8th Annual Rocky Mountain Bioinformatics Conference
Full Agenda
Updated Nov. 21, 2010
go directly to: [Friday - December 10] [Saturday - December 11] | |
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Thursday – December 9, 2010 | |
11:00 am – 1:00 pm | Registration |
1:00 pm – 1:45 pm | Keynote 1 Network as Biomarker for Ovarian Cancer Prognosis Sol Efroni, PhD Bar Ilan University, Ramat Gan, Israel |
1:45 pm – 1:55 pm | Oral Presentation 1 Fun and Games with RDF - Moving Rat Data on to the Semantic Web Presenter: Simon Twigger, Medical College of Wisconsin Authors: Simon Twigger, Joey Geiger, Jennifer Smith |
1:55 pm – 2:05 pm | Oral Presentation 2 Full-Text Biomedical Literature Processing: More than a Scaling Challenge Presenter: Christophe Roeder, University of Colorado, Denver Authors: Christophe Roeder, Tom Christiansen, Helen Johnson, Karin Verspoor, Gully Burns, Lawrence Hunter |
2:05 pm – 2:15 pm | Oral Presentation 3 PhiRAST: A Pipeline for Rapid Annotation of Phage Genomes Using Subsystems Technology Presenter: Ramy Aziz, San Diego State University Authors: Robert Olson, Ross Overbeek, Gordon D. Pusch, the PhAnToMe team*, and Robert A. Edwards |
2:15 pm – 2:25 pm | Oral Presentation 4 Polbase: A Repository of Biochemical, Genetic, and Structural Information about DNA Polymerases Presenter: Bradley Langhorst, New England Biolabs Authors: Bradley Langhorst, Nicole Nichols |
2:25 pm – 2:35 pm | Oral Presentation 5 ORO Miner, An Application for Investigating Cell Communication in Multicellular Organisms Presenter: Michael Rogers, University of Nevada Las Vegas Authors: Prashant Singh, Michael Rogers, Patrick Gradie, Rinu Thomas, Dharmistha Kaul, Brandon Roe, Shruti Patel, Briana Sugihara, Narineh Abadian, Michael Gryk, Martin Schiller |
2:35 pm – 2:45 pm | Oral Presentation 6 Early Detection and Dynamics of Rare Viral Variants by Ultradeep Sequencing Presenter: Peter Hraber, Los Alamos National Lab Authors: Peter Hraber, Will Fischer, Elena Giorgi, Thomas Leitner, Tanmoy Bhattacharya, Bette Korber |
2:45 pm – 3:00 pm | Break (15 minutes) |
3:00 pm – 3:10 pm | Oral Presentation 7 A Process for Unifying Sources of Biomedical Information in an RDF-based Knowledge Base Presenter: Kevin Livingston, University of Colorado Denver Authors: Kevin Livingston, Michael Bada, Lawrence Hunter |
3:10 pm – 3:20 pm | Oral Presentation 8 Testing for Joint Association of All SNP Pairs Presenter: Ronald Schuyler, University of Colorado Authors: Ronald Schuyler, Lawrence Hunter |
3:20 pm – 3:30 pm | Oral Presentation 9 Cognitive Task Flows and Visual Analytics Presenter: Barbara Mirel, University of Michigan Authors: Barbara Mirel, Felix Eichinger |
3:30 pm – 3:40 pm | Oral Presentation 10 CategoryCompare: High-throughput Data Meta-analysis using Gene Annotations Presenter: Robert Flight, University of Louisville Authors: Robert Flight, Jeffrey Petruska, Benjamin Harrison, Eric Rouchk |
3:40 pm – 3:50 pm | Oral Presentation 11 Pairwise Agonist Scanning Predicts Cellular Signaling Responses to Combinatorial Stimuli Presenter: Scott Diamond, University of Pennsylvania Authors: Scott Diamond, Manash Chatterjee |
3:50 pm – 4:00 pm | Oral Presentation 12 A Bayesian Network Framework for Statistical Assessment of the Intent to Stabilize Yersinia Pestis Presenter: Bobbie-jo Webb-Robertson, Pacific Northwest National Laboratory Authors: Bobbie-Jo Webb-Robertson, Lee Ann McCue, Craig McKinstry, Brian Clowers, Heather Colburn, Christina Sorensen, David Wunschel, Karen Wahl |
