Promotion

Description	File type/link
Rocky '09 Promotional Flyer	.pdf

Presentation Slides (.pdf)

updated Feb. 12, 2010

go directly to: [Friday - December 11] [Saturday - December 12]

Thursday – December 10, 2009
Keynote 1	*Polypharmacology: Drug Discovery in the Era of Genomics and Proteomics* Philip E. Bourne, PhD Professor Skaggs School of Pharmacy & Pharmaceutical Sciences, UCSD Associate Director, RCSB Protein Data Bank Editor in Chief, PLoS Computational Biology
Oral Presentation 1	*Helping Biologists Understand their Data: An Update on the Hanalyzer System* William A. Baumgartner, Jr., University of Colorado
Oral Presentation 2	*Thermodynamics-inspired ncRNA Search* Jennifer Smith, Boise State University
Oral Presentation 3	*Algorithm to Improve Gene Consistency Across Bacterial Genomes* Judith D. Cohn, Los Alamos National Laboratory
Oral Presentation 4	*A Genome-wide Analysis of Poised Promoters in Bacteria* Marko Djordjevic, Arkansas State University and The Arkansas Bioscience Institute
Oral Presentation 5	*Structure-Based Prediction of DNA Binding Sites for Families of Transcription Factors* Julia Ponomarenko, University of California, San Diego
Oral Presentation 6	*Genome-wide Discovery of Human Heart Enhancers* Ivan Ovcharenko, NIH
Oral Presentation 7	*Development of Methods for Integrating Diverse Sources of Genome-Scale Data* Daniel Dvorkin, University of Colorado, Denver
Oral Presentation 8	*Visualizing Genomic Sequences in 2D* Josiah Seaman, Colorado State University
Oral Presentation 9	*Automated Inference of Molecular Mechanisms of Disease from Amino Acid Substitutions* Biao Li, Indiana University
Oral Presentation 10	A User Study of Attribute Visualization Tools and Their Role in Understanding Biological Networks Hande Kucuk, Eastern Michigan University
Oral Presentation 11	NeuroIE: Extracting Neuroimaging Study Results from the Literature Yong Gao, Mass General Hospital/Harvard Medical School
Oral Presentation 12	Analysis of a Local Huntingtin Protein Interaction Network Corey Powell, Buck Institute for Age Research
Oral Presentation 13	*In Silico Functional Profiling of Human Disease-Associated and Polymorphic Amino Acid Substitutions* Vidhya G. Krishnan, Buck Institute for Age Research
Keynote 2	Knowledge Acquisition for Knowledge Discovery in Cancer Metastasis Anna Divoli, PhD Postdoctoral Scholar Department of Medicine and Institute of Genomics and Systems Biology The University of Chicago
Oral Presentation 14	*Accelerating Candidate Gene Discovery through Ontological Indexing of Large Scale Data Repositories* Simon Twigger, Medical College of Wisconsin
Oral Presentation 15	Knowledge Network Approach: Pathways and Drugs Nikolai Daraselia, Ariadne
Oral Presentation 16	Can We Accurately Determine the Fittest Genes in Nature Ramy K. Aziz, San Diego State University
Oral Presentation 17	Assessing Models of Protein Interaction Network Evolution Todd A. Gibson, University of Colorado, Denver
Oral Presentation 18	Gene and Genome Trees Conflict at Many Levels Leanne S. Haggerty, NUI Maynooth
Oral Presentation 19	Protein-protein Interactions are Driven by Functional Evolution Yiqiang Zhao, Buck Institute for Age Research
Oral Presentation 20	*Evolutionary Study and Prediction of Protein-protein Interactions in Chromatin Modification Complexes* Xuejian Xiong, Hospital for Sick Children
go directly to: [Thursday - December 10] [Saturday - December 12]

Friday – December 11, 2009
Keynote 3	Spanning Scales - The Combination of Mathematics and High Performance Computing impacts Computational Biology Kirk E. Jordan, PhD, Emerging Solution Executive Computational Science Center IBM T.J. Watson Research Center
Oral Presentation 21	An Individual Based Modelling Approach to Studying the Evolution of Mate Choice Strategy Robert Williamson, Rose-Hulman Institute of Technology
Oral Presentation 22	*MtHaplogroups: A Curated Web Resource for Mitochondrial Variation* Michael V. Osier, Rochester Institute of Technology
Oral Presentation 23	Posterior-Predictive Detection Of Molecular Co-Evolution Using Phylogenetically-Integrated Mutual Information A.P. Jason de Koning, University of Colorado, Denver
Oral Presentation 24	Bioinformatics Characterization Of The Plasmodium Glutathione S-Transferase Emilee Colón, University of Puerto Rico
Oral Presentation 25	*Leveraging Existing Biological Knowledge in Genome Wide Association Studies* Ronald Schuyler, University of Colorado, Denver
Oral Presentation 26	Evaluating Microbial Diversity and Adaptation: New Opportunities for Insight in a Data Rich World Catherine Lozupone, University of Colorado, Boulder
Oral Presentation 27	Wow! That's Really Interesting! Hannah Tipney, University of Colorado, Boulder
Oral Presentation 28	*Global Optimization in Nonlinear Models: Optimization and Evolution in Metabolic Networks* Albert Sorribas, CMB - IRBLLEIDA - University of Lleida
Oral Presentation 29	Virus Discovery by Deep Sequencing and Assembly of Virus-derived Small Silencing RNAs Qingfa Wu, University of California, Riverside
Oral Presentation 30	*Prediction of Protein Protein Interaction Sites and Their Impact on Genetic Disease* Angshuman Bagchi, Buck Institute for Age Research
Oral Presentation 31	*Optimal Nearest Shrunken Centroids Method for High-dimensional Data Classification* Tiejun Tong, University of Colorado, Boulder
Oral Presentation 32	*Retrobiosynthesis: Searching Backwards, Looking Forwards* Dan McShan, University of Colorado, Denver
Keynote 4 (Joint Keynote)	*Strategies for Elaborating Cognitive Requirements of Bioinformatics Tools* Ben Keller, PhD, Associate Professor Computer Science Department Eastern Michigan University and Barbara Mirel Associate Research Scientist School of Education, University of Michigan NCIBI Core Director of Evaluation, Education and Training
Oral Presentation 33	*Experiments with Biological Concept Recognition Tools* Karin Verspoor, University of Colorado, Denver
Oral Presentation 34	*Test Suite Design for Biomedical Ontology Concept Recognition Systems* K. Bretonnel Cohen, University of Colorado, Denver
Oral Presentation 35	*Predicting Protein Linkages in Bacteria: Which Method is Best Depends on Task* Anis Karimpour-Fard, University of Colorado, Denver
Oral Presentation 36	*A Metagenomic Study of a Microbial Mat in a Hawaiian Lava Cave* Gayle K. Philip, NASA Astrobiology Institute
Oral Presentation 37	Mobile Metagenomics: Annotating DNA Sequences On A Cell Phone Josh Hoffman, San Diego State University
Oral Presentation 38	*The Colorado Richly Annotated Full-Text (CRAFT) Corpus: A Resource for BioNLP Research* Michael Bada, University of Colorado, Denver
go directly to: [Thursday - December 10] [Friday - December 11]

