Bioinformatics and Systems Biology Graduate Students

Maria Amaral

Program: Bioinformatics and Systems Biology

Special Funding/Awards:

2018-19 Trainee on NIH Training Grant in Bioinformatics

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

earmingol [at] eng.ucsd.edu (Email)

George Armstrong

Program: Bioinformatics and Systems Biology

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

kasthana [at] eng.ucsd.edu (Email)
website

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

aaylward [at] eng.ucsd.edu (Email)

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

hmbaghdassarian [at] eng.ucsd.edu (Email)

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

balaban [at] ucsd.edu (Email)
website

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)

bbehsaz [at] ucsd.edu (Email)
website

Andrey Bzikadze

Arjun Chandrasekhar

Program: Bioinformatics and Systems Biology

Special Funding/Awards:

2014-16 Trainee on NIH Training Grant in Bioinformatics

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

Rongxin Fang

Program: Bioinformatics and Systems Biology

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

pfiaux [at] ucsd.edu (Email)
website

Robert Foreman

Program: Bioinformatics and Systems Biology

Advisor(s): Roy Wollman

Research Interests: Dynamic Cell Signaling

Degrees:

B.S. Biology - Cellular Physiology

rforeman [at] eng.ucsd.edu (Email)
website

Edahi Gonzalez-Avalos

Program: Bioinformatics and Systems Biology

William Greenwald

Program: Bioinformatics and Systems Biology

Advisor(s): Kelly Frazer

Research Interests: Statistical Genetics, Functional Genetics, Computational, Fine Mapping,

Degrees:

B.S. Computational and Systems Biology, UCLA, 2015

Special Funding/Awards:

Institute for Engineering in Medicine Fellow, 2016
2015-16 Trainee on NIH Training Grant in Bioinformatics
ARCS Fellow, Sept 2016-Present
Institute for Engineering in Medicine Fellow, March 2016
​NIH Ruth L. Kirschstein F31 Fellow, April 2018-Present

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

cag104 [at] eng.ucsd.edu (Email)

Daniel Hakim

Program: Bioinformatics and Systems Biology

Special Funding/Awards:

2018-19 Trainee on NIH Training Grant in Bioinformatics

Jennifer Havens

Program: Bioinformatics and Systems Biology

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

rhillary [at] eng.ucsd.edu (Email)

Jason Hyun

Special Funding/Awards:

2017-19 Trainee on NIH Training Grant in Bioinformatics

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

bkellman [at] eng.ucsd.edu (Email)
website

Azhar Khandekar

Program: Bioinformatics and Systems Biology

Adam Klie

Program: Bioinformatics and Systems Biology

Degrees:

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

aklie [at] eng.ucsd.edu (Email)

Emily Kobayashi

Program: Bioinformatics and Systems Biology

Degrees:

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

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

msl043 [at] eng.ucsd.edu (Email)

Isaac Lopez Moyado

Program: Bioinformatics and Systems Biology

Advisor(s): Scott Rifkin

Jia Lu

Program: Bioinformatics and Systems Biology

Advisor(s): Sheng Zhong

Degrees:

B.E., Biomedical Engineering, Peking University, 2013

Special Funding/Awards:

2015-16 Rita. L. Atkinson Graduate Fellowship

jil340 [at] eng.ucsd.edu (Email)

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

jluebeck [at] eng.ucsd.edu (Email)
website

Clarence Mah

Program: Bioinformatics and Systems Biology

Degrees:

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

Cameron Martino

Program: Bioinformatics and Systems Biology

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

jmccorri [at] eng.ucsd.edu (Email)

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

ileenamitra [at] eng.ucsd.edu (Email)
website

Shamim Mollah

Program: Bioinformatics and Systems Biology

Special Funding/Awards:

2013-14 Trainee on National Library of Medicine (NLM) Training Grant Fellowship Program

smollah [at] eng.ucsd.edu (Email)

Robert Morey

Special Funding/Awards:

2017-19 Trainee on NIH Training Grant in Bioinformatics

Niema Moshiri

Program: Bioinformatics and Systems Biology

Advisor(s): Siavash Mirarab, Pavel Pevzner

Research Interests: Phylogenetics, phylogenomics, and computational genomics

Degrees:

