle Genomics, Bioinformatics Scientist

Yunjiang Qiu
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Interpreting human genetic variations through transcriptional regulation and 3D genome organization
Advisor(s): Bing Ren, Sheng Zhong


John Sauls
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Physiological Orchestration in Bacteria
Advisor(s): Suckjoon Jun, Terence Hwa

Dylan Skola
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Christopher Glass, Wei Wang
Next Position: Illumina, Bioinformatics Scientist

Brian Yik Tak Tsui
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Building bioinformatic tools for massive repurposing of multi-omic data in the Sequence Read Archive
Advisor(s): Hannah Carter, Jill Mesirov
Next Position: Illumina, Bioinformatics scientist

Mengchi Wang
Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Christopher Wei
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Kun Zhang, Vineet Bafna
Next Position: Zhang Lab, Postdoctural Researcher

Jeffrey Yuan
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Genome Assembly of Long Error-Prone Reads Using De Bruijn Graphs and Repeat Graphs
Advisor(s): Pavel Pevzner, Bing Ren
Next Position: Illumina, Bioinformatics Scientist

Jing Zhang
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical Informatics
Thesis: Supporting Diabetes Patient Decisional Needs Through Online Health Communities
Advisor(s): Vineet Bafna, Michael Hogarth

Yuan Zhao
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Computational approaches for elucidating the gene regulatory landscape of mammalian development

Nassim Ajami
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Shankar Subramaniam, Shu Chien
Next Position: CRISPR Therapeutics, Scientist

Laurence Bernstein
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Nuno Bandeira, Steve Briggs
Next Position: Quest Diagnostics, Principal Software Engineer

Stephanie Feudjio Feupe
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical Informatics
Thesis: Deep Characterization of the Contribution of Short Tandem Repeats Across Tissues
Advisor(s): Melissa Gymrek, Vineet Bafna

Justin Huang
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Applications of Network Propagation for the Discovery of Candidate Genes in Human Disease
Advisor(s): Trey Ideker
Next Position: MD Anderson Cancer Center TRACTION, Institute Research Investigator: Systems Biology

Leen Jamal
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: A Journey Through the Brain & Heart and Into The Machine
Advisor(s): Gene Yeo
Next Position: Viastat, Inc, Data Scientist

James Jensen
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Jill Mesirov, Pablo Tamayo
Next Position: Recursion Pharmaceuticals, Data Scientist

Rachel Marty
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: The Role of MHC Variation in Tumor Progression
Advisor(s): Hannah Carter
Next Position: Personalis, Inc, Bioinformatics Scientist

Nathan Mih
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Understanding genetic variation in the proteome: a multi-scale structural systems biology toolkit
Advisor(s): Bernhard Palsson, Philip Bourne
Next Position: Lygos, Inc, Software Engineer

Gabriel Pratt
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Methods for Integrative Analysis of RNA Binding Proteins
Advisor(s): Gene Yeo, Sheng Zhong
Next Position: TwinStrand Biosciences, Bioinformatics Scientist

Jenhan Tao
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Machine learning approaches for relating genomic sequence to enhancer activity and function
Advisor(s): Christopher Glass, Christopher Benner
Next Position: Illumina, Bioinformatics Scientist

James Yurkovich
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: The Systems Biology of Red Cell Metabolism: Physiology under Storage Conditions
Advisor(s): Bernhard Palsson, Jeff Hasty
Next Position: Institute for Systems Biology, Translational Research Fellow

Kai Zhang
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Wei Wang, Pavel Pevzner

Kunal Bhutani
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Limiting Biases in Biological Data Analysis by Pooling Information
Advisor(s): Nicholas Schork, Vineet Bafna
Next Position: FVL59, Inc, Computational Scientist

Olga Botvinnik
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Computational analysis of single-cell alternative splicing
Advisor(s): Gene Yeo, Sheng Zhong
Next Position: Chan-Zuckerberg Biohub, Bioinformatics Data Scientist

Dinh Diep
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Novel molecular and bioinformatics approaches to investigate DNA methylation in human epigenome
Advisor(s): Kun Zhang, Vineet Bafna
Next Position: UC San Diego, Postdoctural Researcher

Kuan-Fu Ding
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical Informatics
Thesis: Quantifying and Accommodating Heterogeneity in High Throughput Drug Response Studies
Advisor(s): Nicholas Schork, Bing Ren
Next Position: Sapiens Data Science, Chief Science Officer

