Alumni - BISB Training Grant Recipients

William Greenwald

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Exploring the Regulatory Genome and Functional Genetic Variation

Abstract

Advisor(s): Kelly Frazer

Current Employer: Monoceros Biosystems, Bioinformatics Scientist

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

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

Current Employer: 10X Genomics, Staff Computational Biologist

Niema Moshiri

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Mathematical Modeling of Viral Evolution and Epidemiology

Abstract

Advisor(s): Siavash Mirarab, Pavel Pevzner

Current Employer: UC San Diego Department of Computer Science & Engineering, Assistant Teaching Professor

Vu Ngo

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Interplays between DNA motifs and epigenetic elements

Abstract

Advisor(s): Wei Wang

Current Employer: Cradle Genomics, Bioinformatics Scientist

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

Advisor(s): Bing Ren, Kun Zhang

Current Employer: Fulcrum Therapeutics, Associate Scientist

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

Advisor(s): Kun Zhang, Vineet Bafna

Current Employer: Zhang Lab, Postdoctural Researcher

Jeffrey Yuan

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Genome Assembly of Long Error-Prone Reads Using De Bruijn Graphs and Repeat Graphs

Abstract

Advisor(s): Pavel Pevzner, Bing Ren

Current Employer: Illumina, Bioinformatics Scientist

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

Advisor(s): Shankar Subramaniam, Shu Chien

Current Employer: CRISPR Therapeutics, Scientist

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

Advisor(s): Nuno Bandeira, Steve Briggs

Current Employer: Quest Diagnostics, Principal Software Engineer

Justin Huang

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Applications of Network Propagation for the Discovery of Candidate Genes in Human Disease

Abstract

Advisor(s): Trey Ideker

Current Employer: MD Anderson Cancer Center TRACTION, Institute Research Investigator: Systems Biology

Leen Jamal

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Gene Yeo

Current Employer: Viastat, Inc, Data Scientist

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

Advisor(s): Jill Mesirov, Pablo Tamayo

Current Employer: Recursion Pharmaceuticals, Data Scientist

Rachel Marty

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: The Role of MHC Variation in Tumor Progression

Abstract

Advisor(s): Hannah Carter

Current Employer: Personalis, Inc, Bioinformatics Scientist

Nathan Mih

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Understanding genetic variation in the proteome: a multi-scale structural systems biology toolkit

Abstract

Advisor(s): Bernhard Palsson, Philip Bourne

Current Employer: Lygos, Inc, Software Engineer

Gabriel Pratt

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Methods for Integrative Analysis of RNA Binding Proteins

Abstract

Advisor(s): Gene Yeo, Sheng Zhong

Current Employer: TwinStrand Biosciences, Bioinformatics Scientist

Jenhan Tao

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Christopher Glass, Christopher Benner

Current Employer: Illumina, Bioinformatics Scientist

James Yurkovich

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Bernhard Palsson, Jeff Hasty

Current Employer: Institute for Systems Biology, Translational Research Fellow

Kunal Bhutani

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Limiting Biases in Biological Data Analysis by Pooling Information

Abstract

Advisor(s): Nicholas Schork, Vineet Bafna

Current Employer: FVL59, Inc, Computational Scientist

Olga Botvinnik

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Computational analysis of single-cell alternative splicing

Abstract

Advisor(s): Gene Yeo, Sheng Zhong

Current Employer: Chan-Zuckerberg Biohub, Bioinformatics Data Scientist

Dinh Diep

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Kun Zhang, Vineet Bafna

Current Employer: UC San Diego, Postdoctural Researcher

Kuan-Fu Ding

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

Thesis: Quantifying and Accommodating Heterogeneity in High Throughput Drug Response Studies

Abstract

Advisor(s): Nicholas Schork, Bing Ren

Current Employer: Sapiens Data Science, Chief Science Officer

Joanne Liu

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Predicting Growth Optimization Strategies with Metabolic/Expression Models