Saturday – December 12, 2009
Keynote 5	ChEMBL - Large-scale Open Access Data for Drug Discovery John P. Overington, PhD CChem. European Bioinformatics Institute (EMBL-EBI)
Oral Presentation 39	*Subgraphs of Protein-protein Interaction Networks with High Connectivity* Suzanne Gallagher, University of Colorado, Boulder
Oral Presentation 40	*TreeHugger: A New Test for Enrichment of Gene Ontology Terms* Daniel Jupiter, Texas A&M Health Science Center
Oral Presentation 41	*Pattern-Based Extraction of Argumentation from the Scientific Literature* Elizabeth White, University of Colorado, Boulder
Oral Presentation 42	*Early Host Response During Influenza Infections* Christian V. Forst, University of Texas
Oral Presentation 43	*Boolean Network Models of Human Aging* Michael Verdicchio, Arizona State University
Oral Presentation 44	*Positive Selection and Functional Shift: Human Heme Peroxidase Case Study* Mary J. O'Connell, Dublin City University
Oral Presentation 45	Delving into the Bacteriome:Protein-protein Interactions in E. coli John Parkinson, Hospital for Sick Children
Oral Presentation 46	*Simplified Clustering with Dirichlet Process and Other Process Mixtures* Matthew Shotwell, Medical University of South Carolina
Oral Presentation 47	*Real Time Metagenomics* Robert Edwards, San Diego State University
Oral Presentation 48	*Structure Discovery in PPI Networks Using Pattern-Based Network Decomposition* Ying Liu, University of Texas, Dallas
Oral Presentation 49	*Data Mining Over Directed Transcription Factor Networks* Rauf Malick, Bahria University
Keynote 6	Informatics Challenges for Pharmacogenetic Russ B. Altman, MD, PhD Professor of Bioengineering Genetics, Medicine (& Computer Science, by courtesy) Chair, Bioengineering Director Biomedical Informatics Training Program Stanford University

return to: [Thursday - December 10] [Friday - December 11] [Saturday - December 12]

Full Agenda

updated October 27, 2009

go directly to: [Friday - December 11] [Saturday - December 12]

Thursday – December 10, 2009
11:00 am – 1:00 pm	Registration
1:00 pm – 1:45 pm	Keynote 1
1:45 pm – 1:55 pm	Oral Presentation 1 Helping Biologists Understand their Data: An Update on the Hanalyzer System Presenter: William A Baumgartner, Jr., University of Colorado Denver Authors: William A Baumgartner Jr, Hannah Tipney, Lawrence Hunter
1:55 pm – 2:05 pm	Oral Presentation 2 Thermodynamics-inspired ncRNA Search Presenter: Jennifer Smith, Boise State University Authors: Jennifer Smith, Pamila Ward
2:05 pm – 2:15 pm	Oral Presentation 3 Algorithm to Improve Gene Consistency Across Bacterial Genomes Presenter: Judith D. Cohn, Los Alamos National Laboratory Authors: Judith D. Cohn, Michael E. Wall, John Dunbar
2:15 pm – 2:25 pm	Oral Presentation 4 A Genome-wide Analysis of Poised Promoters in Bacteria Presenter: Marko Djordjevic, Arkansas State University & The Arkansas Biosciences Institute Authors: Marko Djordjevic
2:25 pm – 2:35 pm	Oral Presentation 5 Structure-Based Prediction of DNA Binding Sites for Families of Transcription Factors Presenter: Julia Ponomarenko, University of California, San Diego Authors: Julia Ponomarenko
2:35 pm – 2:45 pm	Oral Presentation 6 Genome-wide Discovery of Human Heart Enhancers Presenter: Ivan Ovcharenko, NIH Authors: Leelavati Narlikar, Noboru Sakabe, Alexander Blanski, Fabio Arimura, Marcelo Nobrega, Ivan Ovcharenko
2:45 pm – 3:00 pm	Break (15 minutes)
3:00 pm – 3:10 pm	Oral Presentation 7 Development of Methods for Integrating Diverse Sources of Genome-Scale Data Presenter: Daniel Dvorkin, University of Colorado Denver Authors: Daniel Dvorkin, Katerina Kechris
3:10 pm – 3:20 pm	Oral Presentation 8 Visualizing Genomic Sequences in 2D Presenter: Josiah Seaman, Colorado State University Authors: Josiah Seaman
3:20 pm – 3:30 pm	Oral Presentation 9 Automated Inference of Molecular Mechanisms of Disease from Amino Acid Substitutions Presenter: Biao Li, School of Informatics and Computing, Indiana University Authors: Biao Li, Vidhya G. Krishnan, Matthew E. Mort, Fuxiao Xin, Kishore K. Kamati, David N. Cooper, Sean D. Mooney, Predrag Radivojac
3:30 pm – 3:40 pm	Oral Presentation 10 A User Study of Attribute Visualization Tools and Their Role in Understanding Biological Networks Presenter: Hande Kucuk, Eastern Michigan University Authors: Hande Kucuk, Benjamin J. Keller, Terry Weymouth, Barbara Mirel
3:40 pm – 3:50 pm	Oral Presentation 11 NeuroIE: Extracting Neuroimaging Study Results from the Literature Presenter: Yong Gao, Mass General Hospital/Harvard Medical School Authors: Yong Gao; Dave Kennedy
3:50 pm – 4:00 pm	Oral Presentation 12 Analysis of a Local Huntingtin Protein Interaction Network Presenter: Corey Powell, Buck Institute for Age Research Authors: Corey Powell, Robert Hughes, Cendrine Tourette, Russell Bell, Sean Mooney
4:00 pm – 4:10 pm	Oral Presentation 13 In Silico Functional Profiling of Human Disease-Associated and Polymorphic Amino Acid Substitutions Presenter: Vidhya G. Krishnan, Buck Institute for Age Research Authors: Matthew Mort, Uday S. Evani, Vidhya G. Krishnan, Kishore K. Kamati Peter H. Baenziger, Anghuman Bagchi, Brandon Peters, Rakesh Sathyesh, Biao Li, Yanan Sun, Bin Xue, Nigam Shah, Maricel Kann, David N. Cooper, Predrag Radivojac, Sean D. Mooney
4:10 pm – 4:25 pm	Break (15 minutes)
4:25 pm – 5:10 pm	Keynote 2
5:10 pm – 5:20 pm	Oral Presentation 14 Accelerating Candidate Gene Discovery through Ontological Indexing of Large Scale Data Repositories Presenter: Simon Twigger, Medical College of Wisconsin Authors: Simon Twigger, Joey Geiger, Jennifer Smit
5:20 pm – 5:30 pm	Oral Presentation 15 Knowledge Network Approach: Pathways and Drugs Presenter: Nikolai Daraselia, Ariadne Authors: Nikolai Daraselia, Ekaterina Kotelnikova, AntonYuryev
5:30 pm – 5:40 pm	Oral Presentation 16 Can We Accurately Determine the Fittest Genes in Nature? Presenter: Ramy K. Aziz, San Diego State University Authors: Ramy K. Aziz, Mya Breitbart, Robert Edwards
5:40 pm – 5:50 pm	Oral Presentation 17 Assessing Models of Protein Interaction Network Evolution Presenter: Todd A. Gibson, University of Colorado Denver Authors: Todd A. Gibson, Debra S. Goldberg
5:50 pm – 6:00 pm	Oral Presentation 18 Gene and Genome Trees Conflict at Many Levels Presenter: Leanne S. Haggerty, NUI Maynooth Authors: Leanne S. Haggerty, Fergal J. Martin, David A. Fitzpatrick, James O. McInerney
6:00 pm – 6:10 pm	Oral Presentation 19 Protein-protein Interactions are Driven by Functional Evolution Presenter: Yiqiang Zhao, Buck Institute for Age Research Authors: Yiqiang Zhao, Sean Mooney
6:10 pm – 6:20 pm	Oral Presentation 20 Evolutionary Study and Prediction of Protein-protein Interactions in Chromatin Modification Complexes Presenter: Xuejian Xiong, Research Institute at the Hospital for Sick Children Authors: Xuejian Xiong, Tuan On, Shuye Pu, Andrei Turinsky, Yunchen Gong, Andrew Emili, Zhaolei Zhang, Jack Greenblatt, Shoshana J. Wodak, John Parkinson
7:00 pm – 9:00 pm	Dinner
go directly to: [Thursday - December 10] [Saturday - December 12]

