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














Click on the presentation iconto 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