Full Agenda
updated October 27, 2009
| go directly to: [Friday - December 11] [Saturday - December 12] | |
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| Thursday – December 10, 2009 | |
| 11:00 am – 1:00 pm | Registration |
| 1:00 pm – 1:45 pm | Keynote 1 |
| 1:45 pm – 1:55 pm | Oral Presentation 1 Helping Biologists Understand their Data: An Update on the Hanalyzer System Presenter: William A Baumgartner, Jr., University of Colorado Denver Authors: William A Baumgartner Jr, Hannah Tipney, Lawrence Hunter |
| 1:55 pm – 2:05 pm | Oral Presentation 2 Thermodynamics-inspired ncRNA Search Presenter: Jennifer Smith, Boise State University Authors: Jennifer Smith, Pamila Ward |
| 2:05 pm – 2:15 pm | Oral Presentation 3 Algorithm to Improve Gene Consistency Across Bacterial Genomes Presenter: Judith D. Cohn, Los Alamos National Laboratory Authors: Judith D. Cohn, Michael E. Wall, John Dunbar |
| 2:15 pm – 2:25 pm | Oral Presentation 4 A Genome-wide Analysis of Poised Promoters in Bacteria Presenter: Marko Djordjevic, Arkansas State University & The Arkansas Biosciences Institute Authors: Marko Djordjevic |
| 2:25 pm – 2:35 pm | Oral Presentation 5 Structure-Based Prediction of DNA Binding Sites for Families of Transcription Factors Presenter: Julia Ponomarenko, University of California, San Diego Authors: Julia Ponomarenko |
| 2:35 pm – 2:45 pm | Oral Presentation 6 Genome-wide Discovery of Human Heart Enhancers Presenter: Ivan Ovcharenko, NIH Authors: Leelavati Narlikar, Noboru Sakabe, Alexander Blanski, Fabio Arimura, Marcelo Nobrega, Ivan Ovcharenko |
| 2:45 pm – 3:00 pm | Break (15 minutes) |
| 3:00 pm – 3:10 pm | Oral Presentation 7 Development of Methods for Integrating Diverse Sources of Genome-Scale Data Presenter: Daniel Dvorkin, University of Colorado Denver Authors: Daniel Dvorkin, Katerina Kechris |
| 3:10 pm – 3:20 pm | Oral Presentation 8 Visualizing Genomic Sequences in 2D Presenter: Josiah Seaman, Colorado State University Authors: Josiah Seaman |
| 3:20 pm – 3:30 pm | Oral Presentation 9 Automated Inference of Molecular Mechanisms of Disease from Amino Acid Substitutions Presenter: Biao Li, School of Informatics and Computing, Indiana University Authors: Biao Li, Vidhya G. Krishnan, Matthew E. Mort, Fuxiao Xin, Kishore K. Kamati, David N. Cooper, Sean D. Mooney, Predrag Radivojac |
| 3:30 pm – 3:40 pm | Oral Presentation 10 A User Study of Attribute Visualization Tools and Their Role in Understanding Biological Networks Presenter: Hande Kucuk, Eastern Michigan University Authors: Hande Kucuk, Benjamin J. Keller, Terry Weymouth, Barbara Mirel |
| 3:40 pm – 3:50 pm | Oral Presentation 11 NeuroIE: Extracting Neuroimaging Study Results from the Literature Presenter: Yong Gao, Mass General Hospital/Harvard Medical School Authors: Yong Gao; Dave Kennedy |
| 3:50 pm – 4:00 pm | Oral Presentation 12 Analysis of a Local Huntingtin Protein Interaction Network Presenter: Corey Powell, Buck Institute for Age Research Authors: Corey Powell, Robert Hughes, Cendrine Tourette, Russell Bell, Sean Mooney |
| 4:00 pm – 4:10 pm | Oral Presentation 13 In Silico Functional Profiling of Human Disease-Associated and Polymorphic Amino Acid Substitutions Presenter: Vidhya G. Krishnan, Buck Institute for Age Research Authors: Matthew Mort, Uday S. Evani, Vidhya G. Krishnan, Kishore K. Kamati Peter H. Baenziger, Anghuman Bagchi, Brandon Peters, Rakesh Sathyesh, Biao Li, Yanan Sun, Bin Xue, Nigam Shah, Maricel Kann, David N. Cooper, Predrag Radivojac, Sean D. Mooney |
