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ORCID13. PSB 2008: Kohala Coast, Hawaii, USA
- Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Tiffany Murray, Teri E. Klein:
Biocomputing 2008, Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, 4-8 January 2008. World Scientific 2008, ISBN 978-981-277-608-2
Beyond Gap Models: Reconstructing Alignments and Phylogenies Under Genomic-Scale Events
- Michael Brudno, Bernard M. E. Moret, C. Randal Linder, Tandy J. Warnow:
Session Introduction. 1-2 - Adrian V. Dalca, Michael Brudno:
FRESCO: Flexible Alignment with Rectangle Scoring Schemes. 3-14 - Giddy Landan, Dan Graur:
Local Reliability Measures from Sets of Co-Optimal Multiple Sequence Alignments. 15-24 - Serita M. Nelesen, Kevin Liu, D. Zhao, C. Randal Linder, Tandy J. Warnow:
The Effect of the Guide Tree on Multiple Sequence Alignments and Subsequent Phylogenetic Analysis. 25-36 - Amit U. Sinha, Jaroslaw Meller:
Sensitivity Analysis for Reversal Distance and Breakpoint Reuse in Genome Rearrangements. 37-48
Computational Challenges in the Study of Small Regulatory RNAs
- Doron Betel, Christina S. Leslie, Nikolaus Rajewsky:
Session Introduction. 49-51 - Jim C. Huang, Brendan J. Frey, Quaid Morris:
Comparing Sequence and Expression for Predicting microRNA Targets Using GenMIR3. 52-63 - Dang D. Long, Chi Yu Chan, Ye Ding:
Analysis of Microrna-Target Interactions by a Target Structure Based Hybridization Model. 64-74 - Vladimir Vacic, Hailing Jin, Jian-Kang Zhu, Stefano Lonardi:
A Probabilistic Model for Small RNA Flowgram Matching. 75-86
Computational Tools for Next-Generation Sequencing Applications
- Francisco M. de la Vega, Gabor T. Marth, Granger G. Sutton:
Session Introduction. 87-89 - Benjarath Phoophakdee, Mohammed Javeed Zaki:
TRELLIS+: An Effective Approach for Indexing Genome-Scale Sequences Using Suffix Trees. 90-101 - Cristian Coarfa, Aleksandar Milosavljevic:
Pash 2.0: Scaleable Sequence Anchoring for Next-Generation Sequencing Technologgies. 102-113 - Vladimir Jojic, Tomer Hertz, Nebojsa Jojic:
Population Sequencing Using Short Reads: HIV as a Case Study. 114-125 - Andrew J. Olson, J. Brennecke, A. A. Aravin, G. J. Hannon, Ravi Sachidanandam:
Analysis of Large-Scale Sequencing of Small RNAs. 126-136
Knowledge-Driven Analysis and Data Integration for High-Throughput Biological Data
- Michael F. Ochs, John Quackenbush, Ramana Davuluri:
Session Introduction. 137-140 - Vincent J. Carey, Jeff Gentry, Deepayan Sarkar, Robert Gentleman, Srini Ramaswamy:
SGDI: System for Genomic Data Integration. 141-152 - Jayesh Pandey, Mehmet Koyutürk, Wojciech Szpankowski, Ananth Grama:
Annotating Pathways of Interaction Networks. 153-165 - Anneleen Daemen, Olivier Gevaert, Tijl De Bie, Annelies Debucquoy, Jean-Pascal Machiels, Bart De Moor, Karin Haustermans:
Integrating Microarray and Proteomics Data to Predict the Response of Cetuximab in Patients with Rectal Cancer. 166-177 - Madhuchhanda Bhattacharjee, Colin C. Pritchard, Peter S. Nelson:
A Bayesian Framework for Data and Hypotheses Driven Fusion of High Throughput Data: Application to Mouse Organogenesis. 178-189 - Michael A. Province, Ingrid B. Borecki:
Gathering the Gold Dust: Methods for Assessing the Aggregate Impact of Small Effect Genes in Genomic Scans. 190-200 - Robert E. Thurman, William Stafford Noble, John A. Stamatoyannopoulos:
Multi-Scale Correlations in Continuous Genomic Data. 201-215 - Habtom W. Ressom, Rency S. Varghese, Lenka Goldman, Christopher A. Loffredo, Mohamed Abdel-Hamid, Zuzana Kyselova, Yehia Mechref, Milos V. Novotny, Radoslav Goldman:
Analysis of MALDI-TOF Spectrometry Data for Detection of Glycan Biomarkers. 216-227
Molecular Bioinformatics for Diseases: Protein Interactions and Phenomics
- Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Marco Punta, Atul J. Butte, Maricel G. Kann:
Session Introduction. 228-230 - Gil Alterovitz, Michael Xiang, Jonathan Liu, Amelia Chang, Marco Ramoni:
System-Wide Peripheral Biomarker Discovery Using Information Theory. 231-242 - David P. Chen, Susan C. Weber, Philip S. Constantinou, Todd A. Ferris, Henry J. Lowe, Atul J. Butte:
Novel Integration of Hospital Electronic Medical Records and Gene Expression Measurements to Identify Genetic Markers of Maturation. 243-254 - Haiyan Hu, Xiaoman Shawn Li:
Networking Pathways Unveils Association Between Obesity and Non-Insulin Dependent Diabetes Mellitus. 255-266 - Liviu Badea:
Extracting Gene Expression Profiles Common to Colon and Pancreatic Adenocarcinoma Using Simultaneous Nonnegative Matrix Factorization. 267-278 - O. Gaevert, Steven Van Vooren, Bart De Moor:
Integration of Microarray and Textual Data Improves the Prognosis Prediction of Breast, Lung, and Ovarian Cancer Patients. 279-290 - Padmavati Sridhar, Bin Song, Tamer Kahveci, Sanjay Ranka:
Mining Metabolic Networks for Optimal Drug Targets. 291-302 - Rohit Singh, Jinbo Xu, Bonnie Berger:
Global Alignment of Multiple Protein Interaction Networks. 303-314 - Sun Kim, Meng Li, Hyun-il Henry Paik, Kenneth P. Nephew, Huidong Shi, Robin Kramer, Dong Xu, Tim Hui-Ming Huang:
Predicting DNA Methylation Susceptibility Using CpG Flanking Sequences. 315-326
Multiscale Modeling and Simulation: From Molecules to Cells to Organisms?
- Jung-Chi Liao, Jeff Reinbolt, Roy Kerckhoffs, Anushka Michailova, Peter W. Arzberger:
Session Introduction. 327-331 - Dariya S. Glazer, Randall J. Radmer, Russ B. Altman:
Combining Molecular Dynamics and Machine Learning to Improve Protein Function Recognition. 332-343 - Youyong Li, William A. Goddard III:
Prediction of the Structure of G-Protein Coupled Receptors and of Bound Ligands with Applications for Drug Design. 344-353 - Hilary DeRemigio, Peter Kemper, Michael Drew Lamar, Gregory D. Smith:
Markov Chain Models of Coupled Intracellular Calcium Channels: Kronecker Structured Representations and Benchmark Stationary Distribution Calculations. 354-365 - John Jeremy Rice, Yuhai Tu, Corrado Poggesi, Pieter P. deTombe:
Spatially-Compressed Cardiac Myofilament Models Generate Hysteresis that Is Not Found in Real Muscle. 366-377 - Joost Lumens, Tammo Delhaas, Borut Kirin, Theo Arts:
Modeling Ventricular Interaction: A Multiscale Approach from Sarcomere Mechanics to Cardiovascular Systems Hemodynamics. 378-389 - Frank B. Sachse, Eleonora Savio-Galimberti, Joshua I. Goldhaber, John H. B. Bridge:
Sub-Micrometer Anatomical Models of the Sarcolemma of Cardiac Myocytes Based on Confocal Imaging. 390-401 - Shatam Agarwal, Jaijeet S. Roychowdhury:
Efficient Multiscale Simulations of Circadian Rhythms Using Automated Phase Macomodelling Techniques. 402-413 - John H. Gennari, Maxwell Lewis Neal, Brian E. Carlson, Daniel L. Cook:
Integration of Multi-Scale Biosimulation Models via Light-Weight Semantics. 414-425 - A. J. Radar, Joshua T. Harrell:
Comparisons of Protein Family Dynamics. 426-437
Protein-Nucleic Acid Interactions: Integrating Structure, Sequence, and Function
