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8th Annual Rocky Mountain Bioinformatics Conference

Keynote Speakers

Updated Nov. 16, 2010
Thomas C. Bishop, PhD
Center for Computational Science
Tulane University

Title: Interactive Chromatin Modeling: Towards a Computational Karyotype.

CV: http://dna.ccs.tulane.edu/background.html

Abstract: Given a set of nucleosome positions, either from experiment or theory, it is possible to construct in near real time and interactively display 3D models of entire chromosomes at base pair resolution. These models are a first order approximation that assumes each nucleosome is a canonical octasome and that the linker DNA assumes a sequence specific conformation similar to free DNA. Our model allows thermal fluctuations in the nucleosome wrapping (i.e. entry/exit angle) and linker conformation to be introduced. Our current model is likely not an accurate representation of chromatin, but it provides critical insights, such as: properly scaled distance metrics, an indication of how intrinsic bends or other deformations in linker DNA may alter chromatin structure, identification of potential nucleation sites for the folding of DNA into chromatin, the effects of thermal fluctuations, and identification of nucleosome positions that are sterically excluded. Based on available nucleosome positioning data, a computational karyotopye of the sixteen chromosomes in the yeast genome is presented. A web based version of these tools capable of folding and displaying kilobase segments of DNA into chromatin in real time is available at http://dna.ccs.tulane.edu/icm.


Sol Efroni, PhD
Bar Ilan University
Ramat Gan, Israel

CV: http://systemsbiomed.org/sol/

Title:
Network as Biomarker for Ovarian Cancer Prognosis

Abstract: Ovarian cancer causes more deaths than any other gynecologic cancer. As the research community continues to invest extensive efforts in identifying disease etiology, with a current multicenter effort in the form of The Cancer Genome Atlas.

We have used the molecular charachteristics - genomic and epigenomic information from more than 200 women, combined with clinical features, to identify molecular networks most affiliated with prognosis. By quantifying network modifications, we measure the complex, combined, co-dependent behavior of network genes in a manner that is both extremely significant in its affiliation with phenotype, and is highly robust - enough to be able to significantly stratify prognosis in other, independent, datasets.

We show how gene components of the network themselves do not serve as efficient prognostic biomarkers. Only a combined, co-dependent behavior may serve as a biomarker. By affiliating processes' description (signaling pathways) with specific phenotype, we expose these process to further study and specific intervention.

Larry Gold, MD, PhD
CEO and Chairman of the Board, SomaLogic, Inc.
Professor, University of Colorado, Boulder

CV: .pdf

Title:
Thinking, Measuring, Calculating, and Diagnosing: From Platform to New Ideas about Biology

Abstract: Biology makes no sense to a person of logic, the very people filling the seats at this conference. Biology evolved over a very long time, under conditions that changed from time to time, making reverse engineering difficult. Mathematics is logical, even to me, and thus mathematicians can analyze and calculate beautifully, using awful data as their input (a common problem). It is easier to reverse engineer car bumpers than human biology.

We thought for a long time about what inputs should be the basis for deep thinking. Unlike everyone else (or nearly everyone), we decided almost 15 years ago that phenotype was better than genotype, in spite of the power of DNA sequencing technology. During those 15 years, while our colleagues decreed Personalized Medicine to be the study of genotypes, we worked to find an unbiased measurement of molecular phenotype. The platform we developed was broad proteomics, on a scale not possible through any other methodology.

For the scientists at SomaLogic the thrill has been overcoming difficult scientific challenges. For people at this conference the thrill will be to access data that may be logical, or at least coherent. I will provide examples of proteomic similarities among people (and tumors) with broad genotypic differences. The vast dimensionality of genomics can be reduced through proteomics, resulting in (perhaps) insights about human biology.

Shawn Gomez, PhD
University of NC-Chapel Hill

CV: www.bme.unc.edu/index.php/directory/userprofile/smgomez

Title: New Approaches for Comparing Biological Trees and Networks

Abstract: Representation of biological relationships in the form of trees or networks is a core aspect of numerous biological analyses. Continued progress in this area requires improvements in how we can analyze, compare and compute information on these graphs.

We have recently developed a set of related computational methods for the representation and comparison of these trees/networks. The approaches are based on the alignment of representative high-dimensional embeddings or structures that provide the ability to measure global similarity, as well as differences, between graphs. Most recently, we have developed a generalized spectral algorithm for the comparison of weighted graphs. Unlike other methods, this approach takes into account edge information that is often available and may be of significant importance in improving prediction accuracy. We have applied these approaches to problems in phylogenetic tree comparison including the detection of horizontal gene transfer events and the identification protein interaction specificity in coevolving multigene families. Together, these approaches provide a useful set of tools for future application in the analysis of these increasingly common high-dimensional data sets. Finally, such methods have broader applications in computer vision, image analysis and computational chemistry.

Carsten Görg, PhD
University of Colorado School of Medicine

CV: http://compbio.ucdenver.edu/goerg/

Title:
Supporting Research and Analysis Across the Biomedical Literature Using Visual Analytics

Abstract:
Visual Analytics is an emerging academic discipline. It has been defined as "the science of analytical reasoning facilitated by interactive visualizations" and aims at supporting people to analyze and understand data through the help of computer visualizations, and ultimately make decisions based on that analysis and understanding. Visual analytics includes three main components: (1) computational techniques and algorithms for data manipulation, transformation, and analysis; (2) interactive visualizations and user interfaces to present the data; and (3) an analytical reasoning component for understanding how people think, reason, and come to conclusions, in order to design software that best leverages those abilities.

