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.


Fatemeh Amrollahi

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

Thesis: Generalizeable Risk Predictive Deep Learning Models

Abstract: Link

Advisor(s): Shamim Nemati , Gabriel Wardi
Website

Email: earmingo@ucsd.edu

Erick Armingol

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Deciphering Patterns of Cell–Cell Interactions and Communication in Multicellular Organizations

Abstract: Link

Advisor(s): Nathan E. Lewis , Gene Yeo
Website

Email: hmbagdha@ucsd.edu

Hratch Baghdassarian

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Understanding How Context Influences Function Across Biological Scales in Multicellular Mammalian Systems

Abstract: Link

Advisor(s): Nathan E. Lewis , Terence Hwa
Email: ochapman@ucsd.edu

Owen Chapman

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

Thesis: Inter- and intratumoral heterogeneity of circular extrachromosomal DNA in medulloblastoma and other pediatric cancers

Abstract: Link

Advisor(s): Jill Mesirov , Bing Ren
Email: rhillary@ucsd.edu
Website

Email: j6hyun@ucsd.edu

Jason Hyun

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Comparative Pangenomics: Finding structure in the endless diversity of microbial life

Abstract: Link

Advisor(s): Bernhard Palsson , Terry Gaasterland

Jihoon Kim

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

Thesis: Data Standardization, Federated Learning, and Informed Consent Algorithms and Tools to Honor Patient Privacy and Preferences in Clinical Research

Abstract: Link

Advisor(s): Lucila Ohno-Machado , Tsung-Ting Kuo

Rick Zhenzhi Li

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Deciphering genomic grammar in regulatory sequences

Abstract: Link

Advisor(s): Christopher Glass , Christopher Benner
Website

Email: ckmah@ucsd.edu

Clarence Mah

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Computational Frameworks for Functional Subcellular Analysis of Spatial Transcriptomics Data

Abstract: Link

Advisor(s): Hannah Carter , Gene Yeo

Jonathan Pekar

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

Thesis: The zoonotic origins and molecular epidemiology of SARS-CoV-2

Abstract: Link

Advisor(s): Joel Wertheim , Siavash Mirarab
Website

Email: y8qin@ucsd.edu

Yue Qin

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Towards an in silico cell

Abstract: Link

Advisor(s): Trey Ideker , Jill Mesirov

Eleonora Rachtman

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Alignment-free genomic distance estimation: from conventional methods to machine learning

Abstract: Link

Advisor(s): Siavash Mirarab , Vineet Bafna

Gibraan Rahman

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Computational and Statistical Methods for Extracting Biological Signal from High-Dimensional Microbiome Data

Abstract: Link

Advisor(s): Rob Knight , Pieter Dorrestein
Email: cew003@ucsd.edu

Cynthia Wu

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Interrogating the effect of variation in trans-acting factors

Abstract: Link

Advisor(s): Melissa Gymrek , Alon Goren
Email: f5yuan@ucsd.edu

Nancy Yuan

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

Thesis: Using Machine Learning to Elucidate Disease Heterogeneity and Improve Prognostication in Patients with COPD

Abstract: Link

Advisor(s): Terry Gaasterland , Tsung-Ting Kuo
Email: jlz014@ucsd.edu

Jessica Zhou

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Revealing translational and fundamental insights via computational analysis of single-cell sequencing data

Abstract: Link

Advisor(s): Graham McVicker , Bing Ren
Email: jiz509@eng.ucsd.edu

Jingtian Zhou

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Analysis of 3D Genome Structure in Single Cells

Abstract: Link

Advisor(s): Joseph Ecker , Eran Mukamel

Email: garmstro@ucsd.edu

George Armstrong

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Benchmarking and Acceleration of Machine Learning and Analytics Pipelines for Large Microbiome Datasets

Abstract: Link

Advisor(s): Rob Knight , Pieter Dorrestein
Website

Email: kasthana@eng.ucsd.edu

Kanishk Asthana

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Wei Wang , Bing Ren
Website

Email: balaban@ucsd.edu

Metin Balaban

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Siavash Mirarab , Vineet Bafna

