Varun Aggarwala
avarun at mail.med.upenn.edu
B.S. Computer Science and Engineering, Indian Institute of Technology, 2008
Matriculated: 2011
Nathan Berkowitz
nberk at mail.med.upenn.edu
B.A. Molecular Biology, Clark University, 2002
Advisor: Brian Gregory
Matriculated: 2010
Josh Burdick
jburdick at seas.upenn.edu
B.S. Computer Science, University of Maryland, 1999
M.S. Computer and Information Science, University of Pennsylvania, 2003
Advisor: John Murray
Thesis working title:
Spatiotemporal gene expression patterns in developing C. elegans
Matriculated: 2007
Aleah Caulin
alefox at mail.med.upenn.edu
B.S. Biology, Boston College, 2008
Advisor: Carlo Maley
Matriculated: 2008
Jun Chen
chenjun at mail.med.upenn.edu
B.Med. Basic Medical Sciences, Fudan University, 2004
M.E. Pattern Recognition and Machine Intelligence, Shanghai Jiao Tong University, 2007
Advisor: Hongzhe Li
Thesis topic:Statistical analysis of metagenomic data
Matriculated: 2007
Zhang (Eric) Chen
zhch at mail.med.upenn.edu
B.S. Biology, University of Science and Technology of China, 2008
M.S. Bioinformatics, Chinese University of Hong Kong, 2011
Matriculated: 2011
Serena Dollive
sdollive at mail.med.upenn.edu
B.S. Computational Biology, 2008
Advisor: Rick Bushman
Matriculated: 2008
Hannah Dueck
hdueck at mail.med.upenn.edu
B.A. English, Goshen College, 2001
B.S. Biochemistry, Indiana University South Bend, 2009
Advisor: Junhyong Kim
Matriculated: 2009
Joe Glessner
jgle at mail.med.upenn.edu
B.S. Bioinformatics, University of the Sciences in Philadelphia, 2006
M.S. in Bioinformatics, University of the Sciences in Philadelphia, 2007
Advisor: Hakon Hakonarson
Matriculated: 2010
Brett Hannigan
brettth at mail.med.upenn.edu
B.S. Electrical Engineering, Stanford University
Advisor: Bill DeGrado
Research description:My interests lie in the field of functional genomics and protein design. As a member of Dr. DeGrado's lab, I am currently working on algorithms to help design proteins to interact with given peptide sequences.
Matriculated: 2007
Hannah Hutton
huttonh at mail.med.upenn.edu
B.S. Biological Sciences, Cornell University, 2009
Advisors: Sarah TIshkoff and Hongzhe Li
Matriculated: 2010
Yih-Chii Hwang
yihhwang at mail.med.upenn.edu
B.S. Computer Science, National Chengchi University, 2005
M.S. Bioinformatics, National Yang-Ming University, 2007
Advisors: Li-San Wang and Brian Gregory
Matriculated: 2009
Rumen Kostadinov
rumen at mail.med.upenn.edu
B.S. Bioinformatics, Ramapo College, 2005
Advisor : Carlo Maley
Research description : I am interested in the dynamics of clonal evolution in human neoplasms. Four parameters of tumor evolution could be used as biomarkers for cancer prevention: mutation rates, stem cells population size, stem cells generation time and clonal expansions. I am developing computational tools to detect changes in the four parameters in longitudinal samples from Barrett's Esophagus in Carlo Maley's lab at the Wistar Institute.
Matriculated : 2005
Nicholas Lahens
nif at mail.med.upenn.edu
B.S. Bioinformatics and Computer Science, Canisius College, 2007
Advisor: John Hogenesch
Matriculated: 2007
Fan Li
fanli at mail.med.upenn.edu
B.S. Electrical Engineering and Computer Sciences, 2008
Advisors: Li-San Wang and Brian Gregory
Thesis Working Title:
Genome-wide analysis of RNA secondary structure in eukaryotes
Matriculated: 2009
Sarah Middleton
sarahmid at mail.med.upenn.edu
B.S. Biology and Computer Science, 2011
Matriculated: 2011
Le Ba Nguyen
blnguyen at mail.med.upenn.edu
B.S. Electrical Engineering, University of Texas, 1999
M.S. Software Engineering, University of St. Thomas, 2005
Advisors: John Maris and Hongzhe Li
Research Description: I am using Whole Genome computational methods to identify disease variances for Neuroblastoma, and experimental methods to validate/verify those predicted disease variances.
