13. PSB 2008:
Kohala Coast,
Hawaii,
USA
Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Tiffany Murray, Teri E. Klein (Eds.):
Biocomputing 2008, Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, 4-8 January 2008.
World Scientific 2008, ISBN 978-981-277-608-2 BibTeX
Beyond Gap Models:
Reconstructing Alignments and Phylogenies Under Genomic-Scale Events
- Michael Brudno, Bernard M. E. Moret, C. Randal Linder, Tandy Warnow:
Session Introduction.
1-2
Electronic Edition (link) BibTeX
- A. V. Dalca, Michael Brudno:
FRESCO: Flexible Alignment with Rectangle Scoring Schemes.
3-14
Electronic Edition (link) BibTeX
- Giddy Landan, Dan Grauer:
Local Reliability Measures from Sets of Co-Optimal Multiple Sequence Alignments.
15-24
Electronic Edition (link) BibTeX
- Serita M. Nelesen, Kevin Liu, D. Zhao, C. Randal Linder, Tandy Warnow:
The Effect of the Guide Tree on Multiple Sequence Alignments and Subsequent Phylogenetic Analysis.
25-36
Electronic Edition (link) BibTeX
- Amit U. Sinha, Jaroslaw Meller:
Sensitivity Analysis for Reversal Distance and Breakpoint Reuse in Genome Rearrangements.
37-48
Electronic Edition (link) BibTeX
Computational Challenges in the Study of Small Regulatory RNAs
Computational Tools for Next-Generation Sequencing Applications
- Francisco M. de la Vega, Gabor T. Marth, Granger G. Sutton:
Session Introduction.
87-89
Electronic Edition (link) BibTeX
- Benjarath Phoophakdee, Mohammed Javeed Zaki:
TRELLIS+: An Effective Approach for Indexing Genome-Scale Sequences Using Suffix Trees.
90-101
Electronic Edition (link) BibTeX
- Cristian Coarfa, Aleksandar Milosavljevic:
Pash 2.0: Scaleable Sequence Anchoring for Next-Generation Sequencing Technologgies.
102-113
Electronic Edition (link) BibTeX
- Vladimir Jojic, Tomer Hertz, Nebojsa Jojic:
Population Sequencing Using Short Reads: HIV as a Case Study.
114-125
Electronic Edition (link) BibTeX
- A. J. Olson, J. Brennecke, A. A. Aravin, G. J. Hannon, R. Sachidanandam:
Analysis of Large-Scale Sequencing of Small RNAs.
126-136
Electronic Edition (link) BibTeX
Knowledge-Driven Analysis and Data Integration for High-Throughput Biological Data
- Michael Ochs, John Quackenbush, Ramana Davuluri:
Session Introduction.
137-140
Electronic Edition (link) BibTeX
- V. J. Carey, Jeff Gentry, D. Sarkar, Robert Gentleman, S. Ramaswamy:
SGDI: System for Genomic Data Integration.
141-152
Electronic Edition (link) BibTeX
- Jayesh Pandey, Mehmet Koyutürk, Wojciech Szpankowski, Ananth Grama:
Annotating Pathways of Interaction Networks.
153-165
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Madhuchhanda Bhattacharjee, Colin C. Pritchard, Peter Nelson:
A Bayesian Framework for Data and Hypotheses Driven Fusion of High Throughput Data: Application to Mouse Organogenesis.
178-189
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- R. E. Thurman, William Stafford Noble, John A. Stamatoyannopoulos:
Multi-Scale Correlations in Continuous Genomic Data.
201-215
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
Molecular Bioinformatics for Diseases:
Protein Interactions and Phenomics
- Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Marco Punta, Atul Butte, Maricel G. Kann:
Session Introduction.
228-230
Electronic Edition (link) BibTeX
- Gil Alterovitz, Michael Xiang, Jonathan Liu, Amelia Chang, Marco Ramoni:
System-Wide Peripheral Biomarker Discovery Using Information Theory.
231-242
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Haiyan Hu, Xiaoman Shawn Li:
Networking Pathways Unveils Association Between Obesity and Non-Insulin Dependent Diabetes Mellitus.
255-266
Electronic Edition (link) BibTeX
- Liviu Badea:
Extracting Gene Expression Profiles Common to Colon and Pancreatic Adenocarcinoma Using Simultaneous Nonnegative Matrix Factorization.
267-278
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Padmavati Sridhar, Bin Song, Tamer Kahveci, Sanjay Ranka:
Mining Metabolic Networks for Optimal Drug Targets.
291-302
Electronic Edition (link) BibTeX
- Rohit Singh, Jinbo Xu, Bonnie Berger:
Global Alignment of Multiple Protein Interaction Networks.
303-314
Electronic Edition (link) BibTeX
- Sun Kim, Meng Li, Hyun-il Henry Paik, Kenneth P. Nephew, Huidong Shi, Robin Kramer, Dong Xu, T.-H. Huang:
Predicting DNA Methylation Susceptibility Using CpG Flanking Sequences.