Kemal Eren
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Joel Wertheim, Siavash Mirarab
Yupeng He
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Beyond DNA sequence : Exploring and Exploiting Mammalian DNA Methylation
Advisor(s): Joseph Ecker, Wei Wang

Joanne Liu
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Predicting Growth Optimization Strategies with Metabolic/Expression Models
Advisor(s): Karsten Zengler, Nathan E. Lewis
Next Position: Biota Technology, Data Scientist

Wei Wei
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical Informatics
Thesis: Information Retrieval in Biomedical Research: From Articles to Datasets
Advisor(s): Lucila Ohno-Machado, Xiaoqian Jiang

Jason Yao
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Modeling and Measuring Dynamic Cellular Signaling States
Advisor(s): Roy Wollman, Shankar Subramaniam
Next Position: Guavus, Research Data Scientist

Michael Yu
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Hierarchical Models of Biological Systems
Advisor(s): Trey Ideker, Christopher Glass
Next Position: Toyota Technical Institute at Chicago, Research Assistant Professor

Christopher DeBoever
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Genetic regulation of RNA splicing and expression in cancer and stem cells
Advisor(s): Kelly Frazer, Trey Ideker
Next Position: Takeda, Computational Biology Scientist

Andrew Gross
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Understanding disease through data driven biology
Advisor(s): Trey Ideker, Kelly Frazer
Next Position: Illumina, Bioinformatics Scientist

Eric Levy
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Molecular immune signatures of T-cell infiltration in cancer
Advisor(s): Lucila Ohno-Machado, Olivier Harismendy
Next Position: Personalis, Senior Bioinformatics Scientist

Kavitha Mukund
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Systems Biology Approaches to Discerning Striated Muscle Pathologies
Advisor(s): Shankar Subramaniam, Richard Lieber

Cory White
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Investigations of HIV Latency Through Transcriptomic and Proteomic Profiling
Advisor(s): Doug Richman, David Smith

Chia-Yi Allison Wu
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Dissecting the Worn Intestinal Genetic Network with Quantitative Measurement and Modeling
Advisor(s): Scott Rifkin, Jeff Hasty

Karmel Allison
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Enhancers and Transcriptional Regulation in CD4+ T Cell
Advisor(s): Christopher Glass, Stephen Hedrick
Next Position: Google Brain TensorFlow Team, Engineering Manager

Spencer Bliven
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Structure-preserving Rearrangements: Algorithms for Structural Comparison and Protein Analysis
Advisor(s): Philip Bourne, Milton Saier
Next Position: Paul Scherrer Institut PSI, Scientific Computing Engineer

Stefano Bonissone
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Deconvolution of immunome and degradome repertoires using computational proteomics
Advisor(s): Pavel Pevzner, Steve Briggs

Qi Ma
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Understanding the Functional Properties of Enhancers
Advisor(s): Michael Rosenfeld, Gene Yeo
Next Position: UCSD, Postdoctoral Fellow in Rosenfeld Lab

Daria Merkurjev
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Understanding Enhancer Role in the Transcriptional Response
Advisor(s): Michael Rosenfeld, Wei Wang

Edward J O'Brien
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Proteome allocation trade-offs in bacterial evolution and regulation
Advisor(s): Bernhard Palsson, Philip Bourne

Eric Scott
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Joseph Gleeson, Vineet Bafna
Next Position: GRAIL, Inc, Bioinformatics Scientist

Martin Smith
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Sergei L. Kosakovsky Pond, Doug Richman
Next Position: Pacific Biosciences, Staff Engineer: Primary Analysis

Alex Thomas
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Moving Towards Interpretable Mechanisms in Human Systems Biology
Advisor(s): Nathan E. Lewis, Dorothy Sears
Next Position: C.H. Robinson, Principal Data Scientist
Gordon Bean
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Development of experimental and computational tools for high-throughput microbial "omics"
Advisor(s): Trey Ideker, Christopher Woelk
Next Position: Illumina, Bionformatics Scientist

Winston Chen
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Deciphering Molecular Mechanism of Adverse Reactions of Drugs
Advisor(s): Ruben Abagyan, Grace Kuo

Jeremy Davis-Turak
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Alexander Hoffmann, Gene Yeo
Next Position: OnRamp Bioinformatics, Vice President

Stephen Federowicz
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Elucidating mechanisms of transcriptional regulation at the genome-scale
Advisor(s): Bernhard Palsson, Wei Wang
Next Position: Inscripta, Inc, Senior Scientist: Computational Biology

Stephanie Huelga
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Gene Yeo, Christopher Woelk
Next Position: NuGEN, Data Analysis Scientist