Bokan Bao

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

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

Email: abzikadze@ucsd.edu

Andrey Bzikadze

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Pavel Pevzner , Melissa Gymrek
Website

Email: andreabcastro@ucsd.edu

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: Link

Advisor(s): Hannah Carter , Ludmil Alexandrov
Website

Email: Nathaniel.P.DelosSantos@jacobs.ucsd.edu

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: Link

Advisor(s): Christopher Benner , Melissa Gymrek
Website

Email: edahi@eng.ucsd.edu

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: Link

Advisor(s): Anjana Rao , Ferhat Ay
Email: msl043@ucsd.edu

Miin Lin

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

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

Email: cmartino@ucsd.edu

Cameron Martino

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Tracking Microbial Communities Across Human Development in Response to Disturbance and Restoration

Abstract: Link

Advisor(s): Rob Knight , Pieter Dorrestein

Robert Morey

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Understanding trophoblast development using human embryonic stem cells

Abstract: Link

Advisor(s): Louise Laurent , Melissa Gymrek
Email: dnachman@ucsd.edu

Daniela Nachmanson

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Olivier Harismendy , Ludmil Alexandrov

Kivilicim Ozturk

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Hannah Carter , Prashant Mali

Timofey Prodanov

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Vikas Bansal , Melissa Gymrek
Website

Email: michelle.ragsac@gmail.com

Michelle Franc Ragsac

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Decoding the genomic regulatory syntax driving notochord development

Abstract: Link

Advisor(s): Emma Farley , Terry Gaasterland
Email: isshamie@ucsd.edu

Isaac Shamie

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Using Emerging Next-Generation Sequencing Technologies to Enhance the Lifecycle of Biopharmaceuticals

Abstract: Link

Advisor(s): Nathan E. Lewis , Christopher Benner

Chao Zhang

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Siavash Mirarab , Pavel Pevzner
Email: liz227@ucsd.edu

Lina Zheng

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: New insights into 3D chromatin organization and function

Abstract: Link

Advisor(s): Wei Wang , Gene Yeo

Email: aaylward@eng.ucsd.edu

Anthony Aylward

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Kyle Gaulton , Dorothy Sears

Kevin Blansit

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Albert Hsiao
Website

Email: pfiaux@ucsd.edu

Patrick Fiaux

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Graham McVicker , Bing Ren
Website

Email: jluebeck@ucsd.edu

Jens Luebeck

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Reconstructing and Profiling Extrachromosomal DNA

Abstract: Link

Advisor(s): Vineet Bafna , Julie Law
Website

Email: ileenamitra@eng.ucsd.edu

Ileena Mitra

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Identifying and characterizing de novo tandem repeat mutations and their contribution to autism spectrum disorders

Abstract: Link

Advisor(s): Melissa Gymrek
Website

Email: pphaneuf@ucsd.edu

Patrick Phaneuf

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Bernhard Palsson , Nathan E. Lewis
Email: sjroth@eng.ucsd.edu

Samuel Roth

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Christopher Benner , Sven Heinz

Argus Athanas-Crannell

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

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

Email: bbehsaz@ucsd.edu

Bahar Behsaz

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Scalable Computational Methods for Discovering Novel Natural Products

Abstract: Link

Advisor(s): Pavel Pevzner , Rob Knight

Arjun Chandrasekhar

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Saket Navlakha , Glenn Tesler

Michelle Dow

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

Thesis: Integrative Multi-omics Analysis to Understand Cancer and Anticancer Therapy

Abstract: Link

Advisor(s): Hannah Carter

Yingxiang Huang

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

Thesis: Preservation of Patient Level Privacy : Federated Classification and Calibration Models

Abstract: Link

Advisor(s): Lucila Ohno-Machado
Website

Email: bkellman@ucsd.edu
Email: jmccorri@eng.ucsd.edu

Jamison McCorrison

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Exploitation of Metadata in Molecular Genomics Studies

