Bioinformatics and Systems Biology Graduate Students

Ammal Abbasi
Program: Bioinformatics and Systems Biology

Fatemeh Amrollahi
Program: Bioinformatics and Systems Biology with a Specialization in Biomedical Informatics

Erick Armingol
Program: Bioinformatics and Systems Biology
Advisor(s): Nathan E. Lewis
Research Interests: Metabolic modeling and multicellular interactions to predict phenotypes
Degrees:
B.S., Molecular Biotechnology, Universidad de Chile, 2013
Engineer in Molecular Biotechnology, Universidad de Chile, 2015
Special Funding/Awards:
2018-22 Becas Chile - CONICYT (Chilean Government Scholarship)
2018-22 Fulbright Scholarship

George Armstrong
Program: Bioinformatics and Systems Biology

Argus Athanas-Crannell
Program: Bioinformatics and Systems Biology
Special Funding/Awards:
2015-18 Trainee on National Library of Medicine (NLM) Training Grant Fellowship Program

Anthony Aylward
Program: Bioinformatics and Systems Biology
Degrees:
B.S., CCS Mathematics, University of California, Santa Barbara, 2012
Special Funding/Awards:
2013-15 Trainee on NIH Training Grant in Bioinformatics

Hratch Baghdassarian
Program: Bioinformatics and Systems Biology
Degrees:
B.S., Bioengineering, University of California, Berkeley, 2017
B.S., Economics, University of California, Berkeley, 2017
Special Funding/Awards:
2018-20 Trainee on NIH Training Grant in Bioinformatics

Metin Balaban
Program: Bioinformatics and Systems Biology
Advisor(s): Siavash Mirarab
Research Interests: Phylogenetics, Phylogenomics, Comparative Genomics, Microbiome Analysis
Degrees:
B.S., Computer Engineering, Middle East Technical University, 2015
M.S., Computer Science, Swiss Federal Institute of Technology Lausanne, 2017

Bokan Bao
Program: Bioinformatics and Systems Biology

Bahar Behsaz
Program: Bioinformatics and Systems Biology
Advisor(s): Pavel Pevzner, Rob Knight
Research Interests: Computational Mass Spectrometry, (Meta)genome Assembly Algorithms, Microbiome Data Analysis, Metabologenomics
Degrees:
B.Sc., Computer Science, Sharif University of Technology, 2010
M.Sc., Mathematics, Simon Fraser University, 2013
Special Funding/Awards:
Center for for Microbiome and Innovations (CMI) 2018 Grand Challenges Award Grant with Pavel Pevzner
RECOMB 2019 Travel Award
2018 Microbial Sciences Graduate Research Fellowship (2018-2019)
Natural Sciences and Engineering Research Council of Canada Graduate Scholarship (2015-2018)

Kevin Blansit
Program: Bioinformatics and Systems Biology
Special Funding/Awards:
2016-18 Trainee on National Library of Medicine (NLM) Training Grant Fellowship Program

Andrey Bzikadze

Andrea Castro
Program: Bioinformatics and Systems Biology with a Specialization in Biomedical Informatics
Advisor(s): Hannah Carter
Research Interests: Artificial intelligence for precision medicine and drug discovery
Degrees:
B.S., Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, 2017
Minor, Bioinformatics, University of California, Los Angeles, 2017
Special Funding/Awards:
2018-2021 Trainee on National Library of Medicine (NLM) Training Grant Fellowship Program
2017-2018 GEM PhD Engineering Fellowship
2017 Intel Scholar

Owen Chapman
Advisor(s): Jill Mesirov
Degrees:
B.A., Computer Science, Pomona College, 2017
Special Funding/Awards:
2017-20 Trainee on National Library of Medicine (NLM) Training Grant Fellowship Program

Chien-Ju Chen
Program: Bioinformatics and Systems Biology

Brett Copeland
Program: Bioinformatics and Systems Biology
Special Funding/Awards:
2018-19 Trainee on NIH Training Grant in Bioinformatics

Nathaniel Delos Santos
Program: Bioinformatics and Systems Biology with a Specialization in Biomedical Informatics
Advisor(s): Christopher Benner
Research Interests: Transcriptional regulation in immune response, specializing in motif analysis.
Degrees:
B.S., Bioengineering (Biotechnology), University of California, San Diego, 2014
Special Funding/Awards:
2016-19 Trainee on National Library of Medicine (NLM) Training Grant Fellowship Program
2016-20 Katzin Prize Scholar

