8th Annual Rocky Mountain Bioinformatics Conference

Full Agenda

Updated Nov. 21, 2010
go directly to: [Friday - December 10] [Saturday - December 11]

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
Simon Twigger, Medical College of Wisconsin
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

Christophe Roeder, University of Colorado, Denver
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
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
Bradley Langhorst, New England Biolabs
Bradley Langhorst, Nicole Nichols
2:25 pm – 2:35 pm Oral Presentation 5
ORO Miner, An Application for Investigating Cell Communication in Multicellular Organisms
Michael Rogers, University of Nevada Las Vegas
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
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
Kevin Livingston, University of Colorado Denver
Kevin Livingston, Michael Bada, Lawrence Hunter
3:10 pm – 3:20 pm Oral Presentation 8
Testing for Joint Association of All SNP Pairs
Ronald Schuyler, University of Colorado
Ronald Schuyler, Lawrence Hunter
3:20 pm – 3:30 pm Oral Presentation 9
Cognitive Task Flows and Visual Analytics
Barbara Mirel, University of Michigan
Barbara Mirel, Felix Eichinger
3:30 pm – 3:40 pm Oral Presentation 10
CategoryCompare: High-throughput Data Meta-analysis using Gene Annotations
Robert Flight, University of Louisville
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
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
Bobbie-jo Webb-Robertson, Pacific Northwest National Laboratory
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
Daniel Dvorkin, University of Colorado Denver
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]

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
Karin Verspoor, University of Colorado Denver
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
Emily Howe, The Buck Institute
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
Christian Forst, UT Southwestern Medical Center
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
Ken Yokoyama, University of Colorado Denver
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
Elizabeth Siewert, Colorado School of Public Health
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
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

Graciela Gonzalez, Arizona State University
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
Ian Davis, GrassRoots Biotechnology, Inc.
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]

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
Weerayuth Kittichotirat, University of Washington
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
Laura Wojtulewicz, Arizona State University
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
Xiaowei Xu, University of Arkansas at Little Rock
Xiaowei Xu
4:20 pm – 4:30 pm Oral Presentation 46
Adaptive Learning Neural Networks for Binding Site Search in Genomic Sequences
Ivan Erill, University of Maryland Baltimore
Joseph Cornish, Sumeet Bagde, Elisabeth Hobbs, Ivan Erill
4:30 pm – 4:40 pm Oral Presentation 47
Enriching Regulatory Networks with Other Functional Relationships
Ronald Taylor, Pacific Northwest National Laboratory
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
Chanel Mejias-Rosario, Universidad Metropolitana
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

return to: [Thursday - December 9 ] [Friday - December 10]