CONTENTS

• Beyond Gap Models: Reconstructing Alignments and Phylogenies Under Genomic-Scale Events
• Computational Challenges in the Study of Small Regulatory RNAs
• Computational Tools for Next-Generation Sequencing Applications
• Knowledge-Driven Analysis and Data Integration for High-Throughput Biological Data
• Molecular Bioinformatics for Diseases: Protein Interactions and Phenomics
• Multiscale Modeling and Simulation: from Molecules to Cells to Organisms
• Protein-Nucleic Acid Interactions: Integrating Structure, Sequence, and Function
• Tiling Microarray Data Analysis Methods and Algorithms
• Translating Biology: Text Mining Tools that Work

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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Updated: October 1, 2007