Thesis Archive

The UC San Diego Libraries provide access to official copies of all UC San Diego dissertations. Use Roger (in the UC San Diego Libraries Catalog) or eScholarship to search for UC San Diego Bioinformatics dissertations.

2016

Andrew Gross Ph.D., Bioinformatics and Systems Biology (2016)
Understanding disease through data driven biology

Advisors: Trey Ideker
| Kelly Frazer
Library
| Abstract
Chia-Yi Allison Wu Ph.D., (2016)
Dissecting the Worn Intestinal Genetic Network with Quantitative Measurement and Modeling

Advisors: Scott Rifkin
| Jeff Hasty
Library
| Abstract

2015

Karmel Allison Ph.D., Bioinformatics and Systems Biology (2015)
Enhancers and Transcriptional Regulation in CD4+ T Cell

Advisors: Christopher Glass
| Stephen Hedrick
Library
| Abstract
Spencer Bliven Ph.D., Bioinformatics and Systems Biology (2015)
Structure-preserving Rearrangements: Algorithms for Structural Comparison and Protein Analysis

Advisors: Philip Bourne
| Milton Saier
Library
| Abstract
Stefano Bonissone Ph.D., Bioinformatics and Systems Biology (2015)
Deconvolution of immunome and degradome repertoires using computational proteomics

Advisors: Pavel Pevzner
| Steve Briggs
Library
| Abstract
Qi Ma Ph.D., Bioinformatics and Systems Biology (2015)
Understanding the Functional Properties of Enhancers

Advisors: Michael Rosenfeld
| Gene Yeo
Library
| Abstract
Daria Merkurjev Ph.D., Bioinformatics and Systems Biology (2015)
Understanding Enhancer Role in the Transcriptional Response

Advisors: Michael Rosenfeld
| Wei Wang
Library
| Abstract
Eric Scott Ph.D., Bioinformatics and Systems Biology (2015)
Genomic structural characterization of the Greater Middle East to assist in the identification of disease variation

Advisors: Joseph Gleeson
| Vineet Bafna
Library
| Abstract
Martin Smith Ph.D., Bioinformatics and Systems Biology (2015)
Increasing Biological Realism in Models of Sequence Evolution for Improved Statistical and Computational Performance

Advisors: Sergei L. Kosakovsky Pond
| Doug Richman
Library
| Abstract
Alex Thomas Ph.D., Bioinformatics and Systems Biology (2015)
Moving Towards Interpretable Mechanisms in Human Systems Biology

Advisors: Nathan E. Lewis
| Dorothy Sears
Library
| Abstract

2014

Gordon Bean Ph.D., Bioinformatics and Systems Biology (2014)
Development of experimental and computational tools for high-throughput microbial "omics"

Advisors: Trey Ideker
| Christopher Woelk
Library
| Abstract
Winston Chen Ph.D., Bioinformatics and Systems Biology (2014)
Deciphering Molecular Mechanism of Adverse Reactions of Drugs

Advisors: Ruben Abagyan
| Grace Kuo
Library
| Abstract
Jeremy Davis-Turak Ph.D., Bioinformatics and Systems Biology (2014)
Exploring the Mechanisms of pre-mRNA Splicing Using Mathematical Models of Coupled Transcription and Splicing

Advisors: Alexander Hoffmann
| Gene Yeo
Library
| Abstract
Stephen Federowicz Ph.D., Bioinformatics and Systems Biology (2014)
Elucidating mechanisms of transcriptional regulation at the genome-scale

Advisors: Bernhard Palsson
| Wei Wang
Library
| Abstract
Stephanie Huelga Ph.D., Bioinformatics and Systems Biology (2014)
Comprehensive discovery and analysis of RNA binding protein-dependent post-transcriptional events in mammalian systems

Advisors: Gene Yeo
| Christopher Woelk
Library
| Abstract
Boyko Kakaradov Ph.D., Bioinformatics and Systems Biology (2014)
Statistical models for RNA biology: from single nucleotides to single cells

Advisors: Gene Yeo
| Charles Elkan
Library
| Abstract
Joshua Lerman Ph.D., Bioinformatics and Systems Biology (2014)
Genome-scale Models of Metabolism and Gene Expression: Construction and Use for Growth Phenotype Prediction

Advisors: Bernhard Palsson
| Milton Saier
Library
| Abstract
Anand Patel Ph.D., Bioinformatics and Systems Biology (2014)
Genome Rearrangements in Cancer and Human Genomes

Advisors: Vineet Bafna
| Yu-Tsueng Liu
Library
| Abstract
Roy Ronen Ph.D., Bioinformatics and Systems Biology (2014)
Identifying and Characterizing the Genomic Signatures of Natural Selection

