PSB 2008 Online Proceedings

PSB 2008

PSB Proceedings for All Years


CONTENTS


Preface

BEYOND GAP MODELS: RECONSTRUCTING ALIGNMENTS AND PHYLOGENIES UNDER GENOMIC-SCALE EVENTS

Session Introduction
Michael Brudno, Bernard Moret, Randy Linder, Tandy Warnow; Pacific Symposium on Biocomputing 13:1-2(2008)
FRESCO: Flexible Alignment with Rectangle Scoring Schemes
A.V. Dalca, M. Brudno; Pacific Symposium on Biocomputing 13:3-14(2008)
Local Reliability Measures from Sets of Co-Optimal Multiple Sequence Alignments
Giddy Landan, Dan Graur; Pacific Symposium on Biocomputing 13:15-24(2008)
The Effect of the Guide Tree on Multiple Sequence Alignments and Subsequent Phylogenetic Analysis
S. Nelesen, K. Liu, D. Zhao, C. R. Linder, T. Warnow; Pacific Symposium on Biocomputing 13:25-36(2008)
Sensitivity Analysis for Reversal Distance and Breakpoint Reuse in Genome Rearrangements
Amit U. Sinha, Jaroslaw Meller; Pacific Symposium on Biocomputing 13:37-48(2008)

COMPUTATIONAL CHALLENGES IN THE STUDY OF SMALL REGULATORY RNAs

Session Introduction; Pacific Symposium on Biocomputing 13:1-2(2008)
Doron Betel, Christina Leslie, Nikolaus Rajewsky; Pacific Symposium on Biocomputing 13:49-51(2008)
Comparing Sequence and Expression for Predicting microRNA Targets Using GenMIR3
J. C. Huang, B. J. Frey, Q. D. Morris; Pacific Symposium on Biocomputing 13:52-63(2008)
Analysis of Microrna-Target Interactions by a Target Structure Based Hybridization Model
Dang Long, Chi Yu Chan, Ye Ding; Pacific Symposium on Biocomputing 13:64-74(2008)
A Probabilistic Model for Small RNA Flowgram Matching
Vladimir Vacic, Hailing Jin, Jian-Kang Zhu, Stefano Lonardi; Pacific Symposium on Biocomputing 13:75-86(2008)

COMPUTATIONAL TOOLS FOR NEXT-GENERATION SEQUENCING APPLICATIONS

Session Introduction;
Francisco M. De La Vega, Gabor T. Marth, Granger Sutton; Pacific Symposium on Biocomputing 13:87-89(2008)
TRELLIS+: An Effective Approach for Indexing Genome-Scale Sequences Using Suffix Trees
Benjarath Phoophakdee, Mohammed J. Zaki; Pacific Symposium on Biocomputing 13:90-101(2008)
Pash 2.0: Scaleable Sequence Anchoring for Next-Generation Sequencing Technologgies
Cristian Coarfa, Aleksandar Milosavljevic; Pacific Symposium on Biocomputing 13:102-113(2008)
Population Sequencing Using Short Reads: HIV as a Case Study
Vladimir Jojic, Tomer Hertz, Nebojsa Jojic; Pacific Symposium on Biocomputing 13:114-125(2008)
Analysis of Large-Scale Sequencing of Small RNAs
A.J. Olson, J. Brennecke, A.A. Aravin, G.J. Hannon, R. Sachidanandam; Pacific Symposium on Biocomputing 13:126-136(2008)

