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.


Rick Li

Rick Li

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Deciphering genomic grammar in regulatory sequences

Abstract

Advisor(s): Christopher Glass, Christopher Benner

Yue Qin

Yue Qin

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Towards an in silico cell

Abstract

Advisor(s): Trey Ideker, Jill Mesirov

Next Position: Broad Institute of MIT and Harvard, Eric and Wendy Schmidt Center Fellow

Jingtian Zhou

Jingtian Zhou

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Analysis of 3D Genome Structure in Single Cells

Abstract

Advisor(s): Joseph Ecker, Eran Mukamel

Kanishk Asthana

Kanishk Asthana

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Fast Single Cell RNA-Seq measurements using Chrono-seq

Abstract

Advisor(s): Wei Wang, Bing Ren

Metin Balaban

Metin Balaban

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Distance-aware Algorithms for Scalable Evolutionary and Ecological Analyses

Abstract

Advisor(s): Siavash Mirarab, Vineet Bafna

Bokan Bao

Bokan Bao

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Using emerging data analysis technics to improve pediatric disease diagnosis

Abstract

Advisor(s): Nathan E. Lewis, Eric Courchesne

Andrey Bzikadze

Andrey Bzikadze

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Human centromeres: from initial assemblies to structural and evolutionary analysis

Abstract

Advisor(s): Pavel Pevzner, Melissa Gymrek

Andrea Castro

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

Abstract

Advisor(s): Hannah Carter, Ludmil Alexandrov

Nathaniel Delos Santos

Nathaniel Delos Santos

Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical Informatics

Thesis: Score-based Transcription Factor Motif Enrichment Strategies for Analysis of Transcriptional Regulation of Immune Response

Abstract

Advisor(s): Christopher Benner, Melissa Gymrek

Edahí González-Avalos

Edahí González-Avalos

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Integrative Analysis of 5-Hydroxymethylcytosine Signal in the Context of Gene Regulation

Abstract

Advisor(s): Anjana Rao, Ferhat Ay

Miin Lin

Miin Lin

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Decoding Phenotypes via Transcriptomics and Proteomics: Cancer and beyond

Abstract

Advisor(s): Vineet Bafna, David J. Gonzalez

Robert Morey

Robert Morey

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Understanding trophoblast development using human embryonic stem cells

Abstract

Advisor(s): Louise Laurent, Melissa Gymrek

Next Position: University of California, San Diego, Computational and Data Science Research Specialist

Daniela Nachmanson

Daniela Nachmanson

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Profiling archival samples to examine the molecular underpinnings of early carcinogenesis

Abstract

Advisor(s): Olivier Harismendy, Ludmil Alexandrov

Kivilicim Ozturk

Kivilicim Ozturk

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Advancing variant effect interpretation beyond protein-level by incorporating systems-level architecture

Abstract

Advisor(s): Hannah Carter, Prashant Mali

Timofey Prodanov

Timofey Prodanov

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Read mapping, variant calling, and copy number variation detection in segmental duplications

Abstract

Advisor(s): Vikas Bansal, Melissa Gymrek

Michelle Franc Ragsac

Michelle Franc Ragsac

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Decoding the genomic regulatory syntax driving notochord development

Abstract

Advisor(s): Emma Farley, Terry Gaasterland

Next Position: Empirico, Senior Data Scientist

Chao Zhang

Chao Zhang

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Scalable Algorithms for Inference and Simulation under Complex Phylogenetic Models

Abstract

Advisor(s): Siavash Mirarab, Pavel Pevzner

Lina Zheng

Lina Zheng

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: New insights into 3D chromatin organization and function

Abstract

Advisor(s): Wei Wang, Gene Yeo

Anthony Aylward

Anthony Aylward

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Statistical strategies and resources for deciphering mechanisms of diabetes risk loci

Abstract

Advisor(s): Kyle Gaulton, Dorothy Sears

Kevin Blansit

Kevin Blansit

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Advancing Cardiovascular MRI Acquisition Through Deep Convolutional Neural Network-Based Localization

