and 2nd Annual AB3C Conference: X-Meeting fortaleza, brazil - auGust 6-10, 2006 friday (auGust 4) Intelligent Systems for Molecular Biology

Room A Room B1 Room E1 (2nd Floor)

7:00 a.m. Shuttles depart Hotels to Convention Center

7:30 a.m. - 6:00 p.m. Registration - Hall G

3Dsig Alternative Splicing BOSC 9:00 a.m. - 10:30 a.m. Satellite Meeting SIG SIG

10:30 a.m. - 11:00 a.m. Coffee Break - Satellite & SIG meetings (available outside meeting rooms)

3Dsig Alternative Splicing BOSC 11:00 a.m - 12:00 p.m. Satellite Meeting SIG SIG

12:00 p.m. - 1:00 p.m. Lunch - Satellite and SIG meetings (Hall F)

3Dsig Alternative Splicing BOSC 1:00 p.m. - 3:30 p.m. Satellite Meeting SIG SIG

3:30 p.m. - 4:00 p.m. Coffee Break - Satellite & SIG meetings (available outside meeting rooms)

3Dsig Alternative Splicing BOSC 4:00 p.m. - 6:30 p.m. Satellite Meeting SIG SIG

6:30 p.m. Shuttles depart Convention Center to Hotels

1 and 2nd Annual AB3C Conference: X-Meeting fortaleza, brazil - auGust 6-10, 2006 saturday (auGust 5) Intelligent Systems for Molecular Biology

Room A Room B1 Room B2 Room E1 (2nd Floor)

7:00 a.m. Shuttles depart Hotels to Convention Center

7:30 a.m. - 6:00 p.m. Registration - Hall G

Joint BioLINK & 3Dsig Alternative Splicing Bio-ontologies BOSC 9:00 a.m. - 10:30 a.m. Satellite Meeting SIG SIG SIG

10:30 a.m. - 11:00 a.m. Coffee Break - Satellite & SIG meetings (available outside meeting rooms)

Joint BioLINK & 3Dsig Alternative Splicing Bio-ontologies BOSC 11:00 a.m - 12:00 p.m. Satellite Meeting SIG SIG SIG

12:00 p.m. - 1:00 p.m. Lunch - Satellite and SIG meetings (Hall F)

Joint BioLINK & 3Dsig Alternative Splicing Bio-ontologies BOSC 1:00 p.m. - 3:30 p.m. Satellite Meeting SIG SIG SIG

3:30 p.m. - 4:00 p.m. Coffee Break - Satellite & SIG meetings (available outside meeting rooms)

Joint BioLINK & 3Dsig Alternative Splicing Bio-ontologies BOSC 4:00 p.m. - 6:30 p.m. Satellite Meeting SIG SIG SIG

6:30 p.m. Shuttles depart Convention Center to Hotels

7:30 p.m. 3Dsig Satellite Meeting - Dinner (3Dsig Delegates and ticket holders) - Oasis Hotel (Brazil Room)

2 and 2nd Annual AB3C Conference: X-Meeting fortaleza, brazil - auGust 6-10, 2006 sunday (auGust 6) Intelligent Systems for Molecular Biology

Room A Room B1 Room B2 Room B3 Room B5 Room B6 Room E1 Room E2 (2nd Floor)

7:00 a.m. Shuttles depart Hotels to Convention Center

7:30 a.m. - 6:00 p.m. Registration - Hall G

Tutorial Tutorial Tutorial AM5: Computing AM2: Genomes, AM7: Exploring Biological Function: Browsers and Approach Tutorial to the Analysis and Tutorial Databases: Tools For AM1: Biological Tutorial with a Massively Parallel Prediction of Protein AM6: Integration and Automated Data Literature Mining – From AM3: Python High Performance Function Analysis of Diverse Integration Across Tutorial Information Retrieval to Programming for Life Computing Environment Yanay Ofran and Genomic Data Student Council Multiple Genomes AM4: Chemoinformatics Biological Discovery Science Researchers Kirk Jordan and Marco Punta 8:30 a.m. - 10:30 a.m. Symposium (SCS2) Peter Schattner Lars Juhl Jensen Sebastián Bassi Scott Emrich

10:30 a.m. - 10:45 a.m. Coffee Break - Tutorials and Student Council Symposium (available outside meeting rooms)