| 4:10 pm – 4:25 pm | Break (15 minutes) |
| 4:25 pm – 5:10 pm | Keynote 2 |
| 5:10 pm – 5:20 pm | Oral Presentation 14 Accelerating Candidate Gene Discovery through Ontological Indexing of Large Scale Data Repositories Presenter: Simon Twigger, Medical College of Wisconsin Authors: Simon Twigger, Joey Geiger, Jennifer Smit |
| 5:20 pm – 5:30 pm | Oral Presentation 15 Knowledge Network Approach: Pathways and Drugs Presenter: Nikolai Daraselia, Ariadne Authors: Nikolai Daraselia, Ekaterina Kotelnikova, AntonYuryev |
| 5:30 pm – 5:40 pm | Oral Presentation 16 Can We Accurately Determine the Fittest Genes in Nature? Presenter: Ramy K. Aziz, San Diego State University Authors: Ramy K. Aziz, Mya Breitbart, Robert Edwards |
| 5:40 pm – 5:50 pm | Oral Presentation 17 Assessing Models of Protein Interaction Network Evolution Presenter: Todd A. Gibson, University of Colorado Denver Authors: Todd A. Gibson, Debra S. Goldberg |
| 5:50 pm – 6:00 pm | Oral Presentation 18 Gene and Genome Trees Conflict at Many Levels Presenter: Leanne S. Haggerty, NUI Maynooth Authors: Leanne S. Haggerty, Fergal J. Martin, David A. Fitzpatrick, James O. McInerney |
| 6:00 pm – 6:10 pm | Oral Presentation 19 Protein-protein Interactions are Driven by Functional Evolution Presenter: Yiqiang Zhao, Buck Institute for Age Research Authors: Yiqiang Zhao, Sean Mooney |
| 6:10 pm – 6:20 pm | Oral Presentation 20 Evolutionary Study and Prediction of Protein-protein Interactions in Chromatin Modification Complexes Presenter: Xuejian Xiong, Research Institute at the Hospital for Sick Children Authors: Xuejian Xiong, Tuan On, Shuye Pu, Andrei Turinsky, Yunchen Gong, Andrew Emili, Zhaolei Zhang, Jack Greenblatt, Shoshana J. Wodak, John Parkinson |
| 7:00 pm – 9:00 pm | Dinner |
| go directly to: [Thursday - December 10] [Saturday - December 12] | |
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| Friday – December 11, 2009 | |
| 9:00 am – 9:45 am | Keynote 3 |
| 9:45 am – 9:55 am | Oral Presentation 21 An Individual Based Modelling Approach to Studying the Evolution of Mate Choice Strategy Presenter: Robert Williamson, Rose-Hulam Institute of Technology Authors: Robert Williamson |
| 9:55 am – 10:05 am | Oral Presentation 22 MtHaplogroups: A Curated Web Resource for Mitochondrial Variation Presenter: Michael V. Osier, Rochester Institute of Technology Authors: Kyle Dewey, Eric Stevens, Dina L. Newman, Michael V. Osier |
| 10:05 am – 10:15 am | Oral Presentation 23 Posterior-Predictive Detection Of Molecular Co-Evolution Using Phylogenetically-Integrated Mutual Information Presenter: A.P. Jason de Koning, University of Colorado Denver Authors: A.P. Jason de Koning, Todd A. Castoe, Hyun-min Kim, David D. Pollock |
| 10:15 am – 10:25 am | Oral Presentation 24 Bioinformatics Characterization Of The Plasmodium Glutathione S-Transferase Presenter: Emilee Colón, University of Puerto Rico-School of Medicine Authors: Emilee Colón, Adelfa Serrano, Hugh NicholasJr., Troy Wymore, Alexander Ropelewski, Ricardo González Méndez |
| 10:25 am – 10:35 am | Oral Presentation 25 Leveraging Existing Biological Knowledge in Genome Wide Association Studies Presenter: Ronald Schuyler, University of Colorado Anschutz Medical Campus Authors: Ronald Schuyler, Lawrence Hunter, Deborah Glueck |