KNOWLEDGE-DRIVEN ANALYSIS AND DATA INTEGRATION FOR HIGH-THROUGHPUT BIOLOGICAL DATA

Session Introduction
Michael Ochs, John Quackenbush, Ramana Davuluri; Pacific Symposium on Biocomputing 13:137-140(2008)
SGDI: System for Genomic Data Integration
V. J. Carey, J. Gentry, D. Sarkar, R. Gentleman, S. Ramaswamy; Pacific Symposium on Biocomputing 13:141-152(2008)
Annotating Pathways of Interaction Networks
Jayesh Pandey, Mehmet Koyuturk, Wojciech Szpankowski, Ananth Grama; Pacific Symposium on Biocomputing 13:153-165(2008)
Integrating Microarray and Proteomics Data to Predict the Response of Cetuximab in Patients with Rectal Cancer
Anneleen Daeman, Olivier Gevaert, Tijl de Bie, Annelies Debucquoy, Jean-Pascal Machiels, Bart de Moor, Karin Haustermans; Pacific Symposium on Biocomputing 13:166-177(2008)
A Bayesian Framework for Data and Hypotheses Driven Fusion of High Throughput Data: Application to Mouse Organogenesis
Madhuchhanda Bhattacharjee, Colin Pritchard, Peter Nelson; Pacific Symposium on Biocomputing 13:178-189(2008)
Gathering the Gold Dust: Methods for Assessing the Aggregate Impact of Small Effect Genes in Genomic Scans
Michael A. Province, Ingrid B. Borecki; Pacific Symposium on Biocomputing 13:190-200(2008)
Multi-Scale Correlations in Continuous Genomic Data
R. E. Thurman, W. S. Noble, J. A. Stamatoyannopoulos; Pacific Symposium on Biocomputing 13:201-215(2008)
Analysis of MALDI-TOF Spectrometry Data for Detection of Glycan Biomarkers
Habtom W. Ressom, Rency S. Varghese, Lenka Goldman, Christopher A. Loffredo, Mohammed Abdel-Hamid, Zuzana Kyselova, Yehia Mechref, Milos Novotny, Radoslav Goldman; Pacific Symposium on Biocomputing 13:216-227(2008)

MOLECULAR BIOINFORMATICS FOR DISEASES: PROTEIN INTERACTIONS AND PHENOMICS

Session Introduction
Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Marco Punta, Atul Butte, Maricel Kann; Pacific Symposium on Biocomputing 13:228-230(2008)
System-Wide Peripheral Biomarker Discovery Using Information Theory
Gil Alterovitz, Michael Xiang, Jonathan Liu, Amelia Chang, Marco F. Ramoni; Pacific Symposium on Biocomputing 13:231-242(2008)
Novel Integration of Hospital Electronic Medical Records and Gene Expression Measurements to Identify Genetic Markers of Maturation
David P. Chen, Susan C. Weber, Philip S. Constantinou, Todd A. Ferris, Henry J. Lowe, Atul J. Butte; Pacific Symposium on Biocomputing 13:243-254(2008)
Networking Pathways Unveils Association Between Obesity and Non-Insulin Dependent Diabetes Mellitus
Haiyan Hu, Xiaoman Li; Pacific Symposium on Biocomputing 13:255-266(2008)
Extracting Gene Expression Profiles Common to Colon and Pancreatic Adenocarcinoma Using Simultaneous Nonnegative Matrix Factorization
Liviu Badea; Pacific Symposium on Biocomputing 13:267-278(2008)
Integration of Microarray and Textual Data Improves the Prognosis Prediction of Breast, Lung, and Ovarian Cancer Patients
O. Gevaert, S. Van Vooren, B. De Moor; Pacific Symposium on Biocomputing 13:279-290(2008)
Mining Metabolic Networks for Optimal Drug Targets
Padmavati Sridhar, Bin Song, Tamer Kahveci, Sanjay Ranka; Pacific Symposium on Biocomputing 13:291-302(2008)
Global Alignment of Multiple Protein Interaction Networks
Rohit Singh, Jinbu Xu, Bonnie Berger; Pacific Symposium on Biocomputing 13:303-314(2008)
Predicting DNA Methylation Susceptibility Using CpG Flanking Sequences
S. Kim, M. Li, H. Paik, K. Nephew, H. Shi, R. Kramer, D. Xu, T.-H. Huang; Pacific Symposium on Biocomputing 13:315-326(2008)

MULTISCALE MODELING AND SIMULATION: FROM MOLECULES TO CELLS TO ORGANISMS?