SCS2 Tutorial Tutorial Tutorial Tutorial Tutorial Tutorial Tutorial 10:45 a.m. - 12:30 p.m. Continued AM2 Continued AM4 Continued AM1 Continued AM3 Continued AM7 Continued AM5 Continued AM6 Continued

12:30 p.m. - 2:00 p.m. Lunch for delegates attending Student Council Symposium, delegates attending 2 tutorials and ticket holders - Hall F

Tutorial PM11: Computational Tutorial Biology Of Post- PM13: Protein-Protein Tutorial Transcriptional Gene Interactions: Structure Tutorial PM8: Bayesian Networks Tutorial Regulation: At The and Systems PM10: Introduction to For Bioinformatics: An PM9: From Pathways Interplay Of Genomes, Approaches to Analyze Computational Introduction To Databases to Network Networks And Diverse Genomic Data – Open Inference And Learning Models SCS2 Uwe Ohler and Anna Panchenko and Problems Chris Needham and Baltazar Aguda and 2:00 p.m. - 4:00 p.m. Continued Dirk Holste Benjamin Shoemaker Jacques Colinge James Bradford Andrew Goryachev

4:00 p.m. - 4:15 p.m. Coffee Break - Tutorials and Student Council Symposium (available outside meeting rooms)

SCS2 Tutorial Tutorial Tutorial Tutorial Tutorial 4:15 p.m. - 6:00 p.m. Continued PM11 Continued PM13 Continued PM10 Continued PM8 Continued PM9 Continued

6:00 p.m. - 6:30 p.m. Shuttles depart Convention Center to Hotels

3 and 2nd Annual AB3C Conference: X-Meeting fortaleza, brazil - auGust 6-10, 2006 monday (auGust 7) Intelligent Systems for Molecular Biology

Main Auditorium Room E1 Room E2 Room A Room B1 Room B2 Room B3 (Hall D) (2nd Floor)

7:00 a.m. Shuttles depart Hotels to Convention Center

7:30 a.m. - 7:30 p.m. Registration - Hall G

Opening Welcome and Introduction of Keynote 1 - Main Auditorium (Hall D)

8:45 a.m. - 10:05 a.m. Keynote 1: – Molecular machines for protein degradation

9:00 a.m. - 9:00 p.m. Posters on Display - Hall G - 9:00 a.m. - 9:00 p.m.

10:05 a.m. - 10:30 a.m. Coffee Break with Exhibitors - Hall C

Database and Data Integration Paper 2: An experimental metagenome data management and analysis system Victor Markowitz, Natalia Structural Bioinformatics Ivanova, Krishna Palaniappan Systems Biology Paper 1: ZPRED: Predicting Ernest Szeto, Frank Paper 3: Create and assess the distance to the Korzeniewski, Athanasios protein networks through membrane center for Lykidis, Iain Anderson, molecular characteristics of residues in alpha-helical Konstantinos Mavrommatis, individual proteins membrane proteins Victor Kunin, Hector Garcia Yanay Ofran, Guy Yachdav, Erik Granseth, Håkan Viklund, Martin, Inna Dubchak, Phil Eyal Mozes, Ta-tsen Soong, 10:30 a.m. - 10:55 a.m. Arne Elofsson Hugenholtz, Nikos Kyrpides Rajesh Nair,

Structural Bioinformatics Database and Data Paper 4: A combinatorial Integration Systems Biology pattern discovery approach Paper 5: Distance based Paper 6: Dense subgraph for the prediction of algorithms for small computation via stochastic membrane dipping (re-entrant) biomolecule classification and search: application to detect Software Demo Software Demo loops structural similarity search transcriptional modules Software Demo Integrated Microbial Software Demo GINsim: a software for Gorka Lasso, John Antoniw, Emre Karakoc, Artem Logan Everett, Li-San Wang, ArrayExpress Genomes (IMG) System SSAHA2 the qualitative 10:55 a.m. - 11:20 a.m. Jonathan Mullins Cherkasov, S. Cenk Sahinalp Sridhar Hannenhalli Systems Biology Database and Data Paper 9: A decompositional Integration approach to parameter Paper 8: springScape: estimation in pathway Visualisation of modeling: A case study of the Structural Bioinformatics microarray and contextual Akt and MAPK pathways and Paper 7: Comparative bioinformatic data using their crosstalk footprinting of DNA-binding spring embedding and an Geoffrey Koh, Huey Fern Carol proteins information landscape Teong, Marie-Veronique Bruno Contreras-Moreira, Timothy Ebbels, Bernard Clement, David Hsu, 11:20 a.m. - 11:45 a.m. Julio Collado-Vides Buxton, David Jones P S Thiagarajan

