Agenda
[TOP] [ Friday, Dec 5 ] [ Saturday, Dec 6 ] [ Sunday, Dec 7 ]
Click on the presentation icon to access the PDF slides of each talk. |
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| [ Friday, Dec 5 ] [ Saturday, Dec 6 ] [ Sunday, Dec 7 ] | |
| Thursday – December 4, 2008 | |
| 3:00 pm – 6:00 pm | Registration |
| Friday - December 5, 2008 | |
| 7:30 am – 9:30 am | Registration & Continental Breakfast |
| 8:30 am – 9:15 am | Keynote 1 Cellular Network Based Identification of Master Regulators of Physiological and Oncogenic Processes Andrea Califano, Ph.D., Columbia University |
| 9:15 am – 10:25 am | Oral Presentations 1 - 7 |
| Oral Presentation 1 A Comparison of Next-state (dynamic) and Co-temporal (static) Modeling of Time Course Data: Multiple Approaches Provide Complementary Information Presenter: Edward E. Allen, Wake Forest University Additional Author(s): David J. John, William H. Turkett, Stan J. Thomas, Richard F. Loeser, Leslie B. Poole, Elizabeth M. Hiltbold, Jacquelyn S. Fetrow |
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| Oral Presentation 2 Evaluating Relevance Ranking and Query Expansion for MEDLINE Retrieval Presenter: Zhiyong Lu, NCBI Additional Author(s): Kim Won, John Wilbur |
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| Oral Presentation 3 On the Cache-Awareness in DNA Probe Selection Presenter: Carl Bergenhem, University of Connecticut Additional Author(s): Chih Lee and Chun-Hsi Huang |
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| Oral Presentation 4 Laboratree: Extensible Basic Research Application and Data Management Using the OpenSocial Platform Presenter: Jamison R. Hemmert, Indiana University Additional Author(s): Brandon Peters, Joshua D. Waymire, Kishore K. Kamati, Peter H. Baenziger, Craig A. Sanders, Joy A. Nellis, Justin J. Dantzer, Peter J. Serguta, Jessica L. Dantzer, Sean D. Mooney |
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| Oral Presentation 5 Beyond Dictionary Match for Disease Named Entity Recognition Presenter: Robert Leaman, Arizona State University Additional Author(s): Christopher Miller, Graciela Gonzalez |
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| Oral Presentation 6 Graph Theoretic Properties of Known Complexes Presenter: Suzanne Gallagher, University of Colorado Additional Author(s): Debra S. Goldberg |
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| Oral Presentation 7 Discovery of HuR Binding Sites Using a Machine Learning Approach Presenter: Shweta Bhandare, University of Colorado Boulder Additional Author(s): Debra Goldberg, Jon Miller, Paul Johnson, Nick Farina |
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| 10:25 am – 10:45 am | AM Break |
| 10:45 am – 11:45 am | Oral Presentations 8 - 13 |
| Oral Presentation 8 Textual Characteristics of Full-text Biomedical Journal publications in Open Access vs. Traditional Journals Presenter: Karin Verspoor, University of Colorado Denver Additional Author(s): K. Bretonnel Cohen, Larry Hunter |
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| Oral Presentation 9 A Collaborative Framework for Knowledge Guided Exploration Presenter: Scott Fujan, University of Tulsa Additional Author(s): Cody Pollet, Stephen Tyree, John Hale |
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| Oral Presentation 10 JANUS - A System for Annotating, Vetting and Testing Natural Language Processing Systems Presenter: Anni Coden, IBM T.J. Watson Research Center Additional Author(s): Michael Tanenblatt, Anni Coden, Igor Sominsky |
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| Oral Presentation 11 Using Protein Functional Features to Predict Deleterious Mutations Using Saturation Mutagenesis Data Presenter: Uday S. Evani, Indiana University Additional Author(s): Uday S. Evani, Vidhya Krishnan, Sean D. Mooney |
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| Oral Presentation 12 An Abstraction for Quantitatively Capturing Stochastic Bistable Oscillations in Enzymatic Futile Cycle Presenter: Hiroyuki Kuwahara, The Microsoft Research - University of Trento |
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| Oral Presentation 13 Learning Causal Relationships between Genes from Steady State Data: Algorithms, Simulation and Application Presenter: Michael P. Verdicchio, Arizona State University Additional Author(s): Xin Zhang, Seungchan Kim, Chitta Baral |