Abstract: Link

Advisor(s): Nicholas Schork , Vikas Bansal

Website

Email: mkrdonovan@gmail.com

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: Link

Advisor(s): Kelly Frazer

Rongxin Fang

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Single Cell Analysis of Chromatin Accessibility

Abstract: Link

Advisor(s): Bing Ren , Vineet Bafna
Email: rforeman@eng.ucsd.edu

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: Link

Advisor(s): Scott Rifkin , Roy Wollman

William Greenwald

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Exploring the Regulatory Genome and Functional Genetic Variation

Abstract: Link

Advisor(s): Kelly Frazer
Email: nlhepler@gmail.com

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: Link

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

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: Link

Advisor(s): Anjana Rao , Vineet Bafna
Email: jil340@eng.ucsd.edu

Jia Lu

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Understanding cis-Regulatory Activities with Evolutionary Epigenomic Analyses

Abstract: Link

Advisor(s): Sheng Zhong , Bing Ren
Website

Email: smollah@wustl.edu

Shamim Mollah

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Shankar Subramaniam , Vineet Bafna
Website

Email: niema@ucsd.edu

Niema Moshiri

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Mathematical Modeling of Viral Evolution and Epidemiology

Abstract: Link

Advisor(s): Siavash Mirarab , Pavel Pevzner
Website

Email: vqngo@ucsd.edu

Vu Ngo

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Interplays between DNA motifs and epigenetic elements

Abstract: Link

Advisor(s): Wei Wang
Email: yuq003@ucsd.edu

Yunjiang Qiu

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Bing Ren , Sheng Zhong
Email: amraman@post.harvard.edu

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: Link

Advisor(s): Bing Ren , Kun Zhang
Website

Email: jsauls@ucsd.edu

John Sauls

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Physiological Orchestration in Bacteria

Abstract: Link

Advisor(s): Suckjoon Jun , Terence Hwa
Website

Email: ucsd@phageghost.net

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: Link

Advisor(s): Christopher Glass , Wei Wang
Website

Email: btsui@ucsd.edu

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: Link

Advisor(s): Hannah Carter , Jill Mesirov

Mengchi Wang

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Deciphering the Genetic Code of DNA Methylation

Abstract: Link

Advisor(s): Wei Wang , Bing Ren
Email: cjwei@eng.ucsd.edu
Email: jeyuan@eng.ucsd.edu

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: Link

Advisor(s): Pavel Pevzner , Bing Ren

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: Link

Advisor(s): Vineet Bafna , Michael Hogarth

Yuan Zhao

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Bing Ren , Wei Wang

Website

Email: lebernstein@ucsd.edu

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: Link

Advisor(s): Nuno Bandeira , Steve Briggs

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: Link

Advisor(s): Melissa Gymrek , Vineet Bafna
Website

Email: jkh013@ucsd.edu

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: Link

Advisor(s): Trey Ideker
Website

Email: ljamal@eng.ucsd.edu

Leen Jamal

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Gene Yeo
Website

Email: jdjensen@ucsd.edu
Website

Email: ramarty@ucsd.edu

Rachel Marty

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: The Role of MHC Variation in Tumor Progression

Abstract: Link

Advisor(s): Hannah Carter
Website

Email: nmih@ucsd.edu

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: Link

Advisor(s): Bernhard Palsson , Philip Bourne
Website

Email: gpratt@ucsd.edu

Gabriel Pratt

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Methods for Integrative Analysis of RNA Binding Proteins

Abstract: Link

Advisor(s): Gene Yeo , Sheng Zhong
Website

Email: jenhantao@gmail.com

Jenhan Tao

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Christopher Glass , Christopher Benner
Website

Email: james.yurkovich@systemsbiology.org

James Yurkovich

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Bernhard Palsson , Jeff Hasty

Email: kbhutani@ucsd.edu

Kunal Bhutani

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Limiting Biases in Biological Data Analysis by Pooling Information

Abstract: Link

Advisor(s): Nicholas Schork , Vineet Bafna
Website

Email: obotvinn@ucsd.edu

Olga Botvinnik

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Computational analysis of single-cell alternative splicing