Session Introduction
Jung-Chi Liao, Jeff Reinbolt, Roy Kerckhoffs, Anuska Michailova, Peter Arzberger; Pacific Symposium on Biocomputing 13:327-331(2008)
Combining Molecular Dynamics and Machine Learning to Improve Protein Function Recognition
Dariya S. Glazer, Randall J. Radmer, Russ B. Altman; Pacific Symposium on Biocomputing 13:332-343(2008)
Prediction of the Structure of G-Protein Coupled Receptors and of Bound Ligands with Applications for Drug Design
Youyong Li, William A. Goddard III; Pacific Symposium on Biocomputing 13:344-353(2008)
Markov Chain Models of Coupled Intracellular Calcium Channels: Kronecker Structured Representations and Benchmark Stationary Distribution Calculations
Hilary DeRemigio, Peter Kemper, M. Drew Lamar, Gregory D. Smith; Pacific Symposium on Biocomputing 13:354-365(2008)
Spatially-Compressed Cardiac Myofilament Models Generate Hysteresis that Is Not Found in Real Muscle
John Jeremy Rice, Yuhai Tu, Corrado Poggesi, Pieter P. De Tombe; Pacific Symposium on Biocomputing 13:366-377(2008)
Modeling Ventricular Interaction: A Multiscale Approach from Sarcomere Mechanics to Cardiovascular Systems Hemodynamics
Joost Lumens, Tammo Delhaas, Borut Kirn, Theo Arts; Pacific Symposium on Biocomputing 13:378-389(2008)
Sub-Micrometer Anatomical Models of the Sarcolemma of Cardiac Myocytes Based on Confocal Imaging
Frank B. Sachse, Eleonora Savio-Galimberti, Joshua I. Goldhaber, John H. B. Bridge; Pacific Symposium on Biocomputing 13:390-401(2008)
Efficient Multiscale Simulations of Circadian Rhythms Using Automated Phase Macomodelling Techniques
Shatam Agarwal, Jaijeet Roychowdhury; Pacific Symposium on Biocomputing 13:402-413(2008)
Integration of Multi-Scale Biosimulation Models via Light-Weight Semantics
John H. Gennari, Maxwell L. Neal, Brian E. Carlson, Daniel L. Cook; Pacific Symposium on Biocomputing 13:414-425(2008)
Comparisons of Protein Family Dynamics
A. J. Rader, Joshua T. Harrell; Pacific Symposium on Biocomputing 13:426-437(2008)

PROTEIN-NUCLEIC ACID INTERACTIONS: INTEGRATING STRUCTURE, SEQUENCE, AND FUNCTION

Session Introduction
Martha Bulyk, Ernest Fraenkel, Alexander Hartemink, Yael Mandel-Gutfreund; Pacific Symposium on Biocomputing 13:438-440(2008)
Functional Trends in Structural Classes of the DNA Binding Domains of Regulatory Transcription Factors
Rachel Patton McCord, Martha L. Bulyk; Pacific Symposium on Biocomputing 13:441-452(2008)
Using DNA Duplex Stability Information for Transcription Factor Binding Site Discovery
Raluca Gordân, Alexander J. Hartemink; Pacific Symposium on Biocomputing 13:453-464(2008)
A Parametric Joint Model of DNA-Protein Binding, Gene Expression and DNA Sequence Data to Detect Target Genes of a Transcription Factor
Wei Pan, Peng Wei, Arkady Khodursky; Pacific Symposium on Biocomputing 13:465-476(2008)
An Analysis of Information Content Present in Protein-DNA Interactions
Chris Kauffman, George Karypis; Pacific Symposium on Biocomputing 13:477-488(2008)
Use of an Evolutionary Model to Provide Evidence for a Wide Heterogenity of Required Affinities Between Transcription Factors and Their Binding Sites in Yeast
Richard W. Lusk, Michael B. Eisen; Pacific Symposium on Biocomputing 13:489-500(2008)
Striking Similarities in Diverse Telomerase Proteins Revealed by Combining Structure Prediction and Machine Learning Approaches
Jae-Hyung Lee, Michael Hamilton, Colin Gleeson, Cornelia Caragea, Peter Zaback, Jeffrey D. Sander, Xue Li, Feihong Wu, Michael Terribilini. Vasant Honavar, Drena Dobbs; Pacific Symposium on Biocomputing 13:501-512(2008)