- Martha L. Bulyk, Ernest Fraenkel, Alexander J. Hartemink, Yael Mandel-Gutfreund:
Session Introduction. 438-440 - Rachel Patton McCord, Martha L. Bulyk:
Functional Trends in Structural Classes of the DNA Binding Domains of Regulatory Transcription Factors. 441-452 - Raluca Gordân, Alexander J. Hartemink:
Using DNA Duplex Stability Information for Transcription Factor Binding Site Discovery. 453-464 - Wei Pan, Peng Wei, Arkady B. Khodursky:
A Parametric Joint Model of DNA-Protein Binding, Gene Expression and DNA Sequence Data to Detect Target Genes of a Transcription Factor. 465-476 - Christopher Kauffman, George Karypis
:
An Analysis of Information Content Present in Protein-DNA Interactions. 477-488 - Richard W. Lusk, Michael B. Eisen:
Use of an Evolutionary Model to Provide Evidence for a Wide Heterogenity of Required Affinities Between Transcription Factors and Their Binding Sites in Yeast. 489-500 - Jae-Hyung Lee, Michael Hamilton, Colin Gleeson, Cornelia Caragea, Peter Zaback, Jeffry D. Sander, Li C. Xue, Feihong Wu, Michael Terribilini, Vasant G. Honavar, Drena Dobbs:
Striking Similarities in Diverse Telomerase Proteins Revealed by Combining Structure Prediction and Machine Learning Approaches. 501-512
Tiling Microarray Data Analysis Methods and Algorithms
- Srinka Ghosh, Antonio Piccolboni:
Session Introduction. 513-514 - Pei Fen Kuan, Hyonho Chun, Sündüz Keles:
CMARRT: A Tool of Analysis of CHIP-chip Data from Tiling Arrays by Incorporating the Correlation Structure. 515-526 - Georg Zeller, Stefan R. Henz, Sascha Laubinger, Detlef Weigel, Gunnar Rätsch:
Transcript Normalization and Segmentation of Tiling Array Data. 527-538 - Timothy Danford, P. Alexander Rolfe, David K. Gifford:
GSE: A Comprehensive Database System for the Representation, Retrieval, and Analysis of Microarray Data. 539-550
Translating Biology: Text Mining Tools That Work
- K. Bretonnel Cohen, Hong Yu, Philip E. Bourne, Lynette Hirschman:
Session Introduction. 551-555 - Beatrice Alex, Claire Grover, Barry Haddow, Mijail Kabadjor, Ewan Klein, Michael Matthews, Stuart Roebuck, Richard Tobin, Xinglong Wang:
Assisted Curation: Does Text Mining Really Help?. 556-567 - Anna Divoli, Marti A. Hearst, Michael A. Wooldridge:
Evidence for Showing Gene/Protein Name Suggestions in Bioscience Literature Search Interfaces. 568-579 - Joel Dudley, Atul J. Butte:
Enabling Integrative Genomic Analysis of High Impact Human Diseases Through Text Mining. 580-591 - Phoebe M. Roberts, William S. Hayes:
Information Needs and the Role of Text Mining in Drug Development. 592-603 - Scott Brady, Hagit Shatkay:
EpiLoc: A (Working) Text-Based System for Predicting Protein Subcellular Location. 604-615 - Yoshinobu Kano, Ngan L. T. Nguyen, Rune Sætre, Kazuhiro Yoshida, Yusuke Miyao, Yoshimasa Tsuruoka, Yuichiroh Matsubayashi, Sophia Ananiadou, Jun'ichi Tsujii:
Filling the Gaps Between Tools and Users: A Tool Comparator, Using Protein-Protein Interactions as an Example. 616-627 - Xinglong Wang, Michael Matthews:
Comparing Usability of Matching Techniques for Normalising Biomedical Named Entities. 628-639 - J. Gregory Caporaso, Nita Deshpande, J. Lynn Fink, Philip E. Bourne, K. Bretonnel Cohen, Lawrence Hunter:
Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic Tasks. 640-651 - Robert Leaman, Graciela Gonzalez:
BANNER: An Executable Survey of Advances in Biomedical Named Entity Recognition. 652-663
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