9th Annual Rocky Mountain Bioinformatics Conference

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 under $100 per night, and domestic travel fares are the lowest they have been in years.

Schools who have participated in the past combined the experience of attending Rocky 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 2011 offers academic retreats* the following group package benefits (3 available):

• One free student registration
• 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 Rocky conference 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 8.

9th Annual Rocky Mountain Bioinformatics Conference

Contacts

Rocky Conference Coordinator
Stephanie Hagstrom
This email address is being protected from spambots. You need JavaScript enabled to view it.
352-665-1763

Registration Coordinator
Suzi Smith
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9th Annual Rocky Mountain Bioinformatics Conference

Call for Presentations closed on October 7.

For any questions about the submission system and deadlines, please send email to This email address is being protected from spambots. You need JavaScript enabled to view it..

9th Annual Rocky Mountain Bioinformatics Conference

Keynote Speakers

Updated November 21, 2011

	Judith A. Blake, PhD Associate Professor The Jackson Laboratory Bar Harbor, Maine - USA CV: http://research.jax.org/faculty/judith_blake.html Title: "The Future of Research Communication: From Surfing to Deep Diving" Abstract: The Internet has revolutionized the transmission of data and of knowledge. Scientific journal publishers are reeling under the impact of on-line publishing, the inability to handle very large datasets for peer review, and the emergence of download tracking and commentary post-publication as impact metrics. Electronic management of research data and results provide a mechanism for open access to electronic project directories. Very large data sets are increasingly common, and testing reproducibility of reported results is increasingly difficult to undertake. Nonetheless, ontologies, semantic and accession ID mapping, and author-tagging provide immediate points for on-line integration of scientific results, both experimental and inferred, although the distinction is often missing. For scientists associated with large institutions, access to copyrighted biomedical literature continues unabated although the function of the university library is radically changing. Meanwhile, scientists and citizens without access to journal subscriptions have limited access to publically financed scientific results although plenty of scientific discourse is available on the Web. Open access publication, digital data repositories, and electronic journals will help in the dissemination of scientific research results. I will discuss these topics and the impact of these changes on the scientific enterprise.
	Peter Clark, PhD Vulcan Inc. Seattle, Washington - USA CV: www.cs.utexas.edu/users/pclark Title: Project Halo: Constructing and Exploiting a Formal Representation of a Biology Textbook to Understand and Answer Users' Questions Abstract: As part of Project Halo at Vulcan Inc, we are building a large-scale, broad-coverage, formal (logic-based) knowledge-base (KB) that represents a substantial portion of the knowledge in an AP-level biology textbook, and supports question interpretation, reasoning, and question answering. Because users pose questions in English, we are not spared the huge challenge of interpreting natural language; however, the KB does provide significant advantages for this task, in particular creating knowledge-based expectations of what would be coherent to ask, that can be used to coerce a user's question into something meaningful to the computer. In this talk I will describe the project, our approach and progress in constructing the KB, and our successes and challenges in interpreting and answering users' biology questions with it. I will then speculate on the longer-term picture of using the knowledge base to guide interpretation of (parts of) biology texts themselves, with the potential to further expand the KB semi-automatically and ultimately create more knowledgeable machines.
	Emek Demir, PhD Computational Biology Center Memorial Sloan Kettering Cancer Center New York, New York USA CV: http://cbio.mskcc.org/~demir/cv.html Title: Building Cell Maps: Status and Challenges Abstract: Advances in molecular technologies have led to rapid generation of data and information about cellular processes at an increasing rate. Current means of knowledge representation and scientific communication in biology cannot adequately deal with the complexity and volume of this information - a serious bottleneck for developing a causal, predictive understanding of the cell. To address this problem we have developed BioPAX (Biological Pathway Exchange), a standard language for representing and exchanging pathway information. Recently released BioPAX level 3 can represent signaling and metabolic pathways, gene regulation and molecular and genetic interactions in great detail. The latest