Friday – December 11, 2009
9:00 am – 9:45 am	Keynote 3
9:45 am – 9:55 am	Oral Presentation 21 An Individual Based Modelling Approach to Studying the Evolution of Mate Choice Strategy Presenter: Robert Williamson, Rose-Hulam Institute of Technology Authors: Robert Williamson
9:55 am – 10:05 am	Oral Presentation 22 MtHaplogroups: A Curated Web Resource for Mitochondrial Variation Presenter: Michael V. Osier, Rochester Institute of Technology Authors: Kyle Dewey, Eric Stevens, Dina L. Newman, Michael V. Osier
10:05 am – 10:15 am	Oral Presentation 23 Posterior-Predictive Detection Of Molecular Co-Evolution Using Phylogenetically-Integrated Mutual Information Presenter: A.P. Jason de Koning, University of Colorado Denver Authors: A.P. Jason de Koning, Todd A. Castoe, Hyun-min Kim, David D. Pollock
10:15 am – 10:25 am	Oral Presentation 24 Bioinformatics Characterization Of The Plasmodium Glutathione S-Transferase Presenter: Emilee Colón, University of Puerto Rico-School of Medicine Authors: Emilee Colón, Adelfa Serrano, Hugh NicholasJr., Troy Wymore, Alexander Ropelewski, Ricardo González Méndez
10:25 am – 10:35 am	Oral Presentation 25 Leveraging Existing Biological Knowledge in Genome Wide Association Studies Presenter: Ronald Schuyler, University of Colorado Anschutz Medical Campus Authors: Ronald Schuyler, Lawrence Hunter, Deborah Glueck
10:35 am – 10:45 am	Oral Presentation 26 Leveraging Existing Biological Knowledge in Genome Wide Association Studies Presenter: Ronald Schuyler, University of Colorado Anschutz Medical Campus Authors: Ronald Schuyler, Lawrence Hunter, Deborah Glueck
10:45 am – 11:00 am	Break (15 minutes)
11:00 am – 11:10 am	Oral Presentation 27 Wow! That's Really Interesting! Presenter: Hannah Tipney, University of Colorado Authors: Hannah Tipney, Lawrence Hunter
11:10 am – 11:20 am	Oral Presentation 28 Global Optimization in Nonlinear Models: Optimization and Evolution in Metabolic Networks Presenter: Albert Sorribas, CMB - IRBLLEIDA - University of Lleida Authors: Albert Sorribas, Carlos Pozo, Gonzalo Guillén-Gosálbez, Laureano Jimenez, Rui Alves
11:20 am – 11:30 am	Oral Presentation 29 Virus Discovery by Deep Sequencing and Assembly of Virus-derived Small Silencing RNAs Presenter: Qingfa Wu, UC Riverside Authors: Qingfa Wu, Yingjun Luo, Rui Lu, Nelson Lau, Eric C Lai, Wan-Xiang Li, Shou-Wei Ding
11:30 am – 11:40 am	Oral Presentation 30 Prediction of Protein Protein Interaction Sites and Their Impact on Genetic Disease Presenter: Angshuman Bagchi, Buck Institute for Age Research Authors: Angshuman Bagchi, Eunseog Youn, Matthew E. Mort, David N. Cooper, Sean D. Mooney
11:40 am – 11:50 am	Oral Presentation 31 Optimal Nearest Shrunken Centroids Method for High-dimensional Data Classification Presenter: Tiejun Tong, University of Colorado at Boulder Authors: Tiejun Tong, Herbert Pang
11:50 am – 12:00 pm	Oral Presentation 32 Retrobiosynthesis: Searching Backwards, Looking Forwards Presenter: Dan McShan, UC Denver Health Sciences Authors: Dan McShan
12:00 pm – 4:00 pm	Break
4:00 pm – 4:45 pm	Keynote 4
4:45 pm – 4:55 pm	Oral Presentation 33 Experiments with Biological Concept Recognition Tools Presenter: Karin Verspoor, University of Colorado Denver Authors: Karin Verspoor, Kevin B. Cohen, Helen Johnson, Christophe Roeder, Cesar Mejia, William Baumgartner Jr., Larry Hunter
4:55 pm – 5:05 pm	Oral Presentation 34 Test Suite Design for Biomedical Ontology Concept Recognition Systems Presenter: K. Bretonnel Cohen, U. Colorado School of Medicine Authors: K. Bretonnel Cohen, Karin Verspoor, Christophe Roeder, William A. Baumgartner Jr., Lawrence Hunter
5:05 pm – 5:15 pm	Oral Presentation 35 Predicting Protein Linkages in Bacteria: Which Method is Best Depends on Task Presenter: Anis Karimpour-Fard, University of Colorado Denver Authors: Anis Karimpour-Fard, Sonia M. Leach, Ryan T. Gill, Lawrence E Hunter
5:15 pm – 5:25 pm	Oral Presentation 36 A Metagenomic Study of a Microbial Mat in a Hawaiian Lava Cave Presenter: Gayle K. Philip, NASA Astrobiology Institute Authors: Gayle K. Philip, Mark V. Brown, Stuart P. Donachie
5:25 pm – 5:35 pm	Oral Presentation 37 Mobile Metagenomics: Annotating DNA Sequences On A Cell Phone Presenter: Josh Hoffman, San Diego State University Authors: Josh Hoffman, Daniel Cuevas, Robert Edwards
5:35 pm – 5:45 pm	Oral Presentation 38 The Colorado Richly Annotated Full-Text (CRAFT) Corpus: A Resource for BioNLP Research Presenter: Michael Bada, University of Colorado Denver Authors: Michael Bada, Miriam Eckert, Kristin Garcia, Donald Evans, Dmitry Sitnikov, William A. Baumgartner, Jr., Philip V. Ogren, Arrick Lanfranchi, Amanda Howard, William Corvey, Nianwen Xue, Kevin B. Cohen, Karin Verspoor, Judith A. Blake, Martha Palmer
5:45 pm – 8:00 pm	Reception and Poster Session
go directly to: [Thursday - December 10] [Friday - December 11]