4 and 2nd Annual AB3C Conference: X-Meeting fortaleza, brazil - auGust 6-10, 2006 monday (auGust 7) Intelligent Systems for Molecular Biology

Main Auditorium Room E1 Room E2 Room A Room B1 Room B2 Room B3 (Hall D) (2nd Floor)

Database and Data Integration Paper 11: SNP Function Portal: Structural Bioinformatics a web database for exploring Paper 10: The iRMSD: A local the function implication of Systems Biology measure of sequence SNP alleles Paper 12: Bistable Switching alignment accuracy using Pinglang Wang, Manhong Dai, and Excitable Behaviour in structural information Weijian Xuan, Richard C the Activation of Src at Fabrice Armougom, Sebastien McEachin, Anne U Jackson, Mitosis Laura J Scott, Brian Athey, 11:45 a.m. - 12:10 p.m. Moretti, Vladimir Keduas, Hendrik Fuß, Werner Dubitzky, Cedric Notredame Stanley J. Watson, Fan Meng Stephen Downes, Mary Jo Kurth

Database and Data Integration Structural Bioinformatics Paper 14: Integrating Software Demo Paper 13: Improved pruning structured biological data by Systems Biology HP/Synamatix: algorithms and divide-and- kernel Maximum Mean Paper 15: Identification of Enhancement and conquer strategies for dead- Discrepancy metabolic units induced by Software Demo Acceleration of Genome Software Demo environmental signals end elimination, with Karsten Borgwardt, Arthur Web Services at the Assembly using Novel Pygr, the Python Graph application to protein design Gretton, Malte Rasch, Hans- Jose Nacher, Jean-Marc Pattern Indexing and Schwartz, , European Bioinformatics Database Framework for Ivelin Georgiev, Ryan Lilien, Peter Kriegel, Bernhard Institute Retrieval Application Bioinfomatics 12:10 p.m. - 12:35 p.m. Bruce Donald Schoelkopf, Alex Smola Tatsuya Akutsu

ISCB Open Business Birds of a Feather Birds of a Feather Birds of a Feather Birds of a Feather 12:35 p.m. - 2:00 p.m. Lunch - Hall F Meeting Flock Together Flock Together Flock Together Flock Together (12:45 p.m.- 1:45 p.m) Human Health Paper 17: Predicting the Structural Bioinformatics prognosis of breast cancer by Paper 16: Modelling sequential integrating clinical and Systems Biology protein folding under kinetic microarray data with Bayesian Paper 18: Inferring functional control using hp lattice networks pathways from multi- models Olivier Gevaert, Frank De Smet, perturbation data 2:00 p.m. - 2:25 p.m. Fabien Huard, Charlotte Deane, Dirk Timmerman, , Nir Yosef, Alon Kaufman, Graham Wood Bart De Moor Eytan Ruppin

Human Health Paper 20: AClAP, Autonomous Systems Biology Structural Bioinformatics hierarchical agglomerative Paper 21: Dynamical analysis Paper 19: A probabilistic Cluster Analysis based of a generic Boolean model approach to protein Protocol to partition for the control of the backbone tracing in electron conformational datasets mammalian cell cycle density maps Giovanni Bottegoni, Walter Adrien Fauré, Aurélien Naldi, Frank DiMaio, Jude Shavlik, Rocchia, Maurizio Recanatini, Claudine Chaouiya, 2:25 p.m. - 2:50 p.m. George Phillips Andrea Cavalli Denis Thieffry

