|
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
TOP
|
|
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 icon to
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 |
TOP
|