Saturday – December 12, 2009
9:00 am – 9:45 am	Keynote 5 ChEMBL - Large-scale Open Access Data for Drug Discovery John P. Overington, PhD CChem. European Bioinformatics Institute (EMBL-EBI)
9:45 am – 9:55 am	Oral Presentation 39 Subgraphs of Protein-protein Interaction Networks with High Connectivity Presenter: Suzanne Gallagher, University of Colorado Dept. of Computer Science Authors: Suzanne Gallagher, Debra Goldberg
9:55 am – 10:05 am	Oral Presentation 40 TreeHugger: A New Test for Enrichment of Gene Ontology Terms Presenter: Daniel Jupiter, Texas A&M Health Science Center Authors: Daniel Jupiter, Jessica Sahutoglu, Vincent VanBuren
10:05 am – 10:15 am	Oral Presentation 41 Pattern-Based Extraction of Argumentation from the Scientific Literature Presenter: Elizabeth White, University of Colorado at Boulder Authors: Elizabeth White
10:15 am – 10:25 am	Oral Presentation 42 Early Host Response During Influenza Infections Presenter: Christian V. Forst, University of Texas Southwestern Medical Center Authors: Christian V. Forst
10:25 am – 10:35 am	Oral Presentation 43 Boolean Network Models of Human Aging Presenter: Michael Verdicchio, Arizona State University Authors: Michael Verdicchio, Seungchan Kim
10:35 am – 12:00 pm	Poster Session
12:00 pm – 4:00 pm	Break
4:00 pm – 4:10 pm	Oral Presentation 44 Positive Selection and Functional Shift: Human Heme Peroxidase Case Study Presenter: Mary J. O'Connell, Dublin City University Authors: Noeleen B. Loughran, Brendan O'Connor, Ciaran O'Fagain, William M. Nauseef, Mary J. O'Connell
4:10 pm – 4:20 pm	Oral Presentation 45 Delving into the Bacteriome:Protein-protein Interactions in E. coli Presenter: John Parkinson, Hospital for Sick Children Authors: Jose Peregrin-Alvarez, Xuejian Xiong, Chong Su, John Parkinson
4:20 pm – 4:30 pm	Oral Presentation 46 Simplified Clustering with Dirichlet Process and Other Process Mixtures Presenter: Matthew Shotwell, Medical University of South Carolina Authors: Matthew Shotwell, M.S., Elizabeth Slate, Ph.D.
4:30 pm – 4:40 pm	Oral Presentation 47 Real Time Metagenomics Presenter: Robert Edwards, San Diego State University Authors: Robert Edwards, Robert Olson, Terry Disz, Rick Stevens, Ross Overbeek
4:40 pm – 4:50 pm	Oral Presentation 48 Structure Discovery in PPI Networks Using Pattern-Based Network Decomposition Presenter: Ying Liu, University of Texas at Dallas Authors: Ying Liu, Chengcheng Shen, Phil Bachman
4:50 pm – 5:00 pm	Oral Presentation 49 Data Mining Over Directed Transcription Factor Networks Presenter: Rauf Malick, Bahria University Authors: Rauf Malick, Abdul Aziz, Mansoor Ahmed, Aysha Mazhar
5:00 pm – 5:40 pm	Keynote 6 Informatics Challenges for Pharmacogenetic Russ B. Altman, MD, PhD Biomedical Informatics Training Program Stanford University
5:40 pm	Rocky '09 Closing Comments

return to: [Thursday - December 10] [Friday - December 11] [Saturday - December 12]

Poster Presenters and Abstracts

Updated December 9, 2009.

PDF listing of the Poster Presenters and Abstracts (pdf) - Click here.

Listed in alphabetical order by presenter's last name:

Genomewide Haplotype Association Analysis in Sub-threshold Regions
Presenter: Ryan Abo, University of Utah
Authors: Ryan Abo, Nicola J. Camp

Novel Method for MicroRNA Target Prediction Using a Genetic Algorithm
Presenter: Andrea Acquaviva, Politecnico di Torino
Authors: Paula Helena Reyes Herrera, Andrea Acquaviva, Elisa Ficarra, Enrico Macii

Modeling and Design of Peptido-mimetic Compounds to Block Noggin/BMP, Activin/Follistatin and Crossveinless 2/BMP Interactions to Promote Osteogenesis
Presenter: Shaila Ahmed, Queens College, CUNY
Authors: Shaila Ahmed, Boojala Vijay B Reddy, Sreedhara Sangadala, Sanjay Kumar

Assembler for SOLiD Data: by Improving Memory Management of Velvet Assembler
Presenter: Sajia Akhter, San Diego State University
Authors: Sajia Akhter, Robert Edwards

Application of Data Integration Methods to Aid in the Development of Second Generation Biofuels
Presenter: David Astling, National Renewable Energy Laboratory
Authors: David Astling, Peter Graf, Kofi Adragni, Jinsuk Lee, Mark Davis

PhAnToMe (PHage ANnotation TOols and MEthods): A Platform for Phage Annotation and Comparative Genomics
Presenter: Ramy K. Aziz, San Diego State University
Authors: Ramy K. Aziz, Bhakti Dwivedi, Joe Anderson, Bonnie Hurwitz, JP Massar, Matthew Sullivan, Jeff Elhai, Mya Breitbart, Robert Edwards

Prediction of Protein Protein Interaction Sites and Their Impact on Genetic Disease
Presenter: Angshuman Bagchi, Buck Institute for Age Research
Authors: Angshuman Bagchi, Eunseog Youn, Matthew E. Mort, David N. Cooper, Sean D. Mooney