Human Health Paper 23: Integrating copy number polymorphisms into Systems Biology Structural Bioinformatics array CGH analysis using a Paper 24: Computational Software Demo Paper 22: Learning MHC robust HMM inference of the molecular binding Sohrab Shah, Xiang Xuan, Ron logic for synaptic connectivity TreeDomViewer: A tool for Nebojsa Jojic, M. Reyes-Gomez, DeLeeuw, Mehrnoush Khojasteh, in C. elegans Software Demo the visualization of Software Demo Software Demo D. Heckerman, C. Kadie, Wan Lam, Raymond Ng, Vinay Varadan, David Miller III, EBI: Text Mining phylogeny and protein PATIKAweb BioModels Database 2:50 p.m. - 3:15 p.m. O. Furman-Schueler Kevin Murphy Dimitris Anastassiou domain structure

5 and 2nd Annual AB3C Conference: X-Meeting fortaleza, brazil - auGust 6-10, 2006 monday (auGust 7) Intelligent Systems for Molecular Biology

Main Auditorium Room E1 Room E2 Room A Room B1 Room B2 Room B3 (Hall D) (2nd Floor)

3:15 p.m. - 3:40 p.m. Coffee Break with Exhibitors - Hall C

New Frontiers Panel Introduction and Human Health Session Systems Biology Papaer 25: Decoding non- Paper 26: An integrative unique oligonucleotide approach for causal gene Chair: Goran Neshich, hybridization experiments of Embrapa/CNPTIA identification and gene targets related by a regulatory pathway inference phylogenetic tree Key Challenges in exploiting Zhidong Tu, Li Wang, Michelle Alexander Schliep, Arbeitman, Ting Chen, 3:40 p.m. - 4:05 p.m. biomolecular data for Sven Rahmann Medicine and Agriculture Fengzhu Sun , European Bioinformatics Institute,

Conceptual questions and Systems Biology key challenges in Paper 27: An equilibrium Software Demo partitioning model connecting computational biology PLoS Track 1: Knowledge- gene expression and cis-motif Genome Expression Software Demo , Memorial Sloan- Based Analysis of Genome- content Pathway Analysis Tool PIRSF Protein Classification Software Demo Kettering Cancer Center Wide SNP Scanning Data Joe Mellor, Charles DeLisi (GEPAT) System (PCS) 4:05 p.m. - 4:30 p.m. Fan Meng GenePro

PLoS Panel: BioTermNet: a system for biomedical text mining (Asako Koike) Imitating manual curation of text-mined facts in biomedicine (Raul Rodriguez-Esteban) PLoS Track 2: Datamining the SherLoc: Comprehensive Fourth Dimension from Crystal Prediction of Protein Structures: Function- Subcellular Localization by New Frontiers Structure-Entropy Integrating Clues from Relationships in Membrane Sequence Data and the Session Proteins Literature 4:30 p.m. - 4:55 p.m. Continued Ilan Samish (Hagit Shatkay)

Introduction of Keynote 2 - Main Auditorium (Hall D)

4:55 p.m. - 5:50 p.m. Keynote 2: - Structural biology, informatics and the discovery of new medicines

6:00 p.m. - 9:00 p.m. Poster Session with Authors (Odd Numbers) & Reception - Hall G

9:30 p.m. Shuttles depart Convention Center to Hotels

6 and 2nd Annual AB3C Conference: X-Meeting fortaleza, brazil - auGust 6-10, 2006 tuesday (auGust 8) Intelligent Systems for Molecular Biology

Main Auditorium Room E1 Room E2 Room A Room B1 Room B2 Room B3 (Hall D) (2nd Floor)

7:00 a.m. Shuttles depart Hotels to Convention Center

7:30 a.m. - 7:30 p.m. Registration - Hall G

Morning Welcome, Promotion - ISMB/ECCB 2007 - Introduction of Keynote 3 - Main Auditorium (Hall D)

8:45 a.m. - 9:55 a.m. Keynote 3: Kurt Wüthrich – Computational Aspects of NMR Studies with Proteins in Solution

Posters on Display - Hall G - 9:00 a.m. - 9:00 p.m. 9:00 a.m. - 9:00 p.m.

