13. PSB 2008: Kohala Coast, Hawaii, USA

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
  
• 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 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 Ochs, John Quackenbush, Ramana Davuluri:
  Session Introduction. 137-140
  
• Vincent J. Carey, Jeff Gentry, Deepayan Sarkar, Robert Gentleman, S. 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
  
• R. 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, T.-H. 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, Anuska 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, M. 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 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 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
  
• 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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