Abstract: Link

Advisor(s): Gene Yeo , Sheng Zhong
Website

Email: ddiep@ucsd.edu

Dinh Diep

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Kun Zhang , Vineet Bafna
Website

Email: kuding@ucsd.edu

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: Link

Advisor(s): Nicholas Schork , Bing Ren
Email: yuh026@ucsd.edu

Yupeng He

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Joseph Ecker , Wei Wang
Email: jkl055@ucsd.edu

Joanne Liu

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Predicting Growth Optimization Strategies with Metabolic/Expression Models

Abstract: Link

Advisor(s): Karsten Zengler , Nathan E. Lewis
Email: w2wei@ucsd.edu

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: Link

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

Jason Yao

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Modeling and Measuring Dynamic Cellular Signaling States

Abstract: Link

Advisor(s): Roy Wollman , Shankar Subramaniam
Email: mkyu003@ucsd.edu

Michael Yu

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Hierarchical Models of Biological Systems

Abstract: Link

Advisor(s): Trey Ideker , Christopher Glass

Website

Email: cdeboeve@ucsd.edu

Christopher DeBoever

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Kelly Frazer , Trey Ideker
Website

Email: the.andrew.gross@gmail.com

Andrew Gross

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Understanding disease through data driven biology

Abstract: Link

Advisor(s): Trey Ideker , Kelly Frazer
Email: edlevy@ucsd.edu

Eric Levy

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Lucila Ohno-Machado , Olivier Harismendy
Email: k1mukund@ucsd.edu

Kavitha Mukund

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Systems Biology Approaches to Discerning Striated Muscle Pathologies

Abstract: Link

Advisor(s): Shankar Subramaniam , Richard Lieber
Email: cwhite@ucsd.edu

Cory White

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Investigations of HIV Latency Through Transcriptomic and Proteomic Profiling

Abstract: Link

Advisor(s): Doug Richman , David Smith
Email: chia.yi.wu.tw@gmail.com

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: Link

Advisor(s): Scott Rifkin , Jeff Hasty

Website

Email: karmelallison@ucsd.edu

Karmel Allison

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Enhancers and Transcriptional Regulation in CD4+ T Cell

Abstract: Link

Advisor(s): Christopher Glass , Stephen Hedrick
Email: sbliven@ucsd.edu

Spencer Bliven

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Philip Bourne , Milton Saier
Email: stephano.rb@gmail.com

Stefano Bonissone

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Deconvolution of immunome and degradome repertoires using computational proteomics

Abstract: Link

Advisor(s): Pavel Pevzner , Steve Briggs
Website

Email: maqiwinner@gmail.com

Qi Ma

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Understanding the Functional Properties of Enhancers

Abstract: Link

Advisor(s): Michael Rosenfeld , Gene Yeo
Email: dariamerkurjev@gmail.com

Daria Merkurjev

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Understanding Enhancer Role in the Transcriptional Response

Abstract: Link

Advisor(s): Michael Rosenfeld , Wei Wang
Email: ejobrien@ucsd.edu

Edward J O'Brien

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Bernhard Palsson , Philip Bourne
Email: msmith@ucsd.edu
Email: a1xt06@gmail.com

Alex Thomas

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Moving Towards Interpretable Mechanisms in Human Systems Biology

Abstract: Link

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

Email: gbean@ucsd.edu

Gordon Bean

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Trey Ideker , Christopher Woelk
Email: yuc023@ucsd.edu

Winston Chen

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Deciphering Molecular Mechanism of Adverse Reactions of Drugs

Abstract: Link

Advisor(s): Ruben Abagyan , Grace Kuo
Email: jdavistu@ucsd.edu

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: Link

Advisor(s): Alexander Hoffmann , Gene Yeo

Stephen Federowicz

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Bernhard Palsson , Wei Wang
Website

Email: shuelga@gmail.com
Email: boyko@ucsd.edu

Boyko Kakaradov

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Gene Yeo , Charles Elkan
Website

