Poster Abstracts


Arranged in alphabetical order by last name of first author.

Exploring The Protein Universe From General Principles
L. Apeltsin, T. E. Ferrin

Comparison Of Gene Regulatory Networks Between Fruit Fly And Sea Urchin
J. M. Auer

Machine Learning Approaches On Prediction Of Protein-Protein Interactions And Feature Selection With An Eye To Mutational Analyses
Angshuman Bagchi, Corey Powell, Sean D. Mooney, Matthew Mort, David N. Cooper, Eunseog Youn, Fuxiao Xin, Predrag Radivojac

Comparative Pathway Analysis Of Aging Associated Genes In Humans And Model Organisms
A. E. Berman, T. Wittkop, U. S. Evani, S. D. Mooney

Great.Stanford.Edu: Improved Functional Interpretation Of Cis-Regulatory Regions
D. M. Bristor, C. Y. McLean

Predicting Disease-Related Single Amino Acid Polymorphisms Using Protein Structure
E. Capriotti, R. B. Altman

Mooney Laboratory Web Services And Software
Carson Carlisle, S. D. Mooney

Collabarray: A Storage And Collaboration Utility For Gene Expression-Based Research
C. W. Chen, A. E. Berman, S. D. Mooney

Genome-Wide Mouse Encode Data At UC Santa Cruz
Melilssa Cline, Kate Rosenbloom, Tim Drezer, Brian Raney, Cricket Sloan, Venkat Malladi, Galt Barber, Krishna Roskin, Bernard Suh, Angie Hinrichs, Ann Zwieg, Pauline Fujita, Katrina Learned, Brooke Rhead, Vanessa Swing, Antonio Coehlo, Robern Kuhn, Donna Karolchik, David Haussler, W. James Kent

Berkeley PhOg: Phylogenomic Orthology Prediction, With Applications To Inferring Interactions
Ruchira S. Datta, Kimmen Sjölander

Classification And Identification Of Microbes Using A Mass Spectrometry Proteomic Method (MSPM)
Samir V. Deshpande, Rabih E. Jabbour, Michael Stanford, Charles Wick, Alan Zulich

Computational Translation Is The Translation Of What?: Philosophy, Computation, And The Biologically Real
Timothy H. Engström

An Integrated Gene And Protein ID Mapping Tool With Batch Ortholog Prediction
Mathew Fleisch, Uday Evani, Sean D. Mooney

Computational Simulation And Verification Of Hmgb1 Signaling Pathway
Haijun Gong, Paolo Zuliani, Anvesh Komuravelli, Edmund Clarke, James Faeder

Gene Expression And The Meridian Chart
Ming Guo

Simulation Of  "Single Molecule Real Time" (SMRT) Sequencing, And Data Transformations For Use With Existing Workflow Tools
Robert M. Horton

Investigating Consistency Between Curated Binding Profiles And PWMs Derived From Protein-DNA Structure Models
Tsung-Ting Hsieh, Mei-Ju May Chen, Chien-Yu Chen

Characterizing The Human Transcriptional Landscape: The Allele Binding  Cooperativity Test
Konrad Karczewski, Maya Kasowski, Fabian Grubert, Manoj Hariharan, Mark Gerstein, Jan Korbel, Russ Altman, Michael Snyder

High-Throughput Detection Of Epistasis In Studies Of The Genetics Of Complex Traits
Asta Laiho, Attila Gyenesei, András Király, János Abonyi, Colin Semple, Chris Haley, Wenhuan Wei

Automated Inference Of Molecular Mechanisms Of Disease From Amino Acid Substitutions
Biao Li, Vidhya G. Krishnan, Kishore K. Kamati, Matthew E. Mort, Fuxiao Xin, David Cooper, Sean D. Mooney, Predrag Radivojac

Prediction Of Epigenetic Biomarkers In Breast Cancer Cell Lines By Logistic Regression Of Methylation-Expression Associations
Leandro A. Loss, Anguraj Sadanandam, Steffen Durinck, Shivani Nautiyal, Diane Flaucher, Victoria E. H. Carlton, Martin Moorhead, Yontao Lu, Joe W. Gray, Malek Faham, Paul Spellman, Bahram Parvin

