9th Annual Rocky Mountain Bioinformatics Conference
Full Agenda
Updated Jan. 09, 2012
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| Thursday – December 08, 2011 | |
| 11:00 am – 1:00 pm | Registration |
| 1:00 pm – 1:45 pm | Keynote 1 The Future of Research Communication: From Surfing to Deep Diving Judith A. Blake, PhD Associate Professor The Jackson Laboratory Bar Harbor, Maine - USA |
| 1:45 pm – 1:55 pm | Oral Presentation 1 The Rat Genome Curation: RGD Automated Data Integration Pipelines Maximize Coverage Presenter: Marek Tutaj, Medical College of Wisconsin Authors: Marek Tutaj, Mary Shimoyama, Elizabeth Worthey, Jennifer Smith, Howard Jacob PDF of Presentation |
| 1:55 pm – 2:05 pm | Oral Presentation 2 A Sensemaking Model for the Explorative Analysis of Large Gene Lists Presenter: Carsten Görg, University of Colorado Denver Authors: Carsten Görg, Barbara Mirel, Hannah Tipney PDF of Presentation |
| 2:05 pm – 2:15 pm | Oral Presentation 3 The Role of p53 in Oligodendrocyte UPR Presenter: Hasan Jamil, Wayne State University Author: Hasan Jamil PDF of Presentation |
| 2:15 pm – 2:25 pm | Oral Presentation 4 Quantitative Data: Where are they Hidden in Biomedical Literature? Presenter: Komandur Ravidumar, University of Colorado School of Medicine Authors: K.E. Ravikumar, Meenakshi Narayanaswamy, S.V. Ramanan PDF of Presentation |
| 2:25 pm – 2:35 pm | Oral Presentation 5 Multiscale Patient-Specific Blood Systems Biology Presenter: Scott Diamond, University of Pennsylvania Authors: Scott L. Diamond |
| 2:35 pm – 2:45 pm | Oral Presentation 6 A Resource for the Rational Selection of Drug Target Proteins and Leads for the Malaria Parasite, Plasmodium Falciparum Presenter: Fourie Joubert, University of Pretoria Authors: Jeanre Smit, Phele Mpangase, Michal Szolkiewicz, Misha le Grange, Fourie Joubert PDF of Presentation |
| 2:45 pm – 3:00 pm | Break (15 minutes) |
| 3:00 pm – 3:10 pm | Oral Presentation 7 Identifying Treatment Relevant Colorectal Cancer Subtypes Using Iterative Non-negative Matrix Factorization Presenter: Andreas Schlicker, Netherlands Cancer Institute Authors: Andreas Schlicker, Garry Beran, Christine M Chresta, Gael McWalter, Alison Pritchard, Susie Weston, Sarah Runswick, Sara Davenport, Kerry Heathcote, Denis Alferez Castro, George Orphanides, Tim French, Lodewyk FA Wessels |
| 3:10 pm – 3:20 pm | Oral Presentation 8 The Origin of Mammalian Placentation Correlates with Protein Functional Shift and the Emergence of New Control Mechanisms Presenter: Mary O'Connell, Dublin City University Authors: Thomas A. Walsh, Kieran Holohan, Anna O'Brien, Robert Carton, Elinor Velasquez, Claire C. Morgan, Noeleen B. Loughran, Mary J. O'Connell |
| 3:20 pm – 3:30 pm | Oral Presentation 9 Exploring and Profiling Long Non-coding RNA in T Cell Development Using Next Generation Sequencing and Bioinformatics Approaches Presenter: Tzu L. Phang, University of Colorado Denver Authors: Tzu L. Phang, Ping Yao Zeng, Edwin.F. de Zoeten |
| 3:30 pm – 3:40 pm | Oral Presentation 10 Building an Interactome to Identify Signaling Components Presenter: Sarah Wyatt, Ohio University Authors: Sarah Waytt, Kaiyu Shen |
| 3:40 pm – 3:50 pm | Oral Presentation 11 GeneSmash: A RESTful Web Service for Gene Annotations Presenter: Ganiraju Manyam, University of Texas Anderson Cancer Center Authors: Michelle Payton, Ganiraju Manyam, Chris Wakefield, Jack Roth, Lynne Abruzzo, Kevin Coombes |
| 3:50 pm – 4:00 pm | Oral Presentation 12 Integrating Curated Databases and Text Mining Output into a Biomedical Knowledge Base Presenter: Kevin Livingston, University of Colorado Denver Authors: Kevin M. Livingston, Michael Bada, William A. Baumgartner Jr, Yuriy Malenkiy, Lawrence E. Hunter PDF of Presentation |
| 4:00 pm – 4:10 pm | Oral Presentation 13 Using Evolving Protein Networks to Inform the Graph Coloring Problem Presenter: Todd Gibson, University of Colorado Denver Authors: Todd A. Gibson, Debra S. Goldberg |