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| 11:45 pm – 12:30 pm | Keynote 2 Next-generation Extraction: Ad-hoc Knowledge Networks Graciela Gonzalez, Arizona State University |
| 12:30 pm – 4:00 pm | Break |
| 4:00 pm – 5:00 pm | Workshop Session: Computational Bioethics: Issues and Didactic Strategies Presenters: Lawrence Hunter Director, Computational Bioscience Program, UC Denver Mark Yarborough, Director Center for Bioethics and the Humanities, UC Denver |
| 5:00 pm – 6:00 pm | Oral Presentations 14 - 19 |
| Oral Presentation 14 Reflect – Augmented Browsing for the Life Scientist Presenter: Reinhard Schneider, EMBL Heidelberg Additional Author(s): Evangelos Pafilis, Seán I. O’Donoghue, Lars J. Jensen, Heiko Horn, Michael Kuhn, Nigel P. Brown |
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| Oral Presentation 15 Using the OpenSocial Platform to Develop Open, Exchangeable Web Based Biomedical Research Applications Presenter: Joshua Waymire, Indiana University Additional Author(s): Brandon Peters, Jessica L. Dantzer, Sean D. Mooney |
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| Oral Presentation 16 Category Theory and the Notion of Natural in Bioinformatic Models Presenter: Peter Salamon, San Diego State University Additional Author(s): James Nulton, David Aaby, Andrew Detzel, Barbara Bailey |
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| Oral Presentation 17 A Novel Gene Regulatory Model for Embryonic Cell Differentiation in Drosophila Melanogaster Presenter: Tejaswi Gowda, Arizona State University Additional Author(s): Sarma Vrudhula, Seungchan Kim |
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| Oral Presentation 18 Was Vioxx the Culprit? Presenter: Jack Horner, Independent Researcher |
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| Oral Presentation 19 Optimizing Proteomic Biomarker Discovery – Incorporating Prior Experimental Data Presenter: David Gnabasik, University of Colorado Boulder Additional Author(s): Mark Duncan, David Gnabasik |
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| 6:30 pm – 10:00 pm | Banquet Location: Il Poggio Restaurant, Snowmass Village |
| [TOP] [ Friday, Dec 5 ] [ Saturday, Dec 6 ] [ Sunday, Dec 7 ] | |
| Saturday, December 6, 2008 | |
| 7:30 am – 9:30 am | Registration & Continental Breakfast |
| 8:30 am – 9:15 am | Keynote 3 Biomedical Informatics: Its Scientific Evolution and Future Promise Edward H. Shortliffe, MD, PhD, University of Arizona, Phoenix |
| 9:15 am – 10:25 am | Oral Presentations 20 - 26 |
| Oral Presentation 20 Mechanism-based Inference of Drugs to Diseases using Drug-driven Ontologies and Semantic Infrastructure Presenter: Eric Neumann, Science Commons, MIT Additional Author(s): Angela Qu, Ranga Gudivada, Bruce Aronow |
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| Oral Presentation 21 Sequence Cooccurrence and Covariation Suggest Specific Physical Interactions Between Type VI Secretion System Components Presenter: J. Gregory Caporaso, University of Colorado Denver Additional Author(s): Amy Dear, Larry Hunter, Marcelo Sousa, Rob Knight |
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| Oral Presentation 22 Modelling Elastin Self-Assembly Presenter: Hongyan Song, Hospital for Sick Children Additional Author(s): John Parkinson |
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| Oral Presentation 23 A Statistical Framework for Differential Network Analysis (DNA) from Microarray Data using Partial Least Squares Presenter: Susmita Datta, University of Louisville Additional Author(s): Ryan Gill, Vasyl Pihur, Somnath Datta |
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| Oral Presentation 24 A Statistical Approach to Better Assess Environmental Community Taxonomy and Average Genome Size Presenter: Florent Angly, San Diego State University Additional Author(s): Dana Willner, Robert Schmieder, Forest Rohwer |
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| Oral Presentation 25 Sponge Evolution and the Rise of Animals Presenter: Davide Pisani, The National University of Ireland Maynooth Additional Author(s): Erik Sperling, Kevin J. Peterson |
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| Oral Presentation 26 Archaebacterial Homologs are More Central to Eukaryotic Metabolism than Eubacterial Homologs Presenter: James McInerney, National University of Ireland Additional Author(s): James Cotton |
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| 10:25 am – 10:45 am | AM Break |
| 10:45 am – 11:45 am | Oral Presentations 27 - 32 |
