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            Dear 
              Rocky '05 Participant, 
            Welcome to the 
              third annual Rocky Mountain Regional Bioinformatics Meeting, a regional 
              conference of the International Society for Computational Biology. 
              The organizers hope that you enjoy the program, and find the meeting 
              a productive opportunity to meet researchers, students and industrial 
              users of bioinformatics technology in our area. We think we have 
              the best program yet, offering a remarkable cross-section of bioinformatics 
              research. 
            There is clearly 
              a lot of computational bioscience going on in the region. Presenters 
              at this meeting come from New Mexico, Arizona, Nevada, Colorado, 
              Utah, Alaska and Alberta, representing universities, industrial 
              enterprises, government laboratories, medical libraries and even 
              a biological field station. Two of our keynote speakers (Profs. 
              Ben-Hur and Kechris) have just moved to the area to take new faculty 
              positions. The meeting is a chance to get to know your local colleagues, 
              look for collaborative opportunities, and find synergies that can 
              drive our field forward.  
            We've listened 
              carefully to the comments that were made about the previous Rocky 
              meetings, and tried to be responsive. We've moved the meeting space 
              to a hotel so we can stay together through the full three days, 
              and so that transportation is less of an issue. We've retained (and 
              expanded) the education workshop to discuss issues relevant to training 
              the next generation of bioinformaticians. And we've arranged for 
              small group ski lessons so that those of you who want to learn to 
              ski will have a chance to do so among friends and colleagues. We 
              welcome any further suggestions that you have to make next year's 
              meeting even better.  
            We should all 
              be grateful for the support of our sponsors: The International Society 
              for Computational Biology (ISCB), IBM, Affymetrix, Apple, AMD, Dharmacon 
              RNA Technologies, Ariadne Genomics, Cancer Informatics, PLoS 
              Computational Biology, Exagen Diagnostics, Inc. and Wiley Publishing. 
              The meeting would simply not be possible with organizational help 
              from the ISCB, as well as from Kathy Thomas and Susan Trapp at the 
              University of Colorado School of Medicine. It is only with the help 
              of our corporate sponsors that we can make this meeting as affordable 
              as it is. Even more important than the money is the intellectual 
              contribution of these companies. The keynotes from Affymetrix and 
              IBM lay out some of the challenges we face and some the resources 
              we will need to address them. We're grateful for the valuable data 
              and the opportunity for supercomputer time that they offer us as 
              well. 
            Many of you 
              have contributed $5 to join the Rocky Mountain Regional Bioinformatics 
              Group, an affiliate of the ISCB. We have to charge dues of some 
              sort in order for the ISCB to recognize us as an affiliate. So far, 
              the only activity of the Group has been to organize this meeting. 
              If you are interested in volunteering to get something else going, 
              please talk to Larry Hunter. 
            We hope you 
              enjoy the science, the company, and the spectacular scenery of the 
              Rocky Mountains. Welcome! 
            Larry Hunter 
              Steve Billups 
              Rocky '05 co-chairs 
               
              
              
              
              
              
              
              
              
              
              
              
              
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                Click 
                  on the presentation icon to 
                  access the .pdf slides of each talk.  | 
               
               
                | Friday 
                  - December 9, 2005 | 
               
               
                | 2:00 pm 
                  – 6:00 pm | 
                Registration | 
               
               
                | 3:00pm 
                  - 6:00pm  | 
                Workshop 
                  Panel Discussion: 
                  Mining 
                  for Bioinformatics Jobs: Training students with the appropriate 
                  skill set for a successful career in the Bioinformatics Field 
                   | 
               
               
                | 6:30pm 
                  - 10:00pm | 
                Dinner 
                  & Opening Keynote 
                  Computational Bioscience in The Rockies 
                  Larry Hunter, University of Colorado School of Medicine  | 
               
               
                | Saturday 
                  - December 10, 2005 | 
               
               
                | 8:00am 
                  - Noon | 
                Registration | 
               
               
                | 9:00am 
                  - 9:45am  | 
                Invited 
                  Keynote: A Kernel Method for Predicting Protein-Protein 
                  Interactions 
                  Asa Ben-Hur, Colorado State University | 
               
