CONTENTS

• Computational Challenges in Comparative Genomics
• Computational studies of non-coding RNAs
• Dynamics of Biological Networks
• Multi-resolution Modeling of Biological Macromolecules
• Personal Genomics
• Reverse Engineering and Synthesis of Biomolecular Systems

Computational Challenges in Comparative Genomics

Session Introduction

Bernard Moret, Webb Miller, Pavel Pevzner, and David Sankoff; Pacific Symposium on Biocomputing 15:1-2(2010)

Accurate Taxonomic Assignment of Short Pyrosequencing Reads

José C. Clemente , Jesper Jansson, Gabriel Valiente; Pacific Symposium on Biocomputing 15:3-9(2010)

Benchmarking BLAST Accuracy of Genus/Phyla Classification of Metagenomic Reads

Steven D. Essinger, Gail L. Rosen; Pacific Symposium on Biocomputing 15:10-20(2010)

Guided genome halving: provably optimal solutions provide good insights into the preduplication ancestral genome of Saccharomyces cerevisiae

Haris Gavranovic, Eric Tannier; Pacific Symposium on Biocomputing 15:21-30(2010)

A Practical Algorithm for Estimation of the Maximum Likelihood Ancestral Reconstruction Error

Glenn Hickey, Mathieu Blanchette; Pacific Symposium on Biocomputing 15:31-42(2010)

Optimization methods for selecting founder populations for captive breeding of endangered species

Webb Miller, Stephen J. Wright, Yu Zhang, Stephan C. Schuster, Vanessa M. Hayes; Pacific Symposium on Biocomputing 15:43-53(2010)

Computational studies of non-coding RNAs

Session Introduction

Rolf Backofen, Hamidreza Chitsaz, Ivo Hofacker, S. Cenk Sahinalp, Peter F. Stadler; Pacific Symposium on Biocomputing 15:54-56(2010)

RNA Structural Segmentation

Ivan Dotu, William A. Lorenz, Pascal Van Hentenryck, Peter Clote; Pacific Symposium on Biocomputing 15:57-68(2010)

RNAz 2.0: Improved Noncoding RNA Detection

Andreas R. Gruber, Sven Findeiß, Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler; Pacific Symposium on Biocomputing 15:69-79(2010)

Identification and Classification of Small RNAs in Transcriptome Sequence Data

D. Langenberger, C.I. Bermudez-Santana, P.F. Stadler, S. Hoffmann; Pacific Symposium on Biocomputing 15:80-87(2010)

Improvement of Structure Conservation Index with Centroid Estimators

Yohei Okada, Kengo Sato, Yasubumi Sakakibara; Pacific Symposium on Biocomputing 15:88-97(2010)

Dynamic Programming Algorithms for RNA Structure Prediction with Binding Sites

Unyanee Poolsap, Yuki Kato, Tatsuya Akutsu; Pacific Symposium on Biocomputing 15:98-107(2010)

An Algorithm for the Energy Barrier Problem Without Pseudoknots and Temporary Arcs

Chris Thachuk, Jan Manuch, Arash Rafiey, Leigh-Anne Mathieson, Ladislav Stacho, Anne Condon; Pacific Symposium on Biocomputing 15:108-119(2010)

Dynamics of Biological Networks

Session Introduction

Tanya Y. Berger-Wolf, Teresa M. Przytycka, Mona Singh, Donna Slonim; Pacific Symposium on Biocomputing 15:120-122(2010)

Local Optimization for Global Alignment of Protein Interaction Networks

Leonid Chindelevitch, Chung-Shou Liao, Bonnie Berger; Pacific Symposium on Biocomputing 15:123-132(2010)

Identification of Coordinately Dysregulated Subnetworks in Complex Phenotypes

Salim A. Chowdhury, Mehmet Koyuturk; Pacific Symposium on Biocomputing 15:133-144(2010)

Subspace Differential Coexpression Analysis: Problem Definition and a General Approach

Gang Fang, Rui Kuang, Gaurav Pandey, Michael Steinbach, Chad L. Myers, Vipin Kumar; Pacific Symposium on Biocomputing 15:145-156(2010)

Estimation of Protein and Domain Interactions in the Switching Motility System of Myxococcus xanthus

Faruck Morcos, Marcin Sikora, Mark Alber, Dale Kaiser, Jesus A. Izaguirre; Pacific Symposium on Biocomputing 15:157-165(2010)