Boyko Kakaradov
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Statistical models for RNA biology: from single nucleotides to single cells
Advisor(s): Gene Yeo, Charles Elkan
Next Position: Deep Genomics, Senior Scientist

Joshua Lerman
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Bernhard Palsson, Milton Saier
Next Position: Total New Energies USA, Inc. (seconded to Amyris Amyris, Inc.), Computational Biology Post-Doctoral Scientist

Anand Patel
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Genome Rearrangements in Cancer and Human Genomes
Advisor(s): Vineet Bafna, Yu-Tsueng Liu
Next Position: Digital Proteomics, Chief Technology Officer

Roy Ronen
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Identifying and Characterizing the Genomic Signatures of Natural Selection
Advisor(s): Vineet Bafna, Gabriel Haddad
Next Position: Data4Cure, Inc., VP Platform

Philip Samayoa
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Applications of synthetic biology inspired by natural bacterial functionality
Advisor(s): Jeff Hasty, Ruth Williams
Next Position: Generation Bio, Vice President: Strategy and Portolio Development

Matthew Schultz
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Joseph Ecker, Vineet Bafna
Next Position: Human Longevity, Inc., Bioinformatics Scientist

Siddarth Selvaraj
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Analysis of 3D genome organization and gene regulation in mammalian cells
Advisor(s): Bing Ren, Vineet Bafna

Maxim Shokhirev
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Developing a multi-scale understanding of the B cell immune response
Advisor(s): Alexander Hoffmann, Andrew McCulloch
Next Position: Salk Institute for Biological Studies Integrative Genomics & Bioinoformatics Core, Director

Vipul Bhargava
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Quantitative Transcriptomics From Limiting Amounts of mRNA
Advisor(s): Shankar Subramaniam, Mark Mercola
Next Position: Janssen Research and Development LLC (Johnson and Johnson company) , Scientist

Marcus Kinsella
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Computational Techniques to Investigate Structural Variation
Advisor(s): Vineet Bafna, Kelly Frazer
Next Position: Pacific Biosciences, Senior Engineer (Bioinformatics)

Paul Loriaux
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Steady State Control of the Cellular Response to Stress
Advisor(s): Alexander Hoffmann, Pavel Pevzner
Next Position: Second Genome Inc, Lead Data Scientist

Nisha Rajagopal
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Navigating the Human Epigenome through Random Forests

Nitin Udpa
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: The Genetic Basis of Hypoxia Tolerance
Advisor(s): Vineet Bafna, Kelly Frazer
Next Position: Illumina, Bioinformatics Scientist

Jian Wang
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Philip Bourne, Pieter Dorrestein

Yi Wen
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Serial Post-Transcriptional Splicing Establishes Negative Feedback Regulation in HIV-1 Expression
Advisor(s): Leor Weinberger, Doug Richman

Shawn Yost
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Accurate Identification of Somatic Mutations in Clinical Tumor Specimens
Advisor(s): Kelly Frazer, Vineet Bafna

Jocelyne Bruand
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Computational Tools for Analysis of Mass spectrometry Imaging Data
Advisor(s): Vineet Bafna, Eduardo Macagno
Next Position: Illumina, Bioinformatics Scientist

Roger Chang
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Structural systems biology perspective on the metabolic impact of physicochemical stress
Advisor(s): Bernhard Palsson, Philip Bourne
Next Position: Albert Einstein College of Medicine, Assistant Professor of Systems and Computational Biology

Eugene Ke
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Insights from reconstructing cellular networks in transcription, stress and cancer
Advisor(s): Shankar Subramaniam, Inder Verma
Next Position: Salk Institute, Research Associate (Postdoc)

Harish Nagarajan
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Electromicrobiiology: A Systems Perspective
Advisor(s): Bernhard Palsson, Milton Saier
Next Position: Genomatica Inc., Research Scientist I, Computational Technologies
Josué Pérez-Santiago
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: The Human Gut Microbiome: Characterization Challenges and HIV Disease Association
Advisor(s): Doug Richman, Kun Zhang
Next Position: UCSD, Postdoctoral Fellow

Jason Chan
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Effects of a Highly Repetitive Endogenous Tyl Retrotransposon on Genome Stablility
Advisor(s): Richard Kolodner, Trey Ideker

Christine Cheng
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Innate immune gene expression programs defined by both regulated mRNA synthesis and decay
Advisor(s): Alexander Hoffmann, Charles Elkan
Next Position: Broad Institute of MIT and Harvard, Postdoc in Aviv Regev's Lab

