As of July 21, 2006 (schedule subject to change) Tuesday August 8 Main Auditorium (Hall D) Room E1 Room E2 Room A          (2nd Floor) Room B1 Room B2 Room B3 Hall G Hall C Hall F ISCB Committee Meetings 7:30 a.m. - 7:30 p.m. Registration - Hall G Registration & Posters Wireless Internet Available 7:30 a.m. - 9:00 p.m.     9:00 a.m. - 9:00 p.m. Posters on Display - Hall G                   8:45 a.m. - 9:05 a.m. Morning Welcome, Promotion - ISMB/ECCB 2007 - Introduction of Keynote 3 (Main Auditorium - Hall D)         9:05 a.m. - 9:55 a.m. Keynote 3: Kurt Wüthrich – Computational Aspects of NMR Studies with Proteins in Solution (Main Auditorium - Hall D)   Exhibits Open - 9:45 a.m. - 5:15 p.m.       New Frontiers Session Sequence Analysis Molecular and Supramolecular Dynamics (1)     Text Mining & Information Extraction (4)                        Software Demos Software Demos Software Demos Software Demos       9:55 a.m. - 10:20 a.m. New Frontiers Continued:     The future of the funding for biomolecular data and  knowledge infrastructures: proposition for a "Fortaleza declaration” Amos Bairoch, Swiss Institute of Bioinformatics Paper 28: Indel seeds for homology search Denise Mak, Yevgeniy Gelfand, Gary Benson Paper 29: DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations  Iris Antes, Shirley Siu, Thomas Lengauer                 10:20 a.m. - 10:50 a.m. Coffee Break with Exhibitors - Hall C   Coffee Break      10:20 a.m. - 10:50 a.m.     10:50 a.m. - 11:15 a.m. New Frontiers Continued: The changing face of scientific dissemination as it  applies to computational biology Phil Bourne, University of California The future of computing in biology Søren Brunak, Biocentrum-DTU   Paper 30: Interpreting anonymous DNA samples from mass disasters --- probabilistic forensic inference using genetic markers    Tien-ho Lin, Eugene W. Myers, Eric P. Xing Paper 31: Accessing Images in Bioscience Literature through User-Interface Designs and Natural Language Processing Hong Yu, Minsuk Lee OpenMS - A Software Platform for Shotgun Proteomics IBM: Inferring Common Origins Biological Concept Diagram Editor (BCDE)  myGrid and ToolBus/PathPort Interoperability     11:15 a.m. - 11:40 p.m. Paper 32: BaCelLo: a balanced subcellular localization predictor Andrea Pierleoni, Pier Luigi Martelli Piero Fariselli, Rita Casadio Paper 33: Finding the evidences for protein-protein interactions from PubMed abstracts Hyunchul Jang, Jaesoo Lim, Joon-Ho Lim, Soo-Jun Park, Kyu-Chul Lee, Seon-Hee Park           11:40 a.m. - 12:05 p.m. Paper 34: On counting position weight matrix matches in a sequence, with application to discriminative motif finding Saurabh Sinha  Paper 35: Novel unsupervised feature filtering of biological data Roy Varshavsky, Assaf Gottlieb, Michal Linial, David Horn           12:05 p.m. - 12:30 p.m. Paper 36: Finding regulatory motifs with maximum density subgraph Eugene Fratkin, Brian Naughton, Douglas Brutlag, Serafim Botzoglou Paper 37: Integrating image data into biomedical text categorization Hagit Shatkay, Nawei Chen, Dorothea Blostein         12:30 p.m. - 2:00 p.m. Lunch - Hall F   EBI User's Forum ISCB Student Council Open Meeting Birds of a Feather Flock Together - Cancer Biomedical Informatics Grid (caBIG) Birds of a Feather Flock Together - Semantic types: towards a common annotation schema for biomedical literature Birds of a Feather Flock Together - Bioinformatics Core Facilities     Lunch    12:30 p.m. - 2:00 p.m.     