Defining Web-Service Based Biological Analysis Workflows
Presenter: Janaka Balasooriya, Arizona State University
Authors: Janaka Balasooriya, Swanson Morgan, Graciela Gonzalez

Identification of Novel Epitopes of the Ebola Virus for Rational Vaccine Design
Presenter: Sophia Banton, Florida Atlantic University
Authors: Sophia Banton, Zvi Roth PhD

Assessing the Predictive Power of Site-Prediction Methods for Identifying Positive Selection Within Empirical Datasets
Presenter: Matthew L. Bendall, Brigham Young University
Authors: Matthew L. Bendall, Matthew Dyer, Keith A. Crandall

Assessing the Predictive Power of Site-Prediction Methods for Identifying Positive Selection Within Empirical Datasets
Presenter: Matthew L. Bendall, Brigham Young University
Authors: Matthew L. Bendall, Matthew Dyer, Keith A. Crandall

Characterization and Assembly of the First Snake Genome Using Multi-Platform Next-Generation Sequence Data
Presenter: Todd A. Castoe, University of Colorado, Denver School of Medicine
Authors: Todd Castoe, Matthew La Bella, A. P. Jason de Koning, Kathryn Hall, Wanjun Gu, Peter Uetz, David D. Pollock

Visualizing Metagenomes
Presenter: Nicholas Celms, San Diego State University
Authors: Nicholas Celms, Elizabeth Dinsdale, Robert Edwards

Phylogenetic Analysis of Plant Sesquiterpene Synthases
Presenter: Brian Y. Chen, National Resource for Biomedical Supercomputing
Authors: Brian Y. Chen, Ashley Young, Hugh B. Nicholas Jr., Alexander J. Ropelewski, Troy Wymore

Systematic Drug Target Discovery via Chemical and Genetic Interaction Profiles
Presenter: Hon Nian Chua, Harvard Medical School
Authors: Hon Nian Chua, Murat Cokol, Yo Suzuki, Frederick P. Roth

On the Accuracy of Automated Inference of Protein Function
Presenter: Wyatt T. Clark, Indiana University
Authors: Wyatt T. Clark, Predrag Radivojac

Algorithm to Improve Gene Consistency Across Bacterial Genomes
Presenter: Judith D. Cohn, Los Alamos National Laboratory
Authors: Judith D. Cohn, Michael E. Wall, John Dunbar

Bioinformatics Characterization Of The Plasmodium Glutathione S-Transferase
Presenter: Emilee Colón, University of Puerto Rico
Authors: Emilee Colón, Adelfa Serrano, Hugh NicholasJr., Troy Wymore, Alexander Ropelewski, Ricardo González Méndez

Knowledge Network Approach: Pathways and Drugs
Presenter: Nikolai Daraselia, Ariadne
Authors: Nikolai Daraselia, Ekaterina Kotelnikova and AntonYuryev

Multivariate Analysis of Metagenomes - An Undergraduate REU Story
Presenter: Elizabeth Dinsdale, San Diego State University
Authors: Naneh Apkarian, Michelle Creek, Eric Guan, Mayra Hernandez, Kate Isaacs, Chris Peterson, Todd Regh, Robert Edwards, Barbara Bailey, Peter Salamon, Imre Tuba, Elizabeth Dinsdale

A Computational Tool for the Identification of Signature Genes Among Phages
Presenter: Bhakti Dwivedi, University of South Florida
Authors: Bhakti Dwivedi, Robert Edwards, Mya Breitbart

Real Time Metagenomics
Presenter: Robert Edwards, San Diego State University
Authors: Robert Edwards, Robert Olson, Terry Disz, Rick Stevens, Ross Overbeek

Bioinformatic Analysis of SDS-insoluble Protein Aggregates in S. Cerevisiae, C. Elegans, and M. Musculus.
Presenter: Uday S Evani, Buck Institute
Authors: Uday S. Evani, Theodore W. Peters, Pedro Rodrigues, Gregg Czerwieniec, Sean D. Mooney, Gordon Lithgow, Bradford Gibson, Robert Hughes

Pairwise and Higher-Order Correlations Among Drug-Resistance Mutations in HIV-1 Subtype B Protease
Presenter: Omar Haq, Rutgers University
Authors: Omar Haq, Ronald M. Levy, Alexandre V. Morozov, Michael Andrec

Genome Analysis of Mycoplasma Mycoides Subsp. MycoidesSC - A Bioinformatics Approach
Presenter: Muhammad Maqsud Hossain, North South University
Authors: A K M Firoj Mahmud, S A M Khairul Bashar, Muhammad Maqsud Hossain, Abdul Khaleque

A Useful Tool for Calculating Binding-site Residues on Proteins from PDB Structures
Presenter: Jing Hu, Franklin & Marshall College
Authors: Jing Hu, Changhui Yan

A Fast Approach to Protein Structure Alignment Based on One-dimensional Alphabet Code Sequences
Presenter: Kenneth Hung, National Taiwan University
Authors: Kenneth Hung, Jui-Chih Wang, Kun-Nan Tsai, Cheng-Wei Chen, Chung-Ming Chen

Dealing with Data Deluge: Designing and Implementing a Database to Enable Specialized Studies in Metagenomics
Presenter: Bonnie Hurwitz, University of Arizona
Authors: Bonnie Hurwitz, Matthew Sullivan, Robert Edwards, Adam Monier, Alexandra Z. Worden, Sudha Ram

Viral Metagenomics in Marine Mcrobial Samples
Presenter: Julio C. Ignacio, University of Arizona
Authors: Julio C. Ignacio, Alexandra Z. Worden, Matthew B. Sullivan

Using Syntactic Context in OpenDMAP Patterns
Presenter: Helen Johnson, University of Colorado, Denver
Authors: Helen L. Johnson, William Baumgartner, Jr., Christophe Roeder, Karin Verspoor, Kevin Bretonnel Cohen, Larry Hunter

In Silico Functional Profiling of Human Disease-Associated and Polymorphic Amino Acid Substitutions
Presenter: Vidhya G. Krishnan, Buck Institute for Age Research
Authors: Matthew Mort, Uday S. Evani, Vidhya G. Krishnan, Kishore K. Kamati Peter H. Baenziger, Anghuman Bagchi, Brandon Peters, Rakesh Sathyesh, Biao Li, Yanan Sun, Bin Xue, Nigam Shah, Maricel Kann, David N. Cooper, Predrag Radivojac, Sean D. Mooney

A User Study of Attribute Visualization Tools and Their Role in Understanding Biological Networks
Presenter: Hande Kucuk, Eastern Michigan University
Authors: Hande Kucuk, Benjamin J. Keller, Terry Weymouth, Barbara Mirel

Automated Inference of Molecular Mechanisms of Disease from Amino Acid Substitutions
Presenter: Biao Li, Indiana University
Authors: Biao Li, Vidhya G. Krishnan, Matthew E. Mort, Fuxiao Xin, Kishore K. Kamati, David N. Cooper, Sean D. Mooney, Predrag Radivojac