Molecular and New Frontiers Session Supramolecular Continued Dynamics Paper 29: DynaPred: A The future of the funding for structure and sequence biomolecular data and based method for the knowledge infrastructures: Sequence Analysis prediction of MHC class I proposition for a "Fortaleza Paper 28: Indel seeds for binding peptide sequences declaration” homology search and conformations , Swiss Institute of Denise Mak, Yevgeniy Gelfand, Iris Antes, Shirley Siu, 9:55 a.m. - 10:20 a.m. Bioinformatics Gary Benson

10:20 a.m. - 10:50 a.m. Coffee Break with Exhibitors - Hall C

Sequence Analysis Paper 30: Interpreting Text Mining & Information anonymous DNA samples from Extraction mass disasters --- Paper 31: Accessing Images in probabilistic forensic inference Bioscience Literature through using genetic markers User-Interface Designs and Tien-ho Lin, Eugene W. Myers, Natural Language Processing 10:50 a.m. - 11:15 a.m. Eric P. Xing Hong Yu, Minsuk Lee

New Frontiers Session Text Mining & Information Continued Extraction Sequence Analysis Paper 33: Finding the The changing face of Paper 32: BaCelLo: a evidences for protein-protein scientific dissemination as it interactions from PubMed balanced subcellular Software Demo applies to computational localization predictor abstracts Software Demo biology Andrea Pierleoni, Pier Luigi Hyunchul Jang, Jaesoo Lim, OpenMS - A Software Software Demo Software Demo myGrid and Phil Bourne, University of Martelli Piero Fariselli, Joon-Ho Lim, Soo-Jun Park, Platform for Shotgun IBM: Inferring Common Biological Concept ToolBus/PathPort 11:15 a.m. - 11:40 a.m. California Kyu-Chul Lee, Seon-Hee Park Proteomics Origins Diagram Editor (BCDE) Interoperability

7 and 2nd Annual AB3C Conference: X-Meeting fortaleza, brazil - auGust 6-10, 2006 tuesday (auGust 8) Intelligent Systems for Molecular Biology

Main Auditorium Room E1 Room E2 Room A Room B1 Room B2 Room B3 (Hall D) (2nd Floor)

Sequence Analysis Text Mining & Paper 34: On counting Information Extraction position weight matrix Paper 35: Novel unsupervised matches in a sequence, with feature filtering of biological application to discriminative data motif finding Roy Varshavsky, Assaf Gottlieb, 11:40 a.m. - 12:05 p.m. Saurabh Sinha , David Horn

Sequence Analysis Text Mining & Paper 36: Finding regulatory Information Extraction motifs with maximum density Paper 37: Integrating image subgraph data into biomedical text Eugene Fratkin, Brian categorization New Frontiers Session Naughton, Douglas Brutlag, Hagit Shatkay, Nawei Chen, 12:05 p.m. - 12:30 p.m. Continued Serafim Botzoglou Dorothea Blostein

Birds of a Feather Flock Together Birds of a Feather Semantic types: towards a Birds of a Feather ISCB Student Council Flock Together Flock Together common annotation schema Lunch - Hall F EBI User's Forum Open Meeting Cancer Biomedical Informatics for biomedical literature, D. Bioinformatics Core Facilities, 12:30 p.m. - 2:00 p.m. Grid (caBIG), Peter Covitz Rebholz-Schuhman Fran Lewitter

Transcriptomics Sequence Analysis Paper 38: Statistical Paper 39: Apples to apples: mechanical modeling of improving the performance of genome-wide transcription motif finders and their factor occupancy data by significance analysis in the PLoS Track 3: Gene MatrixREDUCE Twilight Zone Expression Trees in Blood Cell Development 2:00 p.m. - 2:25 p.m. Barrett Foat, Alexandre Patrick Ng, Niranjan Nagarajan, Morozov, Harmen Bussemaker Neil Jones, Uri Keich Ivan Costa

Software Demo Transcriptomics Sequence Analysis Extend Your Bioinformatics Paper 40: Quantification of Paper 41: CONTRAfold: RNA PLoS Track 4: Pervasive with Accelrys: Integration transcription factor expression secondary structure unproductive splicing of SR proteins of new tools in a common from arabidopsis images prediction without physics- workflow environment Software Demo Daniel Mace, Ji-Young Lee, based models associated with ultraconserved elements Software Demo expands capabilities and GeneChip Analysis System Software Demo 2:25 p.m. - 2:50 p.m. Richard Twigg, Juliette Colinas, Chuong Do, Daniel Woods, STING_RDB (WGAS) GNARE Philip Benfey, Uwe Ohler Steven Brenner biological context

8 and 2nd Annual AB3C Conference: X-Meeting fortaleza, brazil - auGust 6-10, 2006 tuesday (auGust 8) Intelligent Systems for Molecular Biology