Transcriptomics                  Sequence Analysis (continued) PLoS Track Software Demos Software Demos Software Demos Software Demos         2:00 p.m. - 2:25 p.m. Paper 38: Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE Barrett Foat, Alexandre Morozov, Harmen Bussemaker Paper 39: Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone Patrick Ng, Niranjan Nagarajan, Neil Jones, Uri Keich PLoS Track 3: Gene Expression Trees in Blood Cell Development Ivan Costa STING_RDB Extend Your Bioinformatics with Accelrys: Integration of new tools in a common workflow environment expands capabilities and biological context GeneChip Analysis System (WGAS) GNARE         2:25 p.m. - 2:50 p.m. Paper 40: Quantification of transcription factor expression from arabidopsis images Daniel Mace, Ji-Young Lee, Richard Twigg, Juliette Colinas, Philip Benfey, Uwe Ohler Paper 41: CONTRAfold: RNA secondary structure prediction without physics-based models Chuong Do, Daniel Woods, Serafim Batzoglou PLoS Track 4:   Pervasive unproductive splicing of SR proteins associated with ultraconserved elements Steven Brenner         2:50 p.m. - 3:15 p.m. Paper 42: Identifying cycling genes by combining sequence homology and expression data Yong Lu, Roni Rosenfeld, Ziv Bar-Joseph Paper 43: Context-specific independence mixture modeling for positional weight matrices Benjamin Georgi, Alexander Schliep PLoS Track 5: Population Sequencing from Chromatogram Data Nebojsa Jojic   Genetic Marker Search Engine for Medline  Gobase           3:15 p.m. - 3:40 p.m. Paper 44: Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles Elena Edelman, Alessandro Porrello, Justin Guinney, Bala Balakumaran, Andrea Bild, Phillip Febbo, Sayan Mukherjee Paper 45: ARTS: Accurate recognition of transcription starts in human Soeren Sonnenburg, Alexander Zien, Gunnar Raetsch PLoS Track 6: Sm/lsm genes: a glimpse into early Eukaryotic evolution Stella Veretnik       Coffee Break 3:40 p.m. - 4:05 p.m.     3:40 p.m. - 4:05 p.m. Coffee Break with Exhibitors - Hall C               4:05 p.m. - 4:30 p.m. Paper 46: Efficient identification of DNA binding partners in a sequence database Tobias Mann, William Noble Paper 47: Informative priors based on transcription factor structural class improve de novo motif discovery Leelavati Narlikar, Raluca Gordan, Uwe Ohler, Alexander Hartemink PLoS Track 7: Comparative analysis of the complete transcriptome of the ENCODE regions in chimpanzees and humans Philipp Khaitovich PRIDE and the Ontology Lookup Service Talk to Sun about Life Sciences BlueStarSting: A multiplatform environment for protein structure analysis HARLEM (Hamiltonians to Research LargE Molecules)          4:30 p.m. - 4:55 p.m. Paper 48: Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo Yuan Qi, Patrycja Missiuro, Ashish Kapoor, Craig Hunter, Tommi Jaakkola, David Gifford, Hui Ge Paper 49: ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains Kiyoko Aoki-Kinoshita, Nobuhisa Ueda, Hiroshi Mamitsuka, Minoru Kanehisa PLoS Track 8: The strength of selection on ultraconserved elements Christina Chen Poster Session with Authors (Even Number) & Reception - Hall G        6:00 p.m. - 9:00 p.m.     ISCB Publications - Room B4 6:00 p.m. - 7:00 p.m. ISCB Affiliates & SiGs - Room B6 6:00 p.m. - 7:00 p.m. ISCB Education Committee - Room VIP 6:00 p.m. - 7:00 p.m. 4:55 p.m. - 5:00 p.m. Introduction of Keynote 4 (Main Auditorium - Hall D)     5:00 p.m. - 5:50 p.m. Keynote 4: Overton Award: Mathieu Blanchette – What mammalian genomes tell us about our ancestors, and vice-versa (Main Auditorium - Hall D)     6:00 p.m. - 9:00 p.m. Poster Session with Authors (Even Number) & Reception - Hall G           9:00 p.m. Shuttles depart Convention Center to Hotels