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.
Email: cag104@ucsd.edu
Carlos Guzman
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Deciphering how regulatory DNA encodes regulatory function using massively parallel reporter assays
Abstract: Link
Advisor(s): Sven Heinz , Christopher Benner
Email: b2jia@ucsd.edu
Bojing Jia
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Multiplexed genome imaging and analysis
Abstract: Link
Advisor(s): Bing Ren , Albert Hsiao
Jennifer Nguyen
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Using multi-omic QTL analysis in fetal-like pancreatic progenitor cells to characterize diabetes-associated regulatory variants during early development
Abstract: Link
Advisor(s): Kelly Frazer , Lucila Ohno-Machado
Adam Officer
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Multimodal Data Integration Applied to Cancer Evolution and Signaling
Abstract: Link
Advisor(s): Pablo Tamayo , J. Silvio Gutkind
Anh Pham
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Strengthening Health Research Workflow for Research-Oriented Sharing, Predictive Modeling, and Cross-Institutional Collaboration
Abstract: Link
Advisor(s): Tsung-Ting Kuo , Lucila Ohno-Machado
Joe Solvason
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Elucidating Mechanisms Governing Enhancer Function in Development and Disease
Abstract: Link
Advisor(s): Emma Farley , Hannah Carter
Xingzhao Wen
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Interplay Between RNA and Chromatin: From Genome-Wide Mapping to Functional Implications
Abstract: Link
Advisor(s): Sheng Zhong , Bing Ren
Alexander Wenzel
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Expanding the applicability of gene set enrichment analysis with data-driven gene set refinement and adaptation for sparse data
Abstract: Link
Advisor(s): Jill Mesirov
Fatemeh Amrollahi
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Generalizeable Risk Predictive Deep Learning Models
Abstract: Link
Advisor(s): Shamim Nemati , Gabriel Wardi
Erick Armingol
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: Understanding How Context Influences Function Across Biological Scales in Multicellular Mammalian Systems
Abstract: Link
Advisor(s): Nathan E. Lewis , Terence Hwa
Next Position: MIT, Postdoctoral Associate
Email: ochapman@ucsd.edu
Owen Chapman
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Inter- and intratumoral heterogeneity of circular extrachromosomal DNA in medulloblastoma and other pediatric cancers
Abstract: Link
Advisor(s): Jill Mesirov , Bing Ren
Chien-Ju Chen
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: Deciphering Principles of Regulatory Element Communication through Analysis of Nascent Transcription Dynamics
Abstract: Link
Advisor(s): Christopher Benner , Sven Heinz
Jason Hyun
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 InformaticsThesis: 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 BiologyThesis: Deciphering genomic grammar in regulatory sequences
Abstract: Link
Advisor(s): Christopher Glass , Christopher Benner
Clarence Mah
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 InformaticsThesis: 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 BiologyThesis: Towards an in silico cell
Abstract: Link
Advisor(s): Trey Ideker , Jill Mesirov
Next Position: Broad Institute of MIT and Harvard, Eric and Wendy Schmidt Center Fellow
Eleonora Rachtman
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: 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 BiologyThesis: 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 Gleeson
James 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 BiologyThesis: 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 InformaticsThesis: Using Machine Learning to Elucidate Disease Heterogeneity and Improve Prognostication in Patients with COPD
Abstract: Link
Advisor(s): Terry Gaasterland , Tsung-Ting Kuo
Email: jiz509@eng.ucsd.edu
Jingtian Zhou
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Analysis of 3D Genome Structure in Single Cells
Abstract: Link
Advisor(s): Joseph Ecker , Eran Mukamel
Email: jlz014@ucsd.edu
Jessica Zhou
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Revealing translational and fundamental insights via computational analysis of single-cell sequencing data
Abstract: Link
Advisor(s): Graham McVicker , Bing Ren
Email: garmstro@ucsd.edu
George Armstrong