Loss of Post-translational Modification Sites in Disease
Presenter: Shuyan Li, Indiana University
Authors: Shuyan Li, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac

Machine Learning Approaches to the Assessment of Peptide-Spectrum Matches Without Using a Decoy Database
Presenter: Yong Fuga Li, Indiana University, Bloomington
Authors: Yong Fuga Li, Randy J. Arnold, Predrag Radivojac, Haixu Tang

Structure Discovery in PPI Networks Using Pattern-Based Network Decomposition
Presenter: Ying Liu, University of Texas, Dallas
Authors: Ying Liu, Chengcheng Shen, Phil Bachman

Data Mining Over Directed Transcription Factor Networks
Presenter: Rauf Malick, Bahria University
Authors: Rauf Malick, Abdul Aziz, Mansoor Ahmed, Aysha Mazhar

Promoter Prediction in Halothiobacillus Neapolitanus c2 Based on Stress-Induced DNA Duplex Destabilization
Presenter: Aleksandra Markovets, Mississippi Valley State University
Authors: Aleksandra Markovets, Charles Bland, Abigail Newsome

Towards Realistic Codon Models: Among-Site Variability and Dependency of Synonymous and Non-Synonymous Substitution Rates
Presenter: Itay Mayrose, University of British Columbia
Authors: Itay Mayrose, Adi Doron-Faigenboim, Eran Bacharach, Tal Pupko

The Human Gene Mutation Database (HGMD) and its Exploitation in the Era of Personalized Genomics
Presenter: Matthew Mort, Cardiff University
Authors: P.D. Stenson, M. Mort, E. Ball, K. Howells, A. Phillips, N.S.T. Thomas, D.N. Cooper

Meta-Analytical Tools for Deciphering Transcriptional Networks in a Model Anoxygenic Phototroph
Presenter: Oleg Moskvin, University of Wyoming
Authors: Oleg Moskvin, Dmitry Bolotin, Pavel Ivanov, Mark Gomelsky

The Evolutionary Landscape of Chromatin Modification Machinery
Presenter: Tuan On, University of Toronto
Authors: Tuan On, Xuejian Xiong, Shuye Pu, Andrei Turinsky, Yunchen Gong, Andrew Emili, Zhaolei Zhang, Jack Greenblatt, Shoshana J. Wodak, John Parkinson

Bacterial Evolution: Implication from Lipid ABiosynthesis Pathway Enzymes
Presenter: Stephen O. Opiyo, University of Nebraska, Lincoln
Authors: Stephen Opiyo, Rosevelt Pardy, Hideaki Moriyama,Etsuko Moriyama

CNGen - A New Tool for Copy-number Genotypes Partitioning
Presenter: Louis-Philippe Lemieux Perreault, Montreal Unversity
Authors: Louis-Philippe Lemieux Perreault, Gregor Andelfinger, Géraldine Asselin, Marie-Pierre Dubé

QIIME (Quantitative Insights Into Microbial Ecology) Dynamic Rarefaction Graph
Presenter: Megan Pirrung, University of Colorado, Boulder
Authors: Megan Pirrung, Rob Knight

Structure-Based Prediction of DNA Binding Sites for Families of Transcription Factors
Presenter: Julia Ponomarenko, University of California, San Diego
Authors: Julia Ponomarenko

Automated Identification of Amplifiable Microsatellite Loci and Primer Design from 454 High-Throughput Sequencing Reads
Presenter: Alex Poole, University of Colorado, Denver
Authors: Alex Poole, Todd Castoe, David Pollock

Analysis of a Local Huntingtin Protein Interaction Network
Presenter: Corey Powell, Buck Institute for Age Research
Authors: Corey Powell, Robert Hughes, Cendrine Tourette, Russell Bell, Sean Mooney

Flux Balance Analysis of Plasmodium Falciparum's Metabolic Network
Presenter: Farhan Raja, University of Toronto
Authors: Farhan Raja, John Parkinson, James Wasmuth, Stacy Hung

GeneBook, A High Precision Mammalian Protein Thesaurus
Presenter: Phoebe Roberts, Pfizer, Inc.
Authors: Robert Hernandez, Markella Skempri, Phoebe Roberts

Integrating Web Services into Biomedical Text Mining
Presenter: Christophe Roeder, University of Colorado, Denver
Authors: Christophe Roeder, William Baumgartner Jr, Larry Hunter

Integration of DIYA Output with GMOD Standards
Presenter: Inna Rytsareva, Mississippi Valley State University
Authors: Inna Rytsareva, Charles Bland, Abigail Newsome

Protein Secondary Structure is Robust Under Artificial Evolution While Protein Disorder is Not
Presenter: Christian Schaefer, Columbia University, New York City
Authors: Christian Schaefer, Avner Schlessinger, Burkhard Rost

Visualizing Genomic Sequences in 2D
Presenter: Josiah Seaman, Colorado State University
Authors: Josiah Seaman

Improving the Prediction of MicroRNA-Target Genes by Combining Target Prediction Algorithms
Presenter: Ashok Sharma, Medical College of Georgia
Authors: Ashok Sharma, Ryan Rimando, Richard McIndoe

Simplified Clustering with Dirichlet Process and Other Process Mixtures
Presenter: Matthew Shotwell, Medical University of South Carolina
Authors: Matthew Shotwell, M.S., Elizabeth Slate, Ph.D.

Evolving Spiking Neural Networks for the Prediction of Transcription Factor Binding Sites
Presenter: Heike Sichtig, UF Genetics Institute
Authors: Heike Sichtig, Alberto Riva

MCW Proteomics Analysis Platform - A Hybrid Cloud Computing Architecture for Proteomics Analysis
Presenter: Simon Twigger, Medical College of Wisconsin
Authors: Andrew Vallejos, Brian Halligan, Joey Geiger, Andrew Greene, Simon Twigger

Accelerating Candidate Gene Discovery through Ontological Indexing of Large Scale Data Repositories
Presenter: Simon Twigger, Medical College of Wisconsin
Authors: Simon Twigger, Joey Geiger, Jennifer Smith

Digging for Gold - Data Annotation and Exploration With Ratmine
Presenter: Simon Twigger, Medical College of Wisconsin
Authors: Andrew Vallejos, Jennifer Smith, Richard Smith, Julie Sullivan, Gos Micklem, Simon Twigger

Large-scale Sequencing of T-cell Receptor Repertoires in Diabetic NOD Mice
Presenter: Vijetha Vemulapalli, University of Colorado, Denver
Authors: Vijetha Vemulapalli, Todd A Castoe, Maki Nakayama, George Eisenbarth, David D Pollock

Boolean Network Models of Human Aging
Presenter: Michael Verdicchio, Arizona State University
Authors: Michael Verdicchio, Seungchan Kim

