Table of Contents

• Session IntroductionMichael Brudno, Bernard M. E. Moret, C. Randal Linder, Tandy Warnow. 1-2 [doi]
• FRESCO: Flexible Alignment with Rectangle Scoring SchemesA. V. Dalca, Michael Brudno. 3-14 [doi]
• Local Reliability Measures from Sets of Co-Optimal Multiple Sequence AlignmentsGiddy Landan, Dan Grauer. 15-24 [doi]
• The Effect of the Guide Tree on Multiple Sequence Alignments and Subsequent Phylogenetic AnalysisSerita M. Nelesen, Kevin Liu, D. Zhao, C. Randal Linder, Tandy Warnow. 25-36 [doi]
• Sensitivity Analysis for Reversal Distance and Breakpoint Reuse in Genome RearrangementsAmit U. Sinha, Jaroslaw Meller. 37-48 [doi]
• Session IntroductionDoron Betel, Christina S. Leslie, Nikolaus Rajewsky. 49-51 [doi]
• Comparing Sequence and Expression for Predicting microRNA Targets Using GenMIR3Jim C. Huang, Brendan J. Frey, Quaid Morris. 52-63 [doi]
• Analysis of Microrna-Target Interactions by a Target Structure Based Hybridization ModelDang Long, Chi Yu Chan, Ye Ding. 64-74 [doi]
• A Probabilistic Model for Small RNA Flowgram MatchingVladimir Vacic, Hailing Jin, Jian-Kang Zhu, Stefano Lonardi. 75-86 [doi]
• Session IntroductionFrancisco M. de la Vega, Gabor T. Marth, Granger G. Sutton. 87-89 [doi]
• TRELLIS+: An Effective Approach for Indexing Genome-Scale Sequences Using Suffix TreesBenjarath Phoophakdee, Mohammed Javeed Zaki. 90-101 [doi]
• Pash 2.0: Scaleable Sequence Anchoring for Next-Generation Sequencing TechnologgiesCristian Coarfa, Aleksandar Milosavljevic. 102-113 [doi]
• Population Sequencing Using Short Reads: HIV as a Case StudyVladimir Jojic, Tomer Hertz, Nebojsa Jojic. 114-125 [doi]
• Analysis of Large-Scale Sequencing of Small RNAsAndrew J. Olson, J. Brennecke, A. A. Aravin, G. J. Hannon, Ravi Sachidanandam. 126-136 [doi]
• Session IntroductionMichael Ochs, John Quackenbush, Ramana Davuluri. 137-140 [doi]
• SGDI: System for Genomic Data IntegrationVincent J. Carey, Jeff Gentry, D. Sarkar, Robert Gentleman, S. Ramaswamy. 141-152 [doi]
• Annotating Pathways of Interaction NetworksJayesh Pandey, Mehmet Koyutürk, Wojciech Szpankowski, Ananth Grama. 153-165 [doi]
• Integrating Microarray and Proteomics Data to Predict the Response of Cetuximab in Patients with Rectal CancerAnneleen Daemen, Olivier Gevaert, Tijl De Bie, Annelies Debucquoy, Jean-Pascal Machiels, Bart De Moor, Karin Haustermans. 166-177 [doi]
• A Bayesian Framework for Data and Hypotheses Driven Fusion of High Throughput Data: Application to Mouse OrganogenesisMadhuchhanda Bhattacharjee, Colin C. Pritchard, Peter Nelson. 178-189 [doi]
• Gathering the Gold Dust: Methods for Assessing the Aggregate Impact of Small Effect Genes in Genomic ScansMichael A. Province, Ingrid B. Borecki. 190-200 [doi]
• Multi-Scale Correlations in Continuous Genomic DataR. E. Thurman, William Stafford Noble, John A. Stamatoyannopoulos. 201-215 [doi]
• Analysis of MALDI-TOF Spectrometry Data for Detection of Glycan BiomarkersHabtom W. Ressom, Rency S. Varghese, Lenka Goldman, Christopher A. Loffredo, Mohamed Abdel-Hamid, Zuzana Kyselova, Yehia Mechref, Milos V. Novotny, Radoslav Goldman. 216-227 [doi]
• Session IntroductionYves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Marco Punta, Atul Butte, Maricel G. Kann. 228-230 [doi]
