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15. PSB 2010: Kamuela, Hawaii, USA
- Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Tiffany Murray, Teri E. Klein:
Biocomputing 2010: Proceedings of the Pacific Symposium, Kamuela, Hawaii, USA, 4-8 January 2010. World Scientific Publishing 2010, ISBN 978-981-4295-29-1 - Preface.
Computational Challenges in Comparative Genomics
- Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff:
Session Introduction. 1-2 - José Carlos Clemente, Jesper Jansson, Gabriel Valiente:
Accurate Taxonomic Assignment of Short Pyrosequencing Reads. 3-9 - Steven D. Essinger, Gail L. Rosen:
Benchmarking BLAST Accuracy of Genus/Phyla Classification of Metagenomic Reads. 10-20 - Haris Gavranovic, Eric Tannier:
Guided Genome Halving: Provably Optimal Solutions Provide Good Insights into the Preduplication Ancestral Genome of Saccharomyces Cerevisiae. 21-30 - Glenn Hickey, Mathieu Blanchette:
A Practical Algorithm for Estimation of the Maximum Likelihood Ancestral Reconstruction Error. 31-42 - Webb Miller, Stephen J. Wright, Yu Zhang, Stephan C. Schuster, Vanessa M. Hayes:
Optimization Methods for Selecting Founder Populations for Captive Breeding of Endangered Species. 43-53
Computational Studies of non-coding RNAs
- Rolf Backofen, Hamidreza Chitsaz, Ivo L. Hofacker, Süleyman Cenk Sahinalp, Peter F. Stadler:
Session Introduction. 54-56 - Iván Dotú, W. A. Lorenz, Pascal Van Hentenryck, Peter Clote:
RNA Structural Segmentation. 57-68 - Andreas R. Gruber, Sven Findeiß, Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler:
RNAz 2.0: Improved Noncoding RNA Detection. 69-79 - David Langenberger, Clara Bermudez-Santana, Peter F. Stadler, Steve Hoffmann:
Identification and Classification of Small RNAs in Transcriptome Sequence Data. 80-87 - Yohei Okada, Kengo Sato, Yasubumi Sakakibara:
Improvement of Structure Conservation Index with Centroid Estimators. 88-97 - Unyanee Poolsap, Yuki Kato, Tatsuya Akutsu:
Dynamic Programming Algorithms for RNA Structure Prediction with Binding Sites. 98-107 - Chris Thachuk, Ján Manuch, Arash Rafiey, Leigh-Anne Mathieson, Ladislav Stacho, Anne Condon:
An Algorithm for the Energy Barrier Problem Without Pseudoknots and Temporary Arcs. 108-119
Dynamics of Biological Networks
- Tanya Y. Berger-Wolf, Teresa M. Przytycka, Mona Singh, Donna K. Slonim:
Session Introduction. 120-122 - Leonid Chindelevitch, Chung-Shou Liao, Bonnie Berger:
Local Optimization for Global Alignment of Protein Interaction Networks. 123-132 - Salim A. Chowdhury, Mehmet Koyutürk:
Identification of Coordinately Dysregulated Subnetworks in Complex Phenotypes. 133-144 - Gang Fang, Rui Kuang, Gaurav Pandey, Michael S. Steinbach, Chad L. Myers, Vipin Kumar:
Subspace Differential Coexpression Analysis: Problem Definition and a General Approach. 145-156 - Faruck Morcos, Marcin Sikora, Mark S. Alber, Dale Kaiser, Jesús A. Izaguirre:
Estimation of Protein and Domain Interactions in the Switching Motility System of Myxococcus Xanthus. 157-165 - Saket Navlakha, Carl Kingsford:
Exploring Biological Network Dynamics with Ensembles of Graph Partitions. 166-177 - Natasa Przulj, Oleksii Kuchaiev, Aleksandar Stevanovic, Wayne B. Hayes:
Geometric Evolutionary Dynamics of Protein Interaction Networks. 178-189 - Lakshmi Venkatraman, Hanry Yu, Sourav S. Bhowmick, C. Forbes Dewey Jr., Lisa Tucker-Kellogg:
The Steady States and Dynamics of Urokinase-mediated Plasmin Activation. 190-199
Multi-resolution Modeling of Biological Macromolecules
- Samuel Flores, Julie Bernauer, Xuhui Huang, Ruhong Zhou, Seokmin Shin:
Session Introduction. 200-204 - Olivier Delalande, Nicolas Férey, Benoist Laurent, Marc Gueroult, Brigitte Hartmann, Marc Baaden:
Multi-Resolution Approach for Interactively Locating Functionally Linked Ion Binding Sites by Steering Small Molecules into Electrostatic Potential Maps Using a Haptic Device. 205-215 - Samuel Flores, Yaqi Wan, Rick Russell, Russ B. Altman:
Predicting RNA Structure by Multiple Template Homology Modeling. 216-227 - Xuhui Huang, Yuan Yao, Gregory R. Bowman, Jian Sun, Leonidas J. Guibas, Gunnar E. Carlsson, Vijay S. Pande:
Constructing Multi-Resolution Markov State Models (MSMs) to Elucidate RNA Hairpin Folding Mechanisms. 228-239 - Jesús A. Izaguirre, Christopher R. Sweet, Vijay S. Pande:
Multiscale Dynamics of Macromolecules Using Normal Mode Langevin. 240-251 - Nir Kalisman, Michael Levitt:
Insights into the Intra-Ring Subunit Order of TriC/CCT: Structural and Evolutionary Analysis. 252-259 - Peter M. Kasson, Vijay S. Pande:
Cross-Graining: Efficient Multi-Scale Simulation via Markov State Models. 260-268 - Ying Liu, Ivet Bahar:
Toward Understanding Allosteric Signaling Mechanisms in the ATPase Domain of Molecular Chaperones. 269-280 - Lazaros Mavridis, David W. Ritchie:
3D-Blast: 3D Protein Structure Alignment, Comparison, and Classification Using Spherical Polar Fourier Correlations. 281-292 - Laura Perez-Cano, Albert Solernou, Carles Pons, Juan Fernández-Recio:
Structural Prediction of Protein-RNA Interaction by Computational Docking with Propensity-Based Statistical Potentials. 293-301
Personal Genomics
- Can Alkan, Michael Brudno, Evan E. Eichler, Maricel G. Kann, Süleyman Cenk Sahinalp:
Session Introduction. 302-304 - Yael Garten, Nicholas P. Tatonetti, Russ B. Altman:
Improving the Prediction of Pharmacogenes Using Text-Derived Gene-Drug Relationships. 305-314 - Benjamin J. Grady, Eric Torstenson, Scott M. Dudek, Justin Giles, David Sexton, Marylyn D. Ritchie:
Finding Unique Filter Sets in PLATO: A Precursor to Efficient Interaction Analysis in GWAS Data. 315-326 - Casey S. Greene, Daniel S. Himmelstein, Heather H. Nelson, Karl T. Kelsey, Scott M. Williams, Angeline S. Andrew, Margaret R. Karagas, Jason H. Moore:
Enabling Personal Genomics with an Explicit Test of Epistasis. 327-336 - Shuyan Li, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac:
Loss of Post-Translational Modification Sites in Disease. 337-347 - Xin Li, Yixuan Chen, Jing Li:
Detecting Genome-wide Haplotype Polymorphism by Combined Use of Mendelian Constraints and Local Population Structure. 348-358 - 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:
Sequence Feature Variant Type (SFVT) Analysis of the HLA Genetic Association in Juvenile Idiopathic Arthritis. 359-370 - Gökhan Yavas, Mehmet Koyutürk, Z. Meral Özsoyoglu, Meetha P. Gould, Thomas LaFramboise:
COKGEN: A Software for the Identification of Rare Copy Number Variation from SNP Microarrays. 371-382
Reverse Engineering and Synthesis of Biomolecular Systems
- Gil Alterovitz, Silvio Cavalcanti, Taro Muso, Marco Ramoni, May Wang:
Session Introduction. 383-384 - David A. Ball, Matthew W. Lux, Russell R. Graef, Matthew W. Peterson, Jane D. Valenti, John Dileo, Jean Peccoud:
Co-Design in Synthetic Biology: A System-Level Analysis of the Development of an Environmental Sensing Device. 385-396 - Marta Biasiolo, Mattia Forcato, Lino Possamai, Francesco Ferrari, Luca Agnelli, Marta Lionetti, Katia Todoerti, Antonino Neri, Massimo Marchiori, Stefania Bortoluzzi, Silvio Bicciato:
Critical Analysis of Transcriptional and Post-Transcriptional Regulatory Networks in Multiple Myeloma. 397-408 - Francesca Ceroni, Simone Furini, Silvio Cavalcanti:
A Computational Model of Gene Expression in an Inducible Synthetic Circuit. 409-420 - Alberto Corradin, Barbara Di Camillo, Francesca Rende, Vincenzo Ciminale, Gianna Toffolo, Claudio Cobelli:
Retrovirus HTLV-1 Gene Circuit: A Potential Oscillator for Eukaryotes. 421-432 - Eric A. Davidson, Thomas Van Blarcom, Matthew Levy, Andrew D. Ellington:
Emulsion Based Selection of T7 Promoters of Varying Activity. 433-443 - Archana Ramesh, Robert P. Trevino, Daniel D. Von Hoff, Seungchan Kim:
Clustering Context-Specific Gene Regulatory Networks. 444-455 - Adam Shea, Brian Fett, Marc D. Riedel, Keshab K. Parhi:
Writing and Compiling Code into Biochemistry. 456-464 - Luis Tari, Saadat Anwar, Shanshan Liang, Jörg Hakenberg, Chitta Baral:
Synthesis of Pharmacokinetic Pathways through Knowledge Acquisition and Automated Reasoning. 465-476
Workshops
- Richard A. Goldstein, Phil Husbands, Chrisantha Fernando, Dov J. Stekel:
In Silico Biology. 477-480 - Peter Sterk, Lynette Hirschman, Dawn Field, John C. Wooley:
Genomic Standards Consortium Workshop: Metagenomics, Metadata and Metaanalysis (M3). 481-484 - Adrien Coulet, Nigam H. Shah, Lawrence Hunter, Chitta Baral, Russ B. Altman:
Extraction of Genotype-Phenotype-Drug Relationships from Text: From Entity Recognition to Bioinformatics Application. 485-487
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