Merril Gersten
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Systems Analysis of Model Organisms in the Study of Human disease
Advisor(s): Shankar Subramaniam, Gabriel Haddad
Next Position: UCSD Dept Bioengineering, Postdoc

Julio Ng
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Pavel Pevzner, Pieter Dorrestein

Lukasz Szpankowski
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Coordination of Axonal Transport Revealed by Particle Tracking and Quantitative Immunogluorescence
Advisor(s): Lawrence Goldstein, Shankar Subramaniam
Next Position: Fluidigm, Scientist - R&D, New Technologies

Sourav Bandyopadhyay
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Integrating Physical and Genetic Interaction Networks for Biological Discovery
Advisor(s): Trey Ideker, Vineet Bafna
Next Position: Univerity of California, San Francisco, Assistant Professor

Mary Budagyan (Mary Pacold)
Degree Conferred: Ph.D. Bioinformatics
Thesis: Detecting and Characterizing HIV-1 Intaclade Dual Infection
Advisor(s): Doug Richman, Glenn Tesler
Next Position: Ion Torrent / Life Technologies, Product Manager, Informatics Applications

Han-Yu Chuang
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Pathway-based modeling and diagnosis of cancer development and progression
Advisor(s): Trey Ideker, Thomas Kipps
Next Position: Illumina, Bioinformatics Scientist

Jan Schellenberger
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Monte Carlo Sampling in Systems Biology
Advisor(s): Bernhard Palsson, Vineet Bafna
Next Position: ID Analytics, Scientist

Ruben Valas
Degree Conferred: Ph.D. Bioinformatics
Thesis: The Gospel According to LUCA (the last universal common ancestor)
Advisor(s): Philip Bourne, William Loomis
Next Position: UC San Diego (Bourne Lab), Postdoc

Ali Bashir
Degree Conferred: Ph.D. Bioinformatics
Advisor(s): Vineet Bafna, Pavel Pevzner
Next Position: Pacific Biosciences, Scientist

Nitin Gupta
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Pavel Pevzner, Steve Briggs
Next Position: University of California, San Diego (Aron Lab), Postdoc


Suchit Jhunjhunwala
Degree Conferred: Ph.D. Biology with a specialization in Bioinformatics
Advisor(s): Cornelis Murre, Maho Niwa
Next Position: Synthetic Genomics, Inc., Senior Bioinformatics Scientist

Ryan M. Kelley
Degree Conferred: Ph.D. Bioinformatics
Thesis: Analysis and integration of high-throughput biological data for pathway discovery
Advisor(s): Trey Ideker, Vineet Bafna
Next Position: Illumina, Bioinformatics Scienist 1

Juan Lorenzo Rodriguez Flores
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Daniel O'Connor, Shankar Subramaniam
Next Position: Ludwig Institute for Cancer Research, Postdoc

Ines Thiele
Degree Conferred: Ph.D. Bioinformatics
Advisor(s): Bernhard Palsson, Steve Briggs
Next Position: University of Iceland, Asst Professor

Noah Zaitlen
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Vineet Bafna, Eleazar Eskin
Next Position: Harvard School of Public Health, Postdoc

Christopher Benner
Degree Conferred: Ph.D. Bioinformatics
Thesis: Identification of a Conserved Periodic Promoter Structure in Metazoans
Advisor(s): Christopher Glass, Shankar Subramaniam
Next Position: University of California, San Diego (Glass Lab), Postdoc

Kristine Briedis
Degree Conferred: Ph.D. Bioinformatics
Advisor(s): Philip Bourne, William Loomis
Next Position: University of California, San Diego (Bourne Lab), Postdoc

Mark Chaisson
Degree Conferred: Ph.D. Bioinformatics
Advisor(s): Pavel Pevzner, Vineet Bafna
Next Position: Pacific Biosciences, Senior Algorithms Developer

Max Chang
Degree Conferred: Ph.D. Bioinformatics
Advisor(s): Richard Belew, Lin Chao
Next Position: TSRI, Postdoc

Michele Day
Degree Conferred: Ph.D. Bioinformatics
Thesis: Insights into the functionality and targeting of PKA regulatory subunity Rialpha
Advisor(s): Susan Taylor, Lynn Ten Eyck
Next Position: University of California, San Diego (Taylor Lab), Postdoc

Kasey Hutt
Degree Conferred: Ph.D. Bioinformatics
Advisor(s): Michael Rosenfeld, Terry Gaasterland
Next Position: University of California, San Diego (Rosenfeld Lab), Postdoc

