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Dear Rocky '07 Participant,

Welcome to the fifth annual Rocky Mountain Bioinformatics Conference, a meeting of the International Society for Computational Biology (ISCB). The organizers hope that you enjoy the program, and find the conference a productive opportunity to meet researchers, students and industrial users of bioinformatics technology. We think we have the best program yet, offering a remarkable cross–section of bioinformatics research.

The Rocky series began five years ago as a regional conference, and has grown into an international program with a spotlight on regional development in the computational biosciences. Presenters at this year’s meeting come from the Rocky Mountain regional states/provinces of Alberta, Colorado, Nevada, New Mexico, Utah and Wyoming, as well as from over 10 other states/provinces and at least six countries. These scientists represent a broad spectrum of universities, industrial enterprises, government laboratories, and medical libraries. The meeting is a chance to get to know your colleagues near and far, seek collaborative opportunities, and find synergies that can drive our field forward.

For 2007 we will continue with the changes made in 2006 with extending the meeting to three full days, keeping the short talks to 10 minutes, and keeping with a larger poster session, allowing everyone who wants to present to do so. And we’ve retained the lunchtime ski breaks so that those of you who want to ski, including beginners, will have a chance to do so among friends and colleagues.

We hope you enjoy the science, the company, and the spectacular scenery of the Rocky Mountains. Welcome!

Larry Hunter
Rocky '07 Conference Chair

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Full Agenda

The 2007 Rocky Conference will begin on Friday morning.
Click on the presentation iconto access the slides of each talk.
Thursday – November 29, 2007
3:00 pm – 6:00 pm Registration
Friday, November 30, 2007
7:30 am – 8:30 am Registration
8:30 am – 9:150 am Keynote 1
Andrea Califano, Ph.D.
Columbia University
9:15 am – 10:25 am:
  Oral Presentation 1
Manual Curation is not Sufficient for Annotation of Genomic Databases
Presenter: William Baumgartner Jr, University of Colorado School of Medicine
Additional Author(s): K. Bretonnel Cohen, Lynne M. Fox, George Acquaah–Mensah, Lawrence Hunter
  Oral Presentation 2
Knowledge Integration for Gene Target Selection
Presenter: Graciela Gonzalez,
Arizona State University
Additional Author(s): Juan Uribe
9:50 am – 10:00 am Oral Presentation 3
Estimating the Reliability of kNN Classification
Presenter: Maxim Tsypin, Biodesix
Additional Author(s): Heinrich Roder
10:00 am – 10:10 am Oral Presentation 4
Cross–species Multi–scalar Resolution of the Developing Lung Transcriptome
Presenter: Soumyaroop Bhattacharya, Brigham and Womens Hospital
Additional Author(s): Alvin Kho,
Vincent Carey, Kelan Tantisira,
Roger Gaedigk, J. Steven Leeder,
Scott Weiss, Thomas Mariani
10:10 am – 10:20 am Oral Presentation 5 (cancelled)
A Novel Multivariate Method for Identification of The Informative Set of Genes
Presenter: Darius Dziuda,
Central Connecticut State University
10:20 am – 10:30 am Oral Presentation 6
Salamander Mitochondrial Genomics and the Tree of Life
Presenter: Rachel Mueller,
Colorado State University
10:30 am10:50 am Break
10:50 am 11:00 am Oral Presentation 7
(presentation not available)
Adaptive Evolution and Functional Redesign of Metabolic Proteins in Snakes: Linking Microevolutionary Changes with Macroevolutionary Shifts
Presenter: Todd Castoe, University of Colorado - Health Sciences Center
Additional Author(s): David Pollock
11:00 am 11:10 am Oral Presentation 8
Consistency Assessment Among Multiple Probe Sets Interrogating the Same Gene on the Affymetrix MOE430 GeneChip
Presenter: Xiangqin Cui,
University of Alabama at Birmingham
11:10 am – 11:20 am Oral Presentation 9 (cancelled)
Position-dependent Motif Characterization using Non-negative Matrix Factorization
Presenter: Joel Graber,
The Jackson Laboratory
Additional Author(s): Priyam Singh,
Sean Murphy, Erik McCarthy,
Lucie Hutchins
11:20 am – 11:30 am Oral Presentation 10
Reference Normalization Improves the Accuracy of Copy Number Analysis
Presenter: Stanley Pounds, St. Jude Children's Research Hospital
Additional Author(s): Cheng Cheng
11:30 am – 11:40 am Oral Presentation 11
(cancelled)

