Bioinformatics and Systems Biology Graduate Students

Nassim Ajami

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

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

Bokan Bao

Program: Bioinformatics and Systems Biology

Bahar Behsaz

Program: Bioinformatics and Systems Biology

Advisor(s): Pavel Pevzner

Research Interests: Computational Mass Spectrometry and Proteogenomics, Genome/Metagenome Assembly, Algorithms for Natural Products Discovery

Degrees:

B.Sc., Computer Science, Sharif University of Technology, 2010
M.Sc., Mathematics, Simon Fraser University, 2013

Special Funding/Awards:

Natural Sciences and Engineering Research Council of Canada Graduate Scholarship

Laurence Bernstein

Program: Bioinformatics and Systems Biology

Advisor(s): Nuno Bandeira, Steve Briggs

Research Interests: Development of algorithms for interpretation of proteomics mass spectrometry data

Degrees:

B.A., Computer Science, University of California San Diego, 1988

lebernstein [at] ucsd.edu (Email)
website

Kunal Bhutani

Program: Bioinformatics and Systems Biology

Advisor(s): Nicholas Schork, Vineet Bafna

kbhutani [at] ucsd.edu (Email)

Olga Botvinnik

Program: Bioinformatics and Systems Biology

Advisor(s): Gene Yeo, Sheng Zhong

Research Interests: Single cell alternative splicing through open source, reproducible research

Degrees:

S.B., Mathematics, Massachusetts Institute of Technology, 2010
S.B., Biological Engineering, Massachusetts Institute of Technology, 2010
M.S., Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, 2012

Special Funding/Awards:

2014 NumFOCUS John Hunter Technology Fellow
2014 UCSD Bioinformatics Expo Best Talk, 2nd place
2013 National Defense Science and Engineering Graduate Fellow
2013 Hertz Foundation Fellowship Finalist
2012 National Science Foundation Honorable Mention

obotvinn [at] ucsd.edu (Email)
website

Arjun Chandrasekhar

Program: Bioinformatics and Systems Biology

Christopher DeBoever

Program: Bioinformatics and Systems Biology

Advisor(s): Kelly Frazer, Trey Ideker

Research Interests: Human genetics and genomics

Degrees:

B.S., Mathematical Biology, Harvey Mudd College, 2010

Special Funding/Awards:

CIRM Stem Cell Predoctoral Training Grant (TG2-01154)
UC San Diego Research Integrity Student Award 2015
Achievement Rewards for College Scientists (ARCS) Scholar

cdeboeve [at] ucsd.edu (Email)
website

Dinh Diep

Program: Bioinformatics and Systems Biology

Advisor(s): Kun Zhang, Vineet Bafna

Research Interests: DNA methylation and epigenetics

Degrees:

B.S., Bioengineering, University of California, San Diego, 2009

Special Funding/Awards:

CIRM Pre-doctoral Fellow

ddiep [at] ucsd.edu (Email)
website

Kuan-Fu Ding

Program: Bioinformatics and Systems Biology

Advisor(s): Nicholas Schork

Research Interests: Developing statistical methods in human genetics and genomics research

Degrees:

B.S., Mathematics, University of Texas at Austin, 2008
M.S., Biostatistics, University of Virginia, 2011

Special Funding/Awards:

University of Texas, President Faulkner scholarship (2004-2008)

kuding [at] ucsd.edu (Email)
website

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: Functional Genetics, Fine Mapping

Special Funding/Awards:

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

Yupeng He

Program: Bioinformatics and Systems Biology

Advisor(s): Joseph Ecker, Wei Wang

Research Interests: Computational analysis on epigenomic and genomic data from human and mouse; Bioinformatics

Degrees:

B.S., Biotechnology, Shanghai Jiaotong University, 2011
Minor, Mathematics, Shanghai Jiaotong University, 2011

yuh026 [at] ucsd.edu (Email)
website

Justin Huang

Program: Bioinformatics and Systems Biology

Advisor(s): Trey Ideker

Leen Jamal

Program: Bioinformatics and Systems Biology

Advisor(s): Gene Yeo

Research Interests: Cardiac development, mRNA export, Single-cell sequencing

Degrees:

B.S., Biomedical Engineering, University of Virginia, 2012

Special Funding/Awards:

University of Virginia, Harrison Undergraduate Research Award, 2011-2012
National Science Foundation Graduate Research Fellowship, 2014

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

James Jensen

Program: Bioinformatics and Systems Biology

Advisor(s): Trey Ideker

Benjamin Kellman

Program: Bioinformatics and Systems Biology

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

 

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

Miin Lin

Program: Bioinformatics and Systems Biology

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

Joanne Liu

Program: Bioinformatics and Systems Biology

Advisor(s): Nathan E. Lewis, Terry Gaasterland

Research Interests: Modeling metabolism and gene-expression in gram-positive bacteria

Degrees:

B.S., Genetics, Cell Biology and Development, University of Minnesota - Twin Cities, 2011

Special Funding/Awards:

Frontiers of Innovation Scholars Program

jkl055 [at] 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

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

Jens Luebeck

Program: Bioinformatics and Systems Biology

Advisor(s): Vineet Bafna

Degrees:

B.S, Applied Computational & Mathematical Sciences, University of Washington 2015

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

Rachel Marty

Program: Bioinformatics and Systems Biology

Advisor(s): Hannah Carter

Research Interests: Cancer Genomics

Degrees:

B.S., Computer Science with a specialization in Bioinformatics, University of California, San Diego, 2014

Special Funding/Awards:

