Dear Rocky '06 Participant,

Welcome to the forth annual Rocky Mountain Bioinformatics Meeting, a conference of the International Society for Computational Biology (ISCB). 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. We think we have the best program yet, offering a remarkable cross-section of bioinformatics research.

The Rocky series began four years ago as a regional meeting, 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. Among our keynote speakers Prof. Ptitsyn just moved to the Rocky Mountain area to take a new faculty position, Prof. Wishart is a longstanding member of our regional community, and Dr. Myers got his Ph.D. in the area. 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 2006 we’ve expanded the science by extending the meeting to three full days, increased the duration of the short talks to 10 minutes, and enlarged the poster session, allowing everyone who wants to present to do so. We’ve retained the education workshop to discuss issues central to training the next generation of bioinformaticians, making it more relevant than ever to students and employers. 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 should all be grateful for the support of our sponsors: IBM, Affymetrix, HP, Biodesix and Dharmacon. 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 Biodesix and IBM lay out some of the challenges we face and some of the resources we will need to address them. We are also thankful to the 2006 ISCB Overton Prize winner, Mathieu Blanchette, who donated his financial award to this conference to enable us to keep student registration fees low. The meeting would simply not be possible without organizational help from the ISCB staff, as well as from Kathy Thomas at the University of Colorado School of Medicine.

Many of you have contributed $5 to join the Rocky Mountain Regional Bioinformatics group, an affiliate of the ISCB. 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
Susan C. Trapp
Rocky '06 co-chairs

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AGENDA

For the first time the 2006 Rocky Conference will begin
on Friday morning.

All sessions will be held at the
Silvertree Hotel
, Snowmass, Colorado

Click on the presentation iconto access the .pdf slides of each talk.
Thursday - November 30, 2006
3:00 pm -
6:00 pm
Registration
Friday - December 1, 2006
7:30 am -
8:30 am
Registration
8:30 am -
9:15 am
Invited Keynote 1:
Data Mining, Clinical Modeling and the Future of Healthcare Computing
Peter Haug, MD
, Senior Informaticist for Intermountain Health Care and Professor
Department of Biomedical Informatics, University of Utah
9:15 am -
9:25 am
Oral Presentation Number: 1
Computer Aided Genetic Engineering
Presenter: Dan McShan, University of Colorado School of Medicine
Author(s): Dan McShan
9:25 am -
9:35 am
Oral Presentation Number: 2
Designing C2H2 Zinc Finger Proteins to Target Specific Genomic Sites
Presenter: Peter Zaback, Iowa State University/Bioinformatics and Computational Biology
Author(s): P. Zaback, J. Sander, F. Fu, D. Voytas, D. Dobbs
9:35 am -
9:45 am
Oral Presentation Number: 3
Biological Network Inference and the SEBINI Software Environment
Presenter: Ronald Taylor, Pacific Northwest National Laboratory
Author(s): Ronald Taylor, Anuj Shah, Charles Treatman, and Meridith Blevins
9:45 am -
9:55 am
Oral Presentation Number: 4
The BioCyc Collection of Pathway/Genome Databases
Presenter: Alexander G. Shearer, SRI International
Author(s): Alexander G. Shearer, Ron Caspi, Carol A. Fulcher, Pallavi Kaipa, Peter D. Karp
9:55 am -
10:05 am
Oral Presentation Number: 5
Spatio-Temporal Modelling of Biochemical Pathways: Introducing Cell++
Presenter: John Parkinson, Hospital for Sick Children / University of Toronto
Author(s): Chris Sanford, Matthew Yip and John Parkinson
10:05 am -
10:15 am
Oral Presentation Number: 6
Minimal Oscillatory Currents in Neurons
Presenter: Tom McTavish, UCHSC
Author(s): Tom McTavish
10:15 am -
10:25 am
Oral Presentation Number: 7
Assessment of siRNA Inhibition Prediction Algorithms
Presenter: Kevin Sullivan, Dharmacon, Inc
Author(s): Kevin Sullivan
10:25 am -
10:45 am
Break
10:45 am -
10:55 am
Oral Presentation Number: 8
The Balance Between Activating and Inhibiting Connections Controls the Dynamics of Biological Networks
Presenter: Daniel McDonald, University of Colorado at Boulder
Author(s): Daniel McDonald, Meredith Betterton, Laura Waterbury, Rob Knight
10:55 am -
11:05 am
Oral Presentation Number: 9
Beyond Ontologies: The WayCraft Scientific Knowledge Integration Framework
Presenter: Frank D. Russo, WayCraft Biosoftware
Author(s): Frank D Russo, Steven T Connolly, Ranga Chandra Gudavida, Angela Qu, Anil Jegga, Bruce J Aronow
11:05 am -
11:15 am
Oral Presentation Number: 10
An Experiment in Mining Gene-Disease Relationships from Biomedical Literature
Presenter: Graciela Gonzalez, Arizona State University - School of Computing and Informatics, Dept of Biomedical Informatics
Author(s): Graciela Gonzalez, Juan C. Uribe, Luis Tari, Colleen Brophy, Chitta Baral
11:15 am -
11:25 am
Session Cancelled