TILING MICROARRAY DATA ANALYSIS METHODS AND ALGORITHMS

Session Introduction
Srinka Ghosh, Antonio Piccolboni; Pacific Symposium on Biocomputing 13:513-514(2008)
CMARRT: A Tool of Analysis of CHIP-chip Data from Tiling Arrays by Incorporating the Correlation Structure
Pei Fen Kuan, Hyonho Chun, Sűndűz Keles; Pacific Symposium on Biocomputing 13:515-526(2008)
Transcript Normalization and Segmentation of Tiling Array Data
Georg Zeller, Stefan R. Henz, Sascha Laubinger, Detlef Weigel, Gunnar Rätsch; Pacific Symposium on Biocomputing 13:527-538(2008)
GSE: A Comprehensive Database System for the Representation, Retrieval, and Analysis of Microarray Data
Timothy Danford, Alex Rolfe, David Gifford; Pacific Symposium on Biocomputing 13:539-550(2008)

TRANSLATING BIOLOGY: TEXT MINING TOOLS THAT WORK

Session Introduction
K. Bretonnel Cohen, Hong Yu, Philip E. Bourne, Lynette Hirschman; Pacific Symposium on Biocomputing 13:551-555(2008)
Assisted Curation: Does Text Mining Really Help?
Beatrice Alex, Claire Grover, Barry Haddow, Mijail Kabadjor, Ewan Klein, Michael Matthews, Stuart Roebuck, Richard Tobin, Xinglong Wang; Pacific Symposium on Biocomputing 13:556-567(2008)
Evidence for Showing Gene/Protein Name Suggestions in Bioscience Literature Search Interfaces
Anna Divoli, Marti A. Hearst, Michael A. Wooldridge; Pacific Symposium on Biocomputing 13:568-579(2008)
Enabling Integrative Genomic Analysis of High Impact Human Diseases Through Text Mining
Joel Dudley, Atul J. Butte; Pacific Symposium on Biocomputing 13:580-591(2008)
Information Needs and the Role of Text Mining in Drug Development
Phoebe M. Roberts, William S. Hayes; Pacific Symposium on Biocomputing 13:592-603(2008)
EpiLoc: A (Working) Text-Based System for Predicting Protein Subcellular Location
Scott Brady, Hagit Shatkay; Pacific Symposium on Biocomputing 13:604-615(2008)
Filling the Gaps Between Tools and Users: A Tool Comparator, Using Protein-Protein Interactions as an Example
Yoshinobu Kano, Ngan Nguyen, Rune Saetre, Kazuhiro Yoshida,Yusuke Miyao, Yoshimasa Tsuruoka, Yuichiro Matsubayashi, Sophia Ananiadou, Jun'ichi Tsujii Pacific Symposium on Biocomputing 13:616-627
Comparing Usability of Matching Techniques for Normalising Biomedical Named Entities
Xinglong Wang, Michael Matthews; Pacific Symposium on Biocomputing 13:628-639(2008)
Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic Tasks
J. Gregory Caporaso, Nita Deshpande, J. Lynn Fink, Philip E. Bourne, K. Bretonnel Cohen, Lawrence Hunter; Pacific Symposium on Biocomputing 13:640-651(2008)
BANNER: An Executable Survey of Advances in Biomedical Named Entity Recognition
Robert Leaman, Graciela Gonzalez; Pacific Symposium on Biocomputing 13:652-663(2008)

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