Amit Bahl
Thesis title and defense date: Design and Application of Multi-functional Microarrays for Toxoplasma gondii, January 2008
Irina Bochkis
Post-doctoral Fellow, Kaestner Lab, University of Pennsylvania
Thesis title and defense date: Hepatic Metabolic Regulatory Networks of Foxa2, November 20, 2008.
Ryan Coleman
Thesis title and defense date: Shortest Geometric Paths Analysis in Structural Biology, August 28, 2009.
Sheng Guo
Thesis title and defense date: Computational Analysis and Application of Genotype and Phenotype on Drosophilia Odorant Receptors and RNA, September 26. 2008.
Dexter Hadley
Thesis title and defense date: Genome-scale annotation of genetic factors underluying neurotransmission and neuropsychiatric disease, October 2007
Marcin Imilienski
Thesis title and defense date: In silico analysis of microbial biosynthetic capabilities at the genome scale, December 2005
Miler Lee
Post-doctoral Fellow, Kim Lab, University of Pennsylvania
Thesis title and defense date: Modular Organization and Composability of RNA, October 9, 2009.
Molly Megraw
Uwe Ohler Lab, Duke University
Thesis title and defense date: Regulation of MicroRNA Transcription, June 2007
Recent publications:
Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG. (2009). A transcription factor affinity based code for mammalian transcription initiation. Genome Research, [Epub ahead of print].
M. Megraw, P. Sethupathy, B. Corda, and A.G. Hatzigeorgiou (2007). miRGen: A database for the study of animal microRNA genomic organization and function. Nucleic Acids Research, 35:D149-D155.
P. Sethupathy, M. Megraw, and A.G. Hatzigeorgiou (2006). A guide through current computational approaches for the identification of mammalian microRNA targets. Nature Methods, 3:881-6.
M. Megraw, V. Baev, V. Rusinov, S.T. Jensen, K. Kalantidis, and A.G. Hatzigeorgiou (2006). MicroRNA promoter element discovery in Arabidopsis. RNA, 12:1612-9.
L. Zhang, J. Huang, N. Yang, J. Greshock, M. Megraw, A. Giannakakis, S. Liang, T.L. Naylor, A. Barchetti, M.R. Ward, G. Yao, A. Medina, A. O'brien-Jenkins, D. Katsaros, A. Hatzigeorgiou, P.A. Gimotty, B.L. Weber, G. Coukos. (2006). microRNAs exhibit high frequency genomic alterations in human cancer. PNAS, 103:9136-41.
K. Szafranski, M. Megraw, M. Reczko, and A. G. Hatzigeorgiou (2006). Support Vector Machines for Predicting microRNA Hairpins. Proceedings of the 2006 International Conference on Bioinformatics and Computational Biology, 270-276.
Jeremy Purvis
Post-doctoral Fellow, Galit Lahav Laboratory, Department of Systems Biology, Harvard University
Thesis title and defense date: A Systems Approach to Cellular Signal Transduction, June 2009
Recent publications:
Liu, Y.*, J. Purvis*, A. Shih, J. Weinstein, N. Agrawal, and R. Radhikrishnan (2007). A Multiscale Computational Approach to Dissect Early Events in the Erb Family Receptor Mediated Activation, Differential Signaling, and Relevance to Oncogenic Transformations. Annals of Biomedical Engineering, Vol. 35, No. 6, pp. 1012–1025, June 2007. (* equal contribution)
Purvis, Jeremy, Vibitha Ilango, and Ravi Radhakrishnan. Role of Network Branching in Eliciting Differential Short-Term Signaling Responses in the Hypersensitive Epidermal Growth Factor Receptor Mutants Implicated in Lung Cancer. Biotechnology Progress. Web Release Date: 16-Apr-2008
Shah, Parag P., Michael C. Myers, Mary Pat Beavers, Jeremy E. Purvis, Huiyan Jing, Heather J. Grieser, Elizabeth R. Sharlow, Andrew D. Napper, Donna M. Huryn, Barry S. Cooperman, Amos B. Smith, and Scott L. Diamond. Kinetic Characterization and Molecular Docking of a Novel, Potent, and Selective Slow-binding Inhibitor of Human Cathepsin L. Molecular Pharmacology. Published on Web. April 10, 2008.