We have developed a visual analytics system, named Bio-Jigsaw, to support biologists in the challenging task of finding relevant publications in the large and rapidly growing body of biomedical literature. Search queries on PubMed often return thousands of publications and it can be tedious to filter out irrelevant publications and choose a manageable set to read. Bio-Jigsaw acts like a visual index on a document collection and supports biologists in investigating and understanding connections between biological entities. We apply natural language processing techniques to identify biological entities such as genes and pathways and visualize connections among them via multiple representations. Connections are based on co-occurrence in abstracts and also are drawn from ontologies or annotations in digital libraries. Bio-Jigsaw's interactive visual representations help biologists more rapidly explore and understand connections between biological entities and find relevant publications to read.

Kirk E. Jordan, PhD
Emerging Solutions Executive & Associate Program Director
Computational Science
IBM T.J. Watson Research

CV:
https://researcher.ibm.com/researcher/view.php?person=us-kjordan

Title: Data and Analytics Transforming Healthcare for Smarter Healthcare & Life Science

Abstract: In the life sciences and healthcare area there is a wealth of data.  Yet, we need to make sense of this deluge of data.  This is being done through what is currently termed analytics.  In this talk, I will describe some of the areas that IBM is working to transform healthcare and life sciences through the use of analytics and information technology including high performance computing (HPC) systems infrastructure.  While I will describe some projects underway in these areas, I will also comment that to truly take full advantage of HPC to accelerate the healthcare and life science transformation, we need to make access easier.  I will describe work being done to make HPC accessible to a wide audience and eventually targeting the healthcare and life science practitioner directly. 


[Top]

8th Annual Rocky Mountain Bioinformatics Conference

Call for Presentations

Please check back for updates.

8th Annual Rocky Mountain Bioinformatics Conference

Poster Presenters & Abstracts

Updated Nov. 21, 2010

PDF listing of the Poster Presenters and Abstracts  - Click here


Listed in alphabetical order by presenter's last name:

Towards a Cytokine-Cell Interaction Knowledgebase of the Immune System

Presenter: Asa Adadey, University of Maryland Baltimore County
Authors: Adadey Asa, Shen-Orr Shai, Perry Nick, Davis Mark, Butte Atul

A Novel Algorithm for Finding Prophages in Microbial Genomes that Combines Similarity-Based and Composition-Based Strategies
Presenter: Sajia Akhter, San Diego State University
Authors: Sajia Akhter, Ramy Aziz, Robert Edwards

Integrating the HyperGlossary with a Question Answering System
Presenter: Michael Bauer, University of Arkansas Little Rock
Authors: Michael Bauer, Robert Belford, Roger Hall, Daniel Berleant

Comparative Ontological and Network Analysis of Aging Associated Genes in Humans and Model Organisms
Presenter: Ari Berman, Buck Institute for Age Research
Authors: Ari Berman, Tobias Wittkop, Emily Howe, Sean Mooney

Bioinformatic Elucidation of Consensus Phosphorylation Motifs Utilizing Inter-Species Functional Data

Presenter: Leethaniel Brumfield, NC State University
Authors: Leethaniel Brumfield

eQTL Analysis in Diabetic Nephropathy for Candidate Gene Discovery
Presenter: Allison Burlock, University of Michigan
Authors: Allison Burlock, Benjamin Keller, Matthias Kretzler

Role of Viruses in the Oxygen Minimum Zone off Chile: A Metagenomic Approach
Presenter: Noriko Cassman, San Diego State University
Authors: Noriko Cassman, Alejandra Prieto-Davo, Julia Busch, Forest Rohwer, Osvaldo Ulloa, Gadiel Alarcon, Elizabeth Dinsdale

Pangenome-based Taxonomy
Presenter: Nicholas Celms, San Diego State University
Authors: Nicholas Celms, James Nulton, Peter Salamon, Robert Edwards

Mapping International Protein Index/UniprotKB To Affymetrix Probe-set Identifier(s) To Facilitate Biomarker Identification In Multiple Myeloma
Presenter: Shweta Chavan, University of Arkansas Little Rock
Authors: Shweta Chavan, John Shaughnessy Jr., Bart Barlogie, Ricky Edmondson

Blood Systems Biology for Multiscale Modeling of Heart Attacks
Presenter: Scott Diamond, University of Pennsylvania
Authors: Scott Diamond, Manash Chatterjee, Matt Flamm

Comparative Analysis of the Fractions of Secreted Proteins Encoded by Bacterial Genomes
Presenter: Yasmine Elshakry, San Diego State University and Cairo University
Authors: Ahmed Mahmoud, Yasmine Elshakry, Ramy Aziz

Adaptive Learning Neural Networks for Binding Site Search in Genomic Sequences
Presenter: Ivan Erill, University of Maryland Baltimore
Authors: Joseph Cornish, Sumeet Bagde, Elisabeth Hobbs, Ivan Erill

Comparison of Codon Usage Indices as Predictors of Gene Expression in Mutationally Biased Genomes
Presenter: Ivan Erill, University of Maryland Baltimore
Authors: Mindy Or, Isaac Jensen, Ivan Erill

Predicting Flexibility in Protein Structures
Presenter: Elizabeth Eskow, University of Colorado, Boulder
Authors: Elizabeth Eskow, Asa Ben-Hur, Hubert Yin, Debra Goldberg, Deanne Sammond

Comparative Analysis of Apicomplexan Biological Processes
Presenter: Segun Fatumo, Center for Tropical & Emerging Global Diseases
Authors: Segun Fatumo, Jessica Kissinger

CategoryCompare: High-throughput Data Meta-analysis using Gene Annotations
Presenter: Robert Flight, University of Louisville
Authors: Robert Flight, Jeffrey Petruska, Benjamin Harrison, Eric Rouchka

Building a High-Density, High-Throughput Scalable Genotype Storage and Computing Framework for use in Livestock Genomic Research
Presenter: Fernanda Foertter, Genus plc
Authors: Fernanda Foertter, Matthew Cleveland, Selma Forni, Nader Deeb, Nan Yu, Scott Newman, Chad Cropper