Matriculated : 2006
Gabriel Otte
gotte at mail.med.upenn.edu
B.A. Computational Biology, Cornell University, 2011
Matriculated: 2011
Anthony Olarerin-George
olarerin at mail.med.upenn.edu
B.S. Bioinformatics, Ramapo College, 2005
Advisor : John Hogenesch
Research description : I am currently interested in screening for the role of functional RNAs in the circadian pathway.
Matriculated : 2005
Paul Ryvkin
pry at mail.med.upenn.edu
B.S. Electrical and Computer Engineering
Advisor: Li-San Wang
Research description: My interests include using RNAseq technology to investigate the properties of noncoding RNAs across a variety of organisms. In particular, I'm looking at the transcriptomics of neurodegenerative diseases.
Matriculated: 2007
Recent Publications:
Zheng Q, Ryvkin P, Li F, Dragomir I, Valladares O, Yang J, Cao K, Wang LS, Gregory BD. Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. PLoS Genet. 2010 Sep 30;6(9).
Johnson JE, Cao K, Ryvkin P, Wang LS, Johnson FB. Altered gene expression in the Werner and Bloom syndromes is associated with sequences having G-quadruplex forming potential. Nucleic Acids Res. 2010 Mar;38(4):1114-22. Epub 2009 Dec 4.
Najaf Shah
najaf at mail.med.upenn.edu
B.S. Computer Science, University of Alabama Birmingham, 2004
Advisor: Casim Sarkar
Matriculated: 2007
Scott Sherrill-Mix
shescott at mail.med.upenn.edu
B.S. Biology, Florida State University, 2002
M.S. Biology, Dalhousie University, 2007
Advisor: Rick Bushman
Matriculated: 2009
Sameer Soi
ssoi at mail.med.upenn.edu
B.S. Life Sciences, Penn State University, 2006
Advisor: Sarah Tishkoff
Research description: Human evolution, structural genomic variation and phenotypic variation in diverse African populations.
Matriculated: 2007
Sira Sriswasdi
sirasris at mail.med.upenn.edu
B.S. Mathematics, MIT, 2008
Advisor: Dave Speicher
Matriculated: 2008
Lindsay Stetson
stetsonl at mail.med.upenn.edu
B.S. Computer Science, Seattle University, 2011
Matriculated: 2011
Nicholas Stong
nstong at mail.med.upenn.edu
B.S. Molecular Biology and Applied Math, University of Wisconsin - Madison, 2008
Advisor: Harold Riethman
Research Description:
My broad research interest is in telomeres and their role in aging and cancer development. To further this interest I am developing tools to use high throughput sequencing data to quickly evaluate telomere sequence for integrity and mutation. These tools are being developed on high throughput sequence data from normal and cancer samples.
Matriculated: 2008
Jonathan Toung
toung at mail.med.upenn.edu
B.A. Biochemistry and Economics, University of Pennsylvania, 2010
M.S. Chemistry, University of Pennsylvania, 2010
Advisor: Vivian Cheung
Matriculated: 2010
Recent publications:
J. M. Toung, M. Morley, M. Li, V. G. Cheung, RNA-sequence analysis of human B-cells. Genome Research. 21, 991 (2011).
M. Li, I. X. Wang, Y. Li, A. Bruzel, A. L. Richards, J. M. Toung, V. G. Cheung, Widespread RNA and DNA Sequence Differences in the Human Transcriptome. Science. 333, 53 (2011).
Ellen Tsai
eatsai at mail.med.upenn.edu
B.S. Bioengineering, University of California, San Diego, 2008
Advisor: Nancy Spinner
Matriculated: 2008
Krishna Vijayendran
kvija at mail.med.upenn.edu
B.A. Biology and Philosophy, New York University, 2006
Matriculated: 2009
Ray Zhang
rayzhang at mail.med.upenn.edu
B.S. Applied Mathematics and Biochemistry, SUNY at Stony Brook, 2008
Matriculated: 2009