| 10:35 am – 10:45 am | Oral Presentation 26 Leveraging Existing Biological Knowledge in Genome Wide Association Studies Presenter: Ronald Schuyler, University of Colorado Anschutz Medical Campus Authors: Ronald Schuyler, Lawrence Hunter, Deborah Glueck |
| 10:45 am – 11:00 am | Break (15 minutes) |
| 11:00 am – 11:10 am | Oral Presentation 27 Wow! That's Really Interesting! Presenter: Hannah Tipney, University of Colorado Authors: Hannah Tipney, Lawrence Hunter |
| 11:10 am – 11:20 am | Oral Presentation 28 Global Optimization in Nonlinear Models: Optimization and Evolution in Metabolic Networks Presenter: Albert Sorribas, CMB - IRBLLEIDA - University of Lleida Authors: Albert Sorribas, Carlos Pozo, Gonzalo Guillén-Gosálbez, Laureano Jimenez, Rui Alves |
| 11:20 am – 11:30 am | Oral Presentation 29 Virus Discovery by Deep Sequencing and Assembly of Virus-derived Small Silencing RNAs Presenter: Qingfa Wu, UC Riverside Authors: Qingfa Wu, Yingjun Luo, Rui Lu, Nelson Lau, Eric C Lai, Wan-Xiang Li, Shou-Wei Ding |
| 11:30 am – 11:40 am | Oral Presentation 30 Prediction of Protein Protein Interaction Sites and Their Impact on Genetic Disease Presenter: Angshuman Bagchi, Buck Institute for Age Research Authors: Angshuman Bagchi, Eunseog Youn, Matthew E. Mort, David N. Cooper, Sean D. Mooney |
| 11:40 am – 11:50 am | Oral Presentation 31 Optimal Nearest Shrunken Centroids Method for High-dimensional Data Classification Presenter: Tiejun Tong, University of Colorado at Boulder Authors: Tiejun Tong, Herbert Pang |
| 11:50 am – 12:00 pm | Oral Presentation 32 Retrobiosynthesis: Searching Backwards, Looking Forwards Presenter: Dan McShan, UC Denver Health Sciences Authors: Dan McShan |
| 12:00 pm – 4:00 pm | Break |
| 4:00 pm – 4:45 pm | Keynote 4 |
| 4:45 pm – 4:55 pm | Oral Presentation 33 Experiments with Biological Concept Recognition Tools Presenter: Karin Verspoor, University of Colorado Denver Authors: Karin Verspoor, Kevin B. Cohen, Helen Johnson, Christophe Roeder, Cesar Mejia, William Baumgartner Jr., Larry Hunter |
| 4:55 pm – 5:05 pm | Oral Presentation 34 Test Suite Design for Biomedical Ontology Concept Recognition Systems Presenter: K. Bretonnel Cohen, U. Colorado School of Medicine Authors: K. Bretonnel Cohen, Karin Verspoor, Christophe Roeder, William A. Baumgartner Jr., Lawrence Hunter |
| 5:05 pm – 5:15 pm | Oral Presentation 35 Predicting Protein Linkages in Bacteria: Which Method is Best Depends on Task Presenter: Anis Karimpour-Fard, University of Colorado Denver Authors: Anis Karimpour-Fard, Sonia M. Leach, Ryan T. Gill, Lawrence E Hunter |
| 5:15 pm – 5:25 pm | Oral Presentation 36 A Metagenomic Study of a Microbial Mat in a Hawaiian Lava Cave Presenter: Gayle K. Philip, NASA Astrobiology Institute Authors: Gayle K. Philip, Mark V. Brown, Stuart P. Donachie |
| 5:25 pm – 5:35 pm | Oral Presentation 37 Mobile Metagenomics: Annotating DNA Sequences On A Cell Phone Presenter: Josh Hoffman, San Diego State University Authors: Josh Hoffman, Daniel Cuevas, Robert Edwards |
| 5:35 pm – 5:45 pm | Oral Presentation 38 The Colorado Richly Annotated Full-Text (CRAFT) Corpus: A Resource for BioNLP Research Presenter: Michael Bada, University of Colorado Denver Authors: Michael Bada, Miriam Eckert, Kristin Garcia, Donald Evans, Dmitry Sitnikov, William A. Baumgartner, Jr., Philip V. Ogren, Arrick Lanfranchi, Amanda Howard, William Corvey, Nianwen Xue, Kevin B. Cohen, Karin Verspoor, Judith A. Blake, Martha Palmer |
