Poster Presenters & Abstracts

• CLICK HERE for Rocky 2011 Program Book (.pdf).  Posters start on page 47.

Listed in alphabetical order by presenter's last name:

P01: Identifying Novel Components of the Gravitropic Signal Transduction Pathway via Transcriptome Analysis
Presenter: Zachary Abrams, Ohio University

P02: Developing Maximum Likelihood and Bayesian Supertrees
Presenter: Wasiu Akanni, National University of Ireland, Maynooth

P03: Opportunities and Challenges Associated with Computational RNAseq Data Analysis
Presenter: David Astling, University of Colorado School of Medicine

P04: Jikitou a Question Answering System: The Next Stage in the Evolution of Information Retrieval
Presenter: Michael Bauer, University of Arkansas at Little Rock

P05: Phylogenetic Signal Dissection and the Phylogeny of the Ecdysozoa
Presenter: Lahcen Campbell, The National University of Ireland, Maynooth

P06: A Network-based Survival Predictor and its Application to Cytogenetically-normal Acute Myeloid Leukemia
Presenter: Yongkee Cho, Washington University in St. Louis

P07: CodingMotif: Exact Determination of Overrepresented Nucleotide Motifs in Coding Sequences
Presenter: Jeffrey Chuang, Boston College

P08: Testing the Ortholog Conjecture with Functional Data from Several Pairs of Closely Related Organisms
Presenter: Wyatt Clark, Indiana University

P09: Novel Information Theory Based Metrics for the Evaluation of GO Term Annotations
Presenter: Wyatt Clark, Indiana University

P10: Multiscale Patient-Specific Blood Systems Biology
Presenter: Scott Diamond, University of Pennsylvania

P11: Searching for Population Variation of Small Tandem Segmental Duplications using the 1000 Genomes Project Sequencing Data
Presenter: Michael Dickens, University of Colorado

P12: Gene Duplicability in the Mammalian Protein-protein Interaction Network
Presenter: Aoife Doherty, National University of Ireland, Maynooth

P13: Mixture Models vs. Supervised Learning Methods for Integrative Genomic Analysis
Presenter: Daniel Dvorkin, University of Colorado, Denver

P14: Inferring Protein Backbone Flexibility from Conformational Differences
Presenter: Elizabeth Eskow, University of Colorado Boulder

P15: Improving Automated Protein Function Prediction by integrating Natural Language Processing and Machine Learning
Presenter: Christopher Funk, University of Colorado

P16: A Sensemaking Model for the Explorative Analysis of Large Gene Lists
Presenter: Carsten Goerg, University of Colorado Denver

P17: Mathematical Modeling of Metastatic Growth in Lymphatic Vessels
Presenter: Ruth Griswold, Mount Sinai School of Medicine

P18: Consensus Network Inference Using Multiple Datasets to Elucidate Common and Chemical-specific Effects on Steoroidogenesis
Presenter: Tanwir Habib, US Army ERDC

P19: A Network-based Approach to Finding Fusion Genes
Presenter: Leanne Haggerty, The National University of Ireland, Maynooth

P20: Compact Encoding for Gene Therapy
Presenter: Roger Hall, University of Arkansas at Little Rock

P21: Diversification of Visual Receptors (opsin) Coincides with Major Environmental Factors such as the Cambrian Explosion and the Oxygenation of the Oceans
Presenter:  Sinéad Hamilton, The National University of Ireland, Maynooth

P22: A Random Forest Model for Phosphorylation Site Localization using Mass Spectrometric Data
Presenter: Xin He, Indiana University Bloomington

P23: Characterizing the Phenotype of Beta-Blocker Responsiveness in CHF Patients
Presenter: Michael Hinterberg, University of Colorado-Denver

P24: CTCF can Form Unidirectional Regulatory Elements by Combining with Other Transcription Factors
Presenter: Chih-hao Hsu, NIH

P25: Metabolic Network Analysis of Apicomplexan Parasites to Identify Novel Drug Targets
Presenter: Stacy Hung, University of Toronto

P26: Improvement of Fold Recognition by Incorporating Bayesian Framework on Encoding Protein Fragments of Unknown Structures for Structure Alphabet-based Alignment
Presenter: Kenneth Hung, National Taiwan University