Exploring Biological Network Dynamics with Ensembles of Graph Partitions

Saket Navlakha, Carl Kingsford; Pacific Symposium on Biocomputing 15:166-177(2010)

Geometric Evolutionary Dynamics of Protein Interaction Networks

Natasa Przulj, Oleksii Kuchaiev, Aleksandar Stevanovic, Wayne Hayes; Pacific Symposium on Biocomputing 15:178-189(2010)

The Steady States and Dynamics of Urokinase-mediated Plasmin Activation

Lakshmi Venkatraman, Hanry Yu, Sourav S. Bhowmick, Forbes Dewey Jr., Lisa Tucker-Kellogg; Pacific Symposium on Biocomputing 15:190-199(2010)

Multi-resolution Modeling of Biological Macromolecules

Session Introduction

Samuel Flores, Julie Bernauer, Xuhui Huang, Ruhong Zhou, Seokmin Shin; Pacific Symposium on Biocomputing 15:200-204(2010)

Multi-Resolution Approach for Interactively Locating Functionally Linked Ion Binding Sites by Steering Small Molecules into Electrostatic Potential Maps Using a Haptic Device

Olivier Delalande, Nicolas Ferey, Benoist Laurent, Marc Gueroult, Brigitte Hartmann, Marc Baaden; Pacific Symposium on Biocomputing 15:205-215(2010)

Predicting RNA Structure by Multiple Template Homology Modeling

Samuel C. Flores, Yaqi Wan, Rick Russell, Russ B. Altman; Pacific Symposium on Biocomputing 15:216-227(2010)

Constructing Multi-Resolution Markov State Models (MSMs) to Elucidate RNA Hairpin Folding Mechanisms

Xuhui Huang, Yuan Yao, Gregory R. Bowman, Jian Sun, Leonidas J. Guibas, Gunnar Carlsson, Vijay S. Pande; Pacific Symposium on Biocomputing 15:228-239(2010)

Multiscale Dynamics of Macromolecules Using Normal Mode Langevin

Jesus A Izaguirre, Christopher R. Sweet, Vijay S. Pande; Pacific Symposium on Biocomputing 15:240-251(2010)

Insights into the Intra-Ring Subunit Order of TriC/CCT: Structural and Evolutionary Analysis

Nir Kalisman, Michael Levitt; Pacific Symposium on Biocomputing 15:252-259(2010)

Cross-Graining: Efficient Multi-Scale Simulation via Markov State Models

Peter Kasson, Vijay Pande; Pacific Symposium on Biocomputing 15:260-268(2010)

Toward Understanding Allosteric Signaling Mechanisms in the ATPase Domain of Molecular Chaperones

Ying Liu, Ivet Bahar ; Pacific Symposium on Biocomputing 15:269-280(2010)

3D-Blast: 3D Protein Structure Alignment, Comparison, and Classification Using Spherical Polar Fourier Correlations

Lazaros Mavridis. David W. Ritchie; Pacific Symposium on Biocomputing 15:281-292(2010)

Structural Prediction of Protein-RNA Interaction by Computational Docking with Propensity-Based Statistical Potentials

Laura Perez-Cano, Albert Solernou, Carles Pons, Juan Fernandez-Recio; Pacific Symposium on Biocomputing 15:293-301(2010)

Personal Genomics

Session Introduction

Can Alkan, Michael Brudno, Evan E. Eichler, Maricel G. Kann, S. Cenk Sahinalp; Pacific Symposium on Biocomputing 15:302-304(2010)

Improving the Prediction of Pharmacogenes Using Text-Derived Gene-Drug Relationships

Yael Garten, Nicholas P. Tatonetti, Russ B. Altman; Pacific Symposium on Biocomputing 15:305-314(2010)

Finding Unique Filter Sets in PLATO: A Precursor to Efficient Interaction Analysis in GWAS Data

Benjamin J. Grady, Eric Torstenson, Scott M. Dudek, Justin Giles, David Sexton, Marylyn D. Ritchie; Pacific Symposium on Biocomputing 15:315-326(2010)

Enabling Personal Genomics with an Explicit Test of Epistasis

Casey S. Greene, Daniel S. Himmelstein, Heather H. Nelson, Karl T. Kelsey, Scott M. Williams, Angeline S. Andrew, Margaret R. Karagas, Jason H. Moore; Pacific Symposium on Biocomputing 15:327-336(2010)