Main Auditorium Room E1 Room E2 Room A Room B1 Room B2 Room B3 (Hall D) (2nd Floor)

Transcriptomics Sequence Analysis Paper 42: Identifying cycling Paper 43: Context-specific genes by combining sequence independence mixture homology and expression modeling for positional weight PLoS Track 5: Population data matrices Sequencing from Yong Lu, Roni Rosenfeld, Benjamin Georgi, Chromatogram Data 2:50 p.m. - 3:15 p.m. Ziv Bar-Joseph Alexander Schliep Nebojsa Jojic

Transcriptomics Paper 44: Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide Sequence Analysis expression profiles Paper 45: ARTS: Accurate Elena Edelman, Alessandro recognition of transcription PLoS Track 6: Sm/lsm genes: Software Demo Porrello, Justin Guinney, Bala starts in human a glimpse into early Balakumaran, Andrea Bild, Soeren Sonnenburg, Alexander Eukaryotic evolution Genetic Marker Search Software Demo 3:15 p.m. - 3:40 p.m. Phillip Febbo, Sayan Mukherjee Zien, Gunnar Raetsch Stella Veretnik Engine for Medline GObase

3:40 p.m. - 4:05 p.m. Coffee Break with Exhibitors - Hall C

Sequence Analysis Paper 47: Informative priors PLoS Track 7: Comparative Transcriptomics based on transcription factor analysis of the complete Paper 46: Efficient structural class improve de transcriptome of the ENCODE identification of DNA binding novo motif discovery regions in chimpanzees and partners in a sequence Leelavati Narlikar, Raluca humans database Gordan, Uwe Ohler, Philipp Khaitovich 4:05 p.m. - 4:30 p.m. Tobias Mann, William Noble Alexander Hartemink

Transcriptomics Paper 48: Semi-supervised analysis of gene expression profiles for lineage-specific Sequence Analysis development in the Paper 49: ProfilePSTMM: Caenorhabditis elegans capturing tree-structure Software Demo embryo motifs in carbohydrate sugar PLoS Track 8: The strength of BlueStar STING - A Yuan Qi, Patrycja Missiuro, chains Software Demo Software Demo multiplatform environment Software Demo Ashish Kapoor, Craig Hunter, Kiyoko Aoki-Kinoshita, selection on ultraconserved elements PRIDE and the Ontology Talk to Sun about Life for HARLEM (Hamiltonians to Tommi Jaakkola, David Gifford, Nobuhisa Ueda, Hiroshi Lookup Service Sciences Research LargE Molecules) 4:30 p.m. - 4:55 p.m. Hui Ge Mamitsuka, Minoru Kanehisa Christina Chen analysis

Introduction of Keynote 4 - Main Auditorium (Hall D)

4:55 p.m. - 5:50 p.m. Keynote 4: Overton Award: Mathieu Blanchette – What mammalian genomes tell us about our ancestors, and vice-versa

6:00 p.m. - 9:00 p.m. Poster Session with Authors (Even Numbers) & Reception - Hall G

9:30 p.m. Shuttles depart Convention Center to Hotels

9 and 2nd Annual AB3C Conference: X-Meeting fortaleza, brazil - auGust 6-10, 2006 wednesday (auGust 9) Intelligent Systems for Molecular Biology

Main Auditorium Room E1 Room E2 Room A Room B1 Room B2 Room B3 (Hall D) (2nd Floor)

7:30 a.m. - 1:30 p.m. Registration - Hall G

7:45 a.m. Shuttles depart Hotels to Convention Center

Morning Welcome and Introduction of Keynote 5 - Main Auditorium (Hall D)

8:45 a.m. - 9:50 a.m. Keynote 5: Elena Conti – Molecular mechanisms in RNA degradation

9:00 a.m. - 1:00 p.m. Posters on Display - Hall G - 9:00 a.m. - 2:00 p.m.