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Benchmarking and Acceleration of Machine Learning and Analytics Pipelines for Large Microbiome Datasets
Abstract: Link
Advisor(s): Rob Knight , Pieter Dorrestein
Kanishk Asthana
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: 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 BiologyThesis: 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 BiologyThesis: Human centromeres: from initial assemblies to structural and evolutionary analysis
Abstract: Link
Advisor(s): Pavel Pevzner , Melissa Gymrek
Andrea Castro
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Determinants for Effective Neoantigen Based Anti-Tumor Immune Response
Abstract: Link
Advisor(s): Hannah Carter , Ludmil Alexandrov
Nathaniel Delos Santos
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Score-based Transcription Factor Motif Enrichment Strategies for Analysis of Transcriptional Regulation of Immune Response
Abstract: Link
Advisor(s): Christopher Benner , Melissa Gymrek
Edahí González-Avalos
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: 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 BiologyThesis: 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 BiologyThesis: Understanding trophoblast development using human embryonic stem cells
Abstract: Link
Advisor(s): Louise Laurent , Melissa Gymrek
Next Position: University of California, San Diego, Computational and Data Science Research Specialist
Email: dnachman@ucsd.edu
Daniela Nachmanson
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: 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 BiologyThesis: 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 BiologyThesis: Decoding the genomic regulatory syntax driving notochord development
Abstract: Link
Advisor(s): Emma Farley , Terry Gaasterland
Next Position: Tiffany Amariuta, Postdoctoral Scholar
Email: isshamie@ucsd.edu
Isaac Shamie
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: 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 BiologyThesis: 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 BiologyThesis: 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 BiologyThesis: Advancing Cardiovascular MRI Acquisition Through Deep Convolutional Neural Network-Based Localization
Abstract: Link
Advisor(s): Albert Hsiao
Patrick Fiaux
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: Reconstructing and Profiling Extrachromosomal DNA
Abstract: Link
Advisor(s): Vineet Bafna , Julie Law
Next Position: Bafna Lab, Postdoctoral Scholar
Ileena Mitra
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: 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 BiologyThesis: 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 BiologyThesis: Leveraging Longitudinal Data for Predictive Modeling in Clinical and Mental Health Settings
Abstract: Link
Advisor(s): Nicholas Schork , Lucila Ohno-Machado
Bahar Behsaz
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: 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 InformaticsThesis: 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 InformaticsThesis: Preservation of Patient Level Privacy : Federated Classification and Calibration Models
Abstract: Link
Advisor(s): Lucila Ohno-Machado
Benjamin Kellman
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: Exploitation of Metadata in Molecular Genomics Studies
Abstract: Link
Advisor(s): Nicholas Schork , Vikas Bansal
Margaret Donovan
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: 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 BiologyThesis: 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 BiologyThesis: 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 BiologyThesis: Exploring the Regulatory Genome and Functional Genetic Variation
Abstract: Link
Advisor(s): Kelly Frazer
Next Position: Monoceros Biosystems, Bioinformatics Scientist
Email: nlhepler@gmail.com
Nicolaus Lance Hepler
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: HIV-1 Sequence Analysis: Approaches and Applications from Transmission Network Inference to Epitope Discovery
Abstract: Link
Advisor(s): Sergei L. Kosakovsky Pond , Doug Richman
Next Position: 10X Genomics, Staff Computational Biologist
Isaac Lopez Moyado
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: 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 BiologyThesis: Integrative Approaches to Targeting Chromatin Remodeling in Breast Cancer Therapy
Abstract: Link
Advisor(s): Shankar Subramaniam , Vineet Bafna