Evolution of a Placenta Specific Regulatory Network
Presenter: Thomas Walsh, Dublin City University
Authors: Thomas Walsh, Kieran Holohan, Anna O'Brien, Elinor Velasquez, Mary O'Connell

Pattern-Based Extraction of Argumentation from the Scientific Literature
Presenter: Elizabeth White, University of Colorado, Boulder
Authors: Elizabeth White

An Individual Based Modelling Approach to Studying the Evolution of Mate Choice Strategy
Presenter: Robert Williamson, Rose-Hulam Institute of Technology
Authors: Robert Williamson

Factors that Control Functionality of Sesquiterpene Synthases from Phylogentic and Biophysical Simulations
Presenter: Troy Wymore, National Resource for Biomedical Supercomputing
Authors: Troy Wymore, Brian Y. Chen, Hugh B. Nicholas Jr., Alexander J. Ropelewski, Charles L. Brooks III

Structure-Based Kernels for the Prediction of Catalytic Residues and their Involvement in Disease
Presenter: Fuxiao Xin, Indiana University, Bloomington
Authors: Fuxiao Xin, Steven Myers, Yong Fuga Li, David N. Cooper, Sean D. Mooney, Predrag Radivojac

Evolutionary Study and Prediction of Protein-protein Interactions in Chromatin Modification Complexes
Presenter: Xuejian Xiong, Hospital for Sick Children
Authors: Xuejian Xiong, Tuan On, Shuye Pu, Andrei Turinsky, Yunchen Gong, Andrew Emili, Zhaolei Zhang, Jack Greenblatt, Shoshana J. Wodak, and John Parkinson

SimpleMHC: A Novel Method for In-silico Prediction of Peptide Binding to MHC Class II Molecules
Presenter: Li Xue, Iowa State University
Authors: Li Xue; Arthur Fridman

Protein-protein Interactions are Driven by Functional Evolution
Presenter: Yiqiang Zhao, Buck Institute for Age Research
Authors: Yiqiang Zhao, Sean Mooney

Academic Retreat - An Affordable Opportunity

Plan an off-site retreat, bring your colleagues to Rocky and SAVE!

This is the perfect opportunity to roll your conference attendance funds into a very affordable academic group retreat experience in the spectacular setting of the Colorado Rocky Mountains - during ski season!

Rocky registration rates are among the most reasonable in computational biology, the conference hotel accommodations are well under $100 per night, and domestic travel fares are the lowest they have been in years.

Last year four schools from California to Indiana each combined the experience of attending Rocky together for education and group activities on the slopes, at the hotel, and in Snowmass and Aspen Villages. Education and bonding were abundantly fun and memorable, and all left with a renewed sense of inspiration and collaboration. Rocky’09 is now offering academic retreats* the following group package benefits:

One free student registration ($185 minimum savings)
One free suite upgrade ($200 minimum savings)
Two free ski lift tickets per group or $100 food & beverage credit at the conference hotel
Special scheduling of flash presentations for all members of the group to ensure a full morning or afternoon can be spent outside the conference for a group activity if desired (activity not included)

Contact This email address is being protected from spambots. You need JavaScript enabled to view it. for information or a customized package for your academic group today!

* Academic retreats are defined as a minimum of 10 or more paid attendees from the same school, staying in the conference hotel a minimum of two nights (single or double occupancy), and utilizing at least 5 sleeping rooms per night. All academic retreat offers noted above must be secured by November 11.

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Thank you for registering for the ISCB Rocky'09 Conference. You will recieve an e-mail detailing your information and transaction process. Thank you again for registering for the ISCB Rocky'09 Conference. If you have any questions, please contact the ISCB administrator at This email address is being protected from spambots. You need JavaScript enabled to view it..

Contacts

Rocky Conference Coordinator
Stephanie Hagstrom
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352-665-1763

Registration Coordinator
Suzi Smith
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Sponsor Opportunities

The mission of the Rocky '09 Conference is to bring computational bioscientists together in the inspirational setting of the Colorado Rocky Mountains to share research results, build community, and to become better acquainted. Although the conference is open to scientists from across the country and around the globe, the majority of delegates naturally come from the Rocky Mountain states of Montana, Idaho, Wyoming, Colorado, Utah, Nevada, Arizona, New Mexico and the Canadaian provinces of Alberta and British Columbia. Each Rocky conference has resulted in new collaborations and/or business opportunities for all involved.

A key part of the success of this event is the financial support and active involvement of our industry sponsors. This is a great opportunity to meet the key individuals in the field of Bioinformatics and Computational Biology from the Rocky Mountain Region and beyond, and gain international exposure to your products or services through the ISCB marketing efforts.

Please take a moment to review the opportunities below and sign up on the form provided.

	Platinum: $8,000
	Sponsor of Conference Banquet Prominent logo placement on website Keynote speaker introduction Display space 8' wide x 6' deep Three conference registrations Company logo on printed materials Company logo on signage Company logo on session screen Company brochure in delegate bags Recognition from the podium
	Gold: $5,000
	Sponsor of Conference Poster Session Display space 8' wide x 6' deep Two conference registrations Company logo on printed materials Company logo on signage Company logo on session screen Company one-page flyer in delegate bags
	Silver: $3,000
	Sponsor of Conference Refreshment break Company logo on printed materials Company logo on signage Company logo on session screen Company one-page flyer in delegate bags

Other Sponsorship Opportunities:
	Publisher Display Table: $400
	For publishers only Display space 8' wide x 6' deep Company name on printed materials
	Delegate Bags: $1500
	Company name on bags Company name on printed materials
	Keynote Speaker: $1,000
	Company name on keynote slide Keynote speaker introduction
	Delegate Lanyards: $500
	Company name on lanyards Company name on printed materials
	Conference Program Book: $1000
	Company logo on booklets as sponsor
	Best Presentation Awards: $550
	Company name on Award slide Company name on printed materials Award presentation at closing
	Student Travel Fellowships: $550
	Company name on printed materials

	Customized Sponsorship:
	Other customized sponsorship opportunities may be available. To discuss opportunities please contact Rocky Conference Coordinator Stephanie Hagstrom This email address is being protected from spambots. You need JavaScript enabled to view it. 352-665-1763

Call for Presentations

Call for presentations will be open August 1, 2009.

Keynote Speakers

	Russ B. Altman, MD, PhD Professor of Bioengineering, Genetics, Medicine (& Computer Science, by courtesy) Chair, Bioengineering Director Biomedical Informatics Training Program Stanford University CV (pdf) Title: Informatics Challenges for Pharmacogenetics >>Click here for presentation slides (.pdf) Abstract: Pharmacogenomics is the study of how human genetic variation impacts drug response phenotypes. We are building the PharmGKB (www.pharmgkb.org/) to catalog all knowledge of gene- drug relationships to support discovery and application of pharmacogenomics. From this effort arise important informatics challenges. I will discuss our work in text mining to extract relationships between drugs and gene variants, our use of this information to create tools for predicting gene-drug interactions, and our efforts building tools to assist in genetic association studies particularly focusing on drug response.