version of Pathway Commons, our pathway data integration and aggregation server aims to provide a "merged" network of publicly available databases that support BioPAX. Through an iterative process of aggregation, alignment, matching, and merging- not very different conceptually than putting pieces of a puzzle together - we are building a cell map. Pathway alignment, or finding similar and/or equivalent portions of two pathways, is a crucial step for this goal. PATCH is an algorithm that can align pathways even when there is missing or omitted knowledge. We have successfully applied Patch to find similar pathways between Reactome and NCI/PID, and detected several curation errors in both databases during this process. As we build pathway resources and infrastructure it is becoming increasing possible to utilize a knowledge driven approach to biological problems. With a mechanistic understanding of the cellular events, we can better subtype diseases, predict drug responses, and choose combinations of drugs to optimally interfere with the disease. This would be revolutionary, especially for complex, multi-causal diseases such as cancer.
	Hans Peter Graf, PhD NEC Laboratories America, Inc. Princeton, New Jersey - USA CV: http://www.nec-labs.com/research/machine/ml_website/person.php?person=hpg Title: SOMAmer-based Proteomic Analysis with Machine Learning Collaborators: - Yanjun Qi, PhD, NEC Laboratories America - Alexandru Niculescu-Mizil, PhD, NEC Laboratories America - Igor Durdanovic, NEC Laboratories America - Shintaro Kato, PhD, NEC Tokyo - Iwao Waga, PhD, NEC Tokyo - Alex Stuart, PhD, SomaLogic, Boulder Abstract: SOMAmer technology opens the possibility for a low-cost analysis of thousands of plasma proteins from a small sample of blood. Finding reliable biomarkers among such a large number of proteins is challenging since the plasma proteome has a complex composition and conditions can change quickly, affecting the concentrations of proteins we try to interpret. Finding reliable biomarkers is a problem of feature selection, where we search for combinations of proteins that consistently indicate certain conditions, such as a disease, with high sensitivity and specificity. Typical approaches are univariate algorithms or algorithms that greedily search for groups of proteins. Recently, research has made considerable progress in feature learning where we try learning automatically features that are more indicative of the underlying phenomena. We applied methods based on deep learning and kernel techniques successfully in various image, text and protein analysis applications. Here we demonstrate several multivariate feature selection algorithms based on L1 regularization and kernel techniques for the detection of biomarkers in data from three different cancer studies. Each data set consists of several hundred samples with between 800 and 1,000 different proteins. Due to the small sample sizes, individual runs of feature learning can be unstable, with variations in the selected proteins from one run to the next. Yet with statistical sampling, groups of proteins are identified reproducibly that provide high sensitivity and selectivity. These results are very encouraging since the ability to analyze large numbers of proteins holds great promise for a wide range of proteomic analysis applications.
	Kirk E. Jordan, PhD Emerging Solutions Executive & Associate Program Director Computational Science Center IBM T.J. Watson Research Member, IBM Academy of Technology Massachusetts - USA CV: https://researcher.ibm.com/researcher/view.php?person=us-kjordan Title: A New Day, A New High Performance Computer, What Does It Mean for the Life Sciences? Collaborators: Vipin Sachdeva, Michael Perrone Abstract: A new day is dawning with IBM’s latest High Performance Computing (HPC) System as we see core counts continue to rise. In this talk, I will briefly describe this system and explain how it fits into the road to Exascale. More importantly, I will describe some of the work underway pertinent to the life science. I will describe some of our experience on this new system including bring up Rosetta, a code that predicts protein structures from amino acid sequences in DNA. In addition, while related to our HPC work, I will describe work continuing to make HPC accessible to a wider audience and eventually targeting the healthcare and life science practitioner directly and explain why this work is of importance.