Next Position: Washington University School of Medicine in St. Louis, Assistant Professor
Niema Moshiri
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Mathematical Modeling of Viral Evolution and Epidemiology
Abstract: Link
Advisor(s): Siavash Mirarab , Pavel Pevzner
Next Position: UC San Diego Department of Computer Science & Engineering, Associate Teaching Professor
Vu Ngo
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Interplays between DNA motifs and epigenetic elements
Abstract: Link
Advisor(s): Wei Wang
Next Position: Cradle Genomics, Bioinformatics Scientist
Email: yuq003@ucsd.edu
Yunjiang Qiu
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: Genomic diversity of tumor and normal tissues revealed by single-nuclei RNA-seq computational analysis
Abstract: Link
Advisor(s): Bing Ren , Kun Zhang
Next Position: Fulcrum Therapeutics, Associate Scientist
John Sauls
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Physiological Orchestration in Bacteria
Abstract: Link
Advisor(s): Suckjoon Jun , Terence Hwa
Dylan Skola
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Understanding the Influence of Genetic Variation on Transcriptional Regulation in Humans and Other Metazoans
Abstract: Link
Advisor(s): Christopher Glass , Wei Wang
Next Position: Illumina, Bioinformatics Scientist
Brian Yik Tak Tsui
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Building bioinformatic tools for massive repurposing of multi-omic data in the Sequence Read Archive
Abstract: Link
Advisor(s): Hannah Carter , Jill Mesirov
Next Position: Illumina, Bioinformatics scientist
Mengchi Wang
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: Single Cell Phylogenetic Fate Mapping: Combining Microsatellite and Methylation Profiling for Retrospective Lineage Tracing
Abstract: Link
Advisor(s): Kun Zhang , Vineet Bafna
Next Position: Zhang Lab, Postdoctural Researcher
Email: jeyuan@eng.ucsd.edu
Jeffrey Yuan
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Genome Assembly of Long Error-Prone Reads Using De Bruijn Graphs and Repeat Graphs
Abstract: Link
Advisor(s): Pavel Pevzner , Bing Ren
Next Position: Illumina, Bioinformatics Scientist
Jing Zhang
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: 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 BiologyThesis: 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 BiologyThesis: 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
Next Position: CRISPR Therapeutics, Scientist
Laurence Bernstein
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Penalty-Based Dynamic Programming for the Identification of Post-Translational Modifications in Peptide Mass Spectra
Abstract: Link
Advisor(s): Nuno Bandeira , Steve Briggs
Next Position: Quest Diagnostics, Principal Software Engineer
Stephanie Feudjio Feupe
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Deep Characterization of the Contribution of Short Tandem Repeats Across Tissues
Abstract: Link
Advisor(s): Melissa Gymrek , Vineet Bafna
Justin Huang
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Applications of Network Propagation for the Discovery of Candidate Genes in Human Disease
Abstract: Link
Advisor(s): Trey Ideker
Next Position: MD Anderson Cancer Center TRACTION, Institute Research Investigator: Systems Biology
Leen Jamal
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: A Journey Through the Brain & Heart and Into The Machine
Abstract: Link
Advisor(s): Gene Yeo
Next Position: Viastat, Inc, Data Scientist
James Jensen
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Toward precision medulloblastoma treatment through integrated functional and genomic analysis of realistic preclinical models
Abstract: Link
Advisor(s): Jill Mesirov , Pablo Tamayo
Next Position: Recursion Pharmaceuticals, Data Scientist
Rachel Marty
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: The Role of MHC Variation in Tumor Progression
Abstract: Link
Advisor(s): Hannah Carter
Next Position: Personalis, Inc, Bioinformatics Scientist
Nathan Mih
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Understanding genetic variation in the proteome: a multi-scale structural systems biology toolkit
Abstract: Link
Advisor(s): Bernhard Palsson , Philip Bourne
Next Position: Lygos, Inc, Software Engineer
Gabriel Pratt
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Methods for Integrative Analysis of RNA Binding Proteins
Abstract: Link
Advisor(s): Gene Yeo , Sheng Zhong
Next Position: TwinStrand Biosciences, Bioinformatics Scientist
Jenhan Tao
