|
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 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 |
|