Abstract

Advisor(s): Albert Hsiao

Patrick Fiaux

Patrick Fiaux

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Discovery of novel sequences through the analysis of tiling CRISPR screens

Abstract

Advisor(s): Graham McVicker, Bing Ren

Jens Luebeck

Jens Luebeck

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Reconstructing and Profiling Extrachromosomal DNA

Abstract

Advisor(s): Vineet Bafna, Julie Law

Next Position: Bafna Lab, Postdoctoral Scholar

Patrick Phaneuf

Patrick Phaneuf

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data

Abstract

Advisor(s): Bernhard Palsson, Nathan E. Lewis

Samuel Roth

Samuel Roth

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Identification and Characterization of Systems with Defects in Transcription Termination

Abstract

Advisor(s): Christopher Benner, Sven Heinz

Argus Athanas-Crannell

Argus Athanas-Crannell

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Leveraging Longitudinal Data for Predictive Modeling in Clinical and Mental Health Settings

Abstract

Advisor(s): Nicholas Schork, Lucila Ohno-Machado

Bahar Behsaz

Bahar Behsaz

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Scalable Computational Methods for Discovering Novel Natural Products

Abstract

Advisor(s): Pavel Pevzner, Rob Knight

Arjun Chandrasekhar

Arjun Chandrasekhar

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Derivation and Analysis of Distributed Computing Algorithms in Biological Systems

Abstract

Advisor(s): Saket Navlakha, Glenn Tesler

Michelle Dow

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

Abstract

Advisor(s): Hannah Carter

Yingxiang Huang

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

Abstract

Advisor(s): Lucila Ohno-Machado

Jamison McCorrison

Jamison McCorrison

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Exploitation of Metadata in Molecular Genomics Studies

Abstract

Advisor(s): Nicholas Schork, Vikas Bansal

Margaret Donovan

Margaret Donovan

Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical Informatics

Thesis: Understanding the cellular heterogeneity in fetal-like and adult tissues to study cell-type-specific functional genetic variation

Abstract

Advisor(s): Kelly Frazer

Rongxin Fang

Rongxin Fang

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Single Cell Analysis of Chromatin Accessibility

Abstract

Advisor(s): Bing Ren, Vineet Bafna

Robert Foreman

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

Abstract

Advisor(s): Scott Rifkin, Roy Wollman

William Greenwald

William Greenwald

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Exploring the Regulatory Genome and Functional Genetic Variation

Abstract

Advisor(s): Kelly Frazer

Next Position: Monoceros Biosystems, Bioinformatics Scientist

Nicolaus Lance Hepler

Nicolaus Lance Hepler

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: HIV-1 Sequence Analysis: Approaches and Applications from Transmission Network Inference to Epitope Discovery

Abstract

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

Next Position: 10X Genomics, Staff Computational Biologist

Isaac Lopez Moyado

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

Abstract

Advisor(s): Anjana Rao, Vineet Bafna

Jia Lu

Jia Lu

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Understanding cis-Regulatory Activities with Evolutionary Epigenomic Analyses

Abstract

Advisor(s): Sheng Zhong, Bing Ren

Shamim Mollah

Shamim Mollah

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Integrative Approaches to Targeting Chromatin Remodeling in Breast Cancer Therapy

Abstract

Advisor(s): Shankar Subramaniam, Vineet Bafna

Next Position: Washington University School of Medicine in St. Louis, Assistant Professor

Niema Moshiri

Niema Moshiri

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Mathematical Modeling of Viral Evolution and Epidemiology

Abstract

Advisor(s): Siavash Mirarab, Pavel Pevzner

Next Position: UC San Diego Department of Computer Science & Engineering, Assistant Teaching Professor

Vu Ngo

Vu Ngo

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Interplays between DNA motifs and epigenetic elements

Abstract

Advisor(s): Wei Wang

Next Position: Cradle Genomics, Bioinformatics Scientist

Yunjiang Qiu

Yunjiang Qiu

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Interpreting human genetic variations through transcriptional regulation and 3D genome organization