	Michael R. Mehan, PhD SomaLogic Inc. Boulder, Colorado - USA CV: pdf Title: Advances in Protein Biomarker Discovery: Controlling for Sample Handling Artifacts and Confounding Effects Collaborators: Rachel Ostroff, Alex Stewart, Glenn Sanders, Dom Zichi, Ed Brody, Steve Williams Abstract: Many biomarker discovery studies may fail to validate because the clinical population does not represent the intended clinical use or because hidden preanalytic variability in the discovery samples contaminates the apparent disease specific information in the biomarkers. This preanalytic variability can arise from differences in blood sample processing between study sites, or worse, introduce case/control bias in samples collected differently at the same study site. To better understand the effect of different blood sample processing procedures, we evaluated protein measurement bias in a large multi-center lung cancer study. These analyses revealed that perturbations in serum protocols result in changes to many proteins in a coordinated fashion. Using the SomaLogic SOMAscan platform we developed protein biomarker signatures of processes such as cell lysis, platelet activation, and complement activation and assembled these preanalytic signatures into quantitative multi-dimensional Sample Mapping Vectors (SMV).  The underlying platform technology uses SOMAmers (Slow Off-rate Modified Aptamers) as affinity reagents to quantify approximately 850 proteins. The SMV score provides critical evaluation of both the quality of every blood sample used in discovery, and also enables the evaluation of candidate protein biomarkers for resistance to preanalytic variability.
	Anna Panchenko, PhD Associate Investigator National Center for Biotechnology Information, NLM, NIH Maryland - USA CV: www.ncbi.nlm.nih.gov/CBBresearch/Panchenko/ Title: Deciphering of Human Protein Interactome using Structural Complexes Abstract: Proteins function by interacting with other biomolecules and knowledge of the entire set of interactions combined with the properties of protein binding sites is essential for our understanding of cellular functions and the origins of many diseases. Recently we developed a method (IBIS) which analyzes and predicts interaction partners and locations of binding sites in proteins based on the evolutionary conservation of binding sites in homologous structural complexes. IBIS imposes a number of rigorous criteria in order to increase the reliability of homology-based inference of interactions and provides binding site annotations for five different types of interaction partners (proteins, small molecules, nucleic acids, peptides and ions). It facilitates the mapping of the entire biomolecular interaction network for a given organism and we use this framework to map the human protein interactome and analyze its properties. We show that structurally inferred interaction network is highly modular and has small-world characteristics. Moreover it is more functionally coherent and reliable compared to high-throughput interaction networks. Since structurally inferred interaction network provides the details of binding interfaces, we analyze the effect of cancer associated point mutations on protein-protein binding. We show that cancer related mutations can either destabilize or make the complex more stable and lead to excessive activation or inactivation. Cellular regulatory mechanisms provide a sensitive and specific response to external stimuli and such dynamic regulation can be achieved through reversible covalent modifications. We study the effect of phosphorylation on protein binding and function for different types of complexes from the human proteome. Our analysis of molecular mechanisms of phosphorylation shows that phosphorylation may modulate the binding affinity and trigger the transitions between different conformer and oligomeric states. We also show that phosphorylation sites are not only more likely to be evolutionary conserved than surface residues but even more so than the binding interface.
	Gabriele Scheler, PhD Mountain View, California - USA CV: www.theoretical-biology.org/people/scheler.html Title: Transfer Function Analysis of Signal Transduction - The PSF System Abstract: We present a new approach towards a modular and systematic analysis of biochemical reaction models using a modified steady-state assumption. An ordinary differential equation (ODE) system for both complex formation and enzymatic reactions is automatically transformed into a set of signal-response transfer functions, called protein signaling functions (PSF). Elementary PSFs represent individual biochemical reactions out of context, systemic PSFs are the transformation of the elementary PSF in the context of a system of equations. The use of systemic PSFs reduces the complexity of biological signal systems to manageable chunks which allow modular parameter adjustment. The poster uses two published moderate-sized ODE models on striatal neural plasticity to present the analysis. The models use a different selection of proteins and interactions, but aim to model the same biological system. They are derived from essentially the same experimental data by standard methods of parameter tuning. Re-analysis of the ODEs as PSF systems allows to directly compare shared components between the systems, such as the centrally important cAMP-PKA-DARPP32 connection. The results show that individual pathway components have become tuned to radically different quantitative transfer functions and concentration ranges, due to the influence of the different system embedding. By tuning transfer functions directly in the PSF system, current methods of system construction can be improved and cross-model consistency becomes achievable.