Xiaomi Du
Program: Bioinformatics and Systems Biology
Degrees:
B.S., Biology, Caltech, 2016
Special Funding/Awards:
2019-20 Trainee on NIH Training Grant in Bioinformatics

Patrick Fiaux
Program: Bioinformatics and Systems Biology
Advisor(s): Graham McVicker
Research Interests: Enhancers and Promoters
Degrees:
B.A., Biology with concentration in Computational Biology, Cornell University, 2015

Edahi Gonzalez-Avalos
Program: Bioinformatics and Systems Biology

Carlos Guzman
Program: Bioinformatics and Systems Biology
Advisor(s): Sven Heinz, Christopher Benner
Research Interests: Gene regulation, enhancer biology, chromatin regulation
Degrees:
B.S., Biology, University of Texas-Pan American, 2013
M.S., Biology, University of Texas-Pan American, 2015
Special Funding/Awards:
2017-19 Trainee on NIH Training Grant in Bioinformatics
Sloan Scholars Fellowship
Competitive EDGE Fellowship
2019 Ford Foundation Predoctoral Fellowship

Daniel Hakim
Program: Bioinformatics and Systems Biology
Special Funding/Awards:
2018-20 Trainee on NIH Training Grant in Bioinformatics

Jennifer Havens
Program: Bioinformatics and Systems Biology
Advisor(s): Joel Wertheim
Degrees:
B.S., Mathematical and Computational Biology, Harvey Mudd College, 2018

Ryan Hillary
Program: Bioinformatics and Systems Biology
Advisor(s): Christopher Benner
Research Interests: Transcription Initiation and Regulation, Enhancer Biology, Gene Regulation
Degrees:
B.S., Bioinformatics, Brigham Young University, 2014

Jason Hyun
Program: Bioinformatics and Systems Biology
Advisor(s): Bernhard Palsson
Research Interests: Microbial pan-genomes, antimicrobial resistance
Degrees:
B.S., Chemical-Biological Engineering, Massachusetts Institute of Technology, 2017
Special Funding/Awards:
2017-20 Trainee on NIH Training Grant in Bioinformatics

Pratibha Jagannatha
Program: Bioinformatics and Systems Biology
Special Funding/Awards:
2019-20 Trainee on NIH Training Grant in Bioinformatics

Bojing Jia
Program: Bioinformatics and Systems Biology
Advisor(s): Bing Ren, Albert Hsiao
Research Interests: Spatial transcriptomics, computer vision
Degrees:
B.Sc., Quantitative Biology, McGill University, 2015

Adam Jussila
Program: Bioinformatics and Systems Biology

Benjamin Kellman
Program: Bioinformatics and Systems Biology
Advisor(s): Nathan E. Lewis
Research Interests: Systems Medicine: Pediatric Diagnostics and Insight
Degrees:
B.S., Brain and Cognitive Science in Neurobiology, University of Rochester, 2013
B.A., Biology, University of Rochester, 2013
Min., Mathematics, University of Rochester, 2013
Min., Computer Science, University of Rochester, 2013
Special Funding/Awards:
2013-14 Trainee on NIH Training Grant in Bioinformatics

Azhar Khandekar
Program: Bioinformatics and Systems Biology
Degrees:
B.S., Biochemistry, University of Washington, 2016
Special Funding/Awards:
National Cancer Institute's Cancer Research Training Award

Adam Klie
Program: Bioinformatics and Systems Biology
Advisor(s): Hannah Carter
Degrees:
B.S., Bioengineering: Bioinformatics, University of California, San Diego, 2017
Special Funding/Awards:
2019-20 Trainee on NIH Training Grant in Bioinformatics

Emily Kobayashi
Program: Bioinformatics and Systems Biology
Degrees:
B.S., Bioinformatics, University of California, Santa Cruz, 2019
Special Funding/Awards:
2019-20 Trainee on NIH Training Grant in Bioinformatics

Eric Kofman
Program: Bioinformatics and Systems Biology
Special Funding/Awards:
2019-20 Trainee on NIH Training Grant in Bioinformatics

Zhenzhi Li
Program: Bioinformatics and Systems Biology

Miin Lin
Program: Bioinformatics and Systems Biology
Special Funding/Awards:
2015-17 Trainee on NIH Training Grant in Bioinformatics