Abstract

Advisor(s): Bing Ren, Sheng Zhong

Anugraha Raman

Anugraha Raman

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Genomic diversity of tumor and normal tissues revealed by single-nuclei RNA-seq computational analysis

Abstract

Advisor(s): Bing Ren, Kun Zhang

Next Position: Fulcrum Therapeutics, Associate Scientist

John Sauls

John Sauls

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Physiological Orchestration in Bacteria

Abstract

Advisor(s): Suckjoon Jun, Terence Hwa

Dylan Skola

Dylan Skola

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Christopher Glass, Wei Wang

Next Position: Illumina, Bioinformatics Scientist

Brian Yik Tak Tsui

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

Abstract

Advisor(s): Hannah Carter, Jill Mesirov

Next Position: Illumina, Bioinformatics scientist

Mengchi Wang

Mengchi Wang

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Deciphering the Genetic Code of DNA Methylation

Abstract

Advisor(s): Wei Wang, Bing Ren

Christopher Wei

Christopher Wei

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Single Cell Phylogenetic Fate Mapping: Combining Microsatellite and Methylation Profiling for Retrospective Lineage Tracing

Abstract

Advisor(s): Kun Zhang, Vineet Bafna

Next Position: Zhang Lab, Postdoctural Researcher

Jeffrey Yuan

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

Abstract

Advisor(s): Pavel Pevzner, Bing Ren

Next Position: Illumina, Bioinformatics Scientist

Jing Zhang

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

Abstract

Advisor(s): Vineet Bafna, Michael Hogarth

Yuan Zhao

Yuan Zhao

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Computational approaches for elucidating the gene regulatory landscape of mammalian development

Abstract

Advisor(s): Bing Ren, Wei Wang

Nassim Ajami

Nassim Ajami

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Shankar Subramaniam, Shu Chien

Next Position: CRISPR Therapeutics, Scientist

Laurence Bernstein

Laurence Bernstein

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Nuno Bandeira, Steve Briggs

Next Position: Quest Diagnostics, Principal Software Engineer

Stephanie Feudjio Feupe

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

Abstract

Advisor(s): Melissa Gymrek, Vineet Bafna

Justin Huang

Justin Huang

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Trey Ideker

Next Position: MD Anderson Cancer Center TRACTION, Institute Research Investigator: Systems Biology

Leen Jamal

Leen Jamal

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Gene Yeo

Next Position: Viastat, Inc, Data Scientist

James Jensen

James Jensen

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Jill Mesirov, Pablo Tamayo

Next Position: Recursion Pharmaceuticals, Data Scientist

Rachel Marty

Rachel Marty

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: The Role of MHC Variation in Tumor Progression

Abstract

Advisor(s): Hannah Carter

Next Position: Personalis, Inc, Bioinformatics Scientist

Nathan Mih

Nathan Mih

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Bernhard Palsson, Philip Bourne

Next Position: Lygos, Inc, Software Engineer

Gabriel Pratt

Gabriel Pratt

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Methods for Integrative Analysis of RNA Binding Proteins

Abstract

Advisor(s): Gene Yeo, Sheng Zhong

Next Position: TwinStrand Biosciences, Bioinformatics Scientist

Jenhan Tao

Jenhan Tao

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Christopher Glass, Christopher Benner

Next Position: Illumina, Bioinformatics Scientist

James Yurkovich

James Yurkovich

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Bernhard Palsson, Jeff Hasty

Next Position: Institute for Systems Biology, Translational Research Fellow

Kunal Bhutani

Kunal Bhutani

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Limiting Biases in Biological Data Analysis by Pooling Information

Abstract

Advisor(s): Nicholas Schork, Vineet Bafna

Next Position: FVL59, Inc, Computational Scientist

Olga Botvinnik

Olga Botvinnik

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Computational analysis of single-cell alternative splicing