BANNER: A Portable, Open-source, Biomedical Named Entity Recognition System
Presenter: Robert Leaman,
Arizona State University
Additional Author(s): Graciela Gonzalez
11:40 am – 12:25 pm Keynote 2
Elevated Abstract
Andrey Ptitsyn, Ph.D.
12:25 pm – 4:00 pm Break
4:00 pm – 5:00 pm Workshop Session:
The Bioinformatics Curriculum Collaboration as a Mechanism to Create Open Access Shared Curriculum Materials
5:00 pm – 5:10 pm Oral Presentation 12
Genetic Algorithms Select Protein Features Most Predictive of Enzyme Function
Presenter: Andrew Kernytsky,
Columbia University
Additional Author(s): Burkhard Rost
5:10 pm – 5:20 pm Oral Presentation 13
Thermonucleotideblast: A Tool for Improved Assay-Dependent Searching of Nucleic Acid Sequence Databases
Presenter: Jason Gans,
Los Alamos National Lab
5:20 pm – 5:30 pm Oral Presentation 14
ClearTK: A Framework for Statistical Biomedical Language Processing
Presenter: Philip Ogren, University of Colorado at Boulder
Additional Author(s): Philipp Wetzler
5:30 pm – 5:40 pm Oral Presentation 15
Semi-supervised Learning for Protein Sequence Classification
Presenter: Brian King, State University of New York at Albany
Additional Author(s): Chittibabu Guda
5:40 pm – 6:30 pm Break
6:30 pm – 10:00 pm Dinner at Il Pogio Restaurant
Saturday, December 1, 2007
7:30 am – 8:45 am Registration
8:45 am – 9:30 am Keynote 3
Invited Keynote
Lawrence Hunter, Ph.D.
9:30 am – 9:40 am Oral Presentation 16
Evaluating Coevolution Detection Methods on Protein Alpha Helices
Presenter: J Gregory Caporaso, University of Colorado Health Sciences Center
Additional Author(s): Lawrence Hunter, Rob Knight
9:40 am – 9:50 am Oral Presentation 17
Chasing Arboviruses in Vector Mosquitoes
Presenter: Benedict Khoo, University of Houston - Downtown
Additional Author(s): Jenny Martinez,
Dr. Jeffrey Flosi
9:50 am – 10:00 am Oral Presentation 18 (cancelled)
Combining Interaction and Expression Data to Identify Context-Specific Gene Sub-Networks
Presenter: Hannah Tipney, University of Colorado at Denver and Health Sciences Center
Additional Author(s): Sonia Leach, Weiguo Feng, Richard Spritz,
Trevor Williams, Larry Hunter
10:00 am – 10:10 am Oral Presentation 19
Global Similarity Between Multiple Bionetworks
Presenter: Yunkai Liu,
University of South Dakota
10:10 am – 10:20 am Oral Presentation 20
More Powerful Experimental Designs for Detecting Episodic Positive Selection
Presenter: A.P. Jason de Koning,
University of Colorado,
Health Sciences Center
Additional Author(s): Carol-Beth Stewart.
University of Colorado,
Health Sciences Center
10:20 am – 10:30 am Oral Presentation 21
High-throughput Annotation of Genomic Datasets with Genephony
Presenter: Alberto Riva,
University of Florida
Additional Author(s): Angelo Nuzzo
10:30 am – 10:50 am Break
10:50 am – 11:00 am Oral Presentation 22
Timing the Origin of Vision: A 'Palaeoinformatics' Approach
Presenter: Davide Pisani, The National University of Ireland, Maynooth
11:00 am – 11:10 am Oral Presentation 23
Coding Domain Sequence Prediction and Alternative Splicing Detection in Human Malaria Gambiae
Presenter: Jun Li, University of Minnesota
Additional Author(s): Bing-Bing Wang, Jose Ribeiro, Ken Vernick
11:10 am – 11:20 am Oral Presentation 24
Factors Affecting Prediction of Protein-Protein Interaction Networks by Phylogenetic Profiling
Presenter: Anis Karimpour-Fard, University of Colorado at Health Science Center