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9th Annual Rocky Mountain Bioinformatics Conference

Poster Session

General Information:

• Posters will be available for viewing on Friday evening, December 9 and Saturday morning, December 10. There are two scheduled poster sessions:
  
  • Friday, December 9 from 5:45 pm to 8:00 pm and
  • Saturday, December 10 from 11:05 am to 12:30 pm.
• Poster Presenters should be available for presentation during the scheduled poster sessions.
• Posters are assigned a number per the list on the Poster Presenters and Abstracts page (click here).  There will be lists at the conference.  Please put your poster on the poster board corresponding to the number assigned.
• The poster board dimensions are 4 feet high x 4 feet wide. Tacks will be provided
  for securing your poster to the board.

Schedule:

FURTHER QUESTIONS
Rocky Conference Coordinator
Stephanie Hagstrom
This email address is being protected from spambots. You need JavaScript enabled to view it.
360-239-9177

9th Annual Rocky Mountain Bioinformatics Conference

Full Agenda

Updated Jan. 09, 2012

Indicates that the presentation is available for PDF download.

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>>> Go directly to: [Friday - December 09] [Saturday - December 10]
Thursday – December 08, 2011
11:00 am – 1:00 pm	Registration
1:00 pm – 1:45 pm	Keynote 1 The Future of Research Communication: From Surfing to Deep Diving Judith A. Blake, PhD Associate Professor The Jackson Laboratory Bar Harbor, Maine - USA
1:45 pm – 1:55 pm	Oral Presentation 1 The Rat Genome Curation: RGD Automated Data Integration Pipelines Maximize Coverage Presenter: Marek Tutaj, Medical College of Wisconsin Authors: Marek Tutaj, Mary Shimoyama, Elizabeth Worthey, Jennifer Smith, Howard Jacob PDF of Presentation
1:55 pm – 2:05 pm	Oral Presentation 2 A Sensemaking Model for the Explorative Analysis of Large Gene Lists Presenter: Carsten Görg, University of Colorado Denver Authors: Carsten Görg, Barbara Mirel, Hannah Tipney PDF of Presentation
2:05 pm – 2:15 pm	Oral Presentation 3 The Role of p53 in Oligodendrocyte UPR Presenter: Hasan Jamil, Wayne State University Author: Hasan Jamil PDF of Presentation
2:15 pm – 2:25 pm	Oral Presentation 4 Quantitative Data: Where are they Hidden in Biomedical Literature? Presenter: Komandur Ravidumar, University of Colorado School of Medicine Authors: K.E. Ravikumar, Meenakshi Narayanaswamy, S.V. Ramanan PDF of Presentation
2:25 pm – 2:35 pm	Oral Presentation 5 Multiscale Patient-Specific Blood Systems Biology Presenter: Scott Diamond, University of Pennsylvania Authors: Scott L. Diamond
2:35 pm – 2:45 pm	Oral Presentation 6 A Resource for the Rational Selection of Drug Target Proteins and Leads for the Malaria Parasite, Plasmodium Falciparum Presenter: Fourie Joubert, University of Pretoria Authors: Jeanre Smit, Phele Mpangase, Michal Szolkiewicz, Misha le Grange, Fourie Joubert PDF of Presentation
2:45 pm – 3:00 pm	Break (15 minutes)
3:00 pm – 3:10 pm	Oral Presentation 7 Identifying Treatment Relevant Colorectal Cancer Subtypes Using Iterative Non-negative Matrix Factorization Presenter: Andreas Schlicker, Netherlands Cancer Institute Authors: Andreas Schlicker, Garry Beran, Christine M Chresta, Gael McWalter, Alison Pritchard, Susie Weston, Sarah Runswick, Sara Davenport, Kerry Heathcote, Denis Alferez Castro, George Orphanides, Tim French, Lodewyk FA Wessels
3:10 pm – 3:20 pm	Oral Presentation 8 The Origin of Mammalian Placentation Correlates with Protein Functional Shift and the Emergence of New Control Mechanisms Presenter: Mary O'Connell, Dublin City University Authors: Thomas A. Walsh, Kieran Holohan, Anna O'Brien, Robert Carton, Elinor Velasquez, Claire C. Morgan, Noeleen B. Loughran, Mary J. O'Connell
3:20 pm – 3:30 pm	Oral Presentation 9 Exploring and Profiling Long Non-coding RNA in T Cell Development Using Next Generation Sequencing and Bioinformatics Approaches Presenter: Tzu L. Phang, University of Colorado Denver Authors: Tzu L. Phang, Ping Yao Zeng, Edwin.F. de Zoeten