UPIC + GO: Zeroing in on Informative Markers
Presenter: Dorarean Ford, Mississippi Valley State University
Authors: Dorarean Ford, Renee Arias, Linda Ballard, Brian Scheffler, Mary Duke, Sheron Simpson, Abigail Newsome

Bringing Computation into AP Biology Classes
Presenter: Suzanne Gallagher, University of Colorado
Authors: Suzanne Gallagher, Debra Goldberg

Elastin Polymorphisms Associated with Increased Risk of Cardiovascular Disease
Presenter: Mahboubeh Ghoryshi, University of Toronto
Authors: M Ghoryshi, D He, S Lemaire, D Milewicz, F Keeley, J Parkinson

Interaction Sites in Models of Protein Interaction Network Evolution
Presenter: Todd Gibson, University of Colorado Denver
Authors: Todd Gibson, Debra Goldberg

Quantifying Focal Adhesion Spatiotemporal Dynamics Through Computational Image Analysis
Presenter: Shawn Gomez, University of NC-Chapel Hill
Authors: Matthew Berginski, Eric Vitriol, Klaus Hahn, Shawn Gomez

Detecting Genome-wide Copy Number Variations in a Single Sample Using Next Generation Sequencing Data
Presenter: Rajesh Gottimukkala, Life Technologies
Authors: Rajesh Gottimukkala, Fiona Hyland, Somalee Datta, Asim Siddiqui, Ryan Koehler, Yutao Fu

Internal Duplications in A-helical Membrane Protein Topologies are Common but the Nonduplicated Forms are Rare
Presenter: Aron Hennerdal, Stockholm Center for Biomembrane Research
Authors: Aron Hennerdal, Jenny Falk, Erik Lindahl, Arne Elofsson

Investigating the Potential of Viral Procapsids in Metabolic Channeling
Presenter: Kris Hon, University of Toronto, Department of Biochemistry
Authors: Kris Hon, Diane Bona, Alan Davidson, Karen Maxwell, John Parkinson

mRNA-SEQ Workflow at Mayo Clinic
Presenter: Asif Hossain, Mayo Clinic
Authors: Asif Hossain, Yan Asmann, Sumit Middha, Saurabh Baheti, Zhifu Sun, High-Seng Chai, Xiao-Yu Liu, Ying Li, Asha Nair, Eric Klee and Jean-Pierre Kocher

Cytoscape Plugin for Highly Connected Subgraphs
Presenter: Daniel Houck, University of Colorado at Boulder
Authors: Daniel Houck, Suzanne Gallagher, Debra Goldberg

STOP Using Just GO: A Multi-Ontology Enrichment Analysis Tool For Genes and Proteins
Presenter: Emily Howe, The Buck Institute
Authors: Emily Howe, Uday Evani, Mathew Fleish, Nigam Shah, and Sean Mooney

Early Detection and Dynamics of Rare Viral Variants by Ultradeep Sequencing
Presenter: Peter Hraber, Los Alamos National Lab
Authors: Peter Hraber, Will Fischer, Elena Giorgi, Thomas Leitner, Tanmoy Bhattacharya, Bette Korber

Structure Alignment of Proteins with Low Sequence Identity Based on Encoded Local Structure Alphabets
Presenter: Kenneth Hung, Institute of Biomedical Engineering, National Taiwan University
Authors: Kenneth Hung, Jui-Chih Wang, Cheng-Wei Chen, Cheng-Long Chuang, Kun-Nan Tsai, Chung-Ming Chen

Molecular Basis for Inhibition of Active Carboxyltransferase Domain of Acetyl CoA-Carboxylase by Hydroxy Citric Acid to Prevent Obesity
Presenter: Hitesh Jaiswal, Jaypee Institute of Information
Authors: Hitesh Jaiswal, Kamal Rawal

Investigating Relationships between Obesity and the Built Environment Using Agent-Based Modeling
Presenter: Helmet Karim, University of Pittsburgh
Authors: Helmet Karim, Leming Zhou

Providing Context to Genetic Associations with Gene Expression in Renal Disease
Presenter: Benjamin Keller, Eastern Michigan University
Authors: Benjamin Keller, Sebastian Martini, Matthias Kretzler

Algorithm for Phylogenetic Tree Building and Taxonomic Classification using Curated Phylogenetic Tree
Presenter: David Knox, University of Colorado Anschutz
Authors: David Knox, Robin Dowell

Detecting Case-Specific Key-Pathways using OMICS Expression Data
Presenter: Hande Kucuk, Max Planck Institute
Authors: Hande Kucuk, Nicolas Millman, Mayank Kumar, Jan Baumbach

Phylogenetic Analysis and Structure-Function Relationships in the Oxacillinase Enzyme Family
Presenter: Kimberly Lesnock, Pittsburgh Supercomputing Center
Authors: Kimberly Lesnock, Brian Chen, Agnieszka Szarecka, Troy Wymore

Re-Sequencing Workflow at Mayo Clinic
Presenter: Ying Li, Mayo Clinic
Authors: Ying Li, Yan Asmann, Sumit Middha, Asif Hossain, High Seng Chai, Asha Nair, Saurabh Baheti, and Jean-Perrier Kocher

Modeling Gene-Species Data by Generalized Replicator Dynamics for Efficient Phylogenetic Inference
Presenter: Ying Liu, University of North Texas at Dallas
Authors: Ying Liu

Cancer Gene Expression Data is Not Normally Distributed: Analysis of Data Distributions and their Effects on Gene Selection and Molecular Classification
Presenter: Nicholas Marko, Cleveland Clinic Department of Neurosurgery
Authors: Nicholas Marko, Robert Weil