Oral Presentation Number: 11
Pinning: A Method for Localization of Copy-number Aberration Hotspots in Cancer Genomes
Presenter: Alexander Krasnitz, Cold Spring Harbor Laboratory
Author(s): A. Krasnitz, J. Hicks, X. Zhao, B. Lakshmi, Y.-H. Lee, A.-L. Borresen-Dale, A. Zetterberg, D. Mu, S. Powers, M. Wigler
11:25 am -
11:35 am
Oral Presentation Number: 12
Bioinformatics as a Tool to Predict Gene Function in Williams-Beuren Syndrome
Presenter: Hannah Tipney, University of Colorado at Denver Health Sciences Center
Author(s): Hannah Tipney, Andy Brass, May Tassabehji
11:35 am -
11:45 am
Oral Presentation Number: 13
Unified Maximum Separability Analysis for Molecular Profile Analysis and Biomarker Discovery
Presenter: Qiuyan Huo, Johns Hopkins University School of Medicine
Author(s): Qiuyan Huo, Zhen Zhang
11:45 am -
11:55 am
Oral Presentation Number: 14
Data Integration as a Foundation for Semantic Integration
Presenter: Daniel J. McGoldrick, University of Colorado, Department of Pharmacology
Author(s): Daniel J McGoldrick, Lawrence Hunter
11:55 am -
12:40 pm
Invited Keynote 2:
Dynamics Perturbation Analysis of SCOP Domains
Judith Cohn, Ph.D., Technical Staff Member
Bioscience Division, Los Alamos National Lab
12:40 pm -
4:00 pm
Break
4:00 pm -
5:00 pm
Workshop Session 1:
Creating the Right Bioinformatics Resume to Land the Interview
A. The Resume
B. The Cover Letter
Facilitator: Kirk Jordan
5:00 pm -
5:10 pm
Oral Presentation Number: 15
Dissecting Genetics of Host-Pathogen Interactions
Presenter: Peter T. Hraber, Theoretical Biology & Biophysics, LANL
Author(s): Peter T. Hraber
5:10 pm -
5:20 pm
Oral Presentation Number: 16
Phylogenetic Profiling via Partial Genomes: Applications to the Apicomplexa
Presenter: James Wasmuth, Hospital for Sick Children
Author(s): Jennifer Daub, Matthew Fagnani, Jose Peregrin-Alvarez, Chris Sanford, James Wasmuth, John Parkinson
5:20 pm -
5:30 pm
Oral Presentation Number: 17
Genome-Wide Co-Expression Based Prediction of Differential Expressions
Presenter: Yinglei Lai, The George Washington University, Department of Statistics
Author(s): Yinglei Lai
5:30 pm -
6:00 pm
Break
6:00 pm -
10:00 pm
Dinner and Keynote
Invited Keynote 3:
Kirk Jordan, Ph.D. , Emerging Solutions Executive
IBM Strategic Growth Business/Deep Computing
Saturday, December 2
7:30 am -
8:30 am
Registration
8:30 am -
9:15 am
Invited Keynote 4:
Comparative Mass Spectrometry for Clinical Applications
Heinrich Roder, D.Phil., Chief Technology Officer
Biodesix Inc., Colorado
9:15 am -
9:25 am
Oral Presentation Number: 18
A Semi-Manual Method Using the ANCOVA Framework to Identify Expression Profiles in Time-Course Microarray Experiments
Presenter: Tzu Lip Phang, University of Colorado Health Sciences Center, Department of Medicine
Author(s): Tzu Lip Phang, Katherina Kechris
9:25 am -
9:35 am
Oral Presentation Number: 19
ARB - A Comprehensive Phylogenetic Ssequence Analysis and Probe Design Software Environment
Presenter: Harald Meier, Technische Universitaet Muenchen, Informatik
Author(s): W. Ludwig, R. Westram, Y. Kumar, H. Meier
9:35 am -
9:45 am
Oral Presentation Number: 20
Does the Region of rRNA Sequenced Affect Conclusions from Microbial Community Analysis
Presenter: Zongzhi Liu, University of Colorado
Author(s): Zongzhi Liu, Catherine Lozupone, Micah Hamady, Rob Knight
9:45 am -
9:55 am
Oral Presentation Number: 21
Tight Clusters F Proteins
Presenter: Roman L. Tatusov, NCBI NLM NIH
Author(s): Boris Kiryutin
9:55 am -
10:05 am
Oral Presentation Number: 22
A Bayesian Network Model of Stromatolite Formation
Presenter: Jack K. Horner, Science Applications International Corporation
Author(s): Jack K. Horner
10:05 am -
10:15 am
Oral Presentation Number: 23
Genomic Supertrees of Life