Advisors: Vineet Bafna
| Gabriel Haddad
Library
| Abstract
Philip Samayoa Ph.D., Bioinformatics and Systems Biology (2014)
Applications of synthetic biology inspired by natural bacterial functionality

Advisors: Jeff Hasty
| Ruth Williams
Library
| Abstract
Matthew Schultz Ph.D., Bioinformatics and Systems Biology (2014)
What Your Genome Doesn't Tell You: Population-level and Genome-wide Epigenomic Surveys of Plants and People

Advisors: Joseph Ecker
| Vineet Bafna
Library
| Abstract
Siddarth Selvaraj Ph.D., Bioinformatics and Systems Biology (2014)
Analysis of 3D genome organization and gene regulation in mammalian cells

Advisors: Bing Ren
| Vineet Bafna
Library
| Abstract
Maxim Shokhirev Ph.D., Bioinformatics and Systems Biology (2014)
Developing a multi-scale understanding of the B cell immune response

Advisors: Alexander Hoffmann
| Andrew McCulloch
Library
| Abstract

2013

Vipul Bhargava Ph.D., Bioinformatics and Systems Biology (2013)
Quantitative Transcriptomics From Limiting Amounts of mRNA

Advisors: Shankar Subramaniam
| Mark Mercola
Library
| Abstract
Marcus Kinsella Ph.D., Bioinformatics and Systems Biology (2013)
Computational Techniques to Investigate Structural Variation

Advisors: Vineet Bafna
| Kelly Frazer
Library
| Abstract
Paul Loriaux Ph.D., Bioinformatics and Systems Biology (2013)
Steady State Control of the Cellular Response to Stress

Advisors: Alexander Hoffmann
| Pavel Pevzner
Library
| Abstract
Nisha Rajagopal Ph.D., Bioinformatics and Systems Biology (2013)
Navigating the Human Epigenome through Random Forests

Advisors: Bing Ren
| Wei Wang
Library
| Abstract
Nitin Udpa Ph.D., Bioinformatics and Systems Biology (2013)
The Genetic Basis of Hypoxia Tolerance

Advisors: Vineet Bafna
| Kelly Frazer
Library
| Abstract
Jian Wang Ph.D., Bioinformatics and Systems Biology (2013)
Expanding the toolbox of tandem mass spectrometry with algorithms to identify mass spectra from more than one peptide

Advisors: Philip Bourne
| Pieter Dorrestein
Library
| Abstract
Yi Wen Ph.D., Bioinformatics and Systems Biology (2013)
Serial Post-Transcriptional Splicing Establishes Negative Feedback Regulation in HIV-1 Expression

Advisors: Leor Weinberger
| Doug Richman
Library
| Abstract
Shawn Yost Ph.D., Bioinformatics and Systems Biology (2013)
Accurate Identification of Somatic Mutations in Clinical Tumor Specimens

Advisors: Kelly Frazer
| Vineet Bafna
Library
| Abstract

2012

Jocelyne Bruand Ph.D., Bioinformatics and Systems Biology (2012)
Computational Tools for Analysis of Mass spectrometry Imaging Data

Advisors: Vineet Bafna
| Eduardo Macagno
Library
| Abstract
Roger Chang Ph.D., Bioinformatics and Systems Biology (2012)
Structural systems biology perspective on the metabolic impact of physicochemical stress

Advisors: Bernhard Palsson
| Philip Bourne
Library
| Abstract
Eugene Ke Ph.D., Bioinformatics and Systems Biology (2012)
Insights from reconstructing cellular networks in transcription, stress and cancer

Advisors: Shankar Subramaniam
| Inder Verma
Library
| Abstract
Harish Nagarajan Ph.D., Bioinformatics and Systems Biology (2012)
Electromicrobiiology: A Systems Perspective

Advisors: Bernhard Palsson
| Milton Saier
Library
| Abstract
Josué Pérez-Santiago Ph.D., Bioinformatics and Systems Biology (2012)
The Human Gut Microbiome: Characterization Challenges and HIV Disease Association

Advisors: Doug Richman
| Kun Zhang
Library
| Abstract

2011

Jason Chan Ph.D., Bioinformatics and Systems Biology (2011)
Effects of a Highly Repetitive Endogenous Tyl Retrotransposon on Genome Stablility

Advisors: Richard Kolodner
| Trey Ideker
Library
| Abstract
Christine Cheng Ph.D., Bioinformatics and Systems Biology (2011)
Innate immune gene expression programs defined by both regulated mRNA synthesis and decay

Advisors: Alexander Hoffmann
| Charles Elkan
Library
| Abstract
Merril Gersten Ph.D., Bioinformatics and Systems Biology (2011)
Systems Analysis of Model Organisms in the Study of Human disease