Artificial Neural Network Approach for Promoter Prediction in Prokaryotic Organisms Based on Structural Properties of DNA
Presenter: Aleksandra Markovets, University of Arkansas at Little Rock
Authors: Aleksandra Markovets, Abigail Newsome, Charles Bland

Modelling Gene Expression in Tumor Progression Using Binary States
Presenter: Juan Emmanuel Martinez-Ledesma, ITESM Campus Monterrey
Authors: Emmanuel Martinez-Ledesma, Victor Trevino

Functional Regulatory Circuits Induced by Transcription Factors and Small RNAs
Presenter: Molly Megraw, Duke University
Authors: Molly Megraw, Uwe Ohler

Large Scale Analysis of the Solvation Properties of Folded Proteins

Presenter: Marcelo Melo, UFRJ
Authors: Marcelo Melo, Pedro Pascutti

Inhibition of Myeloperoxidase by Chloroquine a Possible Agent for Anti-inflammatory Action
Presenter: Joseph Minari, Joseph Ayo Babalola University
Authors: Bukoye Oloyede, Adewale Odutuga,Joseph Minari

A Cross Species Identification of Shared Transcriptional Network of Diabetic Nephropathy
Presenter: Viji Nair, University of Michigan
Authors: Viji Nair , Jeffrey B. Hodgin, Hongyu Zhang, Ann Randolph, Raymond C. Harris, Robert G. Nelson, Frank C. Brosius,Matthias Kretzler

Radiant: Interactive Visualization of Taxonomic Abundance
Presenter: Brian Ondov, National Biodefense Analysis & Countermeasures Center
Authors: Brian Ondov, Adam Phillippy, Nicholas Bergman

Topiary Explorer

Presenter: Megan Pirrung, University of Colorado
Authors: Megan Pirrung, Ryan Kennedy, Rob Knight

Insilico Vaccine Design for Campylobacteriosis using Reverse Vaccinology
Presenter: Utkarsh Raj, Amity University
Authors: Utkarsh Saxena

Discovery of New Ligands for PPAR Gamma Based on Thiazolidine-4-one: Virtual Screening, Molecular Docking and Receptor Binding Study
Presenter: Sujatha Ramasamy, Sathyabama University
Authors: S. Ramasamy, U. Raj, A. Srivastava, R. Bhavsar, C. Lokesh, D. Tripathi, S.A.H Naqvi

Bioinformatic and Computational Characterization of Orf6: A Putative Thioesterase
Presenter: Maria Rodriguez-Guilbe, Department of Biochemistry, University of Puerto Rico School of Medicine
Authors: Maria Rodriguez-Guilbe, Ricardo Gonzalez-Mendez Troy Wymore, Eric Schreiter, Abel Baerga

SpliceGrapher: Predicting Splice Graphs from Diverse Evidence
Presenter: Mark Rogers, Colorado State University
Authors: Mark Rogers, Asa Ben-Hur, Anireddy Reddy

A Support Vector Classifier for Korarchaeota Containing Hot Springs
Presenter: Christian Ross, The University of Nevada Las Vegas
Authors: Christian Ross, Brian Hedlund

Evolution of Protein Structure in Metapneumovirus
Presenter: Sunando Roy, Pennsylvania State University
Authors: Sunando Roy, Abinash Padhi, Francesca Chiaromonte, Mary Poss

HIVToolbox, An Integrated Web Application and Database for Investigating HIV
Presenter: David Sargeant, University of Nevada Las Vegas
Authors: David Sargeant, Sandeep Deverasetty, Yang Luo, Angel Villahoz-Baleta, Stephanie Zobrist, Viraj Rathnayake, Jacqueline Russo, Jay Vyas, Mark Muesing, Martin Schiller

Molecular Modeling and Docking Studies of Some Novel Derivatives of N-phenyl-2-(pyrimidin-2-ylsulfanyl) Acetamide as Anti SARS Protease Inhibitors
Presenter: Gyana Satpathy, National Institute of Technology
Authors: Gyana Satpathy, B. Jabes, S Murugesan, Sripad Patnaik

Molecular Dynamics Simulations of Sequentially Varied Human Immunodeficiency Virus-1 Tat Consensus Protein Structures
Presenter: Gyana Satpathy, National Institute of Technology
Authors: Gyana Satpathy, Sripad Patnaik

PRINSEQ, TagCleaner and DeconSeq - Tools for Quality Control and Pre-processing of Metagenomic Datasets
Presenter: Robert Schmieder, San Diego State University
Authors: Robert Schmieder, Robert Edwards

In Silico Inference of Immunological Relationships Between Proteins Based on their Cytotoxic T-Lympthocyte Epitope Repertoires
Presenter: Werner Smidt, University of Pretoria
Authors: Werner Smidt

Characterizing Apicomplexan Parasite Metabolism by Flux Balance Analysis of Toxoplasma Gondii
Presenter: Carl Song, University of Toronto
Authors: Carl Song, Stacy Hung, John Parkinson

Simple Local Assembly Program
Presenter: Adam Spargo, Wellcome Trust Sanger Institute
Authors: Adam Spargo, Zemin Ning

The Nature of Genomes Clusterization by Detrended Fluctuation Analysis
Presenter: Yan Stirmanov, Lomonosov Moscow State University
Authors: Yan Viktorovich Stirmanov

Comparing Genomes Using the Profiles Package in R
Presenter: Chris Stubben, Los Alamos National Lab
Authors: Chris Stubben, Murray Wolinsky

Enriching Regulatory Networks with Other Functional Relationships
Presenter: Ronald Taylor, Pacific Northwest National Laboratory
Authors: Ronald Taylor, Antonio Sanfilippo, Jason McDermott, Bob Baddeley, Rick Riensche, Russ Jenson, Marc Verhagen