Abstract

Advisor(s): Gene Yeo, Sheng Zhong

Next Position: Chan-Zuckerberg Biohub, Bioinformatics Data Scientist

Dinh Diep

Dinh Diep

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Kun Zhang, Vineet Bafna

Next Position: UC San Diego, Postdoctural Researcher

Kuan-Fu Ding

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

Abstract

Advisor(s): Nicholas Schork, Bing Ren

Next Position: Sapiens Data Science, Chief Science Officer

Yupeng He

Yupeng He

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Joseph Ecker, Wei Wang

Joanne Liu

Joanne Liu

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Predicting Growth Optimization Strategies with Metabolic/Expression Models

Abstract

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

Next Position: Biota Technology, Data Scientist

Wei Wei

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

Abstract

Advisor(s): Lucila Ohno-Machado, Xiaoqian Jiang

Jason Yao

Jason Yao

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Modeling and Measuring Dynamic Cellular Signaling States

Abstract

Advisor(s): Roy Wollman, Shankar Subramaniam

Next Position: Guavus, Research Data Scientist

Michael Yu

Michael Yu

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Hierarchical Models of Biological Systems

Abstract

Advisor(s): Trey Ideker, Christopher Glass

Next Position: Toyota Technical Institute at Chicago, Research Assistant Professor

Christopher DeBoever

Christopher DeBoever

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Kelly Frazer, Trey Ideker

Next Position: Takeda, Computational Biology Scientist

Andrew Gross

Andrew Gross

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Understanding disease through data driven biology

Abstract

Advisor(s): Trey Ideker, Kelly Frazer

Next Position: Illumina, Bioinformatics Scientist

Eric Levy

Eric Levy

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Molecular immune signatures of T-cell infiltration in cancer

Abstract

Advisor(s): Lucila Ohno-Machado, Olivier Harismendy

Next Position: Personalis, Senior Bioinformatics Scientist

Kavitha Mukund

Kavitha Mukund

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Systems Biology Approaches to Discerning Striated Muscle Pathologies

Abstract

Advisor(s): Shankar Subramaniam, Richard Lieber

Cory White

Cory White

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Investigations of HIV Latency Through Transcriptomic and Proteomic Profiling

Abstract

Advisor(s): Doug Richman, David Smith

Chia-Yi Allison Wu

Chia-Yi Allison Wu

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Scott Rifkin, Jeff Hasty

Karmel Allison

Karmel Allison

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Enhancers and Transcriptional Regulation in CD4+ T Cell

Abstract

Advisor(s): Christopher Glass, Stephen Hedrick

Next Position: Google Brain TensorFlow Team, Engineering Manager

Spencer Bliven

Spencer Bliven

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Philip Bourne, Milton Saier

Next Position: Paul Scherrer Institut PSI, Scientific Computing Engineer

Stefano Bonissone

Stefano Bonissone

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Deconvolution of immunome and degradome repertoires using computational proteomics

Abstract

Advisor(s): Pavel Pevzner, Steve Briggs

Qi Ma

Qi Ma

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Understanding the Functional Properties of Enhancers

Abstract

Advisor(s): Michael Rosenfeld, Gene Yeo

Next Position: UCSD, Postdoctoral Fellow in Rosenfeld Lab

Daria Merkurjev

Daria Merkurjev

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Understanding Enhancer Role in the Transcriptional Response

Abstract

Advisor(s): Michael Rosenfeld, Wei Wang

Edward J O'Brien

Edward J O'Brien

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Proteome allocation trade-offs in bacterial evolution and regulation

Abstract

Advisor(s): Bernhard Palsson, Philip Bourne

Eric Scott

Eric Scott

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Joseph Gleeson, Vineet Bafna

Next Position: GRAIL, Inc, Bioinformatics Scientist

Martin Smith

Martin Smith

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

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

Next Position: Pacific Biosciences, Staff Engineer: Primary Analysis

Alex Thomas

Alex Thomas

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Moving Towards Interpretable Mechanisms in Human Systems Biology

Abstract

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

Next Position: C.H. Robinson, Principal Data Scientist

Gordon Bean

Gordon Bean

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Trey Ideker, Christopher Woelk

Next Position: Illumina, Bionformatics Scientist

Winston Chen

Winston Chen

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Deciphering Molecular Mechanism of Adverse Reactions of Drugs

