Alumni - BISB Training Grant Recipients

The UC San Diego Libraries provide access to official copies of all UC San Diego dissertations. Use Roger (in the UC San Diego Libraries Catalog) to search for UC San Diego Bioinformatics dissertations.


Arjun Chandrasekhar

Arjun Chandrasekhar

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

William Greenwald

William Greenwald

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Exploring the Regulatory Genome and Functional Genetic Variation

Abstract

Current Employer: Monoceros Biosystems, Bioinformatics Scientist

Nicolaus Lance Hepler

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

Current Employer: 10X Genomics, Staff Computational Biologist

Niema Moshiri

Niema Moshiri

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Mathematical Modeling of Viral Evolution and Epidemiology

Abstract

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

Vu Ngo

Vu Ngo

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Interplays between DNA motifs and epigenetic elements

Abstract

Current Employer: Cradle Genomics, Bioinformatics Scientist

Anugraha Raman

Anugraha Raman

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Genomic diversity of tumor and normal tissues revealed by single-nuclei RNA-seq computational analysis

Abstract

Current Employer: Fulcrum Therapeutics, Associate Scientist

John Sauls

John Sauls

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Physiological Orchestration in Bacteria

Abstract

Christopher Wei

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

Current Employer: Zhang Lab, Postdoctural Researcher

Jeffrey Yuan

Jeffrey Yuan

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Current Employer: Illumina, Bioinformatics Scientist

Yuan Zhao

Yuan Zhao

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Nassim Ajami

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

Current Employer: CRISPR Therapeutics, Scientist

Laurence Bernstein

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

Current Employer: Quest Diagnostics, Principal Software Engineer

Justin Huang

Justin Huang

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

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

Leen Jamal

Leen Jamal

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Current Employer: Viastat, Inc, Data Scientist

James Jensen

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

Current Employer: Recursion Pharmaceuticals, Data Scientist

Rachel Marty

Rachel Marty

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: The Role of MHC Variation in Tumor Progression

Abstract

Current Employer: Personalis, Inc, Bioinformatics Scientist

Nathan Mih

Nathan Mih

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Current Employer: Lygos, Inc, Software Engineer

Gabriel Pratt

Gabriel Pratt

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Methods for Integrative Analysis of RNA Binding Proteins

Abstract

Current Employer: TwinStrand Biosciences, Bioinformatics Scientist

Jenhan Tao

Jenhan Tao

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Current Employer: Illumina, Bioinformatics Scientist

James Yurkovich

James Yurkovich

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Current Employer: Institute for Systems Biology, Translational Research Fellow

Kunal Bhutani

Kunal Bhutani

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Limiting Biases in Biological Data Analysis by Pooling Information

Abstract

Current Employer: FVL59, Inc, Computational Scientist

Olga Botvinnik

Olga Botvinnik

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Computational analysis of single-cell alternative splicing

Abstract

Current Employer: Chan-Zuckerberg Biohub, Bioinformatics Data Scientist

Dinh Diep

Dinh Diep

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Current Employer: UC San Diego, Postdoctural Researcher

Kuan-Fu Ding

Kuan-Fu Ding

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

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

Abstract

Current Employer: Sapiens Data Science, Chief Science Officer

Joanne Liu

Joanne Liu

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Predicting Growth Optimization Strategies with Metabolic/Expression Models

Abstract

Current Employer: Biota Technology, Data Scientist

Jason Yao

Jason Yao

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Modeling and Measuring Dynamic Cellular Signaling States

Abstract

Current Employer: Guavus, Research Data Scientist

Michael Yu

Michael Yu

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Hierarchical Models of Biological Systems

Abstract

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

Christopher DeBoever

Christopher DeBoever

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Current Employer: Takeda, Computational Biology Scientist

Andrew Gross

Andrew Gross

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Understanding disease through data driven biology

Abstract

Current Employer: Illumina, Bioinformatics Scientist

Eric Levy

Eric Levy

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Current Employer: Personalis, Senior Bioinformatics Scientist

Cory White

Cory White

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Investigations of HIV Latency Through Transcriptomic and Proteomic Profiling