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Machine learning approaches for relating genomic sequence to enhancer activity and function
Abstract: Link
Advisor(s): Christopher Glass , Christopher Benner
Next Position: Illumina, Bioinformatics Scientist
Email: james.yurkovich@systemsbiology.org
James Yurkovich
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: The Systems Biology of Red Cell Metabolism: Physiology under Storage Conditions
Abstract: Link
Advisor(s): Bernhard Palsson , Jeff Hasty
Next Position: Institute for Systems Biology, Translational Research Fellow
Kai Zhang
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: Limiting Biases in Biological Data Analysis by Pooling Information
Abstract: Link
Advisor(s): Nicholas Schork , Vineet Bafna
Next Position: FVL59, Inc, Computational Scientist
Olga Botvinnik
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Computational analysis of single-cell alternative splicing
Abstract: Link
Advisor(s): Gene Yeo , Sheng Zhong
Next Position: Chan-Zuckerberg Biohub, Bioinformatics Data Scientist
Dinh Diep
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Novel molecular and bioinformatics approaches to investigate DNA methylation in human epigenome
Abstract: Link
Advisor(s): Kun Zhang , Vineet Bafna
Next Position: UC San Diego, Postdoctural Researcher
Kuan-Fu Ding
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Quantifying and Accommodating Heterogeneity in High Throughput Drug Response Studies
Abstract: Link
Advisor(s): Nicholas Schork , Bing Ren
Next Position: Sapiens Data Science, Chief Science Officer
Kemal Eren
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Understanding the evolution of HIV-1 Env through computational analysis and visualization of long-read amplicon sequences
Abstract: Link
Advisor(s): Joel Wertheim , Siavash Mirarab
Email: yuh026@ucsd.edu
Yupeng He
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: Predicting Growth Optimization Strategies with Metabolic/Expression Models
Abstract: Link
Advisor(s): Karsten Zengler , Nathan E. Lewis
Next Position: Biota Technology, Data Scientist
Email: w2wei@ucsd.edu
Wei Wei
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: 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 BiologyThesis: Modeling and Measuring Dynamic Cellular Signaling States
Abstract: Link
Advisor(s): Roy Wollman , Shankar Subramaniam
Next Position: Guavus, Research Data Scientist
Email: mkyu003@ucsd.edu
Michael Yu
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Hierarchical Models of Biological Systems
Abstract: Link
Advisor(s): Trey Ideker , Christopher Glass
Next Position: Toyota Technical Institute at Chicago, Research Assistant Professor
Christopher DeBoever
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Genetic regulation of RNA splicing and expression in cancer and stem cells
Abstract: Link
Advisor(s): Kelly Frazer , Trey Ideker
Next Position: Takeda, Computational Biology Scientist
Andrew Gross
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Understanding disease through data driven biology
Abstract: Link
Advisor(s): Trey Ideker , Kelly Frazer
Next Position: Illumina, Bioinformatics Scientist
Email: edlevy@ucsd.edu
Eric Levy
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Molecular immune signatures of T-cell infiltration in cancer
Abstract: Link
Advisor(s): Lucila Ohno-Machado , Olivier Harismendy
Next Position: Personalis, Senior Bioinformatics Scientist
Email: k1mukund@ucsd.edu
Kavitha Mukund
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: 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 BiologyThesis: 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 BiologyThesis: Enhancers and Transcriptional Regulation in CD4+ T Cell
Abstract: Link
Advisor(s): Christopher Glass , Stephen Hedrick
Next Position: Google Brain TensorFlow Team, Engineering Manager
Email: sbliven@ucsd.edu
Spencer Bliven
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Structure-preserving Rearrangements: Algorithms for Structural Comparison and Protein Analysis
Abstract: Link
Advisor(s): Philip Bourne , Milton Saier
Next Position: Paul Scherrer Institut PSI, Scientific Computing Engineer
Email: stephano.rb@gmail.com
Stefano Bonissone
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: Understanding the Functional Properties of Enhancers
Abstract: Link
Advisor(s): Michael Rosenfeld , Gene Yeo
Next Position: UCSD, Postdoctoral Fellow in Rosenfeld Lab
Email: dariamerkurjev@gmail.com