| 4:10 pm – 4:25 pm | Break (15 minutes) |
| 4:25 pm – 5:10 pm | Keynote 2 Building Cell Maps: Status and Challenges Emek Demir, PhD Computational Biology Center Memorial Sloan Kettering Cancer Center New York, New York - USA |
| 5:10 pm – 5:20 pm | Oral Presentation 14 Machine Approaches to Recognition of Trypanosomal Variant Surface Glycoprotein Sequences Presenter: Jon Wilkes, Wellcome Trust Centre for Molecular Parasitology Author: Jon Wilkes PDF of Presentation |
| 5:20 pm – 5:30 pm | Oral Presentation 15 Compact Encoding for Gene Therapy Presenter: Roger Hall, University of Arkansas at Little Rock Author: Roger Hall PDF of Presentation |
| 5:30 pm – 5:40 pm | Oral Presentation 16 Microbial Monitoring and Space Exploration Presenter: Sven Bilke, NCI Authors: Sven Bilke, Verena Starke |
| 5:40 pm – 5:50 pm | Oral Presentation 17 CodingMotif: Exact Determination of Overrepresented Nucleotide Motifs in Coding Sequences Presenter: Jeffrey Chuang, Boston College Authors: Yang Ding, Andy Lorenz, Jeffrey Chuang PDF of Presentation |
| 5:50 pm – 6:00 pm | Oral Presentation 18 GO Classes or Biclusters? Alternative Approaches for Exploring Microarray Probeset Subsets Presenter: George Acquaah-Mensah, Massachusetts College of Pharmacy and Health Sciences Author: George Acquaah-Mensah PDF of Presentation |
| 6:00 pm – 6:10 pm | Oral Presentation 19 Accurate Inferring Transcription Regulation from a Compendium of Expression Profiles Presenter: Xueling Li, University of Texas, Medical Branch Authors: Xueling Li, Dirar Homouz, Andrzej Kudlicki PDF of Presentation |
| 6:10 pm – 6:20 pm | Oral Presentation 20 A Proposed Algorithm for Epistasis Detection using Frequent Item-sets and Mutual Information Presenter: James Rudd, North Carolina University Author: James Rudd, Assefa Tesfay, ClarLynda Williams-DeVane, Gaolin Zheng PDF of Presentation |
| 7:00 pm – 9:00 pm | Banquet, Thursday, December 8, 2011 7:00 pm - 9:00 pm Banquet Location: Il Poggio Restaurant, Snowmass Village Note: The Dec 08 banquet has sold out. To be placed on a wait list, please email This email address is being protected from spambots. You need JavaScript enabled to view it.. |
| >>> Go directly to: [Thursday - December 08] [Saturday - December 10] | |
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| Friday – December 09, 2011 | |
| 9:00 am – 9:45 am | Keynote 3 Project Halo: Constructing and Exploiting a Formal Representation of a Biology Textbook to Understand and Answer Users' Questions Peter Clark, PhD Vulcan Inc. Seattle, Washington - USA |
| 9:45 am – 9:55 am | Oral Presentation 21 Molecular Insights to the Drug Resistance of V32I & M46L HIV-1 Protease Mutant to Inhibitor TMC114: Free Energy Calculation and Molecular Dynamics Simulations Presenter: Biswa Meher, Albany State University Authors: Biswa R. Meher, Yixuan Wang |
| 9:55 am – 10:05 am | Oral Presentation 22 Testing the Ortholog Conjecture with Functional Data from Several Pairs of Closely Related Organisms Presenter: Wyatt Clark, Indiana University Authors: Wyatt T. Clark, Predrag Radivojac, Matthew Hahn |
| 10:05 am – 10:15 am | Oral Presentation 23 Functional Profiling of Pharmacogenetic Non-synonymous SNPs Presenter: Chet Seligman, Buck Institute for Research on Aging Authors: Chet Seligman, Janita Thusberg, Jackson Miller, Emidio Capriotti, Jim Auer, Michelle Whirl-Carrillo, Teri Klein, Sean Mooney PDF of Presentation |
| 10:15 am – 10:25 am | Oral Presentation 24 Limitations of Automated Annotation Software When Used with Draft Genomic Assemblies Presenter: Robert Norgren, University of Nebraska Medical Center Author: Robert B. Norgren, Jr. PDF of Presentation |
| 10:25 am – 10:35 am | Oral Presentation 25 Mixed Primary-Secondary Structure Alignment of ncRNA Covariance Models for Model Clustering and Combination Presenter: Jennifer Smith, Boise State University Author: Jennifer Smith PDF of Presentation |