Email: jlerman44@gmail.com

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: Link

Advisor(s): Bernhard Palsson , Milton Saier
Email: adp002@ucsd.edu

Anand Patel

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Genome Rearrangements in Cancer and Human Genomes

Abstract: Link

Advisor(s): Vineet Bafna , Yu-Tsueng Liu
Email: rronen@ucsd.edu

Roy Ronen

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Identifying and Characterizing the Genomic Signatures of Natural Selection

Abstract: Link

Advisor(s): Vineet Bafna , Gabriel Haddad
Email: psamayoa@gmail.com

Philip Samayoa

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Applications of synthetic biology inspired by natural bacterial functionality

Abstract: Link

Advisor(s): Jeff Hasty , Ruth Williams
Website

Email: schultzmattd@gmail.com

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: Link

Advisor(s): Joseph Ecker , Vineet Bafna
Email: sselvaraj@ucsd.edu

Siddarth Selvaraj

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Bing Ren , Vineet Bafna
Email: maxshok@gmail.com

Maxim Shokhirev

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Alexander Hoffmann , Andrew McCulloch

Email: vipul.bhargava@gmail.com

Vipul Bhargava

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Quantitative Transcriptomics From Limiting Amounts of mRNA

Abstract: Link

Advisor(s): Shankar Subramaniam , Mark Mercola
Email: mckinsel@ucsd.edu

Marcus Kinsella

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Computational Techniques to Investigate Structural Variation

Abstract: Link

Advisor(s): Vineet Bafna , Kelly Frazer
Email: ploriaux@ucsd.edu

Paul Loriaux

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Steady State Control of the Cellular Response to Stress

Abstract: Link

Advisor(s): Alexander Hoffmann , Pavel Pevzner
Email: nirajago@ucsd.edu

Nisha Rajagopal

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Navigating the Human Epigenome through Random Forests

Abstract: Link

Advisor(s): Bing Ren , Wei Wang
Email: nudpa@ucsd.edu

Nitin Udpa

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: The Genetic Basis of Hypoxia Tolerance

Abstract: Link

Advisor(s): Vineet Bafna , Kelly Frazer
Email: bugouzhi@gmail.com
Email: yiwen@ucsd.edu

Yi Wen

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Serial Post-Transcriptional Splicing Establishes Negative Feedback Regulation in HIV-1 Expression

Abstract: Link

Advisor(s): Leor Weinberger , Doug Richman
Email: yostshawn@gmail.com

Shawn Yost

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Accurate Identification of Somatic Mutations in Clinical Tumor Specimens

Abstract: Link

Advisor(s): Kelly Frazer , Vineet Bafna

Email: jocelyne@ucsd.edu

Jocelyne Bruand

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Computational Tools for Analysis of Mass spectrometry Imaging Data

Abstract: Link

Advisor(s): Vineet Bafna , Eduardo Macagno
Website

Email: roger.chang@einsteinmed.edu

Roger Chang

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Bernhard Palsson , Philip Bourne
Email: eke@ucsd.edu

Eugene Ke

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Shankar Subramaniam , Inder Verma
Email: nagarajan.harish@gmail.com

Harish Nagarajan

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Electromicrobiiology: A Systems Perspective

Abstract: Link

Advisor(s): Bernhard Palsson , Milton Saier
Email: joperez@ucsd.edu

Josué Pérez-Santiago

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Doug Richman , Kun Zhang

Jason Chan

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Richard Kolodner , Trey Ideker
Email: c3cheng@ucsd.edu

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: Link

Advisor(s): Alexander Hoffmann , Charles Elkan
Email: mgersten@ucsd.edu

Merril Gersten

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Shankar Subramaniam , Gabriel Haddad

Lukasz Szpankowski

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Lawrence Goldstein , Shankar Subramaniam

Website

Email: sourav@gmail.com

Sourav Bandyopadhyay

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Integrating Physical and Genetic Interaction Networks for Biological Discovery