| 5:45 pm – 8:00 pm | Reception and Poster Session |
| go directly to: [Thursday - December 10] [Friday - December 11] | |
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| Saturday – December 12, 2009 | |
| 9:00 am – 9:45 am | Keynote 5 ChEMBL - Large-scale Open Access Data for Drug Discovery John P. Overington, PhD CChem. European Bioinformatics Institute (EMBL-EBI) |
| 9:45 am – 9:55 am | Oral Presentation 39 Subgraphs of Protein-protein Interaction Networks with High Connectivity Presenter: Suzanne Gallagher, University of Colorado Dept. of Computer Science Authors: Suzanne Gallagher, Debra Goldberg |
| 9:55 am – 10:05 am | Oral Presentation 40 TreeHugger: A New Test for Enrichment of Gene Ontology Terms Presenter: Daniel Jupiter, Texas A&M Health Science Center Authors: Daniel Jupiter, Jessica Sahutoglu, Vincent VanBuren |
| 10:05 am – 10:15 am | Oral Presentation 41 Pattern-Based Extraction of Argumentation from the Scientific Literature Presenter: Elizabeth White, University of Colorado at Boulder Authors: Elizabeth White |
| 10:15 am – 10:25 am | Oral Presentation 42 Early Host Response During Influenza Infections Presenter: Christian V. Forst, University of Texas Southwestern Medical Center Authors: Christian V. Forst |
| 10:25 am – 10:35 am | Oral Presentation 43 Boolean Network Models of Human Aging Presenter: Michael Verdicchio, Arizona State University Authors: Michael Verdicchio, Seungchan Kim |
| 10:35 am – 12:00 pm | Poster Session |
| 12:00 pm – 4:00 pm | Break |
| 4:00 pm – 4:10 pm | Oral Presentation 44 Positive Selection and Functional Shift: Human Heme Peroxidase Case Study Presenter: Mary J. O'Connell, Dublin City University Authors: Noeleen B. Loughran, Brendan O'Connor, Ciaran O'Fagain, William M. Nauseef, Mary J. O'Connell |
| 4:10 pm – 4:20 pm | Oral Presentation 45 Delving into the Bacteriome:Protein-protein Interactions in E. coli Presenter: John Parkinson, Hospital for Sick Children Authors: Jose Peregrin-Alvarez, Xuejian Xiong, Chong Su, John Parkinson |
| 4:20 pm – 4:30 pm | Oral Presentation 46 Simplified Clustering with Dirichlet Process and Other Process Mixtures Presenter: Matthew Shotwell, Medical University of South Carolina Authors: Matthew Shotwell, M.S., Elizabeth Slate, Ph.D. |
| 4:30 pm – 4:40 pm | Oral Presentation 47 Real Time Metagenomics Presenter: Robert Edwards, San Diego State University Authors: Robert Edwards, Robert Olson, Terry Disz, Rick Stevens, Ross Overbeek |
| 4:40 pm – 4:50 pm | Oral Presentation 48 Structure Discovery in PPI Networks Using Pattern-Based Network Decomposition Presenter: Ying Liu, University of Texas at Dallas Authors: Ying Liu, Chengcheng Shen, Phil Bachman |
| 4:50 pm – 5:00 pm | Oral Presentation 49 Data Mining Over Directed Transcription Factor Networks Presenter: Rauf Malick, Bahria University Authors: Rauf Malick, Abdul Aziz, Mansoor Ahmed, Aysha Mazhar |
| 5:00 pm – 5:40 pm | Keynote 6 Informatics Challenges for Pharmacogenetic Russ B. Altman, MD, PhD Biomedical Informatics Training Program Stanford University |
| 5:40 pm | Rocky '09 Closing Comments |
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| return to: [Thursday - December 10] [Friday - December 11] [Saturday - December 12] | |