Presenter: Davide Pisani, The National University of Ireland Maynooth
Author(s): Davide Pisani, James A. Cotton, James O. McInerney
10:15 am -
10:25 am
Oral Presentation Number: 24
Modeling Evolution of Gene and Protein Networks
Presenter: Todd A. Gibson, University of Colorado Health Sciences Center
Author(s): Todd A. Gibson, Debra S. Golderg
10:25 am -
10:45 am
Break
10:45 am -
10:55 am
Oral Presentation Number: 25
The Unique-eome: What Makes pecies Different?
Presenter: Martin Gollery, University of Nevada, Reno
Author(s): Martin Gollery, John Cushman, Jeff Harper, Taliah Mittler, Ron Mittler
10:55 am -
11:05 am
Oral Presentation Number: 26
Monte Carlo EM Algorithm for Sequence Motif-finding
Presenter: Chengpeng Bi, Children's Mercy Hospitals
Author(s): Chengpeng Bi
11:05 am -
11:15 am
Oral Presentation Number: 27
Biomarker Discovery in Genomic Data with Partial Clinical Annotation
Presenter: Cole Harris, Exagen Diagnostics, Inc.
Author(s): Cole Harris, Noushin Ghaffari
11:15 am -
11:25 am
Oral Presentation Number: 28
Systematic Gene Selection for Dynamic Gene-Network Refinement
Presenter: Christian V. Forst, Los Alamos National Laboratory
Author(s): Nicole Radde, Jutta Gebert, Christian V. Forst
11:25 am -
11:35 am
Oral Presentation Number: 29
Using an Anatomy Ontology to Predict the Spread of Tumor Cells to Regional Metastatic Sites
Presenter: Ira Kalet, University of Washington
Author(s): Ira Kalet
11:35 am -
11:45 am
Oral Presentation Number: 30
Analyzing Time Course Microarray Data With Temporal Uncertainty
Presenter: Stephen Billups, University of Colorado at Denver and Health Sciences Center, Dept. of Mathematical Sciences
Author(s): Stephen Billups
11:45 am -
11:55 am
Oral Presentation Number: 31
Energy Landscape Calculations for a DNA-Rotaxane using Milestoning Technique
Presenter: Shahid Qamar, Arizona State University
Author(s): Shahid Qamar
11:55 am -
12:40 pm
Invited Keynote 5:
Metabolomics: The Next Frontier for Bioinformatics?
David S. Wishart, Ph.D.
Department of Computing Science and Department of Biological Science
University of Alberta
12:40 pm -
4:00 pm
Break
4:00 pm -
5:00 pm
Workshop Session II:
The Interview & Negotiations
Once you get the offer: A mock interview will be perfromed on a live stage! Followed by a panel discussion of each of the interviewees
A. Discussion
Facilitator: Kirk Jordan
5:00 pm -
5:10 pm
Oral Presentation Number: 32
The SINE of the Opossum
Presenter: David D. Pollock, University of Colorado
Author(s): Wanjun Gu, David A. Ray, Jerilyn A. Walker , Erin Barnes, Andrew J. Gentles, Paul B. Samollow, Jerzy Jurka, Mark A. Batzer, David D. Pollock
5:10 pm -
5:20 pm
Oral Presentation Number: 33
Strong Negative and Positive Selection Can Obscure Ancestral Signal in Phylogenetic Analysis
Presenter: Alexander Tchurbanov, University of Wyoming
Author(s): Alexander Tchurbanov, Katherine Harris, Shruti Rastogi, David Liberles
5:20 pm -
5:30 pm
Oral Presentation Number: 34
Cyberenvironment for Computational Bioscience
Presenter: Thanh N. Truong, Department of Chemistry, University of Utah
Author(s): Thanh N. Truong
5:30 pm -
5:40 pm
Oral Presentation Number: 35
A Computational Method to Identify RNA Binding Sites in Proteins
Presenter: Jeff Sander, Iowa State University
Author(s): J. Sander, M. Terribilini, J.H. Lee, R. Jernigan, V. Honavar, D. Dobbs
5:40 pm -
5:50 pm
Oral Presentation Number: 36
Information Retrieval, Question-Answering, Machine Learning, and Concept Recognition in TREC Genomics 2006
Presenter: J. Gregory Caporaso, University of Colorado Health Sciences Center, Dept. of Biochemistry and Molecular Genetics
Author(s): J. Gregory Caporaso, William A. Baumgartner, Jr., Hyunmin Kim, Zhiyong Lu, Helen L. Johnson, Olga Medvedeva, Anna Lindemann, Lynne Fox, Elizabeth K. White, K. Bretonnel Cohen, and Lawrence Hunter
