Conference Program
| Tuesday, August 11, 2009 | |
| 8:15 AM | Opening Remarks |
| 8:30 AM | Session I: Genomics and Genetics - I |
| 8:30 AM | MSOAR 2.0: Incorporating Tandem Duplications into Ortholog Assignment Based on Genome Rearrangement Guanqun Shi, Liqing Zhang and Tao Jiang |
| 8:55 AM | Combinatorial Reconstruction of Half-Sibling Groups Saad I. Sheikh, Tanya Y. Berger-Wolf, Ashfaq A. Khokhar, Isabel C. Caballero, Mary V. Ashley, Wanpracha Chaovalitwongse and Bhaskar DasGupta |
| 9:20 AM | Ranking Genes by Relevance to a Disease Shivani Agarwal and Shiladitya Sengupta |
| 9:45 AM | COFFEE BREAK |
| 10:15 AM | Session II: Keynote Address – Jonathan Eisen Seeking out the dark matter of the biological universe and the need for a phylogeny driven genomic encyclopedia Download slides (~18.4 MB PDF) |
| 11:00 AM | Session III: Structural Bioinformatics - I |
| 11:00 AM | Modeling and Inference of Sequence-structure Specificity Hetunandan Kamisetty, Bornika Ghosh, Chris Bailey-Kellogg and Christopher James Langmead |
| 11:25 AM | A Systematic Study of Homologous Protein Structures with Insertions/Deletions Ryangguk Kim, Jon McCafferty and Jun-tao Guo |
| 11:50 AM | LUNCH - Dohrmann Grove |
| 1:20 PM | POSTER SESSION Abstracts |
| 2:20 PM | Session IV: Invited Talk – Vijay Pande Simulating the Molecular Basis for Alzheimer's Disease: Application of Novel Simulation and Datamining Techniques, Combined with Petascale Distributed Computing |
| 3:20 PM | Session V: Structural Bioinformatics - II |
| 3:20 PM | A Mesoscopic Model for Molecular Dynamics Studies of RNA Nanostructures Max Paliy, Roderick Melnik, and Bruce Shapiro |
| 3:45 PM | A Set-cover-based Approach for Inexact Graph Matching Misael Mongiově, Raffaele Di Natale, Rosalba Giugno, Alfredo Pulvirenti, Alfredo Ferro and Roded Sharan Best Paper Award |
| 4:10 PM | COFFEE BREAK |
| 4:40 PM | Session VI: Transcriptomics and Proteomics |
| 4:40 PM | Peptide Identification Using Both Spectrum Libraries and Protein Databases Marshall Bern |
| 5:05 PM | Understanding Distal Transcriptional Regulation from Sequence, Expression and Interactome Perspectives Arvind Rao, David J. States, Alfred O. Hero, III, and James Douglas Engel |
| 5:30 PM | A Close-to Optimum Bi-clustering Algorithm for Microarray Gene Expression Data Guojun Li, Qin Ma, Bingqiang Liu, Haibao Tang, Andrew H. Paterson and Ying Xu |
| 5:55 PM | Nonnegative Least Square – A New Look Into SAGE Data Erliang Zeng and Mitsunori Ogihara |
| 6:30 PM | DINNER - Dohrmann Grove |
| Wednesday, August 12, 2009 | |
| 8:30 AM | Session VII: Biological Pathways and Networks - I |
| 8:30 AM | Conditional Pathway Integration Alexandra Skolozub, Ofer Sarig and Ron Y. Pinter |
| 8:55 AM | A Pathway Approach to Identify Conserved Regulatory-metabolic Network Elements Yunlei Li, Jan Bot, Marcel J.T. Reinders and Dick de Ridder |
| 9:20 AM | Managing and Querying Mammalian Metabolic Networks: A Metabolism Query Language and Its Query Processing Ali Cakmak, Gultekin Ozsoyoglu and Richard W. Hanson |
| 9:45 AM | COFFEE BREAK |
| 10:15 AM | Session VIII: Functions and Interactions |
| 10:15 AM | GOstruct: Prediction of Gene Ontology Terms Using Methods for Structured Output Spaces Artem Sokolov and Asa Ben-Hur |
| 10:40 AM | Characterizing the Space of Interatomic Distance Distribution Functions Consistent with Solution Scattering Data Paritosh A. Kavathekar, Bruce A. Craig, Alan M. Friedman, Chris Bailey-Kellogg and Devin J. Balkcom |
| 11:05 AM | Improved Small Molecule Activity Determination via Centroid Nearest Neighbors Classification Phuong Dao, Farhad Hormozdiari, Hossein Jowhari, S.Cenk Sahinalp, Ken Byler and Artem Cherkasov |
| 11:30 AM | LUNCH - Dohrmann Grove |
| 1:00 PM | POSTER SESSION Abstracts |
| 2:00 PM | Session IX: Keynote Address – David Haussler Molecular Evolution and Cancer Genomics |
| 3:00 PM | COFFEE BREAK |
| 3:30 PM | Session X: Genomics and Genetics – II |
| 3:30 PM | A General Graphical Framework for Detecting Copy Number Variations Xiao-Lin Yin and Jing Li |
| 3:55 PM | Characteristic Restriction Endonuclease Cut Order for Classification and Identification of Fungal Sequences Rajib Sengupta, Dhundy Bastola and Hesham Ali |
| 4:20 PM | Session XI: Biological Pathways and Networks – II |
| 4:20 PM | Generalized Queries and Bayesian Statistical Model Checking in Dynamic Bayesian Networks: Application to Personalized Medicine Christopher James Langmead |
| 4:55 PM | Computational Modeling of Pathway Dynamics for Detecting Drug Effects: Paradoxical Effects of LY303511 on TRAIL-Induced Apoptosis Yuan Shi, Simi M. Varghese, Sinong Huang, Jacob White, Shazib Pervaiz and Lisa Tucker-Kellogg |
| 5:20 PM | Closing Remarks |