3:30 pm – 3:40 pm	Oral Presentation 10 Building an Interactome to Identify Signaling Components Presenter: Sarah Wyatt, Ohio University Authors: Sarah Waytt, Kaiyu Shen
3:40 pm – 3:50 pm	Oral Presentation 11 GeneSmash: A RESTful Web Service for Gene Annotations Presenter: Ganiraju Manyam, University of Texas Anderson Cancer Center Authors: Michelle Payton, Ganiraju Manyam, Chris Wakefield, Jack Roth, Lynne Abruzzo, Kevin Coombes
3:50 pm – 4:00 pm	Oral Presentation 12 Integrating Curated Databases and Text Mining Output into a Biomedical Knowledge Base Presenter: Kevin Livingston, University of Colorado Denver Authors: Kevin M. Livingston, Michael Bada, William A. Baumgartner Jr, Yuriy Malenkiy, Lawrence E. Hunter PDF of Presentation
4:00 pm – 4:10 pm	Oral Presentation 13 Using Evolving Protein Networks to Inform the Graph Coloring Problem Presenter: Todd Gibson, University of Colorado Denver Authors: Todd A. Gibson, Debra S. Goldberg
4:10 pm – 4:25 pm	Break (15 minutes)
4:25 pm – 5:10 pm	Keynote 2 Building Cell Maps: Status and Challenges Emek Demir, PhD Computational Biology Center Memorial Sloan Kettering Cancer Center New York, New York - USA
5:10 pm – 5:20 pm	Oral Presentation 14 Machine Approaches to Recognition of Trypanosomal Variant Surface Glycoprotein Sequences Presenter: Jon Wilkes, Wellcome Trust Centre for Molecular Parasitology Author: Jon Wilkes PDF of Presentation
5:20 pm – 5:30 pm	Oral Presentation 15 Compact Encoding for Gene Therapy Presenter: Roger Hall, University of Arkansas at Little Rock Author: Roger Hall PDF of Presentation
5:30 pm – 5:40 pm	Oral Presentation 16 Microbial Monitoring and Space Exploration Presenter: Sven Bilke, NCI Authors: Sven Bilke, Verena Starke
5:40 pm – 5:50 pm	Oral Presentation 17 CodingMotif: Exact Determination of Overrepresented Nucleotide Motifs in Coding Sequences Presenter: Jeffrey Chuang, Boston College Authors: Yang Ding, Andy Lorenz, Jeffrey Chuang PDF of Presentation
5:50 pm – 6:00 pm	Oral Presentation 18 GO Classes or Biclusters? Alternative Approaches for Exploring Microarray Probeset Subsets Presenter: George Acquaah-Mensah, Massachusetts College of Pharmacy and Health Sciences Author: George Acquaah-Mensah PDF of Presentation
6:00 pm – 6:10 pm	Oral Presentation 19 Accurate Inferring Transcription Regulation from a Compendium of Expression Profiles Presenter: Xueling Li, University of Texas, Medical Branch Authors: Xueling Li, Dirar Homouz, Andrzej Kudlicki PDF of Presentation
6:10 pm – 6:20 pm	Oral Presentation 20 A Proposed Algorithm for Epistasis Detection using Frequent Item-sets and Mutual Information Presenter: James Rudd, North Carolina University Author: James Rudd, Assefa Tesfay, ClarLynda Williams-DeVane, Gaolin Zheng PDF of Presentation
7:00 pm – 9:00 pm	Banquet, Thursday, December 8, 2011 7:00 pm - 9:00 pm Banquet Location: Il Poggio Restaurant, Snowmass Village Note: The Dec 08 banquet has sold out. To be placed on a wait list, please email This email address is being protected from spambots. You need JavaScript enabled to view it..
>>> Go directly to: [Thursday - December 08] [Saturday - December 10]
Friday – December 09, 2011
9:00 am – 9:45 am	Keynote 3 Project Halo: Constructing and Exploiting a Formal Representation of a Biology Textbook to Understand and Answer Users' Questions Peter Clark, PhD Vulcan Inc. Seattle, Washington - USA
9:45 am – 9:55 am	Oral Presentation 21 Molecular Insights to the Drug Resistance of V32I & M46L HIV-1 Protease Mutant to Inhibitor TMC114: Free Energy Calculation and Molecular Dynamics Simulations Presenter: Biswa Meher, Albany State University Authors: Biswa R. Meher, Yixuan Wang
9:55 am – 10:05 am	Oral Presentation 22 Testing the Ortholog Conjecture with Functional Data from Several Pairs of Closely Related Organisms Presenter: Wyatt Clark, Indiana University Authors: Wyatt T. Clark, Predrag Radivojac, Matthew Hahn