Fun and Games with RDF - Moving Rat Data on to the Semantic Web
Presenter: Simon Twigger, Medical College of Wisconsin
Authors: Simon Twigger, Joey Geiger, Jennifer Smith

Closing the Gap in Time: From Raw Data to Real Science (Science as a Service - ScaaS)
Presenter: Anjana Varadarajan, EdgeBio
Authors: Anjana Varadarajan, Angelo Scorpio, David DeShazer

Validation of Protein Functional Site Predictions Using Automated Biomedical Literature Analysis
Presenter: Karin Verspoor, University of Colorado Denver
Authors: Karin Verspoor, Judith Cohn, Christophe Roeder, Michael Wall

Improving the Accuracy of Coevolution-Based Methods to Predict Protein-Protein Interactions
Presenter: Guisong Wang, University of Maryland Baltimore County
Authors: Guisong Wang, Mileidy Gonzalez, Maricel Kann

Fold Recognition and Alignment for Transmembrane Proteins
Presenter: Han Wang, University of Missouri
Authors: Han Wang

Concepts at Play in Scientific Argumentation
Presenter: Elizabeth White, University of Colorado, Denver
Authors: Elizabeth White, Lawrence Hunter

DEFOG - Discrete Enrichment of Functionally Organized Genes
Presenter: Tobias Wittkop, Buck Institute for Age Research
Authors: Tobias Wittkop, Ari Berman, Sean Mooney

Extracting Adverse Drug Reactions from User Posts to Health-Related Social Networks
Presenter: Laura Wojtulewicz, Arizona State University
Authors: Robert Leaman, Laura Wojtulewicz, Ryan Sullivan, Annie Skariah, Jian Yang, Graciela Gonzalez

Finding Community Leaders in Social Networks
Presenter: Xiaowei Xu, University of Arkansas at Little Rock
Authors: Xiaowei Xu

Integrative Network Analysis to Predict Endocrine Resistance in Breast Cancer
Presenter: Jason Xuan, Virginia Tech
Authors: Jianhua Xuan, Li Chen, Chen Wang, Yue Wang, Rebecca B. Riggins, Robert Clarke

Purification of Bacterial Apoa-1 and Characterization of Novel Anticancer Drug Delivery System
Presenter: Thurman Young, North Carolina State University
Authors: Thurman Young, Andras Lacko

[Top]

 

 

8th Annual Rocky Mountain Bioinformatics Conference

Poster Session

Updated July 12, 2010

General Information:

  • Posters will be available for viewing on Friday evening, December 10 and Saturday morning, December 11. There are two scheduled poster sessions: Friday, December 10 from 5:45 pm to 8:00pm and Saturday, December 11 from 10:35am-12noon. Poster Presenters should be available for presentation during the scheduled poster sessions.
  • There will be no pre-assigned poster boards, please place your poster on any available boards in the poster session room.
  • The poster board dimensions are 4 feet high x 4 feet wide. Tacks will be provided
    for securing your poster to the board.

Schedule:

Day/Date Time Activity/Location
Thursday:
December 9, 2010
3:00pm – 6:00pm SET UP POSTERS
(Maximum size 4 feet high
x 4 feet wide)
Snowmass Conference Center (across street from Silvertree) Sinclair Room
Friday:
December 10, 2010
9:00am – 12:00pm SET UP POSTERS
(Maximum size 4 feet high
x 4 feet wide)
Snowmass Conference Center (across street from Silvertree) Sinclair Room
Friday:
December 10, 2010
12:00pm – 5:45pm POSTER VIEWING
(no authors present)
Snowmass Conference Center (across street from Silvertree) Sinclair Room
Friday:
December 10, 2010
5:45 pm - 8:00 pm POSTER SESSION
(author present)
Snowmass Conference Center (across street from Silvertree) Sinclair Room
Saturday:
December 11, 2010
10:35 am - 12:00 pm POSTER SESSION
(authors present)
Snowmass Conference Center (across street from Silvertree) Sinclair Room
Saturday:
December 11, 2010
12:00pm REMOVE POSTERS (all posters must be removed so room can be used for 4:00pm event)


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

8th 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
This email address is being protected from spambots. You need JavaScript enabled to view it.

8th Annual Rocky Mountain Bioinformatics Conference

Sponsors

Updated Nov. 23, 2010

PLATINUM SPONSOR:





GOLD SPONSOR:



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.


SPONSOR:


Ion Torrent has pioneered an entirely new approach to sequencing that enables a direct connection between chemical and digital information. Ion Torrent™ technology doesn't use light—it's the first commercial PostLight™ sequencing technology.

Instead, Ion Torrent marries simple chemistry to incredibly powerful, proprietary semiconductor technology—it's Watson meets Moore. The result is a sequencing system that is simpler, faster, more cost effective and scalable than any other technology available. The company's goal is to democratize sequencing and make this critical technology available to every lab.

Ion Torrent sequencing technology requires no proprietary chemistries or optics because it's based on a well-characterized biochemical process. When a nucleotide is incorporated into a strand of DNA by a polymerase, a hydrogen ion is released as a byproduct. That hydrogen ion carries a charge which our proprietary ion sensor can detect. If a nucleotide, for example a C, is added to a DNA template and a signal is detected, you know that nucleotide was incorporated. Our sequencer—essentially the world's smallest solid-state pH meter—has called the base, going directly from chemical information to digital information. Because this is direct detection, each nucleotide incorporation is recorded in seconds and you can do an entire run in about an hour.

The semiconductor has transformed every industry it's touched. Just as the microprocessor enabled desktop computing to displace the mainframe, Ion Torrent semiconductor technology will inevitably democratize sequencing, putting it within the reach of any lab or clinic.