B.S., Bioengineering: Bioinformatics, University of California, San Diego, 2015

Special Funding/Awards:

2015-17 Trainee on NIH Training Grant in Bioinformatics
​UC San Diego Distinguished Teaching Award, 2017

niemamoshiri [at] gmail.com (Email)
website

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

dnachman [at] eng.ucsd.edu (Email)

Jacklyn Newsome

Program: Bioinformatics and Systems Biology

Vu Ngo

Program: Bioinformatics and Systems Biology

Advisor(s): Wei Wang

Special Funding/Awards:

2013-16 Trainee on NIH Training Grant in Bioinformatics

vqngo [at] eng.ucsd.edu (Email)
website

Jennifer Nguyen

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

ejobrien [at] ucsd.edu (Email)

Ryan O'Neil

Program: Bioinformatics and Systems Biology

Advisor(s): Joseph Ecker

Special Funding/Awards:

2012-13 Trainee on NIH Training Grant in Bioinformatics

roneil [at] eng.ucsd.edu (Email)

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

Patrick Phaneuf

Program: Bioinformatics and Systems Biology

Advisor(s): Bernhard Palsson

Research Interests: Discovery and application with experimental evolution, cell and computer engineering

Degrees:

M. E. Computer Engineering, Mercer University, 2009
M. S. Computer Science, University of California, San Diego, 2016

pphaneuf [at] eng.ucsd.edu (Email)
website

Timofey Prodanov

Yue Qin

Program: Bioinformatics and Systems Biology

Degrees:

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

y8qin [at] ucsd.edu (Email)

Yunjiang Qiu

Program: Bioinformatics and Systems Biology

Advisor(s): Bing Ren

Degrees:

B.S., Biology, Peking University, 2013

yuq003 [at] ucsd.edu (Email)

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

mragsac [at] eng.ucsd.edu (Email)
website

Gibraan Rahman

Program: Bioinformatics and Systems Biology

Anugraha Raman

Program: Bioinformatics and Systems Biology

Advisor(s): Bing Ren

Research Interests: Epigenetics, DNA Methylation

Degrees:

A.B, Biomedical Engineering, Harvard College, 2012

Special Funding/Awards:

National Science Foundation Graduate Research Fellowship
2012-13 Trainee on NIH Training Grant in Bioinformatics

amraman [at] ucsd.edu (Email)

Joaquin Reyna

Program: Bioinformatics and Systems Biology

Degrees:

Bioengineering: Bioinformatics Bsc

Special Funding/Awards:

2018-19 Trainee on NIH Training Grant in Bioinformatics

joreyna [at] eng.ucsd.edu (Email)

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

sjroth [at] eng.ucsd.edu (Email)

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

jsauls [at] ucsd.edu (Email)
website

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

isshamie [at] ucsd.edu (Email)

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

solvason [at] eng.ucsd.edu (Email)
website

James Sorrentino

Special Funding/Awards:

2017-19 Trainee on NIH Training Grant in Bioinformatics

James Talwar

Program: Bioinformatics and Systems Biology

Mengchi Wang

Program: Bioinformatics and Systems Biology

Advisor(s): Wei Wang

Colleen Weatherwax

Program: Bioinformatics and Systems Biology

Special Funding/Awards:

2016-17 Trainee on NIH Training Grant in Bioinformatics

Christopher Wei

Program: Bioinformatics and Systems Biology

Advisor(s): Kun Zhang

Degrees:

B.S., Bioengineering (Biotechnology), University of California, San Diego, 2013

Special Funding/Awards:

2013-14 Trainee on NIH Training Grant in Bioinformatics

cjwei [at] eng.ucsd.edu (Email)

Cynthia Wu

Degrees:

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

Chao Zhang

Yuan Zhao

Special Funding/Awards:

2013-15 Trainee on NIH Training Grant in Bioinformatics

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

liz227 [at] eng.ucsd.edu (Email)

Jingtian Zhou

Program: Bioinformatics and Systems Biology

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

jlz014 [at] eng.ucsd.edu (Email)