Large-Scale Evolutionary Simulations Of Complex Microbial Behaviors In Dynamic Environments
V. Mozhayskiy, I. Tagkopoulos

Computational Prediction Of Amyloidogenic Regions In Proteins: A Machine Learning Approach
Smitha Sunil Kumaran Nair, N. V. Subba Reddy

Greatly Improved Allele-Specific Tumor Copy Numbers With DNA Microarrays When A Matched Normal Is Available
Peirre Neuvial, Henrik Bengtsson

Analysis Of A Local Huntington Protein Interaction Network
Corey Powell, C. Tourette, S. D. Mooney, R. Hughes

Topological Analysis Of A Site-Specific Recombination Reaction
Mousa Rebouh

The MutDB Web Tool For SNP Analysis
Tal Ronnen Oron, Vidhya G. Krishnan, Kishore K. Kamati, S. D. Mooney, Biao Li, Predrag Radivojac, Matthew Mort

MiDReG: A Method Of Mining Developmentally Regulated Genes Using Boolean Implications
D. Sahoo, J. Seita, D. Bhattacharya, M. A. Inlay, I. L. Weissman, S. K. Plevritis, D. L. Dill

Using Network Dynamics Toward A Top-Down Approach To Gene Expression Analysis
Sandy Shaw

Genome-Scale Methyltyping By Statistical Inference For Determining Methylation States In Populations
Meromit Singer, Dario Boffelli, Joseph Dhahbi, Alexander Schoenhuth, Gary P. Schroth, David I.K. Martin, Lior Pachter

Hairpin Modeling Improvement For Non-Coding RNA Gene Search With Covariance Models
Jennifer A. Smith

Visualizing Evolutionary And Functional Relationships Between Microbes From A Sequence Network Perspective
Samuel Smits

Network Models Of Clinical Trial Data
Marco D. Sorani, Geoffrey T. Manley, J. Claude Hemphill, Sergio E. Baranzini

Multigenic Analysis Of Consumer Genomes For Health Risk Prediction
M. Swan

Ranking Predicted miRNA Targets Through Their Binding Patterns
Leyan Tang

Performance Of SNP Pathogenicity Prediction Methods
Janita Thusberg, A. Olatubosun, M. Vihinen

Reanalyze Unassigned Reads In Metagenomic Data Using Conserved Gene Adjacency
Daryi Wang, Francis Cheng-Hsuan Weng, Huai-Kuang Tsai, Chien-Hao Su, Ming-Tsung Hsu, Tse-Yi Wang

MyTrack: An Application That Integrates With The UCSC Genome Browser To Promote Organization, Customization And Sharing Of Genomic Data
J. D. Waymire, Y. Liu, Kishore K. Kamati, Sean D. Mooney

Exploiting Nucleosome-Positioning Data For Gene-Finding; A Feasibility Study
Christopher Wilks, Dietlind L. Gerloff

Clustering Biological Data By Unraveling Hidden Transitive Substructures
Tobias Wittkop, Jan Baumbach

Exploiting Cross-Species Conservation To Improve Prediction Accuracy Of Discovering Transcription Factor Binding Sites
Po-Chun Wu, Mei-Ju Chen, Chien-Yu Chen

A New Score For Robust Detection Of Differentially Expressed Genes
Yufei Xiao, Xiaowu Wu, Steven E. Wolf, Yidong Chen

A Novel Profile Hidden Markov Model To Predict MicroRNAs And Their Targets Simultaneously
Shu Yang, Kalpana Agrawal, Tak-Wah Lam, Pak Chung Sham, Kathryn Cheah, Junwen Wang

Prediction Of Disease-Associated Regulatory Mutations In Monogenic And Complex Disease
Yiqiang Zhao, Sean D. Mooney, Matthew Mort, David N. Cooper, Wyatt Clark

An Information Network Of Biomedical Entities For Generating Hypotheses
Julie Zheng, Guonchun Liao


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