8th Annual Rocky Mountain Bioinformatics Conference

Full Agenda

Updated Nov. 21, 2010
go directly to: [Friday - December 10] [Saturday - December 11]

Thursday – December 9, 2010
11:00 am – 1:00 pm Registration
1:00 pm – 1:45 pm Keynote 1
Network as Biomarker for Ovarian Cancer Prognosis

Sol Efroni, PhD
Bar Ilan University, Ramat Gan, Israel
1:45 pm – 1:55 pm Oral Presentation 1
Fun and Games with RDF - Moving Rat Data on to the Semantic Web
Presenter:
Simon Twigger, Medical College of Wisconsin
Authors:
Simon Twigger, Joey Geiger, Jennifer Smith
1:55 pm – 2:05 pm Oral Presentation 2
Full-Text Biomedical Literature Processing: More than a Scaling Challenge

Presenter:
Christophe Roeder, University of Colorado, Denver
Authors:
Christophe Roeder, Tom Christiansen, Helen Johnson, Karin Verspoor, Gully Burns, Lawrence Hunter
2:05 pm – 2:15 pm Oral Presentation 3
PhiRAST: A Pipeline for Rapid Annotation of Phage Genomes Using Subsystems Technology

Presenter: Ramy Aziz, San Diego State University
Authors:
Robert Olson, Ross Overbeek, Gordon D. Pusch, the PhAnToMe team*, and Robert A. Edwards
2:15 pm – 2:25 pm Oral Presentation 4
Polbase: A Repository of Biochemical, Genetic, and Structural Information about DNA Polymerases
Presenter:
Bradley Langhorst, New England Biolabs
Authors:
Bradley Langhorst, Nicole Nichols
2:25 pm – 2:35 pm Oral Presentation 5
ORO Miner, An Application for Investigating Cell Communication in Multicellular Organisms
Presenter:
Michael Rogers, University of Nevada Las Vegas
Authors:
Prashant Singh, Michael Rogers, Patrick Gradie, Rinu Thomas, Dharmistha Kaul, Brandon Roe, Shruti Patel, Briana Sugihara, Narineh Abadian, Michael Gryk, Martin Schiller
2:35 pm – 2:45 pm Oral Presentation 6
Early Detection and Dynamics of Rare Viral Variants by Ultradeep Sequencing
Presenter: Peter Hraber, Los Alamos National Lab
Authors:
Peter Hraber, Will Fischer, Elena Giorgi, Thomas Leitner, Tanmoy Bhattacharya, Bette Korber
2:45 pm – 3:00 pm Break (15 minutes)
3:00 pm – 3:10 pm Oral Presentation 7
A Process for Unifying Sources of Biomedical Information in an RDF-based Knowledge Base
Presenter:
Kevin Livingston, University of Colorado Denver
Authors:
Kevin Livingston, Michael Bada, Lawrence Hunter
3:10 pm – 3:20 pm Oral Presentation 8
Testing for Joint Association of All SNP Pairs
Presenter:
Ronald Schuyler, University of Colorado
Authors:
Ronald Schuyler, Lawrence Hunter
3:20 pm – 3:30 pm Oral Presentation 9
Cognitive Task Flows and Visual Analytics
Presenter:
Barbara Mirel, University of Michigan
Authors:
Barbara Mirel, Felix Eichinger
3:30 pm – 3:40 pm Oral Presentation 10
CategoryCompare: High-throughput Data Meta-analysis using Gene Annotations
Presenter:
Robert Flight, University of Louisville
Authors:
Robert Flight, Jeffrey Petruska, Benjamin Harrison,
Eric Rouchk
3:40 pm – 3:50 pm Oral Presentation 11
Pairwise Agonist Scanning Predicts Cellular Signaling Responses to Combinatorial Stimuli
Presenter: Scott Diamond, University of Pennsylvania
Authors:
Scott Diamond, Manash Chatterjee
3:50 pm – 4:00 pm Oral Presentation 12
A Bayesian Network Framework for Statistical Assessment of the Intent to Stabilize Yersinia Pestis
Presenter:
Bobbie-jo Webb-Robertson, Pacific Northwest National Laboratory
Authors:
Bobbie-Jo Webb-Robertson, Lee Ann McCue, Craig McKinstry, Brian Clowers, Heather Colburn, Christina Sorensen, David Wunschel, Karen Wahl
4:00 pm – 4:10 pm Oral Presentation 13
Identifying Genes in the Drosophila Hh Pathway by Integrating TF Binding and Gene Expression Data
Presenter:
Daniel Dvorkin, University of Colorado Denver
Authors:
Daniel Dvorkin, Brian Biehs, Katerina Kechris
4:10 pm – 4:25 pm Break (15 minutes)
4:25 pm – 5:10 pm Keynote 2
Data and Analytics Transforming Healthcare for Smarter Healthcare & Life Science