4:00 pm – 4:10 pm | Oral Presentation 13 Identifying Genes in the Drosophila Hh Pathway by Integrating TF Binding and Gene Expression Data Presenter: Daniel Dvorkin, University of Colorado Denver Authors: Daniel Dvorkin, Brian Biehs, Katerina Kechris |
4:10 pm – 4:25 pm | Break (15 minutes) |
4:25 pm – 5:10 pm | Keynote 2 Data and Analytics Transforming Healthcare for Smarter Healthcare & Life Science Kirk E. Jordan, PhD Emerging Solutions Executive & Associate Program Director Computational Science IBM T.J. Watson Research |
5:10 pm – 5:20 pm | Oral Presentation 14 Cancer Gene Expression Data is Not Normally Distributed: Analysis of Data Distributions and their Effects on Gene Selection and Molecular Classification Presenter: Nicholas Marko, Cleveland Clinic Department of Neurosurgery Authors: Nicholas Marko, Robert Weil |
5:20 pm – 5:30 pm | Oral Presentation 15 Exploring Machine Learning Classifiers for the Prediction of AGO Bound Transcripts with miRNA Seed Matches Presenter: Abel Licon, Thermo Fisher Scientific Authors: Abel Licon, Kevin Sullivan, Amanda Birmingham |
5:30 pm – 5:40 pm | Oral Presentation 16 SpliceGrapher: Predicting Splice Graphs from Diverse Evidence Presenter: Mark Rogers, Colorado State University Authors: Mark Rogers, Asa Ben-Hur, Anireddy Reddy |
5:40 pm – 5:50 pm | Oral Presentation 17 Plasma Metabolites in the Mammalian Hibernation Cycle Presenter: Anis Karimpour-fard, University of Colorado Denver Authors: Anis Karimpour-Fard, L. Elaine Epperson, Lawrence Hunter, Sandra Martin |
5:50 pm – 6:00 pm | Oral Presentation 18 Detecting Genome-wide Copy Number Variations in a Single Sample Using Next Generation Sequencing Data Presenter: Rajesh Gottimukkala, Life Technologies Authors: Rajesh Gottimukkala, Fiona Hyland, Somalee Datta, Asim Siddiqui, Ryan Koehler, Yutao Fu |
6:00 pm – 6:10 pm | Oral Presentation 19 Interaction Sites in Models of Protein Interaction Network Evolution Presenter: Todd Gibson, University of Colorado Denver Authors: Todd Gibson, Debra Goldberg |
6:10 pm – 6:20 pm | Oral Presentation 20 Investigation of Structural Basis of Oncogenesis Property of GTPase H-Ras Protein: A Molecular Dynamics Simulation Study Presenter: Gyana Satpathy, National Institute of Technology Authors: Gyana Satpathy, Raghunath Satpathy, B.P. Nayak |
7:00 pm – 9:00 pm | Banquet, Thursday, December 9, 2010 7:00 pm - 9:00 pm Banquet Location: Il Poggio Restaurant, Snowmass Village |
go directly to: [Thursday - December 9 ] [Saturday - December 11] | |
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Friday – December 10, 2010 | |
9:00 am – 9:45 am | Keynote 3 Interactive Chromatin Modeling: Towards a Computational Karyotype Thomas C. Bishop, PhD Center for Computational Science Tulane University |
9:45 am – 9:55 am | Oral Presentation 21 Validation of Protein Functional Site Predictions Using Automated Biomedical Literature Analysis Presenter: Karin Verspoor, University of Colorado Denver Authors: Karin Verspoor, Judith Cohn, Christophe Roeder, Michael Wall |
9:55 am – 10:05 am | Oral Presentation 22 Modeling Gene-Species Data by Generalized Replicator Dynamics for Efficient Phylogenetic Inference Presenter: Ying Liu, University of North Texas at Dallas Authors: Ying Liu |
10:05 am – 10:15 am | Oral Presentation 23 Comparative Analysis of Apicomplexan Biological Processes Presenter: Segun Fatumo, Center for Tropical & Emerging Global Diseases Authors: Segun Fatumo, Jessica Kissinger |
10:15 am – 10:25 am | Oral Presentation 24 STOP Using Just GO: A Multi-Ontology Enrichment Analysis Tool For Genes and Proteins Presenter: Emily Howe, The Buck Institute Authors: Emily Howe, Uday Evani, Mathew Fleish, Nigam Shah, and Sean Mooney |