Abstract

Advisor(s): Ruben Abagyan, Grace Kuo

Jeremy Davis-Turak

Jeremy Davis-Turak

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Alexander Hoffmann, Gene Yeo

Next Position: OnRamp Bioinformatics, Vice President

Stephen Federowicz

Stephen Federowicz

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Bernhard Palsson, Wei Wang

Next Position: Inscripta, Inc, Senior Scientist: Computational Biology

Stephanie Huelga

Stephanie Huelga

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Gene Yeo, Christopher Woelk

Next Position: NuGEN, Data Analysis Scientist

Boyko Kakaradov

Boyko Kakaradov

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Gene Yeo, Charles Elkan

Next Position: Deep Genomics, Senior Scientist

Joshua Lerman

Joshua Lerman

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

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

Anand Patel

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Genome Rearrangements in Cancer and Human Genomes

Abstract

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

Next Position: Digital Proteomics, Chief Technology Officer

Roy Ronen

Roy Ronen

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Identifying and Characterizing the Genomic Signatures of Natural Selection

Abstract

Advisor(s): Vineet Bafna, Gabriel Haddad

Next Position: Data4Cure, Inc., VP Platform

Philip Samayoa

Philip Samayoa

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Applications of synthetic biology inspired by natural bacterial functionality

Abstract

Advisor(s): Jeff Hasty, Ruth Williams

Next Position: Generation Bio, Vice President: Strategy and Portolio Development

Matthew Schultz

Matthew Schultz

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Joseph Ecker, Vineet Bafna

Next Position: Human Longevity, Inc., Bioinformatics Scientist

Siddarth Selvaraj

Siddarth Selvaraj

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Bing Ren, Vineet Bafna

Maxim Shokhirev

Maxim Shokhirev

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Alexander Hoffmann, Andrew McCulloch

Next Position: Salk Institute for Biological Studies Integrative Genomics & Bioinoformatics Core, Director

Vipul Bhargava

Vipul Bhargava

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Quantitative Transcriptomics From Limiting Amounts of mRNA

Abstract

Advisor(s): Shankar Subramaniam, Mark Mercola

Next Position: Janssen Research and Development LLC (Johnson and Johnson company) , Scientist

Marcus Kinsella

Marcus Kinsella

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Computational Techniques to Investigate Structural Variation

Abstract

Advisor(s): Vineet Bafna, Kelly Frazer

Next Position: Pacific Biosciences, Senior Engineer (Bioinformatics)

Paul Loriaux

Paul Loriaux

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Steady State Control of the Cellular Response to Stress

Abstract

Advisor(s): Alexander Hoffmann, Pavel Pevzner

Next Position: Second Genome Inc, Lead Data Scientist

Nisha Rajagopal

Nisha Rajagopal

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Navigating the Human Epigenome through Random Forests

Abstract

Advisor(s): Bing Ren, Wei Wang

Nitin Udpa

Nitin Udpa

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: The Genetic Basis of Hypoxia Tolerance

Abstract

Advisor(s): Vineet Bafna, Kelly Frazer

Next Position: Illumina, Bioinformatics Scientist

Shawn Yost

Shawn Yost

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Accurate Identification of Somatic Mutations in Clinical Tumor Specimens

Abstract

Advisor(s): Kelly Frazer, Vineet Bafna

Jocelyne Bruand

Jocelyne Bruand

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Computational Tools for Analysis of Mass spectrometry Imaging Data

Abstract

Advisor(s): Vineet Bafna, Eduardo Macagno

Next Position: Illumina, Bioinformatics Scientist

Roger Chang

Roger Chang

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Bernhard Palsson, Philip Bourne

Next Position: Albert Einstein College of Medicine, Assistant Professor of Systems and Computational Biology

Eugene Ke

Eugene Ke

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Shankar Subramaniam, Inder Verma

Next Position: Salk Institute, Research Associate (Postdoc)

Harish Nagarajan

Harish Nagarajan

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Electromicrobiiology: A Systems Perspective