Jens Luebeck
Program: Bioinformatics and Systems Biology
Advisor(s): Vineet Bafna
Research Interests: Cancer biology and genomic structural variation
Degrees:
B.S, Applied Computational & Mathematical Sciences, University of Washington 2015
Special Funding/Awards:
2015-17 Trainee on NIH Training Grant in Bioinformatics

Clarence Mah
Program: Bioinformatics and Systems Biology
Advisor(s): Hannah Carter, Gene Yeo
Research Interests: Transcriptomics, RNA regulation, RNA localization, reproducible research
Degrees:
B.S., Bioengineering: Bioinformatics, University of California, San Diego 2016
Special Funding/Awards:
NSF Graduate Research Fellowship Program
UCSD Genetics Training Program

Jamison McCorrison
Program: Bioinformatics and Systems Biology
Degrees:
B.S., Bioinformatics and Molecular Biology, Rensselaer Polytechnic Institute, 2008
Special Funding/Awards:
2014-15 Trainee on NIH Training Grant in Bioinformatics

Ileena Mitra
Program: Bioinformatics and Systems Biology
Advisor(s): Melissa Gymrek
Research Interests: Human Genomics
Degrees:
B.S., Biomolecular Engineering, University of California Santa Cruz, 2013
Special Funding/Awards:
2016-17 Trainee on NIH Training Grant in Bioinformatics
2019-20 Autism Science Foundation Predoctoral Fellowship

Robert Morey
Special Funding/Awards:
2017-20 Trainee on NIH Training Grant in Bioinformatics

Daniela Nachmanson
Degrees:
B.S., Biochemistry, University of Washington, 2015
Special Funding/Awards:
2017-18 Trainee on NIH Training Grant in Bioinformatics
2018-21 TRDRP (Tobacco-Related Disease Research Program) Predoctoral Research Fellowship

Jacklyn Newsome
Program: Bioinformatics and Systems Biology

Jennifer Nguyen
Program: Bioinformatics and Systems Biology

Edward J O'Brien
Program: Bioinformatics and Systems Biology
Advisor(s): Bernhard Palsson, Philip Bourne
Special Funding/Awards:
2010-11 Trainee on NIH Training Grant in Bioinformatics

Ryan O'Neil
Program: Bioinformatics and Systems Biology
Advisor(s): Joseph Ecker
Special Funding/Awards:
2012-13 Trainee on NIH Training Grant in Bioinformatics

Adam Officer
Program: Bioinformatics and Systems Biology

Kivilicim Ozturk
Program: Bioinformatics and Systems Biology
Advisor(s): Hannah Carter
Degrees:
B.S., Biological Sciences and Bioengineering, Sabanci University
M.S., Computer Science and Engineering, Sabanci University
Special Funding/Awards:
2017-18 SDCSB Systems Biology Training Grant

Jonathan Pekar
Program: Bioinformatics and Systems Biology

Anh Pham
Program: Bioinformatics and Systems Biology

Patrick Phaneuf
Program: Bioinformatics and Systems Biology
Advisor(s): Bernhard Palsson
Research Interests: Discovery and application with experimental evolution, cell and computer engineering
Degrees:
B.S.E., Computer Engineering, Mercer University, 2009
M.S., Computer Science, University of California, San Diego, 2016

Timofey Prodanov

Yue Qin
Program: Bioinformatics and Systems Biology
Degrees:
B.S., Bioinformatics, University of California, San Diego, 2017

Eleonora Rachtman
Program: Bioinformatics and Systems Biology

Michelle Ragsac
Program: Bioinformatics and Systems Biology
Advisor(s): Emma Farley
Research Interests: Single cell transcriptomics and regulatory genomics of Ciona intestinalis embryogenesis
Degrees:
B.S., Bioengineering: Bioinformatics, University of California, San Diego, 2017

Gibraan Rahman
Program: Bioinformatics and Systems Biology

Joaquin Reyna
Program: Bioinformatics and Systems Biology
Degrees:
Bioengineering: Bioinformatics Bsc
Special Funding/Awards:
2018-20 Trainee on NIH Training Grant in Bioinformatics

Samuel Roth
Program: Bioinformatics and Systems Biology
Advisor(s): Christopher Benner
Research Interests: Genomics, Epigenetics, Transcriptional Regulation
Degrees:
B.A., Biology, Computer Science, Wesleyan University, 2013
M.A., Biology, Wesleyan University, 2014
Special Funding/Awards:
2014-16 Trainee on NIH Training Grant in Bioinformatics

