Alumni - BISB Training Grant Recipients
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.

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

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


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

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

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

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

Niema Moshiri
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Mathematical Modeling of Viral Evolution and Epidemiology
Advisor(s): Siavash Mirarab, Pavel Pevzner
Current Employer: 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
Current Employer: Cradle Genomics, Bioinformatics Scientist


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

Christopher Wei
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Kun Zhang, Vineet Bafna
Current Employer: 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
Current Employer: Illumina, Bioinformatics Scientist

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
Current Employer: CRISPR Therapeutics, Scientist

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

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
Current Employer: 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
Current Employer: Viastat, Inc, Data Scientist

James Jensen
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Jill Mesirov, Pablo Tamayo
Current Employer: 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
Current Employer: 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
Current Employer: 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
Current Employer: 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
Current Employer: 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
Current Employer: Institute for Systems Biology, Translational Research Fellow

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
Current Employer: 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
Current Employer: 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
Current Employer: 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
Current Employer: Sapiens Data Science, Chief Science Officer

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
Current Employer: Biota Technology, Data Scientist

Jason Yao
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Modeling and Measuring Dynamic Cellular Signaling States
Advisor(s): Roy Wollman, Shankar Subramaniam
Current Employer: 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
Current Employer: 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
Current Employer: 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
Current Employer: 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
Current Employer: Personalis, Senior Bioinformatics Scientist

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

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
Current Employer: 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
Current Employer: Paul Scherrer Institut PSI, Scientific Computing Engineer

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
Current Employer: GRAIL, Inc, Bioinformatics Scientist

Martin Smith
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Sergei L. Kosakovsky Pond, Doug Richman
Current Employer: 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
Current Employer: 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
Current Employer: Illumina, Bionformatics Scientist

Jeremy Davis-Turak
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Alexander Hoffmann, Gene Yeo
Current Employer: 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
Current Employer: Inscripta, Inc, Senior Scientist: Computational Biology

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
Current Employer: Deep Genomics, Senior Scientist

Joshua Lerman
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Bernhard Palsson, Milton Saier
Current Employer: 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
Current Employer: Digital Proteomics, Chief Technology Officer

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
Current Employer: Generation Bio, Vice President: Strategy and Portolio Development

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
Current Employer: Salk Institute for Biological Studies Integrative Genomics & Bioinoformatics Core, Director

Marcus Kinsella
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Computational Techniques to Investigate Structural Variation
Advisor(s): Vineet Bafna, Kelly Frazer
Current Employer: 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
Current Employer: Second Genome Inc, Lead Data Scientist

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

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

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
Current Employer: 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
Current Employer: Albert Einstein College of Medicine, Assistant Professor of Systems and Computational Biology

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
Current Employer: UCSD Dept Bioengineering, Postdoc

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
Current Employer: Fluidigm, Scientist - R&D, New Technologies

Jan Schellenberger
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Thesis: Monte Carlo Sampling in Systems Biology
Advisor(s): Bernhard Palsson, Vineet Bafna
Current Employer: 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
Current Employer: UC San Diego (Bourne Lab), Postdoc


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
Current Employer: Illumina, Bioinformatics Scienist 1

Noah Zaitlen
Degree Conferred: Ph.D. Bioinformatics and Systems Biology
Advisor(s): Vineet Bafna, Eleazar Eskin
Current Employer: 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
Current Employer: University of California, San Diego (Glass Lab), Postdoc

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

Kasey Hutt
Degree Conferred: Ph.D. Bioinformatics
Advisor(s): Michael Rosenfeld, Terry Gaasterland
Current Employer: 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
Current Employer: J. Craig Venter Institute, Bioinformatics Engineer

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
Current Employer: Prometheus, Bioinformatics Scientist

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

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