P27: The Role of p53 in Oligodendrocyte UPR
Presenter: Hasan Jamil, Wayne State University

P28: Extending the Value of Spectral Libraries: a Neighbor-based Approach to Predicting Intensities of Peptide Fragmentation Spectra
Presenter: Chao Ji, Indiana University, Bloomington

P29: DAVID-WS: A Stateful Web Service to Facilitate Gene/Protein List Analysis
Presenter: Xiaoli Jiao, NIH/NIAID

P30: Mobyle: A Web Based Frame-work for the Integration of Bioinformatics Software and Databanks
Presenter: Louis Jones, Institut Pasteur

P31: Discovery: A Resource for the Rational Selection of Drug Target Proteins and Leads for the Malaria Parasite, Plasmodium Falciparum
Presenter: Fourie Joubert, University of Pretoria

P32: Finding a Surrogate Metric of Cancer Antigen 125 with Thousand of Proteins
Presenter:  Shintaro Kato, NEC Corporation

P33: An Information-theoretic Measure of TFBS Motif Palindromicity
Presenter: Alastair Kilpatrick, University of Edinburgh

P34: 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

P35: Automated Reaction Mapping for Isomers
Presenter: Tina Kouri, Colorado School of Mines

P36: A Data Integration Approach Reveals Species-specific Pharmacology Between Human and Rat Orthologs
Presenter: Felix Kruger, European Bioinformatics Institute

P37: Accurate Inferring Transcription Regulation from a Compendium of Expression Profiles
Presenter: Xueling Li, University of Texas, Medical Branch

P38: PhenoPred 2: Prediction of Gene-Disease Associations Based on Multiple Networks
Presenter: Biao Li, The Buck Institute for Research on Aging

P39: Exploring an Approximate Subgraph Matching Approach for Biomedical Event Extraction
Presenter: Haibin Liu, University of Colorado School of Medicine

P40: Cancelled

P41: A Physiological Pathway Portal Tool at the Rat Genome Database
Presenter: Weisong Liu, The Medical College of Wisconsin

P42: Evolution and Architecture of the Inner Membrane Complex in Asexual and Sexual Stages of the Malaria Parasite
Presenter: Noeleen Loughran, The Hospital for Sick Children

P43: Label and Edge Mismatch Graphlet Kernels for Functional Residue Prediction in Protein Structures
Presenter: Jose Lugo-Martinez, Indiana University

P44: Role of Pyruvate Dehydrogenase Kinases (PDKs) and Their Respective Micro RNAs in Human Ovarian Cancer
Presenter: Shaukat Malik, Mohammad Ali Jinnah University

P45: Analysis of Human Complex Disorders from the Systems Biology Perspective
Presenter: Natalia Maltsev

P46: GeneSmash: A RESTful Web Service for Gene Annotations
Presenter: Ganiraju Manyam, University of Texas Anderson Cancer Center

P47: TrAC: Transcriptome Analysis with Circos
Presenter: Aleksandra Markovets, University of Arkansas at Little Rock

P48: Predicting Transcription Factor Binding Sites with Hidden Markov Models by using ChIP-Seq data
Presenter: Anthony Mathelier, University of British Columbia

P49: A Comparative Analysis of Knowledge-Based Gene Prioritization Methods:  Is the Supply Greater Than the Demand?
Presenter:  Neel Mehta, Arizona State University

P50: Hierarchical Prediction of Enzyme Classes Using Ensemble Machine Learning Approaches
Presenter: Akram Mohammed, University of Nebraska Medical Center

P51: Inferring the Mammalian Phylogeny using a Heterogeneous Approach
Presenter: Claire Morgan, Dublin City University

P52: An Issue of Caution in the use of Mitochondrial Data to Infer the Mammalian Phylogeny
Presenter: Claire Morgan, Dublin City University

P53: Entropy-based Assessment of Condition-specific Histone Modifications
Presenter: Tadasu Nozaki, Keio University

P54: Prediction of Protein Function using Analysis of Interaction Maps Across Species
Presenter: Kymberleigh Pagel, Indiana University, Bloomington