5:50 pm -
6:00 pm
Oral Presentation Number: 37
FluKB: an Integrated Knowledge Base for Influenza Viruses
Presenter: Guoqing Lu, University of Nebraska at Omaha
Author(s): Guoqing Lu, Kashi R Buyyani, Thaine W Rowley, Ruben Donis, Zhengxin Chen
6:00 pm -
6:10 pm
Oral Presentation Number: 38
Improved Algorithms for Reaction Mapping
Presenter: John D. Crabtree, Colorado School of Mines
Author(s): John D. Crabtree, Dinesh P. Mehta, J. Thomas McKinnon, Anthony M. Dean
6:10 pm -
6:20 pm
Oral Presentation Number: 39
Biased Support Vector Machine and Kernel Methods for for Tumor Classification
Presenter: Srinivas Mukkamala, New Mexico Tech
Author(s): Andrew H Sung, Krishna Yendrapalli, Ram Basnet
6:20 pm - 6:30 pm Oral Presentation Number: 40
Identification of HTH Motifs from Amino Acid Sequence
Presenter: Changhui Yan, Utah State University
Author(s): Changhui Yan, Jing Hu
6:30 pm -
8:30 pm
Reception and Poster Session
Sunday, December 3
7:30 am -
8:30 am
Registration
8:30 am -
9:15 am
Invited Keynote 6:
Computer-Assisted Forensic Analysis of Mass Disasters
Eugene Myers, Ph.D., Group Leader
Howard Hughes Medical Institute, Janelia Farms
9:15 am -
9:25 am
Oral Presentation Number: 41
Improving Protein Function Prediction Methods with Improved Network Weighting and Integrated Literature Data
Presenter: Aaron Gabow, UCDHSC
Author(s): Aaron Gabow, Sonia Leach, Larry Hunter, Debra S. Goldberg
9:25 am -
9:35 am
Oral Presentation Number: 42
A Topology-Based Clustering Algorithm for Analysis Very Large Biological Networks
Presenter: Xiaowei Xu, University of Arkansas at Little Rock
Author(s): Xiaowei Xu, Zhidan Feng, Nurcan Yuruk
9:35 am -
9:45 am
Oral Presentation Number: 43
The Phylogenetic Position of the Mitochondrion
Presenter: James McInerney, National University of Ireland
Author(s): David A. Fitzpatrick, Christopher J. Creevey
9:45 am -
9:55 am
Oral Presentation Number: 44
Co-conservation Analysis of Bacterial Genes Across Phyla Predict Gene Function
Presenter: Anis Karimpour-Fard, University of Colorado Health Science Center
Author(s): Anis Karimpour-Fard, Corrella S. Detweiler, Ryan T. Gill, Lawrence Hunter
9:55 am -
10:05 am
Oral Presentation Number: 45
De Novo Signaling Pathway Reconstruction From Multiple Data Sources
Presenter: Dongxiao Zhu, Stowers Institute for Medical Research
Author(s): Dongxiao Zhu, Michael Rabbat , Alfred O Hero, Robert Nowak , Mario Figueiredo
10:05 am -
10:25 am
Break
10:25 am -
10:35 am
Oral Presentation Number: 46
The Role of Discretization in Modeling Signal Transduction Networks
Presenter: David J. John, Wake Forest University
Author(s): David J. John, Edward E. Allen, Leslie B. Poole, Richard F. Loeser, Jacquelyn Fetrow
10:35 am -
10:45 am
Oral Presentation Number: 47
A Generalized Algorithm of Unsupervised Learning
Presenter: Anca Radulescu, University of Colorado at Boulder
Author(s): Paul Adams, Kingsley Cox, Anca Radulescu
10:45 am -
10:55 am
Oral Presentation Number: 48
Principal Component Models to Identify Co- and Differential- Gene Expression in Time-Course Microarray Data
Presenter: Rajagopalan Srinivasan, National University of Singapore
Author(s): Rajagopalan Srinivasan, Sudhakar Jonnalagadda
10:55 am -
11:05 am
Oral Presentation Number: 49
Finding Informative Sentences in Full-Text Journal Articles
Presenter: Zhiyong Lu, University of Colorado School of Medicine
Author(s): Zhiyong Lu, William A. Baumgartner, Jr., J. Gregory Caporaso, K. Bretonnel Cohen, Lawrence Hunter
11:05 am -
11:50 am
Invited Keynote 7:
Life Works on AC Power
Andrey Ptitsyn, Ph.D., Assistant Professor
Colorado State University
11:50 am -
Noon
Rocky ’06 Closing Comments

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