Daria Merkurjev
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: 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 BiologyThesis: Genomic structural characterization of the Greater Middle East to assist in the identification of disease variation
Abstract: Link
Advisor(s): Joseph Gleeson , Vineet Bafna
Next Position: GRAIL, Inc, Bioinformatics Scientist
Email: msmith@ucsd.edu
Martin Smith
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Increasing Biological Realism in Models of Sequence Evolution for Improved Statistical and Computational Performance
Abstract: Link
Advisor(s): Sergei L. Kosakovsky Pond , Doug Richman
Next Position: Pacific Biosciences, Staff Engineer: Primary Analysis
Email: a1xt06@gmail.com
Alex Thomas
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Moving Towards Interpretable Mechanisms in Human Systems Biology
Abstract: Link
Advisor(s): Nathan E. Lewis , Dorothy Sears
Next Position: C.H. Robinson, Principal Data Scientist
Email: gbean@ucsd.edu
Gordon Bean
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Development of experimental and computational tools for high-throughput microbial "omics"
Abstract: Link
Advisor(s): Trey Ideker , Christopher Woelk
Next Position: Illumina, Bionformatics Scientist
Email: yuc023@ucsd.edu
Winston Chen
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: Exploring the Mechanisms of pre-mRNA Splicing Using Mathematical Models of Coupled Transcription and Splicing
Abstract: Link
Advisor(s): Alexander Hoffmann , Gene Yeo
Next Position: OnRamp Bioinformatics, Vice President
Stephen Federowicz
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Elucidating mechanisms of transcriptional regulation at the genome-scale
Abstract: Link
Advisor(s): Bernhard Palsson , Wei Wang
Next Position: Inscripta, Inc, Senior Scientist: Computational Biology
Stephanie Huelga
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Comprehensive discovery and analysis of RNA binding protein-dependent post-transcriptional events in mammalian systems
Abstract: Link
Advisor(s): Gene Yeo , Christopher Woelk
Next Position: NuGEN, Data Analysis Scientist
Email: boyko@ucsd.edu
Boyko Kakaradov
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Statistical models for RNA biology: from single nucleotides to single cells
Abstract: Link
Advisor(s): Gene Yeo , Charles Elkan
Next Position: Deep Genomics, Senior Scientist
Joshua Lerman
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Genome-scale Models of Metabolism and Gene Expression: Construction and Use for Growth Phenotype Prediction
Abstract: Link
Advisor(s): Bernhard Palsson , Milton Saier
Next Position: Total New Energies USA, Inc. (seconded to Amyris Amyris, Inc.), Computational Biology Post-Doctoral Scientist
Email: adp002@ucsd.edu
Anand Patel
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Genome Rearrangements in Cancer and Human Genomes
Abstract: Link
Advisor(s): Vineet Bafna , Yu-Tsueng Liu
Next Position: Digital Proteomics, Chief Technology Officer
Email: rronen@ucsd.edu
Roy Ronen
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Identifying and Characterizing the Genomic Signatures of Natural Selection
Abstract: Link
Advisor(s): Vineet Bafna , Gabriel Haddad
Next Position: Data4Cure, Inc., VP Platform
Email: psamayoa@gmail.com
Philip Samayoa
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Applications of synthetic biology inspired by natural bacterial functionality
Abstract: Link
Advisor(s): Jeff Hasty , Ruth Williams
Next Position: Generation Bio, Vice President: Strategy and Portolio Development
Matthew Schultz
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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
Next Position: Human Longevity, Inc., Bioinformatics Scientist
Email: sselvaraj@ucsd.edu
Siddarth Selvaraj
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: Developing a multi-scale understanding of the B cell immune response
Abstract: Link
Advisor(s): Alexander Hoffmann , Andrew McCulloch
Next Position: Salk Institute for Biological Studies Integrative Genomics & Bioinoformatics Core, Director
Email: vipul.bhargava@gmail.com
Vipul Bhargava
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Quantitative Transcriptomics From Limiting Amounts of mRNA
Abstract: Link
Advisor(s): Shankar Subramaniam , Mark Mercola
Next Position: Janssen Research and Development LLC (Johnson and Johnson company) , Scientist
Email: mckinsel@ucsd.edu
Marcus Kinsella