Samuel Payne
Degree Conferred: Ph.D. Bioinformatics
Thesis: Advances in Computational Mass Spectrometry: Phosphoprteomics and Proteogenomics
Advisor(s): Vineet Bafna, William Loomis
Next Position: Brigham Young University, Associate Professor

Silpa Suthram
Degree Conferred: Ph.D. Bioinformatics
Thesis: Understanding Cellular Function through the Analysis of Protein Interaction Networks
Advisor(s): Trey Ideker, Philip Bourne
Next Position: Stanford working w/ Dr. Atul Butte, Postdoc

Elaine Thompson
Degree Conferred: Ph.D. Bioinformatics
Thesis: Characterizing Protein Structures by Surface Mapping
Advisor(s): Lynn Ten Eyck, Vineet Bafna
Next Position: University of California, San Diego (Susan Taylor Lab), Postdoc

Derren Barken
Degree Conferred: Ph.D. Bioinformatics
Thesis: Temporal encoding and homeostatic control in the IKK-IkB-NF-kB
Advisor(s): Alexander Hoffmann, Shankar Subramaniam
Next Position: Prometheus, Bioinformatics Scientist

Leah Barrera
Degree Conferred: Ph.D. Bioinformatics
Thesis: Genome-wide mapping and analysis of mammalian promoters
Advisor(s): Bing Ren, Philip Bourne
Next Position: Ambit Biosciences, Scientist

Andrew Joyce
Degree Conferred: Ph.D. Bioinformatics
Advisor(s): Bernhard Palsson, Bing Ren
Next Position: Philip Morris, Post Doc

Ann Thuy Mongan (Thuy Vo)
Degree Conferred: Ph.D. Bioinformatics
Advisor(s): Bernhard Palsson, Andrew McCulloch
Next Position: BioInformative, Founder and CEO

Stephen Tanner
Degree Conferred: Ph.D. Bioinformatics
Thesis: Efficient and Accurate Bioinformatics Algorithms for Peptide Mass Spectrometry
Advisor(s): Vineet Bafna, Julian Schroeder
Next Position: Inscripta, Principal Scientist

John Mongan
Degree Conferred: Ph.D. Bioinformatics
Advisor(s): Andrew McCammon, Gary Huber
Next Position: University of California, San Francisco, Associate Professor

Coleman Mosley
Degree Conferred: Ph.D. Bioinformatics
Advisor(s): Nicholas Schork, Daniel O'Connor
Next Position: Magellan Health-National Imaging Associates, Physician Clinical Reviewer

Degui Zhi
Degree Conferred: Ph.D. Bioinformatics
Thesis: Discovery and Analysis of mosaic arrangements in biological squesces and structures
Advisor(s): Pavel Pevzner, William Loomis
Next Position: University of Texas Health Science Center at Houston, Associate Professor

Albert Hsiao
Degree Conferred: Ph.D. Bioengineering with a specialization in Bioinformatics
Thesis: Comparative functional genomics of energy metabolism and insulin resistance in mammalian systems
Advisor(s): Shankar Subramaniam, Jerrold Olefsky
Next Position: UCSD, Assistant Professor of Radiology, In-Residence

Jason Papin
Degree Conferred: Ph.D. Bioengineering with a specialization in Bioinformatics
Thesis: Systems Analysis of Cellular Signaling Networks
Advisor(s): Bernhard Palsson, Jerrold Olefsky
Next Position: University of Virginia, Assistant Professor

Nathan Price
Degree Conferred: Ph.D. Bioengineering with a specialization in Bioinformatics
Thesis: Unbiased Assessment of Genome-Scale Metabolic Network States
Advisor(s): Bernhard Palsson, Shankar Subramaniam
Next Position: University of Illinois, Urbana-Champaign, Assistant Professor

Iman Famili
Degree Conferred: Ph.D. Bioengineering with a specialization in Bioinformatics
Thesis: Systemic analysis of the stoichiometric matrix and kinetic characterization of metabolic networks.
Advisor(s): Bernhard Palsson, Shankar Subramaniam
Next Position: GT Life Sciences, Inc., Research Director

Markus Herrgard
Degree Conferred: Ph.D. Bioengineering with a specialization in Bioinformatics
Advisor(s): Bernhard Palsson, Shankar Subramaniam
Next Position: synthetic genomics, Senior Bioinformatics Scientist

Markus Covert
Degree Conferred: Ph.D. Bioengineering with a specialization in Bioinformatics
Thesis: Transcriptional Regulation in Escherichia coli: A Systems Biology Approach
Advisor(s): Bernhard Palsson
Next Position: Stanford, Asst Professor