               
                | 9:45am 
                  - 9:52am | 
                Oral 
                  Presentation Number: 1   
                  Mathematical 
                  Techniques for Predicting and Analyzing Ontological Protein 
                  Function Annotations 
                  Presenter: Cliff Joslyn, Los Alamos National Laboratory 
                  Author(s): Cliff Joslyn, Karin Verspoor, Judith Cohn and Sue 
                  Mniszewski | 
               
               
                | 9:52am 
                  - 9:59am  | 
                Oral 
                  Presentation Number: 2   
                  Mathematical 
                  Modeling of DNA Damage Response Pathway in Saccharomyces Cerevisiae 
                  Presenter: Farzin Imani, Yale University School of Medicine 
                  Author(s): Farzin Imani, David Tuck | 
               
              
                | 9:59am 
                  - 10:06am | 
                 Oral 
                  Presentation Number: 3   
                  Whole 
                  Genome Transcript Analysis with Affymetrix Exon Microarrays 
                  Presenter: Charles Sugnet, Affymetrix 
                  Author(s): Sugnet, Charles; Williams, Alan; Turpaz, Yaron; Veitch, 
                  Jim; Clark, Tyson; Schweitzer, Anthony; Cline, Melissa; Wang, 
                  Hui; Wheeler, Raymond; Blume, John. | 
               
               
                | 10:06am 
                  - 10:13am | 
                 Oral 
                    Presentation Number: 4   
                    Integration 
                    of Expression Data and Transcriptional Control Network: Significant 
                    Regulators Driving Expression Changes 
                    Presenter: Andrey Y. Sivachenko, Ariadne Genomics, Inc. 
                    Author(s): A. Y. Sivachenko, A. Yuryev, N. Daraselia, I. Mazo  | 
               
               
                | 10:15am 
                  - 10:35am  | 
                Break | 
               
               
                | 10:35am 
                  - 10:42am  | 
                Oral 
                  Presentation Number: 5   
                  The 
                  Bootstrap and Genomic Data: The Potential for Over-confidence 
                  Presenter: James McInerney, Bioinformatics laboratory 
                  Author(s): David A. Fitzpatrick, Christopher J. Creevey, James 
                  O. McInerney | 
               
               
                | 10:42am 
                   - 10:49am 
                   | 
                Oral 
                  Presentation Number: 6   
                  Protdist: 
                  An Analysis of Error  
                  Presenter: Chad Wagner, San Diego State University 
                  Author(s): Chad Wagner, Anna Salamon, Pat McNairnie, Rob Edwards, 
                  Peter Salamon | 
               
               
                | 10:49am 
                  - 10:56am | 
                Oral 
                  Presentation Number: 7   
                  Integration 
                  and Enrichment of OBO Ontologies 
                  Presenter: Michael Bada, University of Colorado at Denver and 
                  Health Sciences Center 
                  Author(s): Michael Bada and Lawrence Hunter | 
               
               
                | 10:56am 
                  - 11:03am | 
                Oral 
                  Presentation Number: 8   
                  Bioinformatics 
                  Research: An Introduction to NCBI Tools 
                  Presenter: Dana Abbey, Denison Memorial Library 
                  Author(s): Dana Abbey | 
               
               
                | 11:03am 
                  - 11:10am | 
                Oral 
                  Presentation Number: 9   
                  Unison: 
                  Integrated Feature-Based Mining for Target Discovery 
                  Presenter: Reece Hart, Genentech, Inc. 
                  Author(s): Reece Hart | 
               
               
                | 11:10am 
                  - 11:17am | 
                Oral 
                  Presentation Number: 10   
                  A 
                  Sentence Recognizer for Mutant Protein Structure Studies: Toward 
                  Intelligent Systems for the Management of Structural Biology 
                  Data 
                  Presenter: J. Gregory Caporaso, University of Colorado Health 
                  Sciences Center 
                  Author(s): J. Gregory Caporaso, K. Bretonnel Cohen, Lawrence 
                  Hunter | 
               