10:25 am – 10:35 am | Oral Presentation 25 Comparative Ontological and Network Analysis of Aging Associated Genes in Humans and Model Organisms Presenter: Ari Berman, Buck Institute for Age Research Authors: Ari Berman, Tobias Wittkop, Emily Howe, Sean Mooney |
10:35 am – 10:45 am | Oral Presentation 26 Flu and Drugs and Rocky10 Presenter: Christian Forst, UT Southwestern Medical Center Authors: Christian Forst |
10:45 am – 11:00 am | Break (15 minutes) |
11:00 am – 11:10 am | Oral Presentation 27 Analysis Workflow of Methylation and Gene Expression microarray in Pediatric Crohn Disease Presenter: Tzu Lip Phang, University of Colorado Denver Authors: Tzu Phang, Anna Hunter, Ping Yao Zeng, Theresa Kerbowski, Edwin de Zoeten |
11:10 am – 11:20 am | Oral Presentation 28 Evolution of Cis-regulatory Elements Presenter: Ken Yokoyama, University of Colorado Denver Authors: Ken Yokoyama |
11:20 am – 11:30 am | Oral Presentation 29 More Is Not Always Better. Considerations in the Use of Time Course Microarray Data Presenter: Elizabeth Siewert, Colorado School of Public Health Authors: Elizabeth Siewert, Katerina Kechris |
11:30 am – 11:40 am | Oral Presentation 30 Semantic Richness in the Colorado Richly Annotated Full-Text (CRAFT) Corpus Presenter: Michael Bada, University of Colorado Anschutz Medical Campus Authors: Michael Bada, Miriam Eckert, Arrick Lanfranchi, William A. Baumgartner, Jr., Colin Warner, Amanda Howard, William Corvey, Nianwen Xue, K. Bretonnel Cohen, Karin Verspoor, Judith A. Blake, Martha Palmer, Lawrence Hunter |
11:40 am – 11:50 am | Oral Presentation 31 Functional Regulatory Circuits Induced by Transcription Factors and Small RNAs Presenter: Molly Megraw, Duke University Authors: Molly Megraw, Uwe Ohler |
11:50 am – 12:00 pm | Oral Presentation 32 Rapid Comprehensive Selection of Sensitive and Specific Oligonucleotide Signatures from Large Hierarchically Clustered Nucleic Acid Sequence Datasets Presenter: Harald Meier, Technical University of Munchen Authors: Kai Bader, Christian Grothoff, Harald Meier |
12:00 pm – 4:00 pm | Break |
4:00 pm – 4:45 pm | Keynote 4 Supporting Research and Analysis Across the Biomedical Literature Using Visual Analytics Carsten Görg, PhD University of Colorado School of Medicine |
4:45 pm – 4:55 pm | Oral Presentation 33 Classifying Parenthesized Material for Text Mining Presenter: Kevin Bretonnel Cohen University of Colorado School of Medicine Authors: K. Bretonnel Cohen, Tom Christiansen, Lawrence Hunter |
4:55 pm – 5:05 pm | Oral Presentation 34 Towards Integrative Gene Prioritization Presenter: Graciela Gonzalez, Arizona State University Authors: Jang Lee, Graciela Gonzalez |
5:05 pm – 5:15 pm | Oral Presentation 35 Towards a Molecular Classification of Kidney Diseases Based on Network Analysis Presenter: Felix Eichinger, University of Michigan Authors: Felix Eichinger, Ramakrishna Varadarajan, Jignesh Patel, Matthias Kretzler |
5:15 pm – 5:25 pm | Oral Presentation 36 Identifying the Dynamic States of the 3D Genome Organization Presenter: Andrzej Kudlicki, University of Texas Authors: Dirar Homouz, Gang Chen, Andrzej Kudlicki |
5:25 pm – 5:35 pm | Oral Presentation 37 Providing Context to Genetic Associations with Gene Expression in Renal Disease Presenter: Benjamin Keller, Eastern Michigan University Authors: Benjamin Keller, Sebastian Martini, Matthias Kretzler |
5:35 pm – 5:45 pm | Oral Presentation 38 Gene and Promoter Discovery Through High-resolution Expression Profiling Presenter: Ian Davis, GrassRoots Biotechnology, Inc. Authors: Ian Davis |