| Oral Presentation 27 Atomic Density Sheds Light on the Evolutionary Characteristics of Proteins Presenter: Jennifer Commins, Smurfit Inst of Genetics, Trinity College Dublin Additional Author(s): Jennifer Commins and Mario Fares | |
| Oral Presentation 28 Reverse-engineering Protein Interaction Network Evolution Presenter: Todd A. Gibson, University of Colorado Denver Additional Author(s): Debra S. Goldberg |
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| Oral Presentation 29 The Phylogeny of the MHPs and Beyond Presenter: Mary J. O'Connell, Dublin City University Additional Author(s): Noeleen B. Loughran, Brendan O'Connor, Ciaran O'Fagain |
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| Oral Presentation 30 Next Generation Evolutionary Genomics: Why wait for Complete Genomes? Presenter: Todd Castoe, University of Colorado School of Medicine Additional Author(s): Wanjun Gu, Jason de Koning, Vijetha Vemulapalli, David Pollock |
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| Oral Presentation 31 Rapid Inference of Complex Patterns of Protein Evolution from Large Phylogenomic Data Sets Presenter: Jason de Koning, University of Colorado Denver Additional Author(s): Wanjun Gu, David D. Pollock |
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| Oral Presentation 32 Looking for a Needle in a Haystack - Identifying Transcription Factor Binding Sites Using a Phylogenetic Magnifying Glass Presenter: Elizabeth Siewert, University of Colorado Denver Additional Author(s): Katerina Kechris |
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| 11:45 am – 12:30 pm | Keynote 4 New Computational Tools for Investigating the Systems Biology of Heart Development Vincent VanBuren, Texas A & M HSC College of Medicine |
| 12:30 pm – 4:00 pm | Break |
| 4:00 pm – 5:30 pm | Oral Presentations 33 - 41 |
| Oral Presentation 33 Gene Function Prediction Using Prior Knowledge and Expression Data Presenter: Luis Tari, Arizona State University Additional Author(s): Chitta Baral, Seungchan Kim |
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| Oral Presentation 34 Natbox: A Network Analysis Toolbox in R Presenter: Shweta S. Chavan, UALR / UAMS Joint Bioinformatics program Additional Author(s): Marco Scutari, Radhakrishnan Nagarajan |
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| Oral Presentation 35 Towards a Multi-Level Calculus for Cellular Modeling and Simulation Presenter: Rayus Kuplicki, University of Tulsa Additional Author(s): Stephen Tyree, Trevor Sarratt, Scott Fujan, John Hale |
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| Oral Presentation 36 Improving the Prediction of Regulatory SNPs Using Functional Information Presenter: Yiqiang Zhao, Indiana University Additional Author(s): Matt Mort, David Cooper, Sean Mooney |
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| Oral Presentation 37 A Two-stage Adaptive Design can Increase Power for Multiple Comparisons Presenter: Deborah Glueck, Colorado School of Public Health Additional Author(s): Anis Karimpour-Fard |
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| Oral Presentation 38 A New Mapping Tool for Next Generation Sequencing Reads Presenter: Alex Poole, University of Colorado Additional Author(s): Wanjun Gu, and David Pollock |
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| Oral Presentation 39 Predicting Temperature-sensitive Mutations Derived From Single Amino Acid Substitutions Presenter: Ping Ye, Washington State University |
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| Oral Presentation 40 Entity Mention Normalization - Taking Another Step Towards Integrating Data Extracted from Literature with Databases Presenter: Jörg Hakenberg, Arizona State University Additional Author(s): Graciela Gonzalez |
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| Oral Presentation 41 Extended Analysis and Prediction of Gain and Loss of Phosphorylation Sites in Cancer Presenter: Peter H. Baenziger, Indiana University School of Medicine Additional Author(s): Maricel G. Kann, Matthew Hahn, Matthew E. Mort, Predrag Radivojac, Sean D. Mooney |
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| 5:30 pm – 7:30 pm | Poster Session/Reception Location: Eldorado A&B Room, Silvertree Hotel |
| [TOP] [ Friday, Dec 5 ] [ Saturday, Dec 6 ] [ Sunday, Dec 7 ] | |
| Sunday, December 7, 2008 | |
| 7:30 am - 9:30 am | Registration & Continental Breakfast |
| 8:30 am – 9:15 am | Keynote 5 Visual Analytics and Flow Cytometry Visualization using SFA Chris Shaw, Simon Fraser University |