| 10:35 am – 10:45 am | Oral Presentation 26 In Silico Gene Expression Based Analysis on Claudin Family Members Association with Human Thyroid Cancer Presenter: Shaukat Malik, Mohammad Ali Jinnah University Authors: Shaukat Malik, S. Sameen, Z. Khalid |
| 10:45 am – 11:00 am | Break (15 minutes) |
| 11:00 am – 11:10 am | Oral Presentation 27 Data Management and Analysis Solutions for Meta-Analysis of Multi-Domain Data Presenter: ClarLynda Williams-Devane, North Carolina Central University Authors: ClarLynda Williams-DeVane, Archana Radadia, Nina Rountree, Stephen Edwards PDF of Presentation |
| 11:10 am – 11:20 am | Oral Presentation 28 STOP and DEFOG: Web Applications for a Comprehensive Functional Gene Set Analysis Presenter: Tobias Wittkop, Buck Institute for Research on Aging Authors: Tobias Wittkop, Emily Teravest, Ari E. Berman, Uday Evani, K. Mathew Fleisch, Corey Powell, Nigam Shah, Sean D. Moone PDF of Presentation |
| 11:20 am – 11:30 am | Oral Presentation 29 DAVID-WS: A Stateful Web Service to Facilitate Gene/Protein List Analysis Presenter: Xiaoli Jiao, NIH/NIAID Authors: Xiaoli Jiao, Brad T. Sherman, Da Wei Huang, Richard A. Lempicki PDF of Presentation |
| 11:30 am – 11:40 am | Oral Presentation 30 Predicting Transcription Factor Binding Sites with Hidden Markov Models by using ChIP-Seq Data Presenter: Anthony Mathelier, University of British Columbia Authors: Anthony Mathelier, Wyeth W. Wasserman PDF of Presentation |
| 11:40 am – 11:50 am | Oral Presentation 31 The Critical Assessment of Function Annotation Experiment: A Community-wide Effort Towards a Better Functional Annotation of Genes and Genomes Presenter: Predrag Radivojac, Indiana University Authors: Predrag Radivojac, Sean Mooney, Iddo Friedberg |
| 11:50 am – 12:00 pm | Oral Presentation 32 In Silico Rational Drug Design and Modeling Studies of Novel Inhibitors for Multi-target Inhibition in Pseudomonas Aeruginosa Presenter: Premkumar Jayaraman, Nanyang Technological University Authors: Premkumar Jayaraman, Lim Chu Sing Daniel, Meena K. Sakharkar PDF of Presentation |
| 12:00 pm – 12:30 pm | Keynote 4 Advances in Protein Biomarker Discovery: Controlling for Sample Handling Artifacts and Confounding Effects Mike Mehan, PhD SomaLogic Boulder, CO - USA |
| 12:30 pm – 4:00 pm | Break |
| 4:00 pm – 4:45 pm | Keynote 5 Deciphering of Human Protein Interactome using Structural Complexes Anna Panchenko, PhD Associate Investigator National Center for Biotechnology Information NLM, NIH Bethesda, Maryland - USA |
| 4:45 pm – 4:55 pm | Oral Presentation 33 PathCMap: Development of Pathway Signature System for Identifying Druggable Partners of Synthetic Lethal Genes in Cancer Presenter: Jihye Kim, University of Colorado Denver School of Medicine Authors: Jihye Kim, Carlos H C Cano, Aik Choon Tan PDF of Presentation |
| 4:55 pm – 5:05 pm | Oral Presentation 34 Identifying Single Copy Orthologs in Metazoa Presenter: Christopher Creevey, Teagasc Authors: Chris Creevey, Jean Muller, Tobias Doerks, Julie D. Thompson, Detlev Arendt, Peer Bork PDF of Presentation |
| 5:05 pm – 5:15 pm | Oral Presentation 35 Mining Genomes to Understand the Origin of Vision in Metazoa Presenter: Davide Pisani, National University of Ireland, Maynooth Authors: Roberto Feuda, Davide Pisani |
| 5:15 pm – 5:25 pm | Oral Presentation 36 Evolutionary Pattern Embedded in the Lengths of Proteins and Their Structural Units Presenter: Minglei Wang, University of Illinois at Urbana-Champaign Authors: Minglei Wang, Cedric Debes, Frauke Gräter, Gustavo Caetano-Anollés |
| 5:25 pm – 5:35 pm | Oral Presentation 37 A Multiple-template Approach for Protein Threading Presenter: Jian Peng, Toyota Technological Institute at Chicago Authors: Jian Peng, Jinbo Xu PDF of Presentation |