Kirk E. Jordan, PhD
Emerging Solutions Executive & Associate Program Director
Computational Science
IBM T.J. Watson Research
5:10 pm – 5:20 pm Oral Presentation 14
Cancer Gene Expression Data is Not Normally Distributed: Analysis of Data Distributions and their Effects on Gene Selection and Molecular Classification
Presenter: Nicholas Marko, Cleveland Clinic Department of Neurosurgery
Authors: Nicholas Marko, Robert Weil
5:20 pm – 5:30 pm Oral Presentation 15
Exploring Machine Learning Classifiers for the Prediction of AGO Bound Transcripts with miRNA Seed Matches
Presenter: Abel Licon, Thermo Fisher Scientific
Authors: Abel Licon, Kevin Sullivan, Amanda Birmingham
5:30 pm – 5:40 pm Oral Presentation 16
SpliceGrapher: Predicting Splice Graphs from Diverse Evidence
Presenter: Mark Rogers, Colorado State University
Authors: Mark Rogers, Asa Ben-Hur, Anireddy Reddy
5:40 pm – 5:50 pm Oral Presentation 17
Plasma Metabolites in the Mammalian Hibernation Cycle
Presenter: Anis Karimpour-fard, University of Colorado Denver
Authors: Anis Karimpour-Fard, L. Elaine Epperson, Lawrence Hunter, Sandra Martin
5:50 pm – 6:00 pm Oral Presentation 18
Detecting Genome-wide Copy Number Variations in a Single Sample Using Next Generation Sequencing Data
Presenter: Rajesh Gottimukkala, Life Technologies
Authors: Rajesh Gottimukkala, Fiona Hyland, Somalee Datta, Asim Siddiqui, Ryan Koehler, Yutao Fu
6:00 pm – 6:10 pm Oral Presentation 19
Interaction Sites in Models of Protein Interaction Network Evolution
Presenter: Todd Gibson, University of Colorado Denver
Authors: Todd Gibson, Debra Goldberg
6:10 pm – 6:20 pm Oral Presentation 20
Investigation of Structural Basis of Oncogenesis Property of GTPase H-Ras Protein: A Molecular Dynamics Simulation Study
Presenter: Gyana Satpathy, National Institute of Technology
Authors: Gyana Satpathy, Raghunath Satpathy, B.P. Nayak
7:00 pm – 9:00 pm Banquet, Thursday, December 9, 2010
7:00 pm - 9:00 pm Banquet
Location: Il Poggio Restaurant, Snowmass Village
go directly to: [Thursday - December 9 ] [Saturday - December 11]

Friday – December 10, 2010
9:00 am – 9:45 am Keynote 3
Interactive Chromatin Modeling: Towards a Computational Karyotype

Thomas C. Bishop, PhD
Center for Computational Science
Tulane University
9:45 am – 9:55 am Oral Presentation 21
Validation of Protein Functional Site Predictions Using Automated Biomedical Literature Analysis
Presenter:
Karin Verspoor, University of Colorado Denver
Authors:
Karin Verspoor, Judith Cohn, Christophe Roeder, Michael Wall
9:55 am – 10:05 am Oral Presentation 22
Modeling Gene-Species Data by Generalized Replicator Dynamics for Efficient Phylogenetic Inference
Presenter: Ying Liu, University of North Texas at Dallas
Authors: Ying Liu
10:05 am – 10:15 am Oral Presentation 23
Comparative Analysis of Apicomplexan Biological Processes
Presenter: Segun Fatumo, Center for Tropical & Emerging Global Diseases
Authors: Segun Fatumo, Jessica Kissinger
10:15 am – 10:25 am Oral Presentation 24
STOP Using Just GO: A Multi-Ontology Enrichment Analysis Tool For Genes and Proteins
Presenter:
Emily Howe, The Buck Institute
Authors:
Emily Howe, Uday Evani, Mathew Fleish, Nigam Shah, and Sean Mooney
10:25 am – 10:35 am Oral Presentation 25
Comparative Ontological and Network Analysis of Aging Associated Genes in Humans and Model Organisms
Presenter: Ari Berman, Buck Institute for Age Research
Authors: Ari Berman, Tobias Wittkop, Emily Howe, Sean Mooney
10:35 am – 10:45 am Oral Presentation 26
Flu and Drugs and Rocky10
Presenter:
Christian Forst, UT Southwestern Medical Center
Authors:
Christian Forst
10:45 am – 11:00 am Break (15 minutes)
11:00 am – 11:10 am Oral Presentation 27
Analysis Workflow of Methylation and Gene Expression microarray in Pediatric Crohn Disease
Presenter: Tzu Lip Phang, University of Colorado Denver
Authors: Tzu Phang, Anna Hunter, Ping Yao Zeng, Theresa Kerbowski, Edwin de Zoeten
11:10 am – 11:20 am Oral Presentation 28
Evolution of Cis-regulatory Elements
Presenter:
Ken Yokoyama, University of Colorado Denver
Authors:
Ken Yokoyama
11:20 am – 11:30 am Oral Presentation 29
More Is Not Always Better. Considerations in the Use of Time Course Microarray Data
Presenter:
Elizabeth Siewert, Colorado School of Public Health
Authors:
Elizabeth Siewert, Katerina Kechris
11:30 am – 11:40 am Oral Presentation 30
Semantic Richness in the Colorado Richly Annotated Full-Text (CRAFT) Corpus
Presenter: Michael Bada, University of Colorado Anschutz Medical Campus
Authors: Michael Bada, Miriam Eckert, Arrick Lanfranchi, William A. Baumgartner, Jr., Colin Warner, Amanda Howard, William Corvey, Nianwen Xue, K. Bretonnel Cohen, Karin Verspoor, Judith A. Blake, Martha Palmer, Lawrence Hunter
11:40 am – 11:50 am Oral Presentation 31
Functional Regulatory Circuits Induced by Transcription Factors and Small RNAs
Presenter: Molly Megraw, Duke University
Authors: Molly Megraw, Uwe Ohler
11:50 am – 12:00 pm Oral Presentation 32
Rapid Comprehensive Selection of Sensitive and Specific Oligonucleotide Signatures from Large Hierarchically Clustered Nucleic Acid Sequence Datasets

Presenter: Harald Meier, Technical University of Munchen
Authors:
Kai Bader, Christian Grothoff, Harald Meier
12:00 pm – 4:00 pm Break
4:00 pm – 4:45 pm Keynote 4
Supporting Research and Analysis Across the Biomedical Literature Using Visual Analytics

