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: Vivian Cheung
Matriculated: 2007
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
Research description: Currently I am working with Dr. Maley on modeling cancer metastasis using dispersal evolution theory. Our hypothesis is that the temporal and spatial heterogeneity in the primary tumor selects cells with high dispersal rate and metastasis is a byproduct of this selection process. We investigate the effect of different levels of heterogeneity on dispersal evolution. My second wet lab rotation is focused on using the real time PCR to quantify the mRNA levels of several key neuroblastoma susceptible genes in the neuroblastoma of the mouse model.
Matriculated: 2007
ZhongQiang (John) Chen
zqchen at mail.med.upenn.edu
B.S. Electrical Engineering, Shanghai Jiao Tong University, 1999
M.E. Biomedical Engineering, Shanghai Jiao Tong University, 2002
Advisor : David Roos
Research description : Subcellular localization prediction in Apicomplexan (including
Toxoplasma gondii and Plasmodium falcipurum) and prediction of first
exon in secretory protein-coding genes.
Matriculated : 2002
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
Matriculated: 2009
Perry Evans
evansjp at mail.med.upenn.edu
B.S. Computer Science, Rose-Hulman Institute, 2005
Advisor : Lyle Ungar
Research description : I'm using results from coexpression experiments and various protein-protein
interaction experiments to construct graphs of protein relations for a species. I'm interested in comparing the graphs from two species to 1) find subsets of conserved protein relations and 2) learn how protein relations evolve.
Matriculated : 2005
Logan Everett
loganje at mail.med.upenn.edu
B.S. Computer Science, SUNY Binghamton, 2004
Advisors : Sridhar Hannenhalli and Steven Master
Research description : My primary research interest is the regulation of transcription factors by post-translational modifications. I apply concepts from proteomics, gene regulatory networks, motif recognition, and machine learning. In Dr. Hannenhalli's lab I am using Bayesian Networks to integrate different genomic data sources, i.e. sequence, expression, ChIP-chip, and protein array data, into a cohesive model of gene regulation that includes primary regulators (transcription factors) and secondary regulators (modifying enzymes). In Dr. Master's lab I am using tandem mass spectrometry to map specific modification sites on transcription factor proteins in vivo. I am applying these techniques for both genome-scale network inference and for specific biological problems.
http://cagr.pcbi.upenn.edu/PTMswitchboard/
Matriculated : 2005
Publications:
Everett L, Vo A, Hannenhalli S. PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. Nucleic Acids Res. 2009 Jan;37(Database issue):D66-71. Epub 2008 Oct 15.
Everett L, Wang LS, Hannenhalli S. Dense subgraph computation via stochastic search: application to detect transcriptional modules. Bioinformatics. 2006 Jul 15;22(14):e117-23.
Adam Ewing
ewingad at mail.med.upenn.edu
B.A. Biology & Computer Science, Hiram College, 2005
Advisor : Haig Kazazian
Research description : The genomic biology of the LINE-1 retrotransposon
Webpage: http://people.pcbi.upenn.edu/~ewingad/
Matriculated : 2005
Aleah Fox
alefox at mail.med.upenn.edu
B.S. Biology, Boston College, 2008
Advisor: Carlo Maley
Matriculated: 2008
Christina Frost
cfrost at mail.med.upenn.edu
B.A. Mathematics, College of St. Scholastica, 2009
Matriculated: 2009
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
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
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
Matriculated: 2009
Zhandong Liu
zhandong at mail.med.upenn.edu
B.A. Computer Science, Nankai University, 2001
M.S. Computer Science, Wayne State University, 2004
Advisor: Lewis Chodosh
Research description: Pathway signature analysis and survival analysis on breast cancer microarray data.
Matriculated: 2004
Rithun Mukherjee
rithun at mail.med.upenn.edu
B.S. Zoology, University of Delhi, 1998
M.S. Life Sciences, Jawaharlal Nehru University, New Delhi, 2000
Advisor: Frederic Bushman
Research description: HIV diversity studies with deep sequencing
Matriculated : 2006
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
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
Thomas Petty
Penn
tpetty at mail.med.upenn.edu
Geneva
thomas.petty@molbio.unige.ch
B.S. Microbiology & Biochemistry, Pennsylvania State University, 2000
Advisor : Thanos Halazonetis & Jeff Saven
Research description : After receiving my B.S. in microbiology, and minor in molecular biology and
biochemistry (The Pennsylvania State University) , I spent a few years in
industry working for an Agricultural Genetics/Biotechnology (molecular
biology / biochemistry) start-up company, and later as an endocrinology
researcher (developed mouse models / biochemistry) at the Children's
Hospital of Philadelphia. The computational experience I gained while away
from school helped focus my interests in computational biology. I always
held an interest in protein structure and function, and so now I study the
structures of cancer-related proteins using both computational and
experimental approaches. I am currently using statistically based protein
design methods to aid in the solubliization and stabilization of large
proteins. Once purified, I will further characterize the functional
significance of these cancer-related proteins through biochemical and
crystallographic structure-based approaches.
Matriculated : 2003
Paul Ryvkin
pry at mail.med.upenn.edu
B.S. Electrical and Computer Engineering
Advisor: Li-San Wang
Matriculated: 2007
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
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
Kathleen Sprouffske
sprouffk at mail.med.upenn.edu
B.A. Biochemistry & Molecular Biology, Reed College, 1996
Advisor : Carlo Maley
Research description : Cancers are complex systems that emerge from mutations and evolution within the cells of our bodies during an organism's lifetime. Each time a cell divides, it has a small chance of incorporating a new mutation (either genetically or epigenetically) in its progeny. It is thought that mutations must cause six phenotypic changes in order to produce cancer, most of which function to stimulate proliferation and avoid growth restraints. Within this biological framework, I have been using agent-based modeling and evolutionary ideas to explore aspects of tumor development.
Web site:http://kazad-dum.wistar.upenn.edu/kathleen/
Matriculated : 2005
Publications:
Pepper, J.W., Sprouffske, K. & Maley, C.C. Animal Cell Differentiation Patterns Suppress Somatic Evolution. PLoS Comput Biol 3, e250 (2007).
Sira Sriswasdi
sirasris at mail.med.upenn.edu
B.S. Mathematics, MIT, 2008
Advisor: Dave Speicher
Matriculated: 2008
Nicholas Stong
nstong at mail.med.upenn.edu
B.S. Molecular Biology and Applied Math, University of Wisconsin - Madison, 2008
Advisor: Harold Riethman
Matriculated: 2008
Ellen Tsai
eatsai at mail.med.upenn.edu
B.S. Bioengineering, University of California, San Diego, 2008
Advisor: Nancy Spinner
Matriculated: 2008
Gabriel Walton
gwalt at mail.med.upenn.edu
B.S. Biology, University of Miami, 2009
Matriculated: 2009