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Computational Techniques to Investigate Structural Variation
Abstract: Link
Advisor(s): Vineet Bafna , Kelly Frazer
Next Position: Pacific Biosciences, Senior Engineer (Bioinformatics)
Email: ploriaux@ucsd.edu
Paul Loriaux
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Steady State Control of the Cellular Response to Stress
Abstract: Link
Advisor(s): Alexander Hoffmann , Pavel Pevzner
Next Position: Second Genome Inc, Lead Data Scientist
Email: nirajago@ucsd.edu
Nisha Rajagopal
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: The Genetic Basis of Hypoxia Tolerance
Abstract: Link
Advisor(s): Vineet Bafna , Kelly Frazer
Next Position: Illumina, Bioinformatics Scientist
Email: bugouzhi@gmail.com
Jian Wang
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: 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 BiologyThesis: 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 BiologyThesis: Computational Tools for Analysis of Mass spectrometry Imaging Data
Abstract: Link
Advisor(s): Vineet Bafna , Eduardo Macagno
Next Position: Illumina, Bioinformatics Scientist
Roger Chang
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Structural systems biology perspective on the metabolic impact of physicochemical stress
Abstract: Link
Advisor(s): Bernhard Palsson , Philip Bourne
Next Position: Albert Einstein College of Medicine, Assistant Professor of Systems and Computational Biology
Email: eke@ucsd.edu
Eugene Ke
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Insights from reconstructing cellular networks in transcription, stress and cancer
Abstract: Link
Advisor(s): Shankar Subramaniam , Inder Verma
Next Position: Salk Institute, Research Associate (Postdoc)
Email: nagarajan.harish@gmail.com
Harish Nagarajan
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Electromicrobiiology: A Systems Perspective
Abstract: Link
Advisor(s): Bernhard Palsson , Milton Saier
Next Position: Genomatica Inc., Research Scientist I, Computational Technologies
Email: joperez@ucsd.edu
Josué Pérez-Santiago
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: The Human Gut Microbiome: Characterization Challenges and HIV Disease Association
Abstract: Link
Advisor(s): Doug Richman , Kun Zhang
Next Position: UCSD, Postdoctoral Fellow
Jason Chan
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: Innate immune gene expression programs defined by both regulated mRNA synthesis and decay
Abstract: Link
Advisor(s): Alexander Hoffmann , Charles Elkan
Next Position: Broad Institute of MIT and Harvard, Postdoc in Aviv Regev's Lab
Email: mgersten@ucsd.edu
Merril Gersten
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Systems Analysis of Model Organisms in the Study of Human disease
Abstract: Link
Advisor(s): Shankar Subramaniam , Gabriel Haddad
Next Position: UCSD Dept Bioengineering, Postdoc
Julio Ng
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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 BiologyThesis: Coordination of Axonal Transport Revealed by Particle Tracking and Quantitative Immunogluorescence
Abstract: Link
Advisor(s): Lawrence Goldstein , Shankar Subramaniam
Next Position: Fluidigm, Scientist - R&D, New Technologies
Sourav Bandyopadhyay
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Integrating Physical and Genetic Interaction Networks for Biological Discovery
Abstract: Link
Advisor(s): Trey Ideker , Vineet Bafna
Next Position: Univerity of California, San Francisco, Assistant Professor
Mary Budagyan (Mary Pacold)
Degree Conferred: Ph.D. BioinformaticsThesis: Detecting and Characterizing HIV-1 Intaclade Dual Infection
Abstract: Link
Advisor(s): Doug Richman , Glenn Tesler
Next Position: Ion Torrent / Life Technologies, Product Manager, Informatics Applications
Han-Yu Chuang
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Pathway-based modeling and diagnosis of cancer development and progression
Abstract: Link
Advisor(s): Trey Ideker , Thomas Kipps
Next Position: Illumina, Bioinformatics Scientist
Jan Schellenberger
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Monte Carlo Sampling in Systems Biology
Abstract: Link
Advisor(s): Bernhard Palsson , Vineet Bafna
Next Position: ID Analytics, Scientist
Ruben Valas
Degree Conferred: Ph.D. BioinformaticsThesis: The Gospel According to LUCA (the last universal common ancestor)
Abstract: Link
Advisor(s): Philip Bourne , William Loomis
Next Position: UC San Diego (Bourne Lab), Postdoc
Email: abashir@pacificbiosciences.com