• System-Wide Peripheral Biomarker Discovery Using Information TheoryGil Alterovitz, Michael Xiang, Jonathan Liu, Amelia Chang, Marco Ramoni. 231-242 [doi]
• Novel Integration of Hospital Electronic Medical Records and Gene Expression Measurements to Identify Genetic Markers of MaturationDavid P. Chen, Susan C. Weber, Philip S. Constantinou, Todd A. Ferris, Henry J. Lowe, Atul J. Butte. 243-254 [doi]
• Networking Pathways Unveils Association Between Obesity and Non-Insulin Dependent Diabetes MellitusHaiyan Hu, Xiaoman Shawn Li. 255-266 [doi]
• Extracting Gene Expression Profiles Common to Colon and Pancreatic Adenocarcinoma Using Simultaneous Nonnegative Matrix FactorizationLiviu Badea. 267-278 [doi]
• Integration of Microarray and Textual Data Improves the Prognosis Prediction of Breast, Lung, and Ovarian Cancer PatientsO. Gaevert, Steven Van Vooren, Bart De Moor. 279-290 [doi]
• Mining Metabolic Networks for Optimal Drug TargetsPadmavati Sridhar, Bin Song, Tamer Kahveci, Sanjay Ranka. 291-302 [doi]
• Global Alignment of Multiple Protein Interaction NetworksRohit Singh, Jinbo Xu, Bonnie Berger. 303-314 [doi]
• Predicting DNA Methylation Susceptibility Using CpG Flanking SequencesSun Kim, Meng Li, Hyun-il Henry Paik, Kenneth P. Nephew, Huidong Shi, Robin Kramer, Dong Xu, T.-H. Huang. 315-326 [doi]
• Session IntroductionJung-Chi Liao, Jeff Reinbolt, Roy Kerckhoffs, Anuska Michailova, Peter W. Arzberger. 327-331 [doi]
• Combining Molecular Dynamics and Machine Learning to Improve Protein Function RecognitionDariya S. Glazer, Randall J. Radmer, Russ B. Altman. 332-343 [doi]
• Prediction of the Structure of G-Protein Coupled Receptors and of Bound Ligands with Applications for Drug DesignYouyong Li, William A. Goddard III. 344-353 [doi]
• Markov Chain Models of Coupled Intracellular Calcium Channels: Kronecker Structured Representations and Benchmark Stationary Distribution CalculationsHilary DeRemigio, Peter Kemper, M. Drew Lamar, Gregory D. Smith. 354-365 [doi]
• Spatially-Compressed Cardiac Myofilament Models Generate Hysteresis that Is Not Found in Real MuscleJohn Jeremy Rice, Yuhai Tu, Corrado Poggesi, Pieter P. deTombe. 366-377 [doi]
• Modeling Ventricular Interaction: A Multiscale Approach from Sarcomere Mechanics to Cardiovascular Systems HemodynamicsJoost Lumens, Tammo Delhaas, Borut Kirin, Theo Arts. 378-389 [doi]
• Sub-Micrometer Anatomical Models of the Sarcolemma of Cardiac Myocytes Based on Confocal ImagingFrank B. Sachse, Eleonora Savio-Galimberti, Joshua I. Goldhaber, John H. B. Bridge. 390-401 [doi]
• Efficient Multiscale Simulations of Circadian Rhythms Using Automated Phase Macomodelling TechniquesShatam Agarwal, Jaijeet S. Roychowdhury. 402-413 [doi]
• Integration of Multi-Scale Biosimulation Models via Light-Weight SemanticsJohn H. Gennari, Maxwell L. Neal, Brian E. Carlson, Daniel L. Cook. 414-425 [doi]
• Comparisons of Protein Family DynamicsA. J. Radar, Joshua T. Harrell. 426-437 [doi]
• Session IntroductionMartha L. Bulyk, Ernest Fraenkel, Alexander J. Hartemink, Yael Mandel-Gutfreund. 438-440 [doi]