Loss of Post-Translational Modification Sites in Disease

Shuyan Li, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac; Pacific Symposium on Biocomputing 15:337-347(2010)

Detecting Genome-wide Haplotype Polymorphism by Combined Use of Mendelian Constraints and Local Population Structure

Xin Li, Yixuan Chen, Jing Li; Pacific Symposium on Biocomputing 15:348-358(2010)

Sequence Feature Variant Type (SFVT) Analysis of the HLA Genetic Association in Juvenile Idiopathic Arthritis

Glenys Thomson, Nishanth Marthandan, Jill A. Hollenbach, Steven J. Mack, Henry A. Erlich, Richard M. Single, Matthew J. Waller, Steven G.E. Marsh, Paula A. Guidry, David R. Karp, Richard H. Scheuermann, Susan D. Thompson, David N. Glass, Wolfgang Helmberg; Pacific Symposium on Biocomputing 15:359-370(2010)

COKGEN: A Software for the Identification of Rare Copy Number Variation from SNP Microarrays

Gokhan Yavas, Mehmet Koyuturk, Meral Ozsoyoglu, Meetha P. Gould, Thomas Laframboise; Pacific Symposium on Biocomputing 15:371-382(2010)

Reverse Engineering and Synthesis of Biomolecular Systems

Session Introduction

Gil Alterovitz, Silvio Cavalcanti, Taro M. Muso, Marco F. Ramoni, May Wang; Pacific Symposium on Biocomputing 15:383-384(2010)

Co-Design in Synthetic Biology: A System-Level Analysis of the Development of an Environmental Sensing Device

David A. Ball, Matthew W. Lux, Russell R. Graef, Matthew W. Peterson, Jane D. Valenti, John Dileo, Jean Peccoud; Pacific Symposium on Biocomputing 15:385-396(2010)

Critical Analysis of Transcriptional and Post-Transcriptional Regulatory Networks in Multiple Myeloma

Marta Biasiolo, Mattia Forcato , Lino Possamai, Francesco Ferrari, Luca Agnelli, Marta Lionetti, Katia Todoerti, Antonino Neri, Massimo Marchiori, Stefania Bortoluzzi, Silvio Bicciato; Pacific Symposium on Biocomputing 15:397-408(2010)

A Computational Model of Gene Expression in an Inducible Synthetic Circuit

Francesca Ceroni, Simone Furini, Silvio Cavalcanti; Pacific Symposium on Biocomputing 15:409-420(2010)

Retrovirus HTLV-1 Gene Circuit: A Potential Oscillator for Eukaryotes

Alberto Corradin, Barbara Di Camillo, Francesca Rende, Vincenzo Ciminale, Gianna Maria Toffolo, Claudio Cobelli; Pacific Symposium on Biocomputing 15:421-432(2010)

Emulsion Based Selection of T7 Promoters of Varying Activity

Eric A. Davidson, Thomas Van Blarcom, Matthew Levy, Andrew D. Ellington; Pacific Symposium on Biocomputing 15:433-443(2010)

Clustering Context-Specific Gene Regulatory Networks

Archana Ramesh, Robert Trevino, Daniel D. Von Hoff, Seungchan Kim; Pacific Symposium on Biocomputing 15:444-455(2010)

Writing and Compiling Code into Biochemistry

Adam Shea, Brian Fett, Marc D. Riedel and Keshab Parhi; Pacific Symposium on Biocomputing 15:456-464(2010)

Synthesis of Pharmacokinetic Pathways through Knowledge Acquisition and Automated Reasoning

Luis Tari, Saadat Anwar, Shanshan Liang, Jorg Hakenberg, Chitta Baral; Pacific Symposium on Biocomputing 15:465-476(2010)

Workshops

In silico Biology

Richard Goldstein, Phil Husbands, Chrisantha Fernando, and Dov Stekel; Pacific Symposium on Biocomputing 15:477-480(2010)

Genomic Standards Consortium Workshop: Metagenomics, Metadata and Metaanalysis (M3)

Peter Sterk, Lynette Hirschman, Dawn Field, John Wooley; Pacific Symposium on Biocomputing 15:481-484(2010)

Extraction of Genotype-Phenotype-Drug Relationships from Text: From Entity Recognition to Bioinformatics Application

Adrien Coulet, Nigam Shah, Lawrence Hunter, Chitta Baral and Russ B. Altman; Pacific Symposium on Biocomputing 15:485-487(2010)

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Updated: November 17, 2009