5:45 pm – 8:00 pm | Reception and Poster Session Snowmass Conference Center (across street from Silvertree) Sinclair Room |
go directly to: [Thursday - December 9 ] [Friday - December 10] | |
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Saturday – December 11, 2010 | |
9:00 am – 9:45 am | Keynote 5 New Approaches for Comparing Biological Trees and Networks Shawn Gomez, PhD University of NC-Chapel Hill |
9:45 am – 9:55 am | Oral Presentation 39 Using a Low Dimensional Firing Rate Model to Study Interactions in Biophysical Neural Networks Presenter: Anca Radulescu, University of Colorado at Boulder Authors: Anca Radulescu |
9:55 am – 10:05 am | Oral Presentation 40 Investigating Relationships between Obesity and the Built Environment Using Agent-Based Modeling Presenter: Helmet Karim, University of Pittsburgh Authors: Helmet Karim, Leming Zhou |
10:05 am – 10:15 am | Oral Presentation 41 Characterization of Genomic Variability in Clinical Isolates of the Oral Pathogen Aggregatibacter Actinomycetemcomitans Presenter: Weerayuth Kittichotirat, University of Washington Authors: Weerayuth Kittichotirat, Casey Chen, Roger Bumgarner |
10:15 am – 10:25 am | Oral Presentation 42 Extracting Adverse Drug Reactions from User Posts to Health-Related Social Networks Presenter: Laura Wojtulewicz, Arizona State University Authors: Robert Leaman, Laura Wojtulewicz, Ryan Sullivan, Annie Skariah, Jian Yang, Graciela Gonzalez |
10:25 am – 10:35 am | Oral Presentation 43 Simple Local Assembly Program Presenter: Adam Spargo, Wellcome Trust Sanger Institute Authors: Adam Spargo, Zemin Ning |
10:35 am – 12:00 pm | Poster Session Snowmass Conference Center (across street from Silvertree) Sinclair Room |
12:00 pm – 4:00 pm | Break |
4:00 pm – 4:10 pm | Oral Presentation 44 Modelling Gene Expression in Tumor Progression Using Binary States Presenter: Juan Emmanuel Martinez-Ledesma ITESM Campus Monterrey Authors: Emmanuel Martinez-Ledesma, Victor Trevino |
4:10 pm – 4:20 pm | Oral Presentation 45 Finding Community Leaders in Social Networks Presenter: Xiaowei Xu, University of Arkansas at Little Rock Authors: Xiaowei Xu |
4:20 pm – 4:30 pm | Oral Presentation 46 Adaptive Learning Neural Networks for Binding Site Search in Genomic Sequences Presenter: Ivan Erill, University of Maryland Baltimore Authors: Joseph Cornish, Sumeet Bagde, Elisabeth Hobbs, Ivan Erill |
4:30 pm – 4:40 pm | Oral Presentation 47 Enriching Regulatory Networks with Other Functional Relationships Presenter: Ronald Taylor, Pacific Northwest National Laboratory Authors: Ronald Taylor, Antonio Sanfilippo, Jason McDermott, Bob Baddeley, Rick Riensche, Russ Jenson, Marc Verhagen |
4:40 pm – 4:50 pm | Oral Presentation 48 GenoS: Segment-based Representation of Genomics data. Application to Genotyping Data Management Presenter: Hugues Sicotte, Mayo Clinic Authors: Jean-Pierre Kocher, Hugues Sicotte, Yaxiong Lin, Eric Klee |
4:50 pm – 5:00 pm | Oral Presentation 49 Bioinformatics Study of the Ferredoxin-Dependent Bilin Reductase Family Presenter: Chanel Mejias-Rosario, Universidad Metropolitana Authors: Mejias-Rosario Chanel, Nicholas Jr. Hugh, Ropelewski Alexander, Gonzalez-Mendez Ricardo, Vazquez-Quinones Luis |
5:00 pm – 5:45 pm | Keynote 6 Thinking, Measuring, Calculating, and Diagnosing: From Platform to New Ideas about Biology Larry Gold, MD, PhD CEO and Chairman of the Board, SomaLogic, Inc. Professor, University of Colorado, Boulder |
5:45 pm | Rocky '10 Closing Comments |
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return to: [Thursday - December 9 ] [Friday - December 10] |