Advisors: Shankar Subramaniam
| Gabriel Haddad
Library
| Abstract
Julio Ng Ph.D., Bioinformatics and Systems Biology (2011)
Computational Mass Spectrometry: Algorithms for Identification of Peptides not present in Protein Databases

Advisors: Pavel Pevzner
| Pieter Dorrestein
Library
| Abstract
Lukasz Szpankowski Ph.D., Bioinformatics and Systems Biology (2011)
Coordination of Axonal Transport Revealed by Particle Tracking and Quantitative Immunogluorescence

Advisors: Lawrence Goldstein
| Shankar Subramaniam
Library
| Abstract

2010

Sourav Bandyopadhyay Ph.D., Bioinformatics and Systems Biology (2010)
Integrating Physical and Genetic Interaction Networks for Biological Discovery

Advisors: Trey Ideker
| Vineet Bafna
Library
| Abstract
Mary Budagyan (Mary Pacold) Ph.D., Bioinformatics (2010)
Detecting and Characterizing HIV-1 Intaclade Dual Infection

Advisors: Doug Richman
| Glenn Tesler
Library
| Abstract
Han-Yu Chuang Ph.D., Bioinformatics and Systems Biology (2010)
Pathway-based modeling and diagnosis of cancer development and progression

Advisors: Trey Ideker
| Thomas Kipps
Library
| Abstract
Jan Schellenberger Ph.D., Bioinformatics and Systems Biology (2010)
Monte Carlo Sampling in Systems Biology

Advisors: Bernhard Palsson
| Vineet Bafna
Library
| Abstract
Ruben Valas Ph.D., Bioinformatics (2010)
The Gospel According to LUCA (the last universal common ancestor)

Advisors: Philip Bourne
| William Loomis
Library
| Abstract

2009

Ali Bashir Ph.D., Bioinformatics (2009)
Computational Methods for Analyzing and Detecting Genomic Structural Variation: Applications to Cancer

Advisors: Vineet Bafna
| Pavel Pevzner
Library
| Abstract
Nitin Gupta Ph.D., Bioinformatics and Systems Biology (2009)
Computational and Comparative Proteogenomics: Annotating Genomes and Proteomes using Tandem Mass Spectrometry

Advisors: Pavel Pevzner
| Steve Briggs
Library
| Abstract
Gary Hon Ph.D., Bioinformatics and Systems Biology (2009)
Understanding the global architecture of gene regulation in human cells through analysis of chromatin signatures

Advisors: Bing Ren
| Wei Wang
Library
| Abstract
Suchit Jhunjhunwala Ph.D., Biology with a specialization in Bioinformatics (2009)
The 3-D Structure of the Immunoglobulin Heavy Chain Locus:Implications for Long-Range Genomic Interactions

Advisors: Cornelis Murre
| Maho Niwa
Library
| Abstract
Ryan M. Kelley Ph.D., Bioinformatics (2009)
Analysis and integration of high-throughput biological data for pathway discovery

Advisors: Trey Ideker
| Vineet Bafna
Library
| Abstract
Juan Lorenzo Rodriguez Flores Ph.D., Bioinformatics and Systems Biology (2009)
In Silico In Vitro In Vivo and In Populo Regulatory Single Nucleotide Polymorphisms in the Phenylethanolamine N-Methyltransferase Promoter

Advisors: Daniel O'Connor
| Shankar Subramaniam
Library
| Abstract
Ines Thiele Ph.D., Bioinformatics (2009)
A Stoichiometric Model of E. Coli's Macromolecular Synthesis Machinery and its Integration with Metablism

Advisors: Bernhard Palsson
| Steve Briggs
Library
| Abstract
Noah Zaitlen Ph.D., Bioinformatics and Systems Biology (2009)
Methods for the Analysis of Human Genetic Variation in the Search for the Genetic Basis of Human Disease

Advisors: Vineet Bafna
| Eleazar Eskin
Library
| Abstract

2008

Christopher Benner Ph.D., Bioinformatics (2008)
Identification of a Conserved Periodic Promoter Structure in Metazoans

Advisors: Christopher Glass
| Shankar Subramaniam
Library
| Abstract
Kristine Briedis Ph.D., Bioinformatics (2008)
The distribution and evolution of protein kinase and phospatase families in the three superkingdoms of life

Advisors: Philip Bourne
| William Loomis
Library
| Abstract
Mark Chaisson Ph.D., Bioinformatics (2008)
Combinatorial Methods for Compuational Genomics: Mammalian Phylogenetics Using Inversions and Fragment Assembly with Short Reads

Advisors: Pavel Pevzner
| Vineet Bafna
Library
| Abstract
Max Chang Ph.D., Bioinformatics (2008)
Computational Structure-Based Methods to Anticipate HIV Drug Resistance Evolution and Accelerate Inhibitor Discovery