Ontologies Paper 51: A top-level ontology Evolution & Phylogeny of functions and its Paper 50: Constructing near- application in the Open PLoS Track 9: Automated Cell perfect phylogenies with Biomedical Ontologies Biology in Drug Discovery: multiple homoplasy events Patryk Burek, Robert Extracting Biological Ravi Vijaya Satya, Amar Hoehndorf, Frank Loebe, Johann Information from Images of Cell Mukherjee, Gabriela Alexe, Visagie, Heinrich Herre, 9:50 a.m. - 10:15 a.m. , Gyan Bhanot Eugeni Vaisberg Software Demo MARSMotif: Deciphering Software Demo Ontologies Transcriptional Evolution & Phylogeny Paper 53: An ontology for a PLoS Track 10: Predicting IMG/M: An Experimental Subnetworks from Paper 52: BNTagger: Improved robot scientist Biological Networks from Metagenome Data Microarray Expression tagging snp selection using Larisa Soldatova, Amanda Diverse Data: a New Role for Software Demo Management and Analysis Data using Regression 10:15 a.m. - 10:40 a.m. Clare, Andrew Sparkes, the Hsp90 Complex Software Demo bayesian networks The BioMAZE System System Splines STRING database Phil Hyoun Lee, Hagit Shatkay Ross King Chad Myers

Evolution & Phylogeny Paper 54: Mutation Ontologies PLoS Track 11: Gene parameters from sequence Paper 55: Protein classification Expression of C. elegans data using graph theoretic using ontology classification Neurons Carries Significant measures on lineage trees Katherine Wolstencroft, Phillip Information on Reuma Magori Cohen, Yoram Lord, Lydia Tabernero Andy Their Synaptic Connectivity 10:40 a.m. - 11:05 a.m. Louzoun, Steven Kleinstein Brass, Robert Stevens Alon Kaufman

11:05 a.m. - 11:35 a.m. Coffee Break with Exhibitors - Hall C

Introduction of Keynote 6 - Main Auditorium (Hall D)

11:35 a.m. - 12:30 p.m. Keynote 6: Charles DeLisi – New Approaches to Biomarker Discovery

12:30 p.m. Shuttles depart for Hotels and/or Beach Park for Delegates and off-site event ticket holders – 1:15 p.m. Last Departure

6:30 p.m. Shuttles depart to hotels from Beach Parkt

10 and 2nd Annual AB3C Conference: X-Meeting fortaleza, brazil - auGust 6-10, 2006 thursday (auGust 10) Intelligent Systems for Molecular Biology

Main Auditorium Room E1 Room E2 Room A Room B1 Room B2 Room B3 (Hall D) (2nd Floor)

7:30 a.m. - 5:30 p.m. Registration - Hall G

7:45 a.m. Shuttles depart Hotels to Convention Center

8:30 a.m. - 4:00 p.m. Posters on Display - Hall G

Morning Welcome and Introduction of Keynote 7 - Main Auditorium (Hall D)

8:45 a.m. - 9:50 a.m. Keynote 7: Rich Roberts – The need of Bioinformatics for experimental biologists

Proteomics Paper 56: Semi-Supervised LC/MS alignment for Comparative differential proteomics Paper 57: Hairpins in a Bernd Fischer, Jonas haystack: recognizing Grossmann, Volker Roth, Wilhelm microrna precursors in PLoS Track 12: Splice Form Gruissem, Sacha Baginsky, comparative genomics data Prediction using Machine Joachim M. Buhmann Jana Hertel, Peter F. Stadler Learning 9:50 a.m. - 10:15 a.m. Gunnar Rätsch

Proteomics Comparative Genomics Paper 58: Annotating proteins Paper 59: Comparative PLoS Track 13: The Software Demo by mining protein interaction genomics reveals unusually consequences of alternative Latin American Pathway Knowledge Software Demo networks long motifs in mammalian splicing on biological Mustafa Kirac, Gultekin genomes pathways BioInformatics Management System Software Demo The PANTHER 10:15 a.m. - 10:40 a.m. Ozsoyoglu, Jiong Yang Neil Jones, Pavel Pevzner Melissa Cline Introduction Session (PKMS) UniProtKB and InterPro Classification System

10:40 a.m. - 11:10 a.m. Coffee Break with Exhibitors - Hall C

Proteomics Paper 60: A model-based Comparative Genomics approach for mining Paper 61: Relative PLoS Track 14: Analysis of membrane protein contributions of structural pleiotropy during C. elegans crystallization trials designability and functional development and Sitaram Asur, Srinivasan diversity in fixation of gene interpretation with interactome Parthasarathy, Pichai Raman, duplicates networks 11:10 a.m. - 11:35 a.m. Matthew Eric Otey Boris Shakhnovich Hui Ge

