Table of Contents

• Session IntroductionBernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff. 1-2 [doi]
• Accurate Taxonomic Assignment of Short Pyrosequencing ReadsJosé Carlos Clemente, Jesper Jansson, Gabriel Valiente. 3-9 [doi]
• Benchmarking BLAST Accuracy of Genus/Phyla Classification of Metagenomic ReadsSteven D. Essinger, Gail L. Rosen. 10-20 [doi]
• Guided Genome Halving: Provably Optimal Solutions Provide Good Insights into the Preduplication Ancestral Genome of Saccharomyces CerevisiaeHaris Gavranovic, Eric Tannier. 21-30 [doi]
• A Practical Algorithm for Estimation of the Maximum Likelihood Ancestral Reconstruction ErrorGlenn Hickey, Mathieu Blanchette. 31-42 [doi]
• Optimization Methods for Selecting Founder Populations for Captive Breeding of Endangered SpeciesWebb Miller, Stephen J. Wright, Yu Zhang, Stephan C. Schuster, Vanessa M. Hayes. 43-53 [doi]
• Session IntroductionRolf Backofen, Hamidreza Chitsaz, Ivo L. Hofacker, Süleyman Cenk Sahinalp, Peter F. Stadler. 54-56 [doi]
• RNA Structural SegmentationIván Dotú, W. A. Lorenz, Pascal Van Hentenryck, Peter Clote. 57-68 [doi]
• RNAz 2.0: Improved Noncoding RNA DetectionAndreas R. Gruber, Sven Findeiß, Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler. 69-79 [doi]
• Identification and Classification of Small RNAs in Transcriptome Sequence DataDavid Langenberger, Clara Bermudez-Santana, Peter F. Stadler, Steve Hoffmann. 80-87 [doi]
• Improvement of Structure Conservation Index with Centroid EstimatorsYohei Okada, Kengo Sato, Yasubumi Sakakibara. 88-97 [doi]
• Dynamic Programming Algorithms for RNA Structure Prediction with Binding SitesUnyanee Poolsap, Yuki Kato, Tatsuya Akutsu. 98-107 [doi]
• An Algorithm for the Energy Barrier Problem Without Pseudoknots and Temporary ArcsChris Thachuk, Ján Manuch, Arash Rafiey, Leigh-Anne Mathieson, Ladislav Stacho, Anne Condon. 108-119 [doi]
• Session IntroductionTanya Y. Berger-Wolf, Teresa M. Przytycka, Mona Singh, Donna K. Slonim. 120-122 [doi]
• Local Optimization for Global Alignment of Protein Interaction NetworksLeonid Chindelevitch, Chung-Shou Liao, Bonnie Berger. 123-132 [doi]
• Identification of Coordinately Dysregulated Subnetworks in Complex PhenotypesSalim A. Chowdhury, Mehmet Koyutürk. 133-144 [doi]
• Subspace Differential Coexpression Analysis: Problem Definition and a General ApproachGang Fang, Rui Kuang, Gaurav Pandey, Michael Steinbach, Chad L. Myers, Vipin Kumar. 145-156 [doi]
• Estimation of Protein and Domain Interactions in the Switching Motility System of Myxococcus XanthusFaruck Morcos, Marcin Sikora, Mark S. Alber, Dale Kaiser, Jesús A. Izaguirre. 157-165 [doi]
• Exploring Biological Network Dynamics with Ensembles of Graph PartitionsSaket Navlakha, Carl Kingsford. 166-177 [doi]
• Geometric Evolutionary Dynamics of Protein Interaction NetworksNatasa Przulj, Oleksii Kuchaiev, Aleksandar Stevanovic, Wayne Hayes. 178-189 [doi]
• The Steady States and Dynamics of Urokinase-mediated Plasmin ActivationLakshmi Venkatraman, Hanry Yu, Sourav S. Bhowmick, C. Forbes Dewey, Lisa Tucker-Kellogg. 190-199 [doi]
• Session IntroductionSamuel Flores, Julie Bernauer, Xuhui Huang, Ruhong Zhou, Seokmin Shin. 200-204 [doi]
• Multi-Resolution Approach for Interactively Locating Functionally Linked Ion Binding Sites by Steering Small Molecules into Electrostatic Potential Maps Using a Haptic DeviceOlivier Delalande, Nicolas Férey, Benoist Laurent, Marc Gueroult, Brigitte Hartmann, Marc Baaden. 205-215 [doi]
• Predicting RNA Structure by Multiple Template Homology ModelingSamuel Flores, Yaqi Wan, Rick Russell, Russ B. Altman. 216-227 [doi]
• Constructing Multi-Resolution Markov State Models (MSMs) to Elucidate RNA Hairpin Folding MechanismsXuhui Huang, Yuan Yao, Gregory R. Bowman, Jian Sun, Leonidas J. Guibas, Gunnar Carlsson, Vijay S. Pande. 228-239 [doi]
• Multiscale Dynamics of Macromolecules Using Normal Mode LangevinJesús A. Izaguirre, Christopher R. Sweet, Vijay S. Pande. 240-251 [doi]
• Insights into the Intra-Ring Subunit Order of TriC/CCT: Structural and Evolutionary AnalysisNir Kalisman, Michael Levitt. 252-259 [doi]