Additional Author(s): Ryan Gill,
Lawrence Hunter
11:20 am – 11:30 am Oral Presentation 25
SNP Analysis Reveals a Role for Polymorphisms in Evolution of Staphylococcal Pathogenicity
Presenter: Karthikeyan Sivaraman, University of Central Florida
Additional Author(s): Alexander Cole
11:30 am – 11:40 am Oral Presentation 26
Exon Array Analysis: Changing the Landscape of Gene Expression Profiling
Presenter: Tzu Lip Phang, University of Colorado at Denver and Health Sciences Center
Additional Author(s): Richard A. Radcliffe
11:40 am – 11:50 am Oral Presentation 27
Advancing X-ray Crystallography via Protein Structure Prediction
Presenter: Christopher Bottoms,
University of Missouri-Columbia
Additional Author(s): Jingfen Zhang, Rajkumar Bondugula, John Tanner,
Dong Xu
11:50 am – 12:35 pms Keynote 4 (cancelled)
Apple
Michael Gonzales, Ph.D.
12:35 pm – 4:00 pm Break
4:00 pm – 4:20 pm Keynote 5
Biodesix
Heinrich Roder, D. Phil.
4:20 pm – 4:30 pm Oral Presentation 28
Beyond TissueInfo: Functional Prediction Using Tissue Expression Profile Similarity Searches
Presenter: Fabien Campagne,
Weill Medical College of Cornell University
Additional Author(s): Daniel Aguilar,
Lucy Skrabanek, Steven Gross,
Baldo Oliva
4:30 pm – 4:40 pm Oral Presentation 29
(presentation not available)
Modelling Transcription Elongation and Termination Using POLII ChIP-Chip Signals in Yeast
Presenter: Hyunmin Kim, University of Colorado Health Sciences Center
Additional Author(s): David Bentley,
David Pollock
4:40 pm – 4:50 pm Oral Presentation 30
Predictive Analysis on Optimization of Cancer Classi?cation by Machine Learning Methods
Presenter: Lei Liu,
Sun Microsystems, Inc.
4:50 pm – 5:00 pm Oral Presentation 31
Protein Interaction Network Evolution Characterized by Subfunctionalization, Not Neofunctionalization
Presenter: Todd Gibson, UCDHSC at Anschutz Medical Campus
Additional Author(s): Debra Goldberg
5:00 pm – 5:10 pm Oral Presentation 32
Mathematical Modeling of Bird Flu Propagation
Presenter: Urmi Ghosh-Dastidar, New York City College of Technology, CUNY
5:10 pm – 5:20 pm Oral Presentation 33
Systematic Order Dependent Effect in Affymetrix GeneChips
Presenter: Kathe Bjork, UCDHSC
Additional Author(s): Karen Kafadar
5:20 pm – 5:30 pm Oral Presentation 34
Phylogenetic Analysis of Protein Phosphatases of the Malaria Parasite Plasmodium Falciparum
Presenter: Jonathan Wilkes,
University of Glasgow
Additional Author(s): Christian Doerig
5:30 pm – 5:40 pm Oral Presentation 35
(presentation not available)
Detecting Reassortment in Influenza Viruses
Presenter: James McInerney, National University of Ireland Maynooth
Additional Author(s): Victoria Svinti Svinti, James Cotton
5:40 pm – 5:50 pm Oral Presentation 36
A Genomic Survey of Heat Shock Transcription Factor Binding Sites in Saccharomyces Cerevisiae
Presenter: Sujuan Ye,
University of South Dakota
Additional Author(s): Alexander Erkine, YunKai Liu
5:50 pm – 6:00 pm Oral Presentation 37
Predicting Drug-drug Interactions That Occur by Metabolic Inhibition Using Evidence and Truth Maintenance
Presenter: Richard Boyce, University of Washington
Additional Author(s): Ira Kalet,
Carol Collins, John Horn
6:00 pm – 6:10 pm Oral Presentation 38
Bayesian Networks for Genome Expression: A Bayesian Statistical Approach to Modeling Gene Regulatory Pathways in Human Placental Microarray Data
Presenter: Elinor Velasquez,
San Francisco State University
6:15 pm – 8:15 pm Reception and Poster Session
