Alumni

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) to search for UC San Diego Bioinformatics dissertations.


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

Advisor(s): Bing Ren

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

Current Employer: 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

Current Employer: Illumina, Bioinformatics scientist

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

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

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

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

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

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

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

Current Employer: 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

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

Current Employer: 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

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

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

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

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

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

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

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

Current Employer: 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

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

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

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

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

Current Employer: 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

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

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

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

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

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

Current Employer: 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

Current Employer: 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

Current Employer: 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

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

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

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

Current Employer: 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

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

Current Employer: 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

Current Employer: 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

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

Current Employer: 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

Current Employer: 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

Current Employer: Harvard Medical School, Postdoctoral Fellow

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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: University of California, 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: J. Craig Venter Institute, Bioinformatics Engineer

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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: Illumina, Bioinformatics Scientist

Coleman Mosley

Coleman Mosley

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

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

Current Employer: 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

Current Employer: University of Alabama, Asst 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: 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

Current Employer: Stanford, Asst Professor