Poster Presenters and Abstracts

Updated December 9, 2009.

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

Listed in alphabetical order by presenter's last name:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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