Sunday, December 2, 2007
7:30 am – 8:45 am Registration
8:45 am – 9:30 am Keynote 6
Elevated Abtract
Karin Verspoor, Ph.D.
9:30 am – 9:40 am Oral Presentation 39
Molecular Evolution of Mammalian Imprinted Genes: Testing the Theories
Presenter: Mary O'Connell,
Dublin City University
Additional Author(s): Noeleen Loughran, Mark Donoghue, Karl Schmid,
Charles Spillane
9:40 am – 9:50 am Oral Presentation 40
A Statistical Framework for Integrating Different Microarray Data Sets in Differential Expression Analysis
Presenter: Yinglei Lai,
George Washington University
9:50 am – 10:00 am Oral Presentation 41
Assembling the Interactome of Human Extracellular Matrix to Understand its Role in Health and Disease
Presenter: Graham Cromar,
Hospital for Sick Children
Additional Author(s): John Parkinson
10:00 am – 10:10 am Oral Presentation 42
Exact Calculations of Expected Power for the Benjamin-Hochberg Procedure
Presenter: Deborah Glueck, University of Colorado Health Sciences Center
Additional Author(s):
Anis Karimpour-Fard, Larry Hunter,
Jan Mandel, Keith Muller
10:10 am – 10:20 am Oral Presentation 43
Combining Structural Modeling, Evolutionary Information, and Machine Learning to Improve Prediction of Nucleic Acid Binding Sites in Telomerase
Presenter: Deepak Reyon,
Iowa State University
Additional Author(s): Ben Lewis,
Jae-Hyung Lee, Colin Gleeson,
Michael Hamilton, Fadi Towfic,
Cornelia Caregea, Michael Terribilini,
Drena Dobbs, Vasant Honavar
10:20 am – 10:30 am Oral Presentation 44
Analysis of Highly Conserved Functional Sites Predicted by Dynamics Perturbation Analysis (DPA)
Presenter: Judith Cohn,
Los Alamos National Laboratory
Additional Author(s): Michael Wall, Dengming Ming
10:30 am – 10:50 am Break
10:50 am – 11:00 am Oral Presentation 45
Accuracy of Structure-based Sequence Alignment of Automatic Methods
Presenter: Byungkook Lee,
National Cancer Institute/National Institutes of Health
Additional Author(s): Changhoon Kim
11:00 am – 11:10 am Oral Presentation 46
Metabolic Analysis of Tumor Progression
Presenter: Norma Pawley, Los Alamos National Laboratory
Additional Author(s): Munehiro Teshima, Susan Carpenter, Steven Brumby,
Clifford Unkefer, Pat Unkefer, James Freyer
11:10 am – 11:20 am Oral Presentation 47
Computational Examination of Gain and Loss of Phosphorylation Consensus Sites in Cancer
Presenter: Peter Baenziger,
Indiana University School of Medicine
Additional Author(s): Uday Shanker, Matthew Mort, Sean Mooney, Maricel Kann, Matthew Hahn, Predrag Radivojac
11:20 am – 11:30 am Oral Presentation 48
Protein Structural Domain Assignment with a Delaunay Tessellation Derived Lattice
Presenter: Todd Taylor, NIST
Additional Author(s): Iosif Vaisman
11:30 am – 11:40 am Oral Presentation 49
Automated Analysis of Viral Integration Sites in Gene Therapy Research Using the SeqMap Web Resource
Presenter: Sean Mooney, Indiana University
Additional Author(s): Jessica Dantzer, Brandon Peters, Sara Dirscherl,
Scott Cross, Xiaoman Li,
Kenneth Cornetta, Mary Dinauer
11:40 am – 11:50 am Oral Presentation 50
Classification Analysis of HIV RNase H Bioassay
Presenter: Lianyi Han, National Center for Biotechnology Information/National Institutes of Health (NIH)
Additional Author(s): Yanli Wang,
Steve Bryant
11:50 am – 12:35 pm Keynote 7
Invited Speaker
Richard H. Lathrop, Ph.D.
12:35 pm Rocky '07 Closing Comments

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