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

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