               
                | 11:17am 
                  - 11:24am | 
                Oral 
                  Presentation Number: 11   
                  Statistical 
                  Data Visualization of Two Important Proteins as Phylogenetic 
                  Tools in Chloroplast Genomes 
                  Presenter: Beatrice Kilel, George Mason University 
                  Author(s): Beatrice Kilel | 
               
               
                | 11:24am 
                  - 11:31am | 
                Oral 
                  Presentation Number: 12   
                  Inferring 
                  Dynamical Gene Regulatory Networks Subject to Noise 
                  Presenter: Andre S. Ribeiro, Institute for Biocomplexity and 
                  Informatics 
                  Author(s): Stuart A. Kauffman, André S. Ribeiro, Jason 
                  Lloyd-Price | 
               
               
                |  11:31am 
                  - 11:38am | 
                Oral 
                  Presentation Number: 13   
                  UIMA 
                  as a Platform for Biomedical Natural Language Processing 
                  Presenter: William A. Baumgartner, Jr., University of Colorado 
                  Health Sciences Center 
                  Author(s): William A. Baumgartner, Jr., Andrew E. Dolbey, K. 
                  Bretonnel Cohen, and Lawrence Hunter | 
               
               
                | 11:38am 
                  - 11:45am | 
                Oral 
                  Presentation Number: 14   
                  Computational 
                  Identification Of Binding Sites In Proteins 
                  Presenter: Drena Dobbs, Iowa State University 
                  Author(s): M Terribilini, C Yan, F Wu, J-H Lee, J Sander, P 
                  Zaback, V Honavar, D Dobbs | 
               
               
                | 11:45am 
                  - 12:30pm | 
                 Invited 
                  Keynote: Blue 
                  Gene/L Impacting Computational Biology - One Year Later 
                  Kirk Jordan, IBM Strategic Growth Business/Deep Computing | 
               
               
                | 12:30pm 
                  - 4pm | 
                Break | 
               
               
                | 4:00 
                  pm - 4:45 pm | 
                Invited 
                  Keynote: Visualizing Bioinformatics Results 
                  Christoph Sensen, University of Calgary  | 
               
               
                | 4:45 pm 
                  - 4:52 pm | 
                Oral 
                  Presentation Number: 15   
                  Dissection 
                  of the Human Genome Using Repeat Probability Clouds 
                  Presenter: David Pollock, Louisiana State University 
                  Author(s): Wanjun Gu, Dale J. Hedges, Mark A. Batzer and David 
                  D. Pollock | 
               
               
                |  4:52 pm 
                  - 4:59 pm | 
                Oral 
                  Presentation Number: 16   
                  MoBIoS: 
                  A Conventional, Unconventional Database Management System Infrastructure 
                  for Biological Discovery 
                  Presenter: Daniel Miranker, The University Of Texas at Austin 
                  Author(s): Daniel P. Miranker, Rui Mao, , Smriti Ramakrishnan, 
                  Willard S. Willard and Weijia Xu | 
               
               
                | 4:52 pm 
                  - 5:06pm | 
                Oral 
                  Presentation Number: 17   
                  Genome-wide 
                  Analysis of the Distances between Human Transcription Factor 
                  Binding Sites 
                  Presenter: Hyunmin Kim, University of Colorado School of Medicine 
                  Author(s): Hyunmin Kim and Dr.Lawrence Hunter | 
               
               
                | 5:06pm 
                  - 5:13pm | 
                Oral 
                  Presentation Number: 18   
                  BioFPGA- 
                  An Open Source Hardware Project 
                  Presenter: Martin Gollery, University of Nevada, Reno 
                  Author(s): Brian Beck, Martin Gollery  | 
               
               
                | 5:13pm- 
                  5:20pm | 
                Oral 
                  Presentation Number: 19   
                  The 
                  Network Inference Testbed Software Environment 
                  Presenter: Ronald Taylor, Pacific Northwest National Laboratory 
                  Author(s): Ronald Taylor | 
               
               
                | 5:20pm 
                  - 5:27pm | 
                Oral 
                  Presentation Number: 20   
                  Novel 
                  Approaches in Peptide and Protein Identification in Shotgun 
                  Proteomics 
                  Presenter: Karen Meyer-Arendt, University of Colorado, Dept. 
                  of Chemistry and Biochemistry 
                  Author(s): Karen Meyer-Arendt, Shaojun Sun, Chia-Yu Yen, Steven 
                  Russell, William M. Old, Natalie G. Ahn, Katheryn A. Resing | 
               