Abstract

Karmel Allison

Karmel Allison

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Enhancers and Transcriptional Regulation in CD4+ T Cell

Abstract

Current Employer: Google Brain TensorFlow Team, Engineering Manager

Spencer Bliven

Spencer Bliven

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Current Employer: Paul Scherrer Institut PSI, Scientific Computing Engineer

Eric Scott

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

Current Employer: GRAIL, Inc, Bioinformatics Scientist

Martin Smith

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

Current Employer: Pacific Biosciences, Staff Engineer: Primary Analysis

Alex Thomas

Alex Thomas

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Moving Towards Interpretable Mechanisms in Human Systems Biology

Abstract

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

Gordon Bean

Gordon Bean

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Current Employer: Illumina, Bionformatics Scientist

Jeremy Davis-Turak

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

Current Employer: OnRamp Bioinformatics, Vice President

Stephen Federowicz

Stephen Federowicz

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

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

Boyko Kakaradov

Boyko Kakaradov

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Current Employer: Deep Genomics, Senior Scientist

Joshua Lerman

Joshua Lerman

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

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

Anand Patel

Anand Patel

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Genome Rearrangements in Cancer and Human Genomes

Abstract

Current Employer: Digital Proteomics, Chief Technology Officer

Philip Samayoa

Philip Samayoa

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Applications of synthetic biology inspired by natural bacterial functionality

Abstract

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

Maxim Shokhirev

Maxim Shokhirev

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

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

Marcus Kinsella

Marcus Kinsella

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Computational Techniques to Investigate Structural Variation

Abstract

Current Employer: Pacific Biosciences, Senior Engineer (Bioinformatics)

Paul Loriaux

Paul Loriaux

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Steady State Control of the Cellular Response to Stress

Abstract

Current Employer: Second Genome Inc, Lead Data Scientist

Nitin Udpa

Nitin Udpa

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: The Genetic Basis of Hypoxia Tolerance

Abstract

Current Employer: Illumina, Bioinformatics Scientist

Jocelyne Bruand

Jocelyne Bruand

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Computational Tools for Analysis of Mass spectrometry Imaging Data

Abstract

Current Employer: Illumina, Bioinformatics Scientist

Roger Chang

Roger Chang

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Current Employer: Harvard Medical School, Postdoctoral Fellow

Merril Gersten

Merril Gersten

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Current Employer: UCSD Dept Bioengineering, Postdoc

Lukasz Szpankowski

Lukasz Szpankowski

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

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

Jan Schellenberger

Jan Schellenberger

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

Thesis: Monte Carlo Sampling in Systems Biology

Abstract

Current Employer: ID Analytics, Scientist

Ruben Valas

Ruben Valas

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

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

Gary Hon

Gary Hon

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Current Employer: Ludwig Institute for Cancer Research, Postdoc

Ryan M. Kelley

Ryan M. Kelley

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

Current Employer: Illumina, Bioinformatics Scienist 1

Noah Zaitlen

Noah Zaitlen

Degree Conferred: Ph.D. Bioinformatics and Systems Biology

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

Abstract

Current Employer: Harvard School of Public Health, Postdoc

Christopher Benner

Christopher Benner

Degree Conferred: Ph.D. Bioinformatics

Thesis: Identification of a Conserved Periodic Promoter Structure in Metazoans

Abstract

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

Kristine Briedis

Kristine Briedis

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

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

Kasey Hutt

Kasey Hutt

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

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

Samuel Payne

Samuel Payne

Degree Conferred: Ph.D. Bioinformatics

Thesis: Advances in Computational Mass Spectrometry: Phosphoprteomics and Proteogenomics

Abstract

Current Employer: J. Craig Venter Institute, Bioinformatics Engineer

Derren Barken

Derren Barken

Degree Conferred: Ph.D. Bioinformatics

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

Abstract

Current Employer: Prometheus, Bioinformatics Scientist

Stephen Tanner

Stephen Tanner

Degree Conferred: Ph.D. Bioinformatics

Thesis: Efficient and Accurate Bioinformatics Algorithms for Peptide Mass Spectrometry

Abstract

Current Employer: Inscripta, Principal Scientist