Advisors: Richard Belew
| Lin Chao
Library
| Abstract
Michele Day Ph.D., Bioinformatics (2008)
Insights into the functionality and targeting of PKA regulatory subunity Rialpha

Advisors: Susan Taylor
| Lynn Ten Eyck
Library
| Abstract
Kasey Hutt Ph.D., Bioinformatics (2008)
High-throughput genomic assays: Applications and analysis of DSL technology and next-generation sequencing

Advisors: Michael Rosenfeld
| Terry Gaasterland
Library
| Abstract
Samuel Payne Ph.D., Bioinformatics (2008)
Advances in Computational Mass Spectrometry: Phosphoprteomics and Proteogenomics

Advisors: Vineet Bafna
| William Loomis
Library
| Abstract
Silpa Suthram Ph.D., Bioinformatics (2008)
Understanding Cellular Function through the Analysis of Protein Interaction Networks

Advisors: Trey Ideker
| Philip Bourne
Library
| Abstract
Elaine Thompson Ph.D., Bioinformatics (2008)
Characterizing Protein Structures by Surface Mapping

Advisors: Lynn Ten Eyck
| Vineet Bafna
Library
| Abstract

2007

Derren Barken Ph.D., Bioinformatics (2007)
Temporal encoding and homeostatic control in the IKK-IkB-NF-kB

Advisors: Alexander Hoffmann
| Shankar Subramaniam
Library
| Abstract
Leah Barrera Ph.D., Bioinformatics (2007)
Genome-wide mapping and analysis of mammalian promoters

Advisors: Bing Ren
| Philip Bourne
Library
| Abstract
Andrew Joyce Ph.D., Bioinformatics (2007)
Modeling and analysis of the e. coli transcriptional regulatory network: an assessment of its properties, plasticity and role in adaptive evolution

Advisors: Bernhard Palsson
| Bing Ren
Library
| Abstract
Ann Thuy Mongan (Thuy Vo) Ph.D., Bioinformatics (2007)
Systems Analysis of Engergy Metabolism Elucidates the Roles of Mitochondria in Human Health and Disease

Advisors: Bernhard Palsson
| Andrew McCulloch
Library
| Abstract
Stephen Tanner Ph.D., Bioinformatics (2007)
Efficient and Accurate Bioinformatics Algorithms for Peptide Mass Spectrometry

Advisors: Vineet Bafna
| Julian Schroeder
Library
| Abstract

2006

John Mongan Ph.D., Bioinformatics (2006)
Implicit Solvent Method Development and Application: Fast Molecular Surfaces, Constant pH and Accelerated Dynamics, and Rational Drug Design

Advisors: Andrew McCammon
| Gary Huber
Library
| Abstract
Coleman Mosley Ph.D., Bioinformatics (2006)
Global Views of Human Genetic Variation: Single Nucleotide Polumorphises (SNPs) Effects and their Random Nature

Advisors: Nicholas Schork
| Daniel O'Connor
Library
| Abstract
Degui Zhi Ph.D., Bioinformatics (2006)
Discovery and Analysis of mosaic arrangements in biological squesces and structures

Advisors: Pavel Pevzner
| William Loomis
Library
| Abstract

2005

Albert Hsiao Ph.D., Bioengineering with a specialization in Bioinformatics (2005)
Comparative functional genomics of energy metabolism and insulin resistance in mammalian systems

Advisors: Shankar Subramaniam
| Jerrold Olefsky
Library
| Abstract
Jason Papin Ph.D., Bioengineering with a specialization in Bioinformatics (2005)
Systems Analysis of Cellular Signaling Networks

Advisors: Bernhard Palsson
| Jerrold Olefsky
Library
| Abstract
Nathan Price Ph.D., Bioengineering with a specialization in Bioinformatics (2005)
Unbiased Assessment of Genome-Scale Metabolic Network States

Advisors: Bernhard Palsson
| Shankar Subramaniam
Library
| Abstract

2004

Iman Famili Ph.D., Bioengineering with a specialization in Bioinformatics (2004)
Systemic analysis of the stoichiometric matrix and kinetic characterization of metabolic networks.

Advisors: Bernhard Palsson
| Shankar Subramaniam
Library
| Abstract
Markus Herrgard Ph.D., Bioengineering with a specialization in Bioinformatics (2004)
Reconstruction and Systems Analysis of Genome-Scale Metabolic and Regulatory Networks inSaccharomyces cerevisiae

Advisors: Bernhard Palsson
| Shankar Subramaniam
Library
| Abstract

2003

Markus Covert Ph.D., Bioengineering with a specialization in Bioinformatics (2003)
Transcriptional Regulation in Escherichia coli: A Systems Biology Approach

Advisors: Bernhard Palsson

Library
| Abstract