Charles-Alexandre Roy
Program: Bioinformatics and Systems Biology
Advisor(s): Jonathan Sebat
Degrees:
B.S., Bioengineering, University of Maine, 2019
Minor, Chemistry, University of Maine, 2019
Minor, Cell and Molecular Biology, University of Maine, 2019
Minor, Nanotechnology, University of Maine, 2019
Minor, Microbiology, University of Maine, 2019

Dominic Schenone
Program: Bioinformatics and Systems Biology
Degrees:
B.S, Bioengineering, University of California, Santa Cruz, 2017

Isaac Shamie
Program: Bioinformatics and Systems Biology
Degrees:
B.S., Biology, Carnegie Mellon University, 2014
Minor, Computational Neuroscience, Carnegie Mellon University, 2014
Special Funding/Awards:
2016-18 Trainee on NIH Training Grant in Bioinformatics

Omar Shanta
Program: Bioinformatics and Systems Biology
Advisor(s): Jonathan Sebat
Degrees:
B.S., Electrical Engineering, University of California, Irvine, 2015
M.S., Electrical and Computer Engineering, University of California, San Diego, 2019

Jesse Solvason
Program: Bioinformatics and Systems Biology
Advisor(s): Emma Farley
Research Interests: Synthetic Biology, Transcriptional Regulation, Sequencing Based High-Throughput Screens
Degrees:
B.S. Molecular, Cellular, Developmental Biology; Minor in Chemistry

James Sorrentino
Program: Bioinformatics and Systems Biology
Advisor(s): Nathan E. Lewis, Jeffrey Esko
Research Interests: Proteomics, Glycoproteomics, MRSA, Sepsis
Degrees:
B.S., Bioengineering with Bioinformatics minor, University of California, Santa Cruz, 2017
Special Funding/Awards:
2017-20 Trainee on NIH Training Grant in Bioinformatics

James Talwar
Program: Bioinformatics and Systems Biology

Juan Tibocha Bonilla
Program: Bioinformatics and Systems Biology

Colleen Weatherwax
Program: Bioinformatics and Systems Biology
Special Funding/Awards:
2016-17 Trainee on NIH Training Grant in Bioinformatics

Xingzhao Wen
Program: Bioinformatics and Systems Biology
Advisor(s): Sheng Zhong
Research Interests: RNA interactome, Genome organization
Degrees:
B.S., Biomedical Engineering, Southeast University, China, 2018

Alexander Wenzel
Program: Bioinformatics and Systems Biology with a Specialization in Biomedical Informatics
Advisor(s): Jill Mesirov
Research Interests: Bulk and single cell transcriptomic algorithms development
Degrees:
B.S., Computer Science, Northwestern University, 2017
Special Funding/Awards:
2017-20 Trainee on National Library of Medicine (NLM) Training Grant Fellowship Program
Cancer Cell Map Initiative: Cancer Systems Biology Training Program Award

Cynthia Wu
Degrees:
B.S., Bioinformatics, University of California, San Diego, 2017
Minor, Computer Science, University of California, San Diego, 2017

Nancy Yuan
Program: Bioinformatics and Systems Biology with a Specialization in Biomedical Informatics
Advisor(s): Albert Hsiao
Degrees:
M.S., Biology, UC San Diego, 2017
B.S., Biology, University of Texas at Austin, 2015
B.A., History, University of Texas at Austin, 2014
Special Funding/Awards:
2018-21 Trainee on National Library of Medicine (NLM) Training Grant Fellowship Program

Chao Zhang

Lina Zheng
Program: Bioinformatics and Systems Biology
Degrees:
B.S. in Pharmaceutical Science
M.S. in Statistics/Biostatistics
Special Funding/Awards:
2017-19 Trainee on NIH Training Grant in Bioinformatics

Jingtian Zhou
Program: Bioinformatics and Systems Biology
Advisor(s): Joseph Ecker
Research Interests: Single-cell epigenomics
Degrees:
B.S., Pharmaceutical Sciences, Tsinghua University, 2016

Jessica Zhou
Program: Bioinformatics and Systems Biology
Degrees:
B.S., Biomedical Engineering, University of Southern California, 2017
Special Funding/Awards:
2017-18 Trainee on NIH Training Grant in Bioinformatics
2019-20 Fulbright Study/Research Award