Proteomics Paper 62: Peptide sequence Comparative Genomics tag-based blind identification Paper 63: Automatic clustering PLoS Track 15: Integrative of post-translational of orthologs and inparalogs Analysis of NCI-60 Panel Software Demo modification with point shared by multiple proteomes Reveals Candidate Key Latin American IntAct - an extensible Software Demo process model Andrey Alexeyenko, Ivica Genetic Regulators Affected BioInformatics Session open source framework CEP: Conformational Chunmei Liu, Bo Yan, Yinglei Tamas, Gang Liu, by Genomic Alterations for molecular interactions epitope prediction server 11:35 a.m. - 12:00 p.m. Song, Ying Xu, Liming Cai Erik Sonnhammer Doron Lipson Continued

11 and 2nd Annual AB3C Conference: X-Meeting fortaleza, brazil - auGust 6-10, 2006 thursday (auGust 10) Intelligent Systems for Molecular Biology

Main Auditorium Room E1 Room E2 Room A Room B1 Room B2 Room B3 (Hall D) (2nd Floor)

12:00 p.m. - 1:45 p.m. Lunch Reception & Late Breaking Poster Session with Authors - Hall G / Lunch with Exhibitors - Hall C

Comparative Genomics Paper 65: A Sequence-based filtering method for ncRNA Proteomics identification and its PLoS Track 16: Integration of Paper 64: Rapid knot application to searching for FRAP experiments and 3D detection and application to Riboswitch Elements simulations of diffusion in the protein structure prediction Shaojie Zhang, Ilya Borovok, lumen and surface of Firas Khatib, Matt Weirauch, Yair Aharonowitz, Roded Endoplasmic Reticulum 1:45 p.m. - 2:10 p.m. Carol Rohl Sharan, Petros Koumoutsakos

Proteomics Paper 66: A computational Comparative Genomics approach toward label-free Paper 67: Finding novel genes protein quantification using in bacterial communities predicted peptide isolated from the environment detectability Lutz Krause, Naryttza N. Diaz, Haixu Tang, Randy Arnold, Daniela Bartels, Robert A. PLoS Track 17: Comparison of Latin American Software Demo Pedro Alves, Zhiyin Xun, David Edwards, Alfred Pühler, Forest Alternative Splicing Structures BioInformatics Session Swiss-Prot Protein Clemmer, Milos Novotny, James Rohwer, Folker Meyer, in Eukaryotes Software Demo Knowledgebase: ready for 2:10 p.m. - 2:35 p.m. Michael Sammeth Continued Reilly, Predrag Radivojac Jens Stoye VisANT the future

PLoS Track 19: DOE Hanford PLoS Track 20: Probabilistic Site Metagenome: A multiple Genetic Networks analysis of PLoS Track 18: Comparative extreme environment that three Plasmodium falciparum Genomics of GPCRs: ET- hosts wide diversity of strains from dynamical Guided Annotation and Re- microbes and radiotolerant expression signals design of Aminergic Receptors bacteria Hernando del Portillo and 2:35 p.m. - 3:00 p.m. Olivier Lichtarge Mustafa Syed, Natalia Maltsev Roberto Cesar Junior Barrera

PLoS Track 22: Simplified Models of Evolution lead to PLoS Track 23: A Probabilistic Improved Prediction of Functional Gene Network of PLoS Track 21: Recursive Top- Functional Linkage from Worm: An Extensive and Down Quantum Correlated Gain and Loss of Accurate Systemic Model of a Latin American 3:00 p.m. - 3:25 p.m. Clustering of Biological Data Genes among Eukaryotes Multi-cellular Organism BioInformatics Session Michal Linial Daniel Barker Insuk Lee Continued

3:25 p.m. - 3:55 p.m. Coffee with Exhibitors - Hall C

Introduction of Keynote 8 - Main Auditorium (Hall D)

3:55 p.m. - 4:50 p.m. Keynote 8: Sr. Scientist Accomplishment Award: - Whole Genome Optical Mapping

4:50 p.m. - 5:15 p.m. Conference Awards and Closing

5:15 p.m. Shuttles depart Convention Center to Hotels

12