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.
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
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
Chien-Ju Chen
Degree Conferred: Ph.D. Bioinformatics and Systems Biology Thesis: Decoding Amplified targeted Transcripts with Fluorescence in situ Hybridization (DART-FISH) reveals cellular heterogeneity of human cerebral cortex in space Abstract: Link Advisor(s): Kun Zhang , Eran Mukamel
Email: rhillary@ucsd.edu
Ryan Hillary
Degree Conferred: Ph.D. Bioinformatics and Systems Biology Thesis: Deciphering Principles of Regulatory Element Communication through Analysis of Nascent Transcription Dynamics Abstract: Link Advisor(s): Christopher Benner , Sven HeinzJason 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
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
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
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: oshanta@ucsd.edu
Omar Shanta
Degree Conferred: Ph.D. Bioinformatics and Systems Biology Thesis: Genome-wide association of copy number variants across six major psychiatric disorders reveals genotype-phenotype relationships of rare variants Abstract: Link Advisor(s): Jonathan Sebat , Joseph GleesonJames Sorrentino
Thesis: Systems methods for the discovery of coordinated host proteome and glycoproteome response in infectious diseases using mass spectrometry Abstract: Link Advisor(s): Nathan E. Lewis , Jeffrey Esko
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: 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 DorresteinKanishk 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
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
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
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
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
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
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
Jens Luebeck
Degree Conferred: Ph.D. Bioinformatics and Systems Biology Thesis: Reconstructing and Profiling Extrachromosomal DNA Abstract: Link Advisor(s): Vineet Bafna , Julie LawIleena 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
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
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
Benjamin Kellman
Degree Conferred: Ph.D. Bioinformatics and Systems Biology Thesis: Essentiality, Biosynthesis, and Prediction of Glycosylation: A genetic and metabolic encoding of intercellular communication augmentation Abstract: Link Advisor(s): Nathan E. Lewis , Hannah Carter
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
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
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
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 PevznerVu 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
John Sauls
Degree Conferred: Ph.D. Bioinformatics and Systems Biology Thesis: Physiological Orchestration in Bacteria Abstract: Link Advisor(s): Suckjoon Jun , Terence Hwa
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 WangBrian 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
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: Link Advisor(s): Kun Zhang , Vineet Bafna
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
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
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: Link Advisor(s): Shankar Subramaniam , Shu Chien
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
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
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
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: Link Advisor(s): Jill Mesirov , Pablo Tamayo
Rachel Marty
Degree Conferred: Ph.D. Bioinformatics and Systems Biology Thesis: The Role of MHC Variation in Tumor Progression Abstract: Link Advisor(s): Hannah CarterNathan 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
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
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 BennerJames 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 HastyKai Zhang
Degree Conferred: Ph.D. Bioinformatics and Systems Biology Thesis: Novel Network-Based Integrated Analyses of Multi-Omics Data Reveal New Insights into CD8+ T Cell Differentiation and Mouse Embryogenesis Abstract: Link Advisor(s): Wei Wang , Pavel Pevzner
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 BafnaOlga 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
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
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 MethylationAbstract: 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
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
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
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: 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
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