10:05 am – 10:15 am	Oral Presentation 23 Functional Profiling of Pharmacogenetic Non-synonymous SNPs Presenter: Chet Seligman, Buck Institute for Research on Aging Authors: Chet Seligman, Janita Thusberg, Jackson Miller, Emidio Capriotti, Jim Auer, Michelle Whirl-Carrillo, Teri Klein, Sean Mooney PDF of Presentation
10:15 am – 10:25 am	Oral Presentation 24 Limitations of Automated Annotation Software When Used with Draft Genomic Assemblies Presenter: Robert Norgren, University of Nebraska Medical Center Author: Robert B. Norgren, Jr. PDF of Presentation
10:25 am – 10:35 am	Oral Presentation 25 Mixed Primary-Secondary Structure Alignment of ncRNA Covariance Models for Model Clustering and Combination Presenter: Jennifer Smith, Boise State University Author: Jennifer Smith PDF of Presentation
10:35 am – 10:45 am	Oral Presentation 26 In Silico Gene Expression Based Analysis on Claudin Family Members Association with Human Thyroid Cancer Presenter: Shaukat Malik, Mohammad Ali Jinnah University Authors: Shaukat Malik, S. Sameen, Z. Khalid
10:45 am – 11:00 am	Break (15 minutes)
11:00 am – 11:10 am	Oral Presentation 27 Data Management and Analysis Solutions for Meta-Analysis of Multi-Domain Data Presenter: ClarLynda Williams-Devane, North Carolina Central University Authors: ClarLynda Williams-DeVane, Archana Radadia, Nina Rountree, Stephen Edwards PDF of Presentation
11:10 am – 11:20 am	Oral Presentation 28 STOP and DEFOG: Web Applications for a Comprehensive Functional Gene Set Analysis Presenter: Tobias Wittkop, Buck Institute for Research on Aging Authors: Tobias Wittkop, Emily Teravest, Ari E. Berman, Uday Evani, K. Mathew Fleisch, Corey Powell, Nigam Shah, Sean D. Moone PDF of Presentation
11:20 am – 11:30 am	Oral Presentation 29 DAVID-WS: A Stateful Web Service to Facilitate Gene/Protein List Analysis Presenter: Xiaoli Jiao, NIH/NIAID Authors: Xiaoli Jiao, Brad T. Sherman, Da Wei Huang, Richard A. Lempicki PDF of Presentation
11:30 am – 11:40 am	Oral Presentation 30 Predicting Transcription Factor Binding Sites with Hidden Markov Models by using ChIP-Seq Data Presenter: Anthony Mathelier, University of British Columbia Authors: Anthony Mathelier, Wyeth W. Wasserman PDF of Presentation
11:40 am – 11:50 am	Oral Presentation 31 The Critical Assessment of Function Annotation Experiment: A Community-wide Effort Towards a Better Functional Annotation of Genes and Genomes Presenter: Predrag Radivojac, Indiana University Authors: Predrag Radivojac, Sean Mooney, Iddo Friedberg
11:50 am – 12:00 pm	Oral Presentation 32 In Silico Rational Drug Design and Modeling Studies of Novel Inhibitors for Multi-target Inhibition in Pseudomonas Aeruginosa Presenter: Premkumar Jayaraman, Nanyang Technological University Authors: Premkumar Jayaraman, Lim Chu Sing Daniel, Meena K. Sakharkar PDF of Presentation
12:00 pm – 12:30 pm	Keynote 4 Advances in Protein Biomarker Discovery: Controlling for Sample Handling Artifacts and Confounding Effects Mike Mehan, PhD SomaLogic Boulder, CO - USA
12:30 pm – 4:00 pm	Break
4:00 pm – 4:45 pm	Keynote 5 Deciphering of Human Protein Interactome using Structural Complexes Anna Panchenko, PhD Associate Investigator National Center for Biotechnology Information NLM, NIH Bethesda, Maryland - USA
4:45 pm – 4:55 pm	Oral Presentation 33 PathCMap: Development of Pathway Signature System for Identifying Druggable Partners of Synthetic Lethal Genes in Cancer Presenter: Jihye Kim, University of Colorado Denver School of Medicine Authors: Jihye Kim, Carlos H C Cano, Aik Choon Tan PDF of Presentation
4:55 pm – 5:05 pm	Oral Presentation 34 Identifying Single Copy Orthologs in Metazoa Presenter: Christopher Creevey, Teagasc Authors: Chris Creevey, Jean Muller, Tobias Doerks, Julie D. Thompson, Detlev Arendt, Peer Bork PDF of Presentation
5:05 pm – 5:15 pm	Oral Presentation 35 Mining Genomes to Understand the Origin of Vision in Metazoa Presenter: Davide Pisani, National University of Ireland, Maynooth Authors: Roberto Feuda, Davide Pisani
