2004 Annual Retreat

Held on October 15, 2004, the Greater Philadelphia Bioinformatics Alliance 2 nd Annual Retreat provided academic and industry scientists the opportunity to exchange ideas and showcase the region's bioinformatics research talent. This year's retreat drew over 130 bioinformatics researchers and innovators from universities, research institutions, start-up companies, and large pharmaceutical firms.

Technical talks in three tracks highlighted both academic and industry-based bioinformatics research in Greater Philadelphia:

Genomic Analysis

GLEAN: Improved eukaryotic gene prediction by statistical consensus of gene evidence, by A. Mackey, F. Pereira and D. Roos ( University of Pennsylvania )

Computational and experimental studies of alternative splicing on genome-wide scale, by M. Pritsker and I. Lemischka ( Princeton University )

NdPASA: A novel pair-wise protein sequence alignment algorithm that incorporates neighbor-dependent amino acid propensities, by J. Feng and J. Wang ( Temple University )

Large Scale Data Analysis

Biomarker pattern discovery, by Allen Moser (Cira Discovery Sciences, Inc.)

Identification of signaling pathways from microarray data, by A. Kossenkov and M. Ochs ( Fox Chase Cancer Center )

Characterization of gene functional expression profiles of Plasmodium Falciparum, by H. Xie, S. Vucentic, H. Sun, P. Hedge and Z. Obradovic ( Temple University )

Networks

Applications of hybrid systems methods to medium-size biochemical networks, by A. Halasz, V. Kumar, M. Imielinski, P. Finin, C. Belta, O. Sokolsky and H. Rubin

Practical fuzzy logic models of biological systems: network reconstruction from heterogeneous experimental data, by B. Sokhansanj ( Drexel University )

Transcriptional regulatory network analysis of mammalian neuronal adaptation, by R. Vadigepalli, A. Simparo, M. Covarrubias, R. Khan, N. Janes, J. Hoek, G. Gonye and J. Schwaber ( Thomas Jefferson University )

A panel discussion titled, “Can Bioinformatics and Computational Biology Innovations be Commercialized in Greater Philadelphia?” included bioinformatics entrepreneurs, intellectual property experts, and early-stage venture capitalists. The lively, interactive conversation provided retreat attendees insights into the current environment around commercializing bioinformatics innovations. Panel members included:

David F. Counts, Ph.D., Director of Life Sciences, Ben Franklin Technology Partners of Southeastern Pennsylvania

Jennifer Hartt, M.S., Associate Director, Business Development and Equity, Center for Technology Transfer, University of Pennsylvania

Ned Haubein, Ph.D., Chief Scientist, BIOSoftware Systems

Gary Kurtzman, M.D., Managing Director and COO, BioAdvance – The Biotechnology Greenhouse of Southeastern Pennsylvania

Wade Rogers, Ph.D., CEO, Cira Discovery Sciences

Christopher Starr, MBA, J.D., Managing Director and Vice President of Investments, Innovation Philadelphia

George Taulbee, J.D., Partner, Alston & Bird, LLP