Abstract

Advisor(s): Bernhard Palsson, Milton Saier

Next Position: Genomatica Inc., Research Scientist I, Computational Technologies

Josué Pérez-Santiago

Josué Pérez-Santiago

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Doug Richman, Kun Zhang

Next Position: UCSD, Postdoctoral Fellow

Jason Chan

Jason Chan

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Richard Kolodner, Trey Ideker

Christine Cheng

Christine Cheng

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Alexander Hoffmann, Charles Elkan

Next Position: Broad Institute of MIT and Harvard, Postdoc in Aviv Regev's Lab

Merril Gersten

Merril Gersten

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Shankar Subramaniam, Gabriel Haddad

Next Position: UCSD Dept Bioengineering, Postdoc

Lukasz Szpankowski

Lukasz Szpankowski

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Lawrence Goldstein, Shankar Subramaniam

Next Position: Fluidigm, Scientist - R&D, New Technologies

Sourav Bandyopadhyay

Sourav Bandyopadhyay

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Integrating Physical and Genetic Interaction Networks for Biological Discovery

Abstract

Advisor(s): Trey Ideker, Vineet Bafna

Next Position: Univerity of California, San Francisco, Assistant Professor

Mary Budagyan (Mary Pacold)

Mary Budagyan (Mary Pacold)

Degree Conferred: Ph.D. Bioinformatics

Thesis: Detecting and Characterizing HIV-1 Intaclade Dual Infection

Abstract

Advisor(s): Doug Richman, Glenn Tesler

Next Position: Ion Torrent / Life Technologies, Product Manager, Informatics Applications

Han-Yu Chuang

Han-Yu Chuang

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Trey Ideker, Thomas Kipps

Next Position: Illumina, Bioinformatics Scientist

Jan Schellenberger

Jan Schellenberger

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Monte Carlo Sampling in Systems Biology