Ali Bashir
Degree Conferred: Ph.D. BioinformaticsThesis: Computational Methods for Analyzing and Detecting Genomic Structural Variation: Applications to Cancer
Abstract: Link
Advisor(s): Vineet Bafna , Pavel Pevzner
Next Position: Pacific Biosciences, Scientist
Email: ngupta@ucsd.edu
Nitin Gupta
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Computational and Comparative Proteogenomics: Annotating Genomes and Proteomes using Tandem Mass Spectrometry
Abstract: Link
Advisor(s): Pavel Pevzner , Steve Briggs
Next Position: University of California, San Diego (Aron Lab), Postdoc
Email: garyhon1@gmail.com
Gary Hon
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Understanding the global architecture of gene regulation in human cells through analysis of chromatin signatures
Abstract: Link
Advisor(s): Bing Ren , Wei Wang
Next Position: Ludwig Institute for Cancer Research, Postdoc
Email: jsuchit@ucsd.edu
Suchit Jhunjhunwala
Degree Conferred: Ph.D. Biology with a specialization in BioinformaticsThesis: The 3-D Structure of the Immunoglobulin Heavy Chain Locus:Implications for Long-Range Genomic Interactions
Abstract: Link
Advisor(s): Cornelis Murre , Maho Niwa
Next Position: Synthetic Genomics, Inc., Senior Bioinformatics Scientist
Email: kelleyRyanM@gmail.com
Ryan M. Kelley
Degree Conferred: Ph.D. BioinformaticsThesis: Analysis and integration of high-throughput biological data for pathway discovery
Abstract: Link
Advisor(s): Trey Ideker , Vineet Bafna
Next Position: Illumina, Bioinformatics Scienist 1
Email: jlrflores@gmail.com
Juan Lorenzo Rodriguez Flores
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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
Next Position: Ludwig Institute for Cancer Research, Postdoc
Ines Thiele
Degree Conferred: Ph.D. BioinformaticsThesis: A Stoichiometric Model of E. Coli's Macromolecular Synthesis Machinery and its Integration with Metablism
Abstract: Link
Advisor(s): Bernhard Palsson , Steve Briggs
Next Position: University of Iceland, Asst Professor
Email: noahaz@gmail.com
Noah Zaitlen
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: 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
Next Position: Harvard School of Public Health, Postdoc
Email: cbenner@ucsd.edu
Christopher Benner
Degree Conferred: Ph.D. BioinformaticsThesis: Identification of a Conserved Periodic Promoter Structure in Metazoans
Abstract: Link
Advisor(s): Christopher Glass , Shankar Subramaniam
Next Position: University of California, San Diego (Glass Lab), Postdoc
Email: kristinebriedis@gmail.com
Kristine Briedis
Degree Conferred: Ph.D. BioinformaticsThesis: The distribution and evolution of protein kinase and phospatase families in the three superkingdoms of life
Abstract: Link
Advisor(s): Philip Bourne , William Loomis
Next Position: University of California, San Diego (Bourne Lab), Postdoc
Email: mchaisso@gmail.com
Mark Chaisson
Degree Conferred: Ph.D. BioinformaticsThesis: Combinatorial Methods for Compuational Genomics: Mammalian Phylogenetics Using Inversions and Fragment Assembly with Short Reads
Abstract: Link
Advisor(s): Pavel Pevzner , Vineet Bafna
Next Position: Pacific Biosciences, Senior Algorithms Developer
Email: mchang@scripps.edu
Max Chang
Degree Conferred: Ph.D. BioinformaticsThesis: Computational Structure-Based Methods to Anticipate HIV Drug Resistance Evolution and Accelerate Inhibitor Discovery
Abstract: Link
Advisor(s): Richard Belew , Lin Chao
Next Position: TSRI, Postdoc
Email: meday2001@gmail.com
Michele Day
Degree Conferred: Ph.D. BioinformaticsThesis: Insights into the functionality and targeting of PKA regulatory subunity Rialpha
Abstract: Link
Advisor(s): Susan Taylor , Lynn Ten Eyck
Next Position: University of California, San Diego (Taylor Lab), Postdoc
Email: khutt@ucsd.edu
Kasey Hutt
Degree Conferred: Ph.D. BioinformaticsThesis: High-throughput genomic assays: Applications and analysis of DSL technology and next-generation sequencing
Abstract: Link
Advisor(s): Michael Rosenfeld , Terry Gaasterland
Next Position: University of California, San Diego (Rosenfeld Lab), Postdoc
Samuel Payne
Degree Conferred: Ph.D. BioinformaticsThesis: Advances in Computational Mass Spectrometry: Phosphoprteomics and Proteogenomics
Abstract: Link
Advisor(s): Vineet Bafna , William Loomis
Next Position: Brigham Young University, Associate Professor
Email: silpasuthram@yahoo.com
Silpa Suthram
Degree Conferred: Ph.D. BioinformaticsThesis: Understanding Cellular Function through the Analysis of Protein Interaction Networks
