Table of Contents

• ISMB 2005H. V. Jagadish, David J. States, Burkhard Rost. 1-2 [doi]
• ISMB 2005 OrganizationH. V. Jagadish, David J. States, Burkhard Rost. 3