               
                | 5:27pm 
                  - 5:34pm | 
                Oral 
                  Presentation Number: 21  
                  The 
                  Ecology of Place and Place-based Database Management Systems 
                  Presenter: Ian Billick, Rocky Mountain Biological Laboratory 
                  Author(s): Ian Billick | 
               
               
                | 5:34pm 
                  - 5:41pm | 
                Oral 
                  Presentation Number: 22   
                  Analysis 
                  of Human Promoters and Gene Expressions by an Integrative Approach: 
                  Constructing an Index Toward Gene Expression Patterns 
                  Presenter: Kihoon Yoon, The University of Texas at San Antonio 
                  Author(s): Kihoon Yoon, Stephen Kwek | 
               
               
                | 5:45pm 
                  - 6:30pm | 
                Invited 
                  Keynote: Sequence Analysis of Human Alternative 
                  Splices Predicted from Exon Junction Arrays 
                  Katerina Kechris, University of California, San Francisco | 
               
               
                |  
                  6:30pm - 8:30pm | 
                Reception 
                  and Posters with Authors | 
               
               
                |  Sunday, 
                  December 11 | 
               
               
                |  9:00am 
                  - 9:45am | 
                Invited 
                  Keynote: Emerging Technology and Applications of 
                  Affymetrix GeneChips: Implications for Data Management and Analysis 
                  Steve Lincoln, Affymetrix, Inc | 
               
               
                | 9:45am 
                  - 9:52am  | 
                Oral 
                  Presentation Number: 23   
                  Molecular 
                  Dynamics Evidence for Enzymatic Enabling of the Re-Configuration 
                  of the HIV Coat Glycoprotein gp120 
                  Presenter: Jack K. Horner, Science Applications International 
                  Corporation 
                  Author(s): Jack K. Horner  | 
               
               
                | 9:52am 
                  - 9:59am | 
                Oral 
                  Presentation Number: 24   
                  SCANS: 
                  System for Compression and Analysis of Nucleotide Sequences 
                  Presenter: Valerio Aimale, SeiraD, Inc 
                  Author(s): Valerio Aimale, Callum Bell & Joe Gatewood | 
               
               
                | 9:59am 
                  - 10:06am | 
                Oral 
                  Presentation Number: 25   
                  Bacterial 
                  Genes in a Eukaryotesy 
                  Presenter: Philip, Gayle, National University of Ireland 
                  Author(s): Gayle K. Philip and Dr. James O. McInerney  | 
               
               
                | 10:06am 
                  - 10:13am | 
                Oral 
                  Presentation Number: 26  
                  ATGC: 
                  A Web Tool for Multiple Genome Comparison 
                  Presenter: Lu, Guoqing - University of Nebraska at Omaha 
                  Author(s): Guoqing Lu, Liying Jiang, Etsuko Moriyama, Luwen 
                  Zhang | 
               
               
                | 10:13am 
                  - 10:20am | 
                Oral 
                  Presentation Number: 27   
                  Inferring 
                  Three-way Gene Interactions from Microarray Data Sets 
                  Presenter: Jiexin Zhang, The University of Texas M.D. Anderson 
                  Cancer Center 
                  Author(s): Jiexin Zhang, Yuan Ji, Li Zhang  | 
               
               
                | 10:20am 
                  - 10:27am  | 
                Oral 
                  Presentation Number: 28 
                  Computational 
                  Alchemy 
                  Presenter: Dan McShan, UCHSC 
                  Author(s): Dan McShan  | 
               
               
                | 10:27am 
                  - 10:34am | 
                Oral 
                  Presentation Number: 29 
                  To be announced  | 
               
               
                | 10:34am 
                  - 10:41am | 
                Oral 
                  Presentation Number: 30   
                  Mining 
                  Protein Transport Data from GeneRIFs 
                  Presenter: Zhiyong Lu, U of Colorado School of Medicine 
                  Author(s): Zhiyong Lu; Larry Hunter  | 
               