Praveen Sethupathy
Post-doctoral Research Fellow,Dr. Francis S. Collins Labratory at the National Human Genome Research Institute (NHGRI) within the National Institutes of Health (NIH)
Thesis title and defense date: Analysis on the Role of Gene Regulatory Elements in Human Health and Evolution, March 2008
Recent publications:
P. Sethupathy and S. Hannenhalli (2008). A tutorial of the Poisson Random Field model in population genetics. Technical Report No. MS-CIS-08-01, University of Pennsylvania Department of Computer and Information Science.
P. Sethupathy, H. Giang, J.B. Plotkin, and S. Hannenhalli. (2008). Genome-wide analysis of natural selection on human cis-elements. Submitted.
P. Sethupathy*, C. Borel*, M. Gagnebin, G.R. Grant, S. Deutsch, T.S. Elton, A.G. Hatzigeorgiou, and S.E. Antonarakis (2007). Human miR-155 on chromosome 21 differentially interacts with its polymorphic target in the AGTR1 3’UTR – a mechanism for functional SNPs related to phenotypes. American Journal of Human Genetics, 81:405-413. (* equal contribution)
Y. Kawahara*, B. Zinshteyn*, P. Sethupathy, H. Iizasa, A.G. Hatzigeorgiou, and K. Nishikura (2007). Redirection of silencing targets by adenosine-to-inosine editing of microRNAs. Science, 315:1137-1140. (* equal contribution)
M. Megraw, P. Sethupathy, B. Corda, and A.G. Hatzigeorgiou (2006). miRGen: a database for the study of microRNA genomic organization and function. Nucleic Acids Research, 35:D149-D155.
P. Sethupathy, M. Megraw and A.G. Hatzigeorgiou (2006). A guide through current computational approaches for the identification of mammalian microRNA targets. Nature Methods, 3:881-886.
P. Sethupathy, B. Corda and A.G. Hatzigeorgiou (2006). TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA, 12:192-197.
P. Sethupathy*, M. Megraw*, M.I. Barrasa, and A.G. Hatzigeorgiou (2005). Computational Identification of Regulatory Factors Involved in MicroRNA Transcription. Lecture Notes in Computer Science, 3746:457-468. (* equal contribution)
Daniel Simola
Post-doctoral Fellow, Kim Lab, University of Pennsylvania
Thesis title and defense date: Evolution of Genome-Wide Gene Regulation in the Budding Yeast Cell- Division Cycle, September 3, 2009.
Geetu Tuteja
Post-doctoral Fellow, Kaestner Lab, University of Pennsylvania
Thesis title and defense date: Illuminating Transcriptional Regulation with Genome-wide Binding Data, December 15, 2008.
Zhi Wei
Assistant Professor, Computer Science Department, New Jersey Institute of Technology
Thesis title and defense date: Statistics Methods for Network-Based Analysis on Genomic Data, March 2008
Recent publications:
Wei, Z. and Li, H. A Hidden Spatial-temporal Markov Random Field Model for Network-based Analysis of Time Course Gene Expression Data. Annals of Applied Statistics, 2008 2: 408-429
Wei, Z. and Li, M. Genome-wide Association Analysis of Rheumatoid Arthritis in a Canadian Population, BMC Proceedings, 2007, 1(Suppl 1):S19
Wei, Z. and Li, H. A Markov Random Field Model for Network-based Analysis of Genomic Data, Bioinformatics, 2007 23:1537-1544
Wei, Z. and Li, H. Nonparametric Pathway-Based Regression Models for Analysis of Genomic Data. Biostatistics, 2007 8: 265-284
Wei, Z. and Jensen, S.T. GAME: detecting cis-regulatory elements using a genetic algorithm. Bioinformatics, 2006 22:1577-1584