P55: Deciphering of Human Protein Interactome using Structural Complexes
Presenter:  Anna Panchenko, National Center for Biotechnology Information, Institutes of Health

P56: Regulation of Protein-Protein Binding by Phosphorylation and Oligomerization
Presenter:  Anna Panchenko, National Center for Biotechnology Information, Institutes of Health, USA

P57: CysNO-DB: A Database of S-nitrosylation Sites
Presenter: Sanjit Pandey, University of Nebraska Medical Center

P58: A Database Framework for identifying Coding Sequence from NextGen mRNA Sequences
Presenter: Sanjit Pandey, University of Nebraska Medical Center

P59: ModPred: Predicting Post-translational Modification Sites from Protein Sequence
Presenter: Vikas Pejaver, Indiana University

P60: A Multiple-template Approach for Protein Threading
Presenter: Jian Peng, Toyota Technological Institute at Chicago

P61: A Tool for Assessment and Validation of Sequencing-Based Methods in Family Disease Studies
Presenter: Alexander Poole, University of Colorado Anschutz Medical Campus

P62: Alternative Splicing Detection Using RNAseq: An Assembly Approach
Presenter: Likit Preeyanon, Michigan State University

P63: In Silico Rational Drug Design and Modeling Studies of Novel Inhibitors for Multi-target Inhibition in Pseudomonas Aeruginosa
Presenter: Jayaraman Premkumar, Nanyang Technological University

P64: Quantitative Data: Where are they Hidden in Biomedical Literature?
Presenter: Komandur Ravikumar, University of Colorado School of Medicine

P65: Transcriptome Profile of Bovine Respiratory Disease Pathogen - Mannheimia Haemolytica PHL213
Presenter: Joseph Reddy, Mississippi State University

P66: SpacerSeeker: Detecting and Identifying Immunity Conferred by CRISPR Loci
Presenter: Zachary Romer, Loyola University Chicago

P67: MutDB: A Database for Assessing the Impact of Genetic Variants
Presenter: Tal Ronnen Oron, Buck Institute for Research on Aging

P68: Support for Larger Epistatic Modeling Using an OpenCL Implementation of Multifactor Dimensionality Reduction
Presenter: James Rudd, North Carolina Central University

P69: Identifying Treatment Relevant Colorectal Cancer Subtypes Using Iterative Non-negative Matrix Factorization
Presenter: Andreas Schlicker, Netherlands Cancer Institute

P70: A New Probabilistic Model in Predictive Microbiology (NPMPM)
Presenter: Nadine Schoene, Goethe University Frankfurt

P71: Simpsons Paradox and Correlation Cancellation in Genome-Wide Association Study Data
Presenter: Ronald Schuyler, University of Colorado Denver

P72: Predicting Chromosome Territories using Sequence Similarity
Presenter: Josiah Seaman, University of Colorado

P73: Functional Profiling of Pharmacogenetic Non-synonymous SNPs
Presenter: Chet Seligman, Buck Institute for Research on Aging

P74: Semi-supervised Learning Improves Gene Expression-based Prediction of Cancer Recurrence
Presenter: Mingguang Shi, Vanderbilt University

P75: Comprehensive Analysis of Associations Between Alternative Splicing and Histone Modifications
Presenter: Yuki Shindo, Keio University, Japan

P76: Developing a Decision Support System for Strategic Selection of Drug Targets to Combat Tropical Diseases
Presenter: Floriano Silva-jr, FIOCRUZ

P77: Concatabominations: A Character Recoding Strategy Implemented in the Safe Taxonomic Reduction Approach for Identifying Unstable Taxa
Presenter: Karen Siu-Ting Salvatierra, National University of Ireland Maynooth

P78: Investigation into Construction of MHC ligand Predictiors and Implications of Protocols used to Evaluate Them
Presenter: Werner Smidt, University of Pretoria

P79: Mining for Class-specific Motifs in Protein Sequence Classification
Presenter: Satish Srinivasan, University of Nebraska Medical Center

P80: Relationships Between Positioning of Synonymous Codon and Gene Translation Efficiency in Bacteria
Presenter: Satoshi Tamaki, Keio University