	Philip E. Bourne PhD Professor, Skaggs School of Pharmacy & Pharmaceutical Sciences, UCSD Associate Director RCSB Protein Data Bank Editor in Chief PLoS Computational Biology www.sdsc.edu/pb CV (html) Title: Polypharmacology: Drug Discovery in the Era of Genomics and Proteomics Abstract: The notion of one drug binding to one receptor to treat one disease becomes questionable as we understand more about the human genome and proteome. Rather we need to consider a collective effect associated with binding to multiple receptors which exist in a variety of different pathways by bringing to bear computational and systems biology. I will illustrate this with a bioinformatics approach [1] that is akin to reverse engineering the drug discovery process. Rather than take a large library of ligand molecules and screen them against a known protein receptor, we take a known drug-receptor complex and search the human proteome for other proteins with similar binding sites. These off-targets are then mapped to pathways and systems and may explain a side effect of a drug or point to a possible repositioning of that drug to treat a different condition. Biological outcomes to date include repositioning Parkinson's disease drugs to treat TB [2] and to explain why Torcetrapib failed after 15 years of development and $850M was spent [3]. References: [1] L. Xie and P.E. Bourne 2008 Detecting Evolutionary Linkages Across Fold and Functional Space with Sequence Order Independent Profile-profile Alignments. PNAS, 105(14) 5441-5446. [2] S.L Kinnings, N. Buchmeier, N. Liu, P.J. Tonge L. Xie and P.E. Bourne 2009 Discovery of Novel Drug Leads to Treat Multi-drug and Extensively Drug Resistant Tuberculosis by Repositioning Safe Pharmaceuticals: A Chemical Genomics Approach with Subsequent Biological Validation. PLoS Comp. Biol. 5(7) e1000423. [3] L. Xie, J. Li, L. Xie, and P.E.Bourne 2009 Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors, PLoS Comp. Biol. 5(5) e1000387.

	Anna Divoli, PhD Postdoctoral Scholar Department of Medicine and Institute of Genomics and Systems Biology The University of Chicago http://home.uchicago.edu/~divoli/ CV (pdf) Title: Knowledge Acquisition for Knowledge Discovery in Cancer Metastasis Abstract: The clinical importance of understanding cancer metastasis and the complex nature of the process have made it an extremely important research subject. We employ Knowledge Acquisition techniques to organize and represent the existing knowledge as it appears in the heads of experts and unveil any compelling trends and controversies. We interviewed 28 experts on several aspects of metastasis and asked them to share with us their subjective opinions. We were interested in their understanding of metastasis and their possible explanations for not yet scientifically answered research questions and unexplained clinical manifestations, as well as their views on the future of the metastasis research field. Detailed analysis of the interview data reveals areas of agreement but also of disagreement, several known theories' devotees and a few challengers, along with a number of interesting viewpoints and the inevitable introduction of some new questions. Besides the biologically interesting perspectives, we examine the language that experts use while communicating to us their views.

	Kirk E. Jordan, PhD Emerging Solution Executive Computational Science Center IBM T.J. Watson Research Center CV (pdf) Title: Spanning Scales - The Combination of Mathematics and High Performance Computing impacts Computational Biology Abstract: Computation is playing an ever increasing and vital role in the biological and healthcare sciences. In many instances, scientists are developing mathematical models and using high performance computing to carry out analysis and simulations that provide insight into biological systems. The complexity of these models often demands increasing compute power and sophisticated mathematics for the solution. In collaboration, biological scientists are using thousands of processors to look at their problems in new ways, leading to science breakthroughs. In this talk, I will briefly describe some of the trends we see in high performance computing and some of the challenges looming on the horizon. I then describe a solution in collaboration with colleagues used in investigating blood perfusion in the brain as an example of a new approach for computational biology. In conclusion, I will point out how this approach is an example of coupling high performance computing and mathematics to tackle multi-scale biological science problems.
	JOINT KEYNOTE: Ben Keller, PhD Associate Professor Computer Science Department Eastern Michigan University http://people.emich.edu/bkeller/ CV (pdf) AND Barbara Mirel Associate Research Scientist School of Education University of Michigan NCIBI Core Director of Evaluation, Education and Training CV (pdf) Title - Strategies for Elaborating Cognitive Requirements of Bioinformatics Tools >>Click here for presentation slides (.pdf) Abstract: Most bioinformatics tools have been designed for isolated problems, and were not built with consideration to the broader context of their use. This fact creates a situation in which the tasks that scientists perform do not map well to the tools available to them. Our challenge as tool designers and developers is to understand how to better engineer these tools to support user cognition for larger tasks such as those in translational systems biology. This talk will discuss the two strategies we have followed to derive cognitive user requirements: first, by synthesizing best practices identified in the literature, and, second, by generalizing from Mirel’s extensive fields studies of scientists conducting exploratory analysis with tools developed at the National Center for Integrative Biomedical Informatics. The first draws on discrete, independent observations to create general strategies applicable to broader sets of tools, while the second focuses on tools dealing with gene relationships and scientists’ classification and comparison as a prelude to causative reasoning. Our goal is to reflect on how best to apply cognitive engineering to the development of translational bioinformatics and systems biology tools. This application of cognitive engineering includes developing user-centered rationales for requirements. Here we step back to look at and propose specific needs assessment processes that can be used to move incrementally from a model of scientific user cognition to high level user requirements, and ultimately to detailed uses cases and functional specifications for tools. (This work partially supported by NIH grant U54 DA021519.)

	John P. Overington, PhD CChem. Team Leader, Computational Chemical Biology European Bioinformatics Institute (EMBL-EBI) web site: www.overingtonlab.org blog: www.chemblog.org CV (pdf) Title: ChEMBL - Large-scale Open Access Data for Drug Discovery Abstract: The link between the biological and chemical worlds is of central importance in many fields, not least that of healthcare. For example, a major focus in systems biology research is the signalling networks and pathways describing the interactions and functions of large numbers of genes and proteins. Similarly, within healthcare-related chemistry research there is much interest in efficiently identifying drug-like compounds that specifically interact with these proteins/genes. However there has been relatively little research explicitly directed at understanding the linkages between these two historically distinct domains. Key to our work in this area has been the construction of a large and general structure activity relationship database, linking pharmacological activities of compounds through to their targets, and understanding how particular compounds recognise their cognate receptors. Application of rules derived from these databases leads to rapid, economic, and effective identification of quality target and lead combinations for subsequent pharmacological validation. These data have also been mapped to the currently drugged genome, launched drugs, and large numbers of clinical development candidates. These databases are now in the public domain with the specific aim of enabling new translational research. Current status and future challenges for these informatics resources will be discussed.