5:15 pm – 5:25 pm	Oral Presentation 36 Evolutionary Pattern Embedded in the Lengths of Proteins and Their Structural Units Presenter: Minglei Wang, University of Illinois at Urbana-Champaign Authors: Minglei Wang, Cedric Debes, Frauke Gräter, Gustavo Caetano-Anollés
5:25 pm – 5:35 pm	Oral Presentation 37 A Multiple-template Approach for Protein Threading Presenter: Jian Peng, Toyota Technological Institute at Chicago Authors: Jian Peng, Jinbo Xu PDF of Presentation
5:35 pm – 5:45 pm	Oral Presentation 38 A New Probabilistic Model in Predictive Microbiology (NPMPM) Presenter: Nadine Schoene, Goethe University Frankfurt Authors: Nadine Schoene, Alexander Bockmayr, Bernd Appel, Annemarie Kaesbohrer PDF of Presentation
5:45 pm – 8:00 pm	Reception and Poster Session Snowmass Conference Center (across street from Silvertree), Sinclair Room
>>> Go directly to: [Thursday - December 08] [Friday - December 09]
Saturday – December 10, 2011
9:00 am – 9:45 am	Keynote 6 A New Day, A New High Performance Computer, What Does It Mean for the Life Sciences? Kirk E. Jordan, PhD Emerging Solutions Executive & Associate Program Director Computational Science Center IBM T.J. Watson Research Member, IBM Academy of Technology Massachusetts - USA
9:45 am – 9:55 am	Oral Presentation 39 Rediscovery of the p53 Transcriptome Presenter: Mary Allen, University of Colorado Authors: Mary Allen, Robin Dowell, Joaquin Espinosa
9:55 am – 10:05 am	Oral Presentation 40 Developing Maximum Likelihood and Bayesian Supertrees Presenter: Wasiu Akanni, National University of Ireland, Maynooth Authors: Wasiu Akanni, Davide Pisani, Peter Forster, Mark Wilkinson PDF of Presentation
10:05 am – 10:15 am	Oral Presentation 41 Prediction of Operons in Microbial Genomes by Integrating Diverse Information Sources Presenter: Anis Karimpour-Fard, University of Colorado Anschutz Medical Campus Authors: Anis Karimpour-Fard, Lawrence E. Hunter PDF of Presentation
10:15 am – 10:25 am	Oral Presentation 42 Gene Language Model Presenter: Siamak Rezaei, Talai Author: Siamak Rezaei PDF of Presentation
10:25 am – 10:35 am	Oral Presentation 43 Live and Let Die Presenter: Christian Forst, University of Texas Southwestern Medical Center Authors: Nassim Sohaee, Christian V. Forst
10:35 am – 11:05 am	Keynote 7 SOMAmer-based Proteomic Analysis with Machine Learning Hans Peter Graf, PhD NEC Laboratories America, Inc. Princeton, New Jersey - USA
11:05 am – 12:30 pm	Poster Session Snowmass Conference Center (across street from Silvertree) Sinclair Room
12:30 pm – 4:00 pm	Break
4:00 pm – 4:10 pm	Oral Presentation 44 Broad Semantic Class Assignment for Biomedical Text Presenter: Kevin Bretonnel Cohen, University of Colorado School of Medicine Authors: K. Bretonnel Cohen, Thomas Christiansen, Lawrence E. Hunter
4:10 pm – 4:20 pm	Oral Presentation 45 On the Accuracy of Protein Tertiary Structure Comparison Presenter: Aleksandar Poleksic, University of Northern Iowa Authors: Aleksandar Poleksic, Mauricio Arriagada
4:20 pm – 4:30 pm	Oral Presentation 46 A Distributed Framework for Computation on the Results of Large Scale NLP Presenter: Christophe Roeder, University of Colorado, Anschutz Medical Campus Authors: Christophe Roeder, William Baumgartner Jr, Kevin Livingston
4:30 pm – 4:40 pm	Oral Presentation 47 Probabilistic Search Frameworks for Protein Conformational Spaces Presenter: Amarda Shehu, George Mason University Authors: Amarda Shehu
4:40 pm – 4:50 pm	Oral Presentation 48 Predicting HIV-1, Human Protein Interactome Through Indirect and Direct Evidences Presenter: Oznur Tastan, Microsoft Research New England Authors: Oznur Tastan, Jaime Carbonell, Judith Klein
4:50 pm – 5:00 pm	Oral Presentation 49 Using Information Theory to Map Reads to a Reference Sequence Presenter: John Conery, University of Oregon Author: John Conery
5:00 pm – 5:45 pm	Keynote 8 Transfer Function Analysis of Signal Transduction - The PSF System Gabriele Scheler, PhD Mountain View, California - USA
5:45 pm	Rocky 2011 Closing Comments
>>> Go directly to: [Thursday - December 08] [Friday - December 09] [Saturday - December 10]