Carsten Görg, PhD
University of Colorado School of Medicine
4:45 pm – 4:55 pm Oral Presentation 33
Classifying Parenthesized Material for Text Mining
Presenter: Kevin Bretonnel Cohen
University of Colorado School of Medicine
Authors: K. Bretonnel Cohen, Tom Christiansen, Lawrence Hunter
4:55 pm – 5:05 pm Oral Presentation 34
Towards Integrative Gene Prioritization

Presenter:
Graciela Gonzalez, Arizona State University
Authors:
Jang Lee, Graciela Gonzalez
5:05 pm – 5:15 pm Oral Presentation 35
Towards a Molecular Classification of Kidney Diseases Based on Network Analysis
Presenter: Felix Eichinger, University of Michigan
Authors: Felix Eichinger, Ramakrishna Varadarajan, Jignesh Patel, Matthias Kretzler
5:15 pm – 5:25 pm Oral Presentation 36
Identifying the Dynamic States of the 3D Genome Organization
Presenter: Andrzej Kudlicki, University of Texas
Authors: Dirar Homouz, Gang Chen, Andrzej Kudlicki
5:25 pm – 5:35 pm Oral Presentation 37
Providing Context to Genetic Associations with Gene Expression in Renal Disease
Presenter: Benjamin Keller, Eastern Michigan University
Authors: Benjamin Keller, Sebastian Martini, Matthias Kretzler
5:35 pm – 5:45 pm Oral Presentation 38
Gene and Promoter Discovery Through High-resolution Expression Profiling
Presenter:
Ian Davis, GrassRoots Biotechnology, Inc.
Authors:
Ian Davis
5:45 pm – 8:00 pm Reception and Poster Session
Snowmass Conference Center (across street from Silvertree)
Sinclair Room
go directly to: [Thursday - December 9 ] [Friday - December 10]

Saturday – December 11, 2010
9:00 am – 9:45 am Keynote 5
New Approaches for Comparing Biological Trees and Networks


Shawn Gomez, PhD
University of NC-Chapel Hill
9:45 am – 9:55 am Oral Presentation 39
Using a Low Dimensional Firing Rate Model to Study Interactions in Biophysical Neural Networks
Presenter: Anca Radulescu, University of Colorado at Boulder
Authors: Anca Radulescu
9:55 am – 10:05 am Oral Presentation 40
Investigating Relationships between Obesity and the Built Environment Using Agent-Based Modeling
Presenter: Helmet Karim, University of Pittsburgh
Authors: Helmet Karim, Leming Zhou
10:05 am – 10:15 am Oral Presentation 41
Characterization of Genomic Variability in Clinical Isolates of the Oral Pathogen Aggregatibacter Actinomycetemcomitans
Presenter:
Weerayuth Kittichotirat, University of Washington
Authors:
Weerayuth Kittichotirat, Casey Chen, Roger Bumgarner
10:15 am – 10:25 am Oral Presentation 42
Extracting Adverse Drug Reactions from User Posts to Health-Related Social Networks
Presenter:
Laura Wojtulewicz, Arizona State University
Authors:
Robert Leaman, Laura Wojtulewicz, Ryan Sullivan, Annie Skariah, Jian Yang, Graciela Gonzalez
10:25 am – 10:35 am Oral Presentation 43
Simple Local Assembly Program
Presenter: Adam Spargo, Wellcome Trust Sanger Institute
Authors: Adam Spargo, Zemin Ning
10:35 am – 12:00 pm Poster Session
Snowmass Conference Center (across street from Silvertree)
Sinclair Room
12:00 pm – 4:00 pm Break
4:00 pm – 4:10 pm Oral Presentation 44
Modelling Gene Expression in Tumor Progression Using Binary States

Presenter: Juan Emmanuel Martinez-Ledesma
ITESM Campus Monterrey
Authors: Emmanuel Martinez-Ledesma, Victor Trevino
4:10 pm – 4:20 pm Oral Presentation 45
Finding Community Leaders in Social Networks
Presenter:
Xiaowei Xu, University of Arkansas at Little Rock
Authors:
Xiaowei Xu
4:20 pm – 4:30 pm Oral Presentation 46
Adaptive Learning Neural Networks for Binding Site Search in Genomic Sequences
Presenter:
Ivan Erill, University of Maryland Baltimore
Authors:
Joseph Cornish, Sumeet Bagde, Elisabeth Hobbs, Ivan Erill
4:30 pm – 4:40 pm Oral Presentation 47
Enriching Regulatory Networks with Other Functional Relationships
Presenter:
Ronald Taylor, Pacific Northwest National Laboratory
Authors:
Ronald Taylor, Antonio Sanfilippo, Jason McDermott, Bob Baddeley, Rick Riensche, Russ Jenson, Marc Verhagen
4:40 pm – 4:50 pm Oral Presentation 48
GenoS: Segment-based Representation of Genomics data. Application to Genotyping Data Management
Presenter: Hugues Sicotte, Mayo Clinic
Authors: Jean-Pierre Kocher, Hugues Sicotte, Yaxiong Lin, Eric Klee
4:50 pm – 5:00 pm Oral Presentation 49
Bioinformatics Study of the Ferredoxin-Dependent Bilin Reductase Family
Presenter:
Chanel Mejias-Rosario, Universidad Metropolitana
Authors:
Mejias-Rosario Chanel, Nicholas Jr. Hugh, Ropelewski Alexander, Gonzalez-Mendez Ricardo, Vazquez-Quinones Luis
5:00 pm – 5:45 pm Keynote 6
Thinking, Measuring, Calculating, and Diagnosing: From Platform to New Ideas about Biology

Larry Gold, MD, PhD
CEO and Chairman of the Board, SomaLogic, Inc.
Professor, University of Colorado, Boulder
5:45 pm Rocky '10 Closing Comments

return to: [Thursday - December 9 ] [Friday - December 10]

8th Annual Rocky Mountain Bioinformatics Conference

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