• Cross-Graining: Efficient Multi-Scale Simulation via Markov State ModelsPeter M. Kasson, Vijay S. Pande. 260-268 [doi]
• Toward Understanding Allosteric Signaling Mechanisms in the ATPase Domain of Molecular ChaperonesYing Liu, Ivet Bahar. 269-280 [doi]
• 3D-Blast: 3D Protein Structure Alignment, Comparison, and Classification Using Spherical Polar Fourier CorrelationsLazaros Mavridis, David W. Ritchie. 281-292 [doi]
• Structural Prediction of Protein-RNA Interaction by Computational Docking with Propensity-Based Statistical PotentialsLaura Perez-Cano, Albert Solernou, Carles Pons, Juan Fernández-Recio. 293-301 [doi]
• Session IntroductionCan Alkan, Michael Brudno, Evan E. Eichler, Maricel G. Kann, Süleyman Cenk Sahinalp. 302-304 [doi]
• Improving the Prediction of Pharmacogenes Using Text-Derived Gene-Drug RelationshipsYael Garten, Nicholas P. Tatonetti, Russ B. Altman. 305-314 [doi]
• Finding Unique Filter Sets in PLATO: A Precursor to Efficient Interaction Analysis in GWAS DataBenjamin J. Grady, Eric Torstenson, Scott M. Dudek, Justin Giles, David Sexton, Marylyn D. Ritchie. 315-326 [doi]
• Enabling Personal Genomics with an Explicit Test of EpistasisCasey S. Greene, Daniel S. Himmelstein, Heather H. Nelson, Karl Kelsey, Scott M. Williams, Angeline S. Andrew, Margaret R. Karagas, Jason H. Moore. 327-336 [doi]
• Loss of Post-Translational Modification Sites in DiseaseShuyan Li, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac. 337-347 [doi]
• Detecting Genome-wide Haplotype Polymorphism by Combined Use of Mendelian Constraints and Local Population StructureXin Li, Yixuan Chen, Jing Li. 348-358 [doi]
• Sequence Feature Variant Type (SFVT) Analysis of the HLA Genetic Association in Juvenile Idiopathic ArthritisGlenys 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. 359-370 [doi]
• COKGEN: A Software for the Identification of Rare Copy Number Variation from SNP MicroarraysGökhan Yavas, Mehmet Koyutürk, Z. Meral Özsoyoglu, Meetha P. Gould, Thomas LaFramboise. 371-382 [doi]
• Session IntroductionGil Alterovitz, Silvio Cavalcanti, Taro Muso, Marco Ramoni, May Wang. 383-384 [doi]
• Co-Design in Synthetic Biology: A System-Level Analysis of the Development of an Environmental Sensing DeviceDavid A. Ball, Matthew W. Lux, Russell R. Graef, Matthew W. Peterson, Jane D. Valenti, John Dileo, Jean Peccoud. 385-396 [doi]
• Critical Analysis of Transcriptional and Post-Transcriptional Regulatory Networks in Multiple MyelomaMarta Biasiolo, Mattia Forcato, Lino Possamai, Francesco Ferrari, Luca Agnelli, Marta Lionetti, Katia Todoerti, Antonino Neri, Massimo Marchiori, Stefania Bortoluzzi, Silvio Bicciato. 397-408 [doi]
• A Computational Model of Gene Expression in an Inducible Synthetic CircuitFrancesca Ceroni, Simone Furini, Silvio Cavalcanti. 409-420 [doi]
• Retrovirus HTLV-1 Gene Circuit: A Potential Oscillator for EukaryotesAlberto Corradin, Barbara Di Camillo, Francesca Rende, Vincenzo Ciminale, Gianna Toffolo, Claudio Cobelli. 421-432 [doi]
• Emulsion Based Selection of T7 Promoters of Varying ActivityEric A. Davidson, Thomas Van Blarcom, Matthew Levy, Andrew D. Ellington. 433-443 [doi]
• Clustering Context-Specific Gene Regulatory NetworksArchana Ramesh, Robert Trevino, Daniel D. Von Hoff, Seungchan Kim. 444-455 [doi]
• Writing and Compiling Code into BiochemistryAdam Shea, Brian Fett, Marc D. Riedel, Keshab Parhi. 456-464 [doi]
• Synthesis of Pharmacokinetic Pathways through Knowledge Acquisition and Automated ReasoningLuis Tari, Saadat Anwar, Shanshan Liang, Jörg Hakenberg, Chitta Baral. 465-476 [doi]
• In Silico BiologyRichard Goldstein, Phil Husbands, Chrisantha Fernando, Dov J. Stekel. 477-480 [doi]
• Genomic Standards Consortium Workshop: Metagenomics, Metadata and Metaanalysis (M3)Peter Sterk, Lynette Hirschman, Dawn Field, John Wooley. 481-484 [doi]
• Extraction of Genotype-Phenotype-Drug Relationships from Text: From Entity Recognition to Bioinformatics ApplicationAdrien Coulet, Nigam H. Shah, Lawrence Hunter, Chitta Baral, Russ B. Altman. 485-487 [doi]