315-326
Electronic Edition (link) BibTeX
Multiscale Modeling and Simulation:
From Molecules to Cells to Organisms?
- Jung-Chi Liao, Jeff Reinbolt, Roy Kerckhoffs, Anuska Michailova, Peter W. Arzberger:
Session Introduction.
327-331
Electronic Edition (link) BibTeX
- Dariya S. Glazer, Randall J. Radmer, Russ B. Altman:
Combining Molecular Dynamics and Machine Learning to Improve Protein Function Recognition.
332-343
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Hilary DeRemigio, Peter Kemper, M. Drew Lamar, Gregory D. Smith:
Markov Chain Models of Coupled Intracellular Calcium Channels: Kronecker Structured Representations and Benchmark Stationary Distribution Calculations.
354-365
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Joost Lumens, Tammo Delhaas, Borut Kirin, Theo Arts:
Modeling Ventricular Interaction: A Multiscale Approach from Sarcomere Mechanics to Cardiovascular Systems Hemodynamics.
378-389
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Shatam Agarwal, Jaijeet S. Roychowdhury:
Efficient Multiscale Simulations of Circadian Rhythms Using Automated Phase Macomodelling Techniques.
402-413
Electronic Edition (link) BibTeX
- John H. Gennari, Maxwell L. Neal, Brian E. Carlson, Daniel L. Cook:
Integration of Multi-Scale Biosimulation Models via Light-Weight Semantics.
414-425
Electronic Edition (link) BibTeX
- A. J. Radar, Joshua T. Harrell:
Comparisons of Protein Family Dynamics.
426-437
Electronic Edition (link) BibTeX
Protein-Nucleic Acid Interactions:
Integrating Structure,
Sequence,
and Function
- Martha L. Bulyk, Ernest Fraenkel, Alexander J. Hartemink, Yael Mandel-Gutfreund:
Session Introduction.
438-440
Electronic Edition (link) BibTeX
- Rachel Patton McCord, Martha L. Bulyk:
Functional Trends in Structural Classes of the DNA Binding Domains of Regulatory Transcription Factors.
441-452
Electronic Edition (link) BibTeX
- Raluca Gordân, Alexander J. Hartemink:
Using DNA Duplex Stability Information for Transcription Factor Binding Site Discovery.
453-464
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Christopher Kauffman, George Karypis:
An Analysis of Information Content Present in Protein-DNA Interactions.
477-488
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Jae-Hyung Lee, Michael Hamilton, Colin Gleeson, Cornelia Caragea, Peter Zaback, Jeffry D. Sander, Xue Li, Feihong Wu, Michael Terribilini, Vasant Honavar, Drena Dobbs:
Striking Similarities in Diverse Telomerase Proteins Revealed by Combining Structure Prediction and Machine Learning Approaches.
501-512
Electronic Edition (link) BibTeX
Tiling Microarray Data Analysis Methods and Algorithms
- Srinka Ghosh, Antonio Piccolboni:
Session Introduction.
513-514
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Georg Zeller, Stefan R. Henz, Sascha Laubinger, Detlef Weigel, Gunnar Rätsch:
Transcript Normalization and Segmentation of Tiling Array Data.
527-538
Electronic Edition (link) BibTeX
- Timothy Danford, Alex Rolfe, David K. Gifford:
GSE: A Comprehensive Database System for the Representation, Retrieval, and Analysis of Microarray Data.
539-550
Electronic Edition (link) BibTeX
Translating Biology:
Text Mining Tools That Work
- K. Bretonnel Cohen, Hong Yu, Philip E. Bourne, Lynette Hirschman:
Session Introduction.
551-555
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Anna Divoli, Marti A. Hearst, Michael A. Wooldridge:
Evidence for Showing Gene/Protein Name Suggestions in Bioscience Literature Search Interfaces.
568-579
Electronic Edition (link) BibTeX
- Joel Dudley, Atul J. Butte:
Enabling Integrative Genomic Analysis of High Impact Human Diseases Through Text Mining.
580-591
Electronic Edition (link) BibTeX
- Phoebe M. Roberts, William S. Hayes:
Information Needs and the Role of Text Mining in Drug Development.
592-603
Electronic Edition (link) BibTeX
- Scott Brady, Hagit Shatkay:
EpiLoc: A (Working) Text-Based System for Predicting Protein Subcellular Location.
604-615
Electronic Edition (link) BibTeX
- Yoshinobu Kano, Ngan Nguyen, Rune Sætre, Kazuhiro Yoshida, Yusuke Miyao, Yoshimasa Tsuruoka, Yuichiro 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
Electronic Edition (link) BibTeX
- Xinglong Wang, Michael Matthews:
Comparing Usability of Matching Techniques for Normalising Biomedical Named Entities.
628-639
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Robert Leaman, Graciela Gonzalez:
BANNER: An Executable Survey of Advances in Biomedical Named Entity Recognition.
652-663
Electronic Edition (link) BibTeX
Copyright © Sat May 16 23:35:21 2009
by Michael Ley (ley@uni-trier.de)