Abstract

Advisor(s): Bernhard Palsson, Vineet Bafna

Next Position: ID Analytics, Scientist

Ruben Valas

Ruben Valas

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

Advisor(s): Philip Bourne, William Loomis

Next Position: UC San Diego (Bourne Lab), Postdoc

Ali Bashir

Ali Bashir

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

Advisor(s): Vineet Bafna, Pavel Pevzner

Next Position: Pacific Biosciences, Scientist

Nitin Gupta

Nitin Gupta

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Pavel Pevzner, Steve Briggs

Next Position: University of California, San Diego (Aron Lab), Postdoc

Gary Hon

Gary Hon

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Bing Ren, Wei Wang

Next Position: Ludwig Institute for Cancer Research, Postdoc

Suchit Jhunjhunwala

Suchit Jhunjhunwala

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

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

Abstract

Advisor(s): Cornelis Murre, Maho Niwa

Next Position: Synthetic Genomics, Inc., Senior Bioinformatics Scientist

Ryan M. Kelley

Ryan M. Kelley

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

Advisor(s): Trey Ideker, Vineet Bafna

Next Position: Illumina, Bioinformatics Scienist 1

Juan Lorenzo Rodriguez Flores

Juan Lorenzo Rodriguez Flores

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

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

Next Position: Ludwig Institute for Cancer Research, Postdoc

Ines Thiele

Ines Thiele

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

Advisor(s): Bernhard Palsson, Steve Briggs

Next Position: University of Iceland, Asst Professor

Noah Zaitlen

Noah Zaitlen

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Vineet Bafna, Eleazar Eskin

Next Position: Harvard School of Public Health, Postdoc

Christopher Benner

Christopher Benner

Degree Conferred: Ph.D. Bioinformatics

Thesis: Identification of a Conserved Periodic Promoter Structure in Metazoans

Abstract

Advisor(s): Christopher Glass, Shankar Subramaniam

Next Position: University of California, San Diego (Glass Lab), Postdoc

Kristine Briedis

Kristine Briedis

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

Advisor(s): Philip Bourne, William Loomis

Next Position: University of California, San Diego (Bourne Lab), Postdoc

Mark Chaisson

Mark Chaisson

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

Advisor(s): Pavel Pevzner, Vineet Bafna

Next Position: Pacific Biosciences, Senior Algorithms Developer

Michele Day

Michele Day

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

Advisor(s): Susan Taylor, Lynn Ten Eyck

Next Position: University of California, San Diego (Taylor Lab), Postdoc

Kasey Hutt

Kasey Hutt

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

Advisor(s): Michael Rosenfeld, Terry Gaasterland

Next Position: University of California, San Diego (Rosenfeld Lab), Postdoc

Samuel Payne

Samuel Payne

Degree Conferred: Ph.D. Bioinformatics

Thesis: Advances in Computational Mass Spectrometry: Phosphoprteomics and Proteogenomics

Abstract

Advisor(s): Vineet Bafna, William Loomis

Next Position: Brigham Young University, Associate Professor

Silpa Suthram

Silpa Suthram

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

Advisor(s): Trey Ideker, Philip Bourne

Next Position: Stanford working w/ Dr. Atul Butte, Postdoc

Elaine Thompson

Elaine Thompson

Degree Conferred: Ph.D. Bioinformatics

Thesis: Characterizing Protein Structures by Surface Mapping

Abstract

Advisor(s): Lynn Ten Eyck, Vineet Bafna

Next Position: University of California, San Diego (Susan Taylor Lab), Postdoc

Derren Barken

Derren Barken

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

Advisor(s): Alexander Hoffmann, Shankar Subramaniam

Next Position: Prometheus, Bioinformatics Scientist

Leah Barrera

Leah Barrera

Degree Conferred: Ph.D. Bioinformatics

Thesis: Genome-wide mapping and analysis of mammalian promoters

Abstract

Advisor(s): Bing Ren, Philip Bourne

Next Position: Ambit Biosciences, Scientist

Ann Thuy Mongan (Thuy Vo)

Ann Thuy Mongan (Thuy Vo)

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

Advisor(s): Bernhard Palsson, Andrew McCulloch

Next Position: BioInformative, Founder and CEO

Stephen Tanner

Stephen Tanner

Degree Conferred: Ph.D. Bioinformatics

Thesis: Efficient and Accurate Bioinformatics Algorithms for Peptide Mass Spectrometry

Abstract

Advisor(s): Vineet Bafna, Julian Schroeder

Next Position: Inscripta, Principal Scientist

John Mongan

John Mongan

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

Advisor(s): Andrew McCammon, Gary Huber

Next Position: University of California, San Francisco, Associate Professor

Coleman Mosley

Coleman Mosley

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

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

Next Position: Magellan Health-National Imaging Associates, Physician Clinical Reviewer

Degui Zhi

Degui Zhi

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

Advisor(s): Pavel Pevzner, William Loomis

Next Position: University of Texas Health Science Center at Houston, Associate Professor

Albert Hsiao

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

Abstract

Advisor(s): Shankar Subramaniam, Jerrold Olefsky

Next Position: UCSD, Assistant Professor of Radiology, In-Residence

Jason Papin

Jason Papin

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

Thesis: Systems Analysis of Cellular Signaling Networks

Abstract

Advisor(s): Bernhard Palsson, Jerrold Olefsky

Next Position: University of Virginia, Assistant Professor

Nathan Price

Nathan Price

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

Thesis: Unbiased Assessment of Genome-Scale Metabolic Network States

Abstract

Advisor(s): Bernhard Palsson, Shankar Subramaniam

Next Position: University of Illinois, Urbana-Champaign, Assistant Professor

Iman Famili

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.

Abstract

Advisor(s): Bernhard Palsson, Shankar Subramaniam

Next Position: GT Life Sciences, Inc., Research Director

Markus Herrgard

Markus Herrgard

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

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

Abstract

Advisor(s): Bernhard Palsson, Shankar Subramaniam

Next Position: synthetic genomics, Senior Bioinformatics Scientist

Markus Covert

Markus Covert

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

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

Abstract

Advisor(s): Bernhard Palsson

Next Position: Stanford, Asst Professor