Abstract

Advisor(s): Karsten Zengler, Nathan E. Lewis

Current Employer: Biota Technology, Data Scientist

Jason Yao

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Modeling and Measuring Dynamic Cellular Signaling States

Abstract

Advisor(s): Roy Wollman, Shankar Subramaniam

Current Employer: Guavus, Research Data Scientist

Michael Yu

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Hierarchical Models of Biological Systems

Abstract

Advisor(s): Trey Ideker, Christopher Glass

Current Employer: Toyota Technical Institute at Chicago, Research Assistant Professor

Christopher DeBoever

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Kelly Frazer, Trey Ideker

Current Employer: Takeda, Computational Biology Scientist

Andrew Gross

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Understanding disease through data driven biology

Abstract

Advisor(s): Trey Ideker, Kelly Frazer

Current Employer: Illumina, Bioinformatics Scientist

Eric Levy

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Lucila Ohno-Machado, Olivier Harismendy

Current Employer: Personalis, Senior Bioinformatics Scientist

Cory White

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Investigations of HIV Latency Through Transcriptomic and Proteomic Profiling

Abstract

Advisor(s): Doug Richman, David Smith

Karmel Allison

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Enhancers and Transcriptional Regulation in CD4+ T Cell

Abstract

Advisor(s): Christopher Glass, Stephen Hedrick

Current Employer: Google Brain TensorFlow Team, Engineering Manager

Spencer Bliven

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Philip Bourne, Milton Saier

Current Employer: Paul Scherrer Institut PSI, Scientific Computing Engineer

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

Advisor(s): Joseph Gleeson, Vineet Bafna

Current Employer: GRAIL, Inc, Bioinformatics Scientist

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

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

Current Employer: Pacific Biosciences, Staff Engineer: Primary Analysis

Alex Thomas

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Moving Towards Interpretable Mechanisms in Human Systems Biology

Abstract

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

Current Employer: C.H. Robinson, Principal Data Scientist

Gordon Bean

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Trey Ideker, Christopher Woelk

Current Employer: Illumina, Bionformatics Scientist

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

Advisor(s): Alexander Hoffmann, Gene Yeo

Current Employer: OnRamp Bioinformatics, Vice President

Stephen Federowicz

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Bernhard Palsson, Wei Wang

Current Employer: Inscripta, Inc, Senior Scientist: Computational Biology

Boyko Kakaradov

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Gene Yeo, Charles Elkan

Current Employer: Deep Genomics, Senior Scientist

Joshua Lerman

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Genome-scale Models of Metabolism and Gene Expression: Construction and Use for Growth Phenotype Prediction

Abstract

Advisor(s): Bernhard Palsson, Milton Saier

Current Employer: Total New Energies USA, Inc. (seconded to Amyris Amyris, Inc.), Computational Biology Post-Doctoral Scientist

Anand Patel

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Genome Rearrangements in Cancer and Human Genomes

Abstract

Advisor(s): Vineet Bafna, Yu-Tsueng Liu

Current Employer: Digital Proteomics, Chief Technology Officer

Philip Samayoa

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Applications of synthetic biology inspired by natural bacterial functionality

Abstract

Advisor(s): Jeff Hasty, Ruth Williams

Current Employer: Generation Bio, Vice President: Strategy and Portolio Development

Maxim Shokhirev

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Alexander Hoffmann, Andrew McCulloch

Current Employer: Salk Institute for Biological Studies Integrative Genomics & Bioinoformatics Core, Director

Marcus Kinsella

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Computational Techniques to Investigate Structural Variation

Abstract

Advisor(s): Vineet Bafna, Kelly Frazer

Current Employer: Pacific Biosciences, Senior Engineer (Bioinformatics)

Paul Loriaux

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Steady State Control of the Cellular Response to Stress