Abstract: Link
Advisor(s): Trey Ideker , Philip Bourne
Next Position: Stanford working w/ Dr. Atul Butte, Postdoc
Email: elainet@mccammin.ucsd.edu
Elaine Thompson
Degree Conferred: Ph.D. BioinformaticsThesis: Characterizing Protein Structures by Surface Mapping
Abstract: Link
Advisor(s): Lynn Ten Eyck , Vineet Bafna
Next Position: University of California, San Diego (Susan Taylor Lab), Postdoc
Email: dbarken@gmail.com
Derren Barken
Degree Conferred: Ph.D. BioinformaticsThesis: Temporal encoding and homeostatic control in the IKK-IkB-NF-kB
Abstract: Link
Advisor(s): Alexander Hoffmann , Shankar Subramaniam
Next Position: Prometheus, Bioinformatics Scientist
Email: leahob@gmail.com
Leah Barrera
Degree Conferred: Ph.D. BioinformaticsThesis: Genome-wide mapping and analysis of mammalian promoters
Abstract: Link
Advisor(s): Bing Ren , Philip Bourne
Next Position: Ambit Biosciences, Scientist
Email: arjoyce26@gmail.com
Andrew Joyce
Degree Conferred: Ph.D. BioinformaticsThesis: 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
Next Position: Philip Morris, Post Doc
Ann Thuy Mongan (Thuy Vo)
Degree Conferred: Ph.D. BioinformaticsThesis: Systems Analysis of Engergy Metabolism Elucidates the Roles of Mitochondria in Human Health and Disease
Abstract: Link
Advisor(s): Bernhard Palsson , Andrew McCulloch
Next Position: BioInformative, Founder and CEO
Email: stanner@illumina.com
Stephen Tanner
Degree Conferred: Ph.D. BioinformaticsThesis: Efficient and Accurate Bioinformatics Algorithms for Peptide Mass Spectrometry
Abstract: Link
Advisor(s): Vineet Bafna , Julian Schroeder
Next Position: Inscripta, Principal Scientist
John Mongan
Degree Conferred: Ph.D. BioinformaticsThesis: 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
Next Position: University of California, San Francisco, Associate Professor
Email: cmosley@ucsd.edu
Coleman Mosley
Degree Conferred: Ph.D. BioinformaticsThesis: Global Views of Human Genetic Variation: Single Nucleotide Polymorphisms' (SNPs) Effects and their Random Nature
Abstract: Link
Advisor(s): Nicholas Schork , Daniel O'Connor
Next Position: Magellan Health-National Imaging Associates, Physician Clinical Reviewer
Degui Zhi
Degree Conferred: Ph.D. BioinformaticsThesis: Discovery and Analysis of mosaic arrangements in biological squesces and structures
Abstract: Link
Advisor(s): Pavel Pevzner , William Loomis
Next Position: University of Texas Health Science Center at Houston, Associate Professor
Email: alhsiao@stanford.edu
Albert Hsiao
Degree Conferred: Ph.D. Bioengineering with a specialization in BioinformaticsThesis: Comparative functional genomics of energy metabolism and insulin resistance in mammalian systems
Abstract: Link
Advisor(s): Shankar Subramaniam , Jerrold Olefsky
Next Position: UCSD, Assistant Professor of Radiology, In-Residence
Email: papin@virginia.edu
Jason Papin
Degree Conferred: Ph.D. Bioengineering with a specialization in BioinformaticsThesis: Systems Analysis of Cellular Signaling Networks
Abstract: Link
Advisor(s): Bernhard Palsson , Jerrold Olefsky
Next Position: University of Virginia, Assistant Professor
Email: ndprice@illinois.edu
Nathan Price
Degree Conferred: Ph.D. Bioengineering with a specialization in BioinformaticsThesis: Unbiased Assessment of Genome-Scale Metabolic Network States
Abstract: Link
Advisor(s): Bernhard Palsson , Shankar Subramaniam
Next Position: University of Illinois, Urbana-Champaign, Assistant Professor
Email: ifamili@gtlifesciences.com
Iman Famili
Degree Conferred: Ph.D. Bioengineering with a specialization in BioinformaticsThesis: Systemic analysis of the stoichiometric matrix and kinetic characterization of metabolic networks.
Abstract: Link
Advisor(s): Bernhard Palsson , Shankar Subramaniam
Next Position: GT Life Sciences, Inc., Research Director
Markus Herrgard
Degree Conferred: Ph.D. Bioengineering with a specialization in BioinformaticsThesis: Reconstruction and Systems Analysis of Genome-Scale Metabolic and Regulatory Networks inSaccharomyces cerevisiae
Abstract: Link
Advisor(s): Bernhard Palsson , Shankar Subramaniam
Next Position: synthetic genomics, Senior Bioinformatics Scientist
Email: mcovert@stanford.edu
Markus Covert
Degree Conferred: Ph.D. Bioengineering with a specialization in BioinformaticsThesis: Transcriptional Regulation in Escherichia coli: A Systems Biology Approach
Abstract: Link
Advisor(s): Bernhard Palsson
Next Position: Stanford, Asst Professor