| 5:35 pm – 5:45 pm | Oral Presentation 38 A New Probabilistic Model in Predictive Microbiology (NPMPM) Presenter: Nadine Schoene, Goethe University Frankfurt Authors: Nadine Schoene, Alexander Bockmayr, Bernd Appel, Annemarie Kaesbohrer PDF of Presentation |
| 5:45 pm – 8:00 pm | Reception and Poster Session Snowmass Conference Center (across street from Silvertree), Sinclair Room |
| >>> Go directly to: [Thursday - December 08] [Friday - December 09] | |
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| Saturday – December 10, 2011 | |
| 9:00 am – 9:45 am | Keynote 6 A New Day, A New High Performance Computer, What Does It Mean for the Life Sciences? Kirk E. Jordan, PhD Emerging Solutions Executive & Associate Program Director Computational Science Center IBM T.J. Watson Research Member, IBM Academy of Technology Massachusetts - USA |
| 9:45 am – 9:55 am | Oral Presentation 39 Rediscovery of the p53 Transcriptome Presenter: Mary Allen, University of Colorado Authors: Mary Allen, Robin Dowell, Joaquin Espinosa |
| 9:55 am – 10:05 am | Oral Presentation 40 Developing Maximum Likelihood and Bayesian Supertrees Presenter: Wasiu Akanni, National University of Ireland, Maynooth Authors: Wasiu Akanni, Davide Pisani, Peter Forster, Mark Wilkinson PDF of Presentation |
| 10:05 am – 10:15 am | Oral Presentation 41 Prediction of Operons in Microbial Genomes by Integrating Diverse Information Sources Presenter: Anis Karimpour-Fard, University of Colorado Anschutz Medical Campus Authors: Anis Karimpour-Fard, Lawrence E. Hunter PDF of Presentation |
| 10:15 am – 10:25 am | Oral Presentation 42 Gene Language Model Presenter: Siamak Rezaei, Talai Author: Siamak Rezaei PDF of Presentation |
| 10:25 am – 10:35 am | Oral Presentation 43 Live and Let Die Presenter: Christian Forst, University of Texas Southwestern Medical Center Authors: Nassim Sohaee, Christian V. Forst |
| 10:35 am – 11:05 am | Keynote 7 SOMAmer-based Proteomic Analysis with Machine Learning Hans Peter Graf, PhD NEC Laboratories America, Inc. Princeton, New Jersey - USA |
| 11:05 am – 12:30 pm | Poster Session Snowmass Conference Center (across street from Silvertree) Sinclair Room |
| 12:30 pm – 4:00 pm | Break |
| 4:00 pm – 4:10 pm | Oral Presentation 44 Broad Semantic Class Assignment for Biomedical Text Presenter: Kevin Bretonnel Cohen, University of Colorado School of Medicine Authors: K. Bretonnel Cohen, Thomas Christiansen, Lawrence E. Hunter |
| 4:10 pm – 4:20 pm | Oral Presentation 45 On the Accuracy of Protein Tertiary Structure Comparison Presenter: Aleksandar Poleksic, University of Northern Iowa Authors: Aleksandar Poleksic, Mauricio Arriagada |
| 4:20 pm – 4:30 pm | Oral Presentation 46 A Distributed Framework for Computation on the Results of Large Scale NLP Presenter: Christophe Roeder, University of Colorado, Anschutz Medical Campus Authors: Christophe Roeder, William Baumgartner Jr, Kevin Livingston |
| 4:30 pm – 4:40 pm | Oral Presentation 47 Probabilistic Search Frameworks for Protein Conformational Spaces Presenter: Amarda Shehu, George Mason University Authors: Amarda Shehu |
| 4:40 pm – 4:50 pm | Oral Presentation 48 Predicting HIV-1, Human Protein Interactome Through Indirect and Direct Evidences Presenter: Oznur Tastan, Microsoft Research New England Authors: Oznur Tastan, Jaime Carbonell, Judith Klein |
| 4:50 pm – 5:00 pm | Oral Presentation 49 Using Information Theory to Map Reads to a Reference Sequence Presenter: John Conery, University of Oregon Author: John Conery |
| 5:00 pm – 5:45 pm | Keynote 8 Transfer Function Analysis of Signal Transduction - The PSF System Gabriele Scheler, PhD Mountain View, California - USA |
| 5:45 pm | Rocky 2011 Closing Comments |
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| >>> Go directly to: [Thursday - December 08] [Friday - December 09] [Saturday - December 10] | |