Abstract

Advisor(s): Alexander Hoffmann, Pavel Pevzner

Current Employer: Second Genome Inc, Lead Data Scientist

Nitin Udpa

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: The Genetic Basis of Hypoxia Tolerance

Abstract

Advisor(s): Vineet Bafna, Kelly Frazer

Current Employer: Illumina, Bioinformatics Scientist

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

Advisor(s): Philip Bourne, Pieter Dorrestein

Jocelyne Bruand

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Computational Tools for Analysis of Mass spectrometry Imaging Data

Abstract

Advisor(s): Vineet Bafna, Eduardo Macagno

Current Employer: Illumina, Bioinformatics Scientist

Roger Chang

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Bernhard Palsson, Philip Bourne

Current Employer: Harvard Medical School, Postdoctoral Fellow

Merril Gersten

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Shankar Subramaniam, Gabriel Haddad

Current Employer: UCSD Dept Bioengineering, Postdoc

Lukasz Szpankowski

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Advisor(s): Lawrence Goldstein, Shankar Subramaniam

Current Employer: Fluidigm, Scientist - R&D, New Technologies

Jan Schellenberger

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Monte Carlo Sampling in Systems Biology

Abstract

Advisor(s): Bernhard Palsson, Vineet Bafna

Current Employer: ID Analytics, Scientist

Ruben Valas

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

Advisor(s): Philip Bourne, William Loomis

Current Employer: UC San Diego (Bourne Lab), Postdoc

Gary Hon

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Understanding the global architecture of gene regulation in human cells through analysis of chromatin signatures

Abstract

Advisor(s): Bing Ren, Wei Wang

Current Employer: Ludwig Institute for Cancer Research, Postdoc

Ryan M. Kelley

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

Advisor(s): Trey Ideker, Vineet Bafna

Current Employer: Illumina, Bioinformatics Scienist 1

Noah Zaitlen

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Methods for the Analysis of Human Genetic Variation in the Search for the Genetic Basis of Human Disease

Abstract

Advisor(s): Vineet Bafna, Eleazar Eskin

Current Employer: Harvard School of Public Health, Postdoc

Christopher Benner

Degree Conferred: Ph.D. Bioinformatics

Thesis: Identification of a Conserved Periodic Promoter Structure in Metazoans

Abstract

Advisor(s): Christopher Glass, Shankar Subramaniam

Current Employer: University of California, San Diego (Glass Lab), Postdoc

Kristine Briedis

Degree Conferred: Ph.D. Bioinformatics

Thesis: The distribution and evolution of protein kinase and phospatase families in the three superkingdoms of life

Abstract

Advisor(s): Philip Bourne, William Loomis

Current Employer: University of California, San Diego (Bourne Lab), Postdoc

Kasey Hutt

Degree Conferred: Ph.D. Bioinformatics

Thesis: High-throughput genomic assays: Applications and analysis of DSL technology and next-generation sequencing

Abstract

Advisor(s): Michael Rosenfeld, Terry Gaasterland

Current Employer: University of California, San Diego (Rosenfeld Lab), Postdoc

Samuel Payne

Degree Conferred: Ph.D. Bioinformatics

Thesis: Advances in Computational Mass Spectrometry: Phosphoprteomics and Proteogenomics

Abstract

Advisor(s): Vineet Bafna, William Loomis

Current Employer: J. Craig Venter Institute, Bioinformatics Engineer

Derren Barken

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

Advisor(s): Alexander Hoffmann, Shankar Subramaniam

Current Employer: Prometheus, Bioinformatics Scientist

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

Advisor(s): Bernhard Palsson, Bing Ren

Current Employer: Philip Morris, Post Doc

Stephen Tanner

Degree Conferred: Ph.D. Bioinformatics

Thesis: Efficient and Accurate Bioinformatics Algorithms for Peptide Mass Spectrometry

Abstract

Advisor(s): Vineet Bafna, Julian Schroeder

Current Employer: Inscripta, Principal Scientist