P81: The Rat Genome Curation:RGD Automated Data Integration Pipelines Maximize Coverage
Presenter: Marek Tutaj, Medical College of Wisconsin

P82: Using Transposable Elements to Understand Genomic Evolution
Presenter: Vijetha Vemulapalli, University of Colorado Denver

P83: Determining The Minimal Functional Elements in Protein Families
Presenter: Suleyman Vural, University of Nebraska

P84: Machine Approaches to Recognition of Trypanosomal Variant Surface Glycoprotein Sequences
Presenter: Jon Wilkes, Wellcome Trust Centre for Molecular Parasitology

P85: STOP and DEFOG: Web Applications for a Comprehensive Functional Gene Set Analysis
Presenter: Tobias Wittkop, Buck Institute for Research on Aging

P86: Building an Interactome to Identify Signaling Components
Presenter: Sarah Wyatt, Ohio University

P87: Post-translational Modifications Induce Significant yet not Extreme Changes to Protein Structure
Presenter: Fuxiao Xin, Indiana University Bloomington

P88: Co-evolution of SP1 and DNA Binding Sites
Presenter: Ken Yokoyama, University of Colorado Denver

P89: Coexpression of Linked Genes is not Explained by Similar Chromatin Environments
Presenter: Yiqiang Zhao, Buck institute

P90: What's New at EcoGene
Presenter: Jindan Zhou, University of Miami Miller School of Medicine

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The next Rocky conference will be announced here soon.

9th Annual Rocky Mountain Bioinformatics Conference

ANNOUNCEMENTS: • Dec 01: Online registration has closed. Onsite registration will take place Thursday, December 08, 11:00 AM. • Dec 01: The Rocky 2011 Program Book is now available (.pdf) • Nov 15: 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.. • MARC Travel Fellowship Application (.doc) - Deadline Nov. 04 •Download the Rocky 2011 Promotional Flyer (.pdf)

SPONSORS: Platinum:

Gold:

Silver:

Book Prizes as Student Prizes:

Welcome to Rocky 2011!

Welcome to the ninth annual Rocky Mountain Bioinformatics Conference, a meeting of the International Society for Computational Biology (ISCB). The organizers hope that you enjoy the program, and find the conference a productive opportunity to meet researchers, students and industrial users of bioinformatics technology.



The Rocky series began nine years ago as a regional conference, and has grown into an international program with a spotlight on regional development in the computational biosciences. The presenters of the Rocky conference are scientists representing a broad spectrum of universities, industrial enterprises, government laboratories, and medical libraries from around the world. 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.

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

Larry Hunter
Rocky 2011 Conference Chair

Rocky 2010 Comments

9th Annual Rocky Mountain Bioinformatics Conference

Registration

• Online registration - Online registration is now closed. Onsite registration will be available starting at 11:00 am on Thursday, December 8.
  
  
• Registration forms
  (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.. )
  • Word
  • .pdf

9th Annual Rocky Mountain Bioinformatics Conference

Key Dates

Updated Sept. 19 2011

9th Annual Rocky Mountain Bioinformatics Conference

Sponsors

Updated November 15, 2011

PLATINUM SPONSOR:

IBM’s Deep Computing organization is the high performance computing organization in IBM Systems and Technology Group. This group is responsible for the strategy, marketing and identification of areas that can benefit from IBM's high end technology. The life sciences is such an area, and IBM is and will continue to bring valued solutions to life sciences.

IBM's Research Division is a partner with IBM’s Deep Computing organization, developing the next generation of high performance computers. In addition, the Research Division has many groups investigating numerous application areas in collaboration with IBM's customers and partners. This includes IBM’s Computational Biology Center with IBM’s new Computational Science Center.

GOLD SPONSORS:



NEC Corporation (TSE: 6701) is one of the world's leading providers of Internet, broadband network and enterprise business solutions dedicated to meeting the specialized needs of its diverse and global base of customers.