• Functional Trends in Structural Classes of the DNA Binding Domains of Regulatory Transcription FactorsRachel Patton McCord, Martha L. Bulyk. 441-452 [doi]
• Using DNA Duplex Stability Information for Transcription Factor Binding Site DiscoveryRaluca Gordân, Alexander J. Hartemink. 453-464 [doi]
• A Parametric Joint Model of DNA-Protein Binding, Gene Expression and DNA Sequence Data to Detect Target Genes of a Transcription FactorWei Pan, Peng Wei, Arkady B. Khodursky. 465-476 [doi]
• An Analysis of Information Content Present in Protein-DNA InteractionsChristopher Kauffman, George Karypis. 477-488 [doi]
• Use of an Evolutionary Model to Provide Evidence for a Wide Heterogenity of Required Affinities Between Transcription Factors and Their Binding Sites in YeastRichard W. Lusk, Michael B. Eisen. 489-500 [doi]
• Striking Similarities in Diverse Telomerase Proteins Revealed by Combining Structure Prediction and Machine Learning ApproachesJae-Hyung Lee, Michael Hamilton, Colin Gleeson, Cornelia Caragea, Peter Zaback, Jeffry D. Sander, Xue Li, Feihong Wu, Michael Terribilini, Vasant Honavar, Drena Dobbs. 501-512 [doi]
• Session IntroductionSrinka Ghosh, Antonio Piccolboni. 513-514 [doi]
• CMARRT: A Tool of Analysis of CHIP-chip Data from Tiling Arrays by Incorporating the Correlation StructurePei Fen Kuan, Hyonho Chun, Sündüz Keles. 515-526 [doi]
• Transcript Normalization and Segmentation of Tiling Array DataGeorg Zeller, Stefan R. Henz, Sascha Laubinger, Detlef Weigel, Gunnar Rätsch. 527-538 [doi]
• GSE: A Comprehensive Database System for the Representation, Retrieval, and Analysis of Microarray DataTimothy Danford, Alex Rolfe, David K. Gifford. 539-550 [doi]
• Session IntroductionK. Bretonnel Cohen, Hong Yu, Philip E. Bourne, Lynette Hirschman. 551-555 [doi]
• Assisted Curation: Does Text Mining Really Help?Beatrice Alex, Claire Grover, Barry Haddow, Mijail Kabadjor, Ewan Klein, Michael Matthews, Stuart Roebuck, Richard Tobin, Xinglong Wang. 556-567 [doi]
• Evidence for Showing Gene/Protein Name Suggestions in Bioscience Literature Search InterfacesAnna Divoli, Marti A. Hearst, Michael A. Wooldridge. 568-579 [doi]
• Enabling Integrative Genomic Analysis of High Impact Human Diseases Through Text MiningJoel Dudley, Atul J. Butte. 580-591 [doi]
• Information Needs and the Role of Text Mining in Drug DevelopmentPhoebe M. Roberts, William S. Hayes. 592-603 [doi]
• EpiLoc: A (Working) Text-Based System for Predicting Protein Subcellular LocationScott Brady, Hagit Shatkay. 604-615 [doi]
• Filling the Gaps Between Tools and Users: A Tool Comparator, Using Protein-Protein Interactions as an ExampleYoshinobu Kano, Ngan Nguyen, Rune Sætre, Kazuhiro Yoshida, Yusuke Miyao, Yoshimasa Tsuruoka, Yuichiro Matsubayashi, Sophia Ananiadou, Jun-ichi Tsujii. 616-627 [doi]
• Comparing Usability of Matching Techniques for Normalising Biomedical Named EntitiesXinglong Wang, Michael Matthews. 628-639 [doi]
• Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic TasksJ. Gregory Caporaso, Nita Deshpande, J. Lynn Fink, Philip E. Bourne, K. Bretonnel Cohen, Lawrence Hunter. 640-651 [doi]
• BANNER: An Executable Survey of Advances in Biomedical Named Entity RecognitionRobert Leaman, Graciela Gonzalez. 652-663 [doi]