Bioinformatics and Systems Biology Graduate Students

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Maria Luisa Amaral

Program: Bioinformatics and Systems Biology

Advisor(s): Bing Ren

Special Funding/Awards:

2018-19 Trainee on NIH Training Grant in Bioinformatics

Erick Armingol

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

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George Armstrong

Program: Bioinformatics and Systems Biology


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Kanishk Asthana

Program: Bioinformatics and Systems Biology

Advisor(s): Wei Wang

Research Interests: Epigenetics, Gene Regulation

Degrees:

B.E., Biotechnology. Delhi College of Engineering, 2012
M.S., Biomedical Engineering, Duke University, 2014

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Argus Athanas-Crannell

Program: Bioinformatics and Systems Biology

Special Funding/Awards:

2015-18 Trainee on National Library of Medicine (NLM) Training Grant Fellowship Program


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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

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:

2018-19 Trainee on NIH Training Grant in Bioinformatics

Metin Balaban

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

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Bokan Bao

Program: Bioinformatics and Systems Biology


Bahar Behsaz

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)

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Kevin Blansit

Program: Bioinformatics and Systems Biology

Special Funding/Awards:

2016-18 Trainee on National Library of Medicine (NLM) Training Grant Fellowship Program


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Andrey Bzikadze


Andrea Castro

Andrea Castro

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:

2017-2018 GEM PhD Engineering Fellowship
2017 Intel Scholar


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Arjun Chandrasekhar

Program: Bioinformatics and Systems Biology

Special Funding/Awards:

2014-16 Trainee on NIH Training Grant in Bioinformatics


Owen Chapman

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

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Chien-Ju Chen

Program: Bioinformatics and Systems Biology


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Brett Copeland

Program: Bioinformatics and Systems Biology

Special Funding/Awards:

2018-19 Trainee on NIH Training Grant in Bioinformatics


Nathaniel Delos Santos

Nathaniel Delos Santos

Program: Bioinformatics and Systems Biology

Advisor(s): Christopher Benner

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
2016-2018 Katzin Prize Scholar

Margaret Donovan

Margaret Donovan

Program: Bioinformatics and Systems Biology

Advisor(s): Kelly Frazer

Research Interests: Examining functional regulatory variation in iPSC-derived tissues using computational genomics

Degrees:

B.S., Biomolecular Engineering, University of California, Santa Cruz, 2013
Minor, Bioinformatics, University of California, Santa Cruz, 2013

Special Funding/Awards:

2015-18 Trainee on National Library of Medicine (NLM) Training Grant Fellowship Program

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Michelle Dow

Program: Bioinformatics and Systems Biology

Special Funding/Awards:

2015-18 Trainee on National Library of Medicine (NLM) Training Grant Fellowship Program


Xiaomi Du

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

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Rongxin Fang

Program: Bioinformatics and Systems Biology


Patrick Fiaux

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

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Edahi Gonzalez-Avalos

Program: Bioinformatics and Systems Biology


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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

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Daniel Hakim

Program: Bioinformatics and Systems Biology

Special Funding/Awards:

2018-19 Trainee on NIH Training Grant in Bioinformatics


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Jennifer Havens

Program: Bioinformatics and Systems Biology


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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

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Yingxiang Huang

Special Funding/Awards:

2014-17 Trainee on National Library of Medicine (NLM) Training Grant Fellowship Program


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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:

2017-19 Trainee on NIH Training Grant in Bioinformatics

Bojing Jia

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

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Adam Jussila

Program: Bioinformatics and Systems Biology


Benjamin Kellman

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

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Azhar Khandekar

Program: Bioinformatics and Systems Biology


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Adam Klie

Program: Bioinformatics and Systems Biology

Degrees:

B.S., Bioengineering: Bioinformatics, University of California, San Diego, 2017

Emily Kobayashi

Emily Kobayashi

Program: Bioinformatics and Systems Biology

Degrees:

B.S., Bioinformatics, University of California, Santa Cruz, 2019


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Zhenzhi Li

Program: Bioinformatics and Systems Biology


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Miin Lin

Program: Bioinformatics and Systems Biology

Special Funding/Awards:

2015-17 Trainee on NIH Training Grant in Bioinformatics

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Isaac Lopez Moyado

Program: Bioinformatics and Systems Biology

Advisor(s): Scott Rifkin


Jens Luebeck

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

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Clarence Mah

Program: Bioinformatics and Systems Biology

Degrees:

B.S., Bioengineering: Bioinformatics, University of California, San Diego 2016


Cameron Martino

Cameron Martino

Program: Bioinformatics and Systems Biology

Advisor(s): Rob Knight

Jamison McCorrison

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

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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

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Robert Morey

Special Funding/Awards:

2017-19 Trainee on NIH Training Grant in Bioinformatics


Daniela Nachmanson

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

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Jacklyn Newsome

Program: Bioinformatics and Systems Biology


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Jennifer Nguyen

Program: Bioinformatics and Systems Biology


Edward J O'Brien

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

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Ryan O'Neil

Program: Bioinformatics and Systems Biology

Advisor(s): Joseph Ecker

Special Funding/Awards:

2012-13 Trainee on NIH Training Grant in Bioinformatics

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Adam Officer

Program: Bioinformatics and Systems Biology


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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


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Jonathan Pekar

Program: Bioinformatics and Systems Biology


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Anh Pham

Program: Bioinformatics and Systems Biology


Patrick Phaneuf

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

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Timofey Prodanov


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Yue Qin

Program: Bioinformatics and Systems Biology

Degrees:

B.S., Bioinformatics, University of California, San Diego, 2017

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Eleonora Rachtman

Program: Bioinformatics and Systems Biology


Michelle Ragsac

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

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Gibraan Rahman

Program: Bioinformatics and Systems Biology


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Joaquin Reyna

Program: Bioinformatics and Systems Biology

Degrees:

Bioengineering: Bioinformatics Bsc

Special Funding/Awards:

2018-19 Trainee on NIH Training Grant in Bioinformatics

Samuel Roth

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

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

John Sauls

John Sauls

Program: Bioinformatics and Systems Biology

Advisor(s): Suckjoon Jun

Research Interests: Bacterial Physiology, Directed Evolution

Degrees:

B.S., Bioengineering, University of Pennsylvania, 2011
M.S., Bioengineering, University of Pennsylvania, 2011

Special Funding/Awards:

2016-18 Trainee on NIH Training Grant in Bioinformatics

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Dominic Schenone

Program: Bioinformatics and Systems Biology

Degrees:

B.S, Bioengineering, University of California, Santa Cruz, 2017

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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

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

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

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James Sorrentino

Special Funding/Awards:

2017-19 Trainee on NIH Training Grant in Bioinformatics


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James Talwar

Program: Bioinformatics and Systems Biology


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Colleen Weatherwax

Program: Bioinformatics and Systems Biology

Special Funding/Awards:

2016-17 Trainee on NIH Training Grant in Bioinformatics


Xingzhao Wen

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

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

Cynthia Wu

Degrees:

B.S., Bioinformatics, University of California, San Diego, 2017
Minor, Computer Science, University of California, San Diego, 2017


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Fang Yuan

Program: Bioinformatics and Systems Biology


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Chao Zhang


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Yuan Zhao

Special Funding/Awards:

2013-15 Trainee on NIH Training Grant in Bioinformatics


Lina Zheng

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

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Jingtian Zhou

Program: Bioinformatics and Systems Biology

Advisor(s): Joseph Ecker

Research Interests: Single-cell epigenomics

Degrees:

B.S., Pharmaceutical Sciences, Tsinghua University, 2016

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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