| 9:15 am – 10:15 am | Oral Presentations 42 - 48 |
| Oral Presentation 42 MutDB: Enhanced Biochemical Analysis of Structural and Functional Features of Genetic Variations Presenter: Kishore Kamati, Indiana University Additional Author(s): Rakesh Sathyesh, Matthew Mort, Arti Singh, Adebayo Olowoyeye, Jessica Dantzer, Charles Moad, Vidhya G. Krishnan, Peter H. Baenziger, Maricel G. Kann, Predrag Radivojac, Randy Heiland, Sean D. Mooney |
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| Oral Presentation 43 Molecular Characterization of Insertional Mutagenesis Sites in Gene Therapy Studies Presenter: Jessica Dantzer, Indiana University School of Medicine Center Additional Author(s): Brandon Peters, Sara Dirscherl, Jonathan Nowacki, Scott Cross, Xiaoman Li, Kenneth Cornetta, Mary C. Dinauer, Sean D. Mooney |
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| Oral Presentation 44 Steps Toward Broad-spectrum Countermeasures: Discovering Virulence-associated Genes Present in Diverse Pathogens Presenter: Chris Stubben, Los Alamos National Lab Additional Author(s): Melanie Duffield, Murray Wolinsky |
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| Oral Presentation 45 Modeling the Malaria Parasite-Mosquito Midgut Cell Interactions Presenter: Ezekiel Adebiyi, Covenant University Additional Author(s): Gbenga Oluwagbemi, Seydou Doumbia |
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| Oral Presentation 46 Use of NMPDR Subsystems-based Annotation and Genome Comparison Tools for Understanding Streptococcus Pyogenes Virulome Presenter: Ramy Aziz, San Diego State University and Cairo University Additional Author(s): Leslie K. Mcneil, Ross Overbeek, Rick Stevens, Veronika Vonstein, Malak Kotb, Robert A. Edwards |
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| Oral Presentation 47 Sensitive and Specific Cross-Species cDNA-to-Genome Alignment with Spaced Seeds Presenter: Leming Zhou, University of Pittsburgh Additional Author(s): Liliana Florea | |
| Oral Presentation 48 Prediction of Functional Sites in Predicted Protein Structures Using Dynamics Perturbation Analysis Presenter: Judith D. Cohn, Los Alamos National Laboratory Additional Author(s): Michael E. Wall |
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| 10:35 am - 10:45 am | AM Break |
| 10:45 am – 11:45 am | Oral Presentations 49 - 55 |
| Oral Presentation 49 Reconstructing the Metabolic Network: a Probabilistic Approach to Improve Enzyme Prediction Presenter: Stacy Hung, Hospital for Sick Children Additional Author(s): James Wasmuth, John Parkinson |
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| Oral Presentation 50 The Topology of the Bacterial Co-conserved Protein Network and its Implications for Predicting Protein Function Presenter: Anis Karimpour-Fard, University of Colorado Denver Additional Author(s): Sonia M. Leach, Ryan T. Gill, Lawrence E. Hunter |
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| Oral Presentation 51 High Throughput Metagenome Analysis Presenter: Rob Edwards, San Diego State University |
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| Oral Presentation 52 Computational Assessment of Screening Statistics with NoiseMaker Presenter: Phoenix Kwan, ThermoFisher Scientific Additional Author(s): Amanda Birmingham |
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| Oral Presentation 53 COBRA: A Web-based Tool for Genotype/phenotype Data Management Presenter: Brandon Peters, IU School of Medicine Additional Author(s): Rebecca Fletcher, Kirthi Krishnamraju, Anne Nguyen, Jason Robarge, Lang Li, Mark Crowder, Todd Skaar, David Flockhart, Sean Mooney |
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| Oral Presentation 54 Analysis of Workflows on Inexpensive, Massive Computational Grids in the Cloud Presenter: Jason A. Stowe, Cycle Computing Additional Author(s): Ian D. Alderman, Dr. Irene M. Ong |
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| Oral Presentation 55 Analyses of Features for Prediction of Protein-protein Interactions in Protein Hetero-complexes and Their Impact on Human Disease Presenter: Angshuman Bagchi, Indiana University School of Medicine Additional Author(s): Eunseog Youn, Sean D. Mooney | |
| 11:45 am – 12:30 pm | Keynote 6 Hybrid Computers Need Hybrid Algorithms Kirk E. Jordan, Computational Science Center, IBM T.J. Watson Research Center |
| 12:30 pm | Adjourn |
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