Abstract: Link

Advisor(s): Trey Ideker , Vineet Bafna

Mary Budagyan (Mary Pacold)

Degree Conferred: Ph.D. Bioinformatics

Thesis: Detecting and Characterizing HIV-1 Intaclade Dual Infection

Abstract: Link

Advisor(s): Doug Richman , Glenn Tesler

Han-Yu Chuang

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract: Link

Advisor(s): Trey Ideker , Thomas Kipps

Jan Schellenberger

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Monte Carlo Sampling in Systems Biology

Abstract: Link

Advisor(s): Bernhard Palsson , Vineet Bafna

Ruben Valas

Degree Conferred: Ph.D. Bioinformatics

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

Abstract: Link

Advisor(s): Philip Bourne , William Loomis

Email: abashir@pacificbiosciences.com
Email: ngupta@ucsd.edu
Email: garyhon1@gmail.com

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: Link

Advisor(s): Bing Ren , Wei Wang
Email: jsuchit@ucsd.edu

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: Link

Advisor(s): Cornelis Murre , Maho Niwa
Email: kelleyRyanM@gmail.com

Ryan M. Kelley

Degree Conferred: Ph.D. Bioinformatics

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

Abstract: Link

Advisor(s): Trey Ideker , Vineet Bafna
Email: jlrflores@gmail.com
Website

Email: ines.thiele@googlemail.com
Email: noahaz@gmail.com

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: Link

Advisor(s): Vineet Bafna , Eleazar Eskin

Email: cbenner@ucsd.edu

Christopher Benner

Degree Conferred: Ph.D. Bioinformatics

Thesis: Identification of a Conserved Periodic Promoter Structure in Metazoans

Abstract: Link

Advisor(s): Christopher Glass , Shankar Subramaniam
Email: kristinebriedis@gmail.com
Email: mchang@scripps.edu
Email: meday2001@gmail.com
Website

Email: samuel.payne@gmail.com
Email: silpasuthram@yahoo.com
Email: elainet@mccammin.ucsd.edu

Elaine Thompson

Degree Conferred: Ph.D. Bioinformatics

Thesis: Characterizing Protein Structures by Surface Mapping

Abstract: Link

Advisor(s): Lynn Ten Eyck , Vineet Bafna

Email: dbarken@gmail.com

Derren Barken

Degree Conferred: Ph.D. Bioinformatics

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

Abstract: Link

Advisor(s): Alexander Hoffmann , Shankar Subramaniam
Email: leahob@gmail.com

Leah Barrera

Degree Conferred: Ph.D. Bioinformatics

Thesis: Genome-wide mapping and analysis of mammalian promoters

Abstract: Link

Advisor(s): Bing Ren , Philip Bourne
Email: stanner@illumina.com

Stephen Tanner

Degree Conferred: Ph.D. Bioinformatics

Thesis: Efficient and Accurate Bioinformatics Algorithms for Peptide Mass Spectrometry

Abstract: Link

Advisor(s): Vineet Bafna , Julian Schroeder

Email: cmosley@ucsd.edu
Website

Email: zhidegui@gmail.com

Email: alhsiao@stanford.edu

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: Link

Advisor(s): Shankar Subramaniam , Jerrold Olefsky
Email: papin@virginia.edu

Jason Papin

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

Thesis: Systems Analysis of Cellular Signaling Networks

Abstract: Link

Advisor(s): Bernhard Palsson , Jerrold Olefsky
Email: ndprice@illinois.edu

Nathan Price

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

Thesis: Unbiased Assessment of Genome-Scale Metabolic Network States

Abstract: Link

Advisor(s): Bernhard Palsson , Shankar Subramaniam

Email: ifamili@gtlifesciences.com

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: Link

Advisor(s): Bernhard Palsson , Shankar Subramaniam
Website

Email: markus.herrgard@gmail.com

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: Link

Advisor(s): Bernhard Palsson , Shankar Subramaniam

Email: mcovert@stanford.edu

Markus Covert

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

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

Abstract: Link

Advisor(s): Bernhard Palsson