9th Annual Rocky Mountain Bioinformatics Conference

Conference Hotel

The Silvertree Hotel is located in Snowmass Village, thirty feet from the Snowmass Conference Center and is on the Snowmass Village Mall and Fanny Hill, which has more than fifty shops, boutiques, and restaurants and is the hub for many exciting activities. Fanny Hill offers direct access to ski lifts.

Transportation within Snowmass Village is easy and free, with frequent service at the Village Bus Stop. Buses to Aspen leave from the end of the mall.

THE SILVERTREE HOTEL HOUSING INFORMATION

Group Room Rates - PLEASE NOTE: Group discount rates are available until November 8, 2011.   Please call the hotel directly (1-800-525-9402) to inquire if rooms are still available at the discount rate.

• Single/Double occupancy $92.00 per night. Extra person charge is $25 per person per night. Children under 12 stay free in parents' room. The hotel rates will be subject to all state, county and city taxes in effect at the time of the Rocky 2011 meeting.
• State tax is currently 12.8% and is subject to change.
• Please mention the 'Rocky11' conference to get the group rate
  
  

Reservation Information:

• *****Click here for "On-line Hotel Reservations" Reference "Rocky11"*****
• Phone: 1-800-525-9402
• A one night deposit of the room rate will be due at the time of the reservation.
• Cut-off date to receive reduced group rate is November 8, 2011. After this date, rooms, if available, are at prevailing rates.
• Check-in is 4:00 pm, Check-out is 11:00 am
  
  

Complimentary shuttle available from Aspen Airport to Snowmass Village.

9th Annual Rocky Mountain Bioinformatics Conference

Agenda at a Glance

Updated Dec. 07, 2011
(Schedule and locations are subject to change. Please check back for updates.)

• CLICK HERE for Rocky 2011 Program Book (.pdf).