               
                | 10:45am 
                  – 11:05am | 
                Coffee 
                  Break | 
               
               
                | 11:05am 
                  - 11:12am | 
                Oral 
                  Presentation Number: 31 
                  Transcriptional 
                  Control and Behavioral Changes in Selectively Bred Mice 
                  Presenter: Razvan Lapadat, UCDHSC- Department of Pharmacology 
                  Author(s): Razvan Lapadat, Sanjiv Bhave, Lawrence Hunter, Paula 
                  Hoffman, Boris Tabakoff  | 
               
               
                | 11:12am 
                  - 11:19am | 
                Oral 
                  Presentation Number: 32 
                  The 
                  Survival Value of Dormancy: Human Hematopoetic Stem Cells and 
                  Hibernating Ground Squirrels 
                  Presenter: Tom Marr, University of Alaska 
                  Author(s): Tom Marr  | 
               
               
                | 11:19am 
                  - 11:26am | 
                Oral 
                  Presentation Number: 33   
                  Gene 
                  Classification by Decision Tree Data Mining Methods: Identification 
                  of Genes Likely to be Involved in Human Genetic Disease 
                  Presenter: Julius Goth, North Carolina State University 
                  Author(s): Julius Goth, ClarLynda Williams-DeVane, Jihye Kim | 
               
               
                | 11:26am 
                  - 11:33am | 
                Oral 
                  Presentation Number: 34 
                  To be announced  | 
               
               
                | 11:33am 
                  - 11:40am | 
                Oral 
                  Presentation Number: 35   
                  Challenges 
                  in Analyzing Methylation cDNA Microarray 
                  Presenter: Mihail Popescu, University of Missouri 
                  Author(s): Mihail Popescu, Gerald Arthur, Charles Caldwell  | 
               
               
                | 11:40am 
                  - 11:47am | 
                Oral 
                  Presentation Number: 36 
                  Simple 
                  Disease Prediction Models for Cancer Screens? 
                  Presenter: James Lyons-Weiler, University of Pittsburgh Cancer 
                  Institute 
                  Author(s): James Lyons-Weiler  | 
               
               
                | 11:47am 
                  - 11:54am | 
                Oral 
                  Presentation Number: 37   
                  A 
                  Molecular Concept Map for Human Biology and Disease 
                  Presenter: Daniel Rhodes, University of Michigan 
                  Author(s): Daniel R. Rhodes, Shanker Kalyana-Sundaram, Vasudeva 
                  Mahavisno, Nicole Kasper, Terrence R. Barrette, Debashis Ghosh 
                  and Arul M. Chinnaiyan  | 
               
               
                | 11:54am 
                  - 12:01pm | 
                Oral 
                  Presentation Number: 38   
                  Development 
                  of a Proteome Database from a Genome Sequence or ESTs for Protein 
                  Identification and in silico Predictions 
                  Presenter: Dong Chen - Utah State University 
                  Author(s): Dong Chen, Jon L. Pearson, Desai Prerak, Jake Michaelson, 
                  and Bart C. Weimer  | 
               
               
                | 12:01pm 
                  - 12:08pm | 
                Oral 
                  Presentation Number: 39 
                  Identifying 
                  Temporally Dependent Variation in Noisy Gene Expression Data 
                  Without Replicates 
                  Presenter: Stephen Billups, University of Colorado at Denver 
                  and Health Sciences Center 
                  Author(s): Stephen Billups   
                   | 
               
               
                | 12:08pm 
                  - 12:15pm | 
                Oral 
                  Presentation Number: 40   
                  A 
                  Study to Identify Interactions Between Transcription Factors 
                  and Non-housekeeping Genes to Determine Expression Regulation 
                  of Cancer Genes 
                  Presenter: Kihoon Yoon, University of Texas at San Antonio 
                  Author(s): Amitava Karmaker, Kihoon Yoon, Stephen Kwek  | 
               
               
                | 12:15pm 
                  - 1:00pm | 
                Closing 
                  Keynote 
                  Gene Myers, University of California, Berkeley | 
               
             
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