NEC delivers tailored solutions in the key fields of computer, networking and electron devices, by integrating its technical strengths in IT and Networks, and by providing advanced semiconductor solutions through NEC Electronics Corporation. The NEC Group employs more than 140,000 people worldwide. For additional information, please visit the NEC home page at: www.nec.com.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

SomaLogic, Inc. is a privately-held biomarker discovery and clinical proteomics company based in Boulder, Colorado. The company's mission is to use its proprietary Slow-Offrate Modified Aptamer ("SOMAmer") technology to develop enhanced protein analysis tools and reagents for the life sciences community, to facilitate target validation, and to develop and commercialize clinical diagnostic products that will improve the delivery of healthcare by offering timely and accurate diagnostic information to physicians and their patients. Further information about SomaLogic can be found at www.somalogic.com.

SILVER SPONSOR:

Biodesix is a personalized medicine company focused on the development of diagnostic products that inform treatment decisions and improve patient care. The Company’s goal is to give physicians more information about the patient and their disease; understanding the clinically meaningful information contained within each patient's molecular profile leads to better care and better outcomes. The Company’s unique approach is based on ProTS®, proprietary technology which exploits the power of mass spectrometry and enables the discovery of specific molecular profiles. Biodesix collaborates with clinical investigators to address critical clinical questions, and partners with biotechnology and pharmaceutical companies to develop diagnostics to select patients most likely to benefit from novel therapies. For more information about Biodesix, please visit www.Biodesix.com.

Books as Student Prizes:

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9th Annual Rocky Mountain Bioinformatics Conference

Location & Travel

Go directly to: Driving Directions | Ground Transportation | Airline Information | Other

TIPS FOR TRAVELING AT HIGH ALTITUDE
Aspen/Snowmass are 9,100 feet above sea level and Altitude sickness is something that visitors to Colorado commonly experience. Read tips for helping ease altitude sickness.
www.altituderesearch.org/traveling-to-altitude

NOTE: Independence Pass is closed in December, please do not attempt to drive through Leadville

From Denver & Eagle Airports and all points east of Aspen:

1. Take I-70 west to Glenwood Springs.
2. Take Exit 116 at Glenwood Springs, follow the signs for Hwy. 82 (right at 1st traffic light, right again at 2nd traffic light, onto Grand Ave./Hwy. 82, crossing bridge over Colorado River), toward Aspen.
3. Follow Hwy. 82 for approximately 38 miles. DO NOT turn at the first sign for Snowmass (note mileage); this will take you to "Old Snowmass." Follow the signs for Snowmass Village/Snowmass Ski Area.
4. Turn right onto Brush Creek Road at the traffic light, following signs toward Snowmass Village/Snowmass Ski Area.
5. Follow Brush Creek Road for approximately 6 miles.
6. In Snowmass Village you will pass a Conoco gas station on your right. Continue straight up the hill. At the top of the hill the road forks. Stay on Brush Creek Road, to the left, following the arrow on the "To Upper Village" sign.
7. Take the next right turn onto Upper Snowmelt Road.
8. Take the next left onto Elbert Lane. Continue to the end of the street to The Silvertree Hotel.

Directions From Colorado Springs:

1. Take I-25 North from Colorado Springs about 70 miles
   to Exit 194 (C470 West)
2. Take C470 West to I-70 West
3. Go to Step 1 (above) under "From Denver & Eagle Airports and all
   points east of Aspen:"

Map of Aspen

Map of the United States

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(877) 277-3690 or (970) 544-2057

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AIRLINE INFORMATION
If traveling by air to the conference, you have three options.

1. Fly to Denver and drive to Aspen/Snowmass (approx. 220 miles). -
   http://flydenver.com for airport/airline information and ground
   transportation options.
2. Fly directly to Aspen/Snowmass Airport - www.flyaspensnowmass.com
3. Fly to Eagle/Vail airport and drive to Aspen/Snowmass (approx. 55 miles)
   - http://flyvail.com for airport/airline information, ground transportation
   options and driving directions to Snowmass.

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Other helpful information.
Silvertree Hotel - Hotel transportation is provided complimentary to the Silvertree Hotel (conference hotel) from the Aspen/Pitkin County Airport. Advance reservations for the shuttle are not required, a telephone is available at the airport to request shuttle service.

Silvertree Hotel : www.silvertreehotel.com
Travel Information: www.flyaspensnowmass.com
Colorado Tourism: www.colorado.com

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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

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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