NSF Graduate Research Fellowship

ramarty [at] ucsd.edu (Email)
website

Jamison McCorrison

Program: Bioinformatics and Systems Biology

Degrees:

B.S., Bioinformatics and Molecular Biology, Rensselaer Polytechnic Institute, 2008

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

Nathan Mih

Program: Bioinformatics and Systems Biology

Advisor(s): Bernhard Palsson, Philip Bourne

Research Interests: Drug off-targets, protein structure, systems pharmacology

Degrees:

B.S., Biochemistry & Molecular Biology, University of California, Irvine, 2012

nmih [at] ucsd.edu (Email)
website

Ileena Mitra

Program: Bioinformatics and Systems Biology

Degrees:

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

ileenamitra [at] gmail.com (Email)

Shamim Mollah

Program: Bioinformatics and Systems Biology

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

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

niemamoshiri [at] gmail.com (Email)
website

Kavitha Mukund

Program: Bioinformatics and Systems Biology

Advisor(s): Shankar Subramaniam

Research Interests: skeletal muscle pathopysiology, networks

Degrees:

B.E, Electrical and Electronics, Visvesvaraya Technological University, India, 2006
M.S., Biomedical Informatics, Arizona State University, 2010

k1mukund [at] ucsd.edu (Email)

Vu Ngo

Program: Bioinformatics and Systems Biology

Advisor(s): Wei Wang

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

Edward J O'Brien

Program: Bioinformatics and Systems Biology

Advisor(s): Bernhard Palsson, Philip Bourne

ejobrien [at] ucsd.edu (Email)

Ryan O'Neil

Program: Bioinformatics and Systems Biology

Advisor(s): Joseph Ecker

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

Kivilicim Ozturk

Program: Bioinformatics and Systems Biology

Gabriel Pratt

Program: Bioinformatics and Systems Biology

Advisor(s): Gene Yeo

Research Interests: RNA Biology and Neurodegeneration

Degrees:

BS, Computer Science, University of Washington 2011

Special Funding/Awards:

Achievement Rewards for College Scientists (ARCS) Scholar
NSF Graduate Research Fellowship
 

gpratt [at] ucsd.edu (Email)
website

Yunjiang Qiu

Program: Bioinformatics and Systems Biology

Advisor(s): Bing Ren

Degrees:

B.S., Biology, Peking University, 2013

yuq003 [at] ucsd.edu (Email)

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

amraman [at] ucsd.edu (Email)

Samuel Roth

Program: Bioinformatics and Systems Biology

Advisor(s): Trey Ideker

Research Interests: Systems Biology; Evolution; Gene Ontology

Degrees:

B.A., Biology, Computer Science, Wesleyan University, 2013
M.A., Biology, Wesleyan University, 2014

 

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

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

isshamie [at] ucsd.edu (Email)

Dylan Skola

Program: Bioinformatics and Systems Biology

Advisor(s): Trey Ideker

Research Interests: Evolution of Biological Networks

Degrees:

B.S., Biology, Humboldt State University, 2002

dskola [at] ucsd.edu (Email)
website

Jenhan Tao

Program: Bioinformatics and Systems Biology

Advisor(s): Christopher Glass

Research Interests: Transcription Factor Mechanisms in Macrophages

Degrees:

B.S., Bioengineering, University of California, Berkeley, 2012

jenhantao [at] gmail.com (Email)
website

Brian Yik Tak Tsui

Program: Bioinformatics and Systems Biology

Advisor(s): Hannah Carter

Research Interests: Integrative Analysis of 'Omics in Cancer

Degrees:

B.S., Computer Science, University of California, San Diego, 2014

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

Mengchi Wang

Program: Bioinformatics and Systems Biology

Advisor(s): Wei Wang

Colleen Weatherwax

Program: Bioinformatics and Systems Biology

Christopher Wei

Program: Bioinformatics and Systems Biology

Advisor(s): Kun Zhang

Degrees:

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

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

Cory White

Program: Bioinformatics and Systems Biology

Advisor(s): Doug Richman, David Smith

Research Interests: Transcriptome and proteome profiling of HIV Latency

Degrees:

B.S., Physics, California Institute of Technology, 2005

Special Funding/Awards:

FISP UCSD grant 2015
Bioinformatics training grant, extension scholarship 2013
Bioinformatics training grant, initial first year 2012

cwhite [at] ucsd.edu (Email)

Jason Yao

Program: Bioinformatics and Systems Biology

Advisor(s): Roy Wollman

Michael Yu

Advisor(s): Trey Ideker

mkyu003 [at] ucsd.edu (Email)

Jeffrey Yuan

Program: Bioinformatics and Systems Biology

Advisor(s): Pavel Pevzner

Research Interests: Genome Assembly for Long Reads

Degrees:

Sc.B., Computational Biology, Brown University, 2007

Special Funding/Awards:

NSF Graduate Fellow

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

James Yurkovich

Program: Bioinformatics and Systems Biology

Advisor(s): Bernhard Palsson

Degrees:

B.S., Electrical Engineering, University of Notre Dame, 2013

jyurkovich [at] ucsd.edu (Email)

Kai Zhang

Advisor(s): Wei Wang

Research Interests: Regulatory Network, Algebraic Biology, Epigenetics

Degrees:

B.S., Biological Science, Xiamen University, 2009
M.S., Molecular Biology and Biochemistry, 2012

Special Funding/Awards:

Dr. Huang Memorial Scholarship

kaz007 [at] ucsd.edu (Email)
website

Yuan Zhao

Jingtian Zhou

Program: Bioinformatics and Systems Biology

Illia Ziamtsov

Program: Bioinformatics and Systems Biology