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
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: Link Advisor(s): Joseph Gleeson , Vineet Bafna
Email: msmith@ucsd.edu
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: Link Advisor(s): Sergei L. Kosakovsky Pond , Doug Richman
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
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: Link Advisor(s): Gene Yeo , Christopher Woelk
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
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
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
Jian Wang
Degree Conferred: Ph.D. Bioinformatics and Systems Biology Thesis: Expanding the toolbox of tandem mass spectrometry with algorithms to identify mass spectra from more than one peptide Abstract: Link Advisor(s): Philip Bourne , Pieter Dorrestein
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
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
Julio Ng
Degree Conferred: Ph.D. Bioinformatics and Systems Biology Thesis: Computational Mass Spectrometry: Algorithms for Identification of Peptides not present in Protein Databases Abstract: Link Advisor(s): Pavel Pevzner , Pieter Dorrestein
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
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
Ali Bashir
Degree Conferred: Ph.D. Bioinformatics Thesis: Computational Methods for Analyzing and Detecting Genomic Structural Variation: Applications to Cancer Abstract: Link Advisor(s): Vineet Bafna , Pavel Pevzner
Email: ngupta@ucsd.edu
Nitin Gupta
Degree Conferred: Ph.D. Bioinformatics and Systems Biology Thesis: Computational and Comparative Proteogenomics: Annotating Genomes and Proteomes using Tandem Mass Spectrometry Abstract: Link Advisor(s): Pavel Pevzner , Steve Briggs
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
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: Link Advisor(s): Daniel O'Connor , Shankar Subramaniam
Ines Thiele
Degree Conferred: Ph.D. Bioinformatics Thesis: A Stoichiometric Model of E. Coli's Macromolecular Synthesis Machinery and its Integration with MetablismAbstract: Link Advisor(s): Bernhard Palsson , Steve Briggs
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
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: Link Advisor(s): Philip Bourne , William Loomis
Email: mchaisso@gmail.com
Mark Chaisson
Degree Conferred: Ph.D. Bioinformatics Thesis: Combinatorial Methods for Compuational Genomics: Mammalian Phylogenetics Using Inversions and Fragment Assembly with Short Reads Abstract: Link Advisor(s): Pavel Pevzner , Vineet Bafna
Email: mchang@scripps.edu
Max Chang
Degree Conferred: Ph.D. Bioinformatics Thesis: Computational Structure-Based Methods to Anticipate HIV Drug Resistance Evolution and Accelerate Inhibitor Discovery Abstract: Link Advisor(s): Richard Belew , Lin Chao
Email: meday2001@gmail.com
Michele Day
Degree Conferred: Ph.D. Bioinformatics Thesis: Insights into the functionality and targeting of PKA regulatory subunity Rialpha Abstract: Link Advisor(s): Susan Taylor , Lynn Ten Eyck
Email: khutt@ucsd.edu
Kasey Hutt
Degree Conferred: Ph.D. Bioinformatics Thesis: High-throughput genomic assays: Applications and analysis of DSL technology and next-generation sequencing Abstract: Link Advisor(s): Michael Rosenfeld , Terry Gaasterland
Samuel Payne
Degree Conferred: Ph.D. Bioinformatics Thesis: Advances in Computational Mass Spectrometry: Phosphoprteomics and Proteogenomics Abstract: Link Advisor(s): Vineet Bafna , William Loomis
Email: silpasuthram@yahoo.com
Silpa Suthram
Degree Conferred: Ph.D. Bioinformatics Thesis: Understanding Cellular Function through the Analysis of Protein Interaction Networks Abstract: Link Advisor(s): Trey Ideker , Philip Bourne
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: arjoyce26@gmail.com
Andrew Joyce
Degree Conferred: Ph.D. Bioinformatics Thesis: Modeling and analysis of the e. coli transcriptional regulatory network: an assessment of its properties, plasticity and role in adaptive evolution Abstract: Link Advisor(s): Bernhard Palsson , Bing Ren
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: Link Advisor(s): Bernhard Palsson , Andrew McCulloch
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
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: Link Advisor(s): Andrew McCammon , Gary Huber
Email: cmosley@ucsd.edu
Coleman Mosley
Degree Conferred: Ph.D. Bioinformatics Thesis: Global Views of Human Genetic Variation: Single Nucleotide Polymorphisms' (SNPs) Effects and their Random Nature Abstract: Link Advisor(s): Nicholas Schork , Daniel O'Connor
Degui Zhi
Degree Conferred: Ph.D. Bioinformatics Thesis: Discovery and Analysis of mosaic arrangements in biological squesces and structures Abstract: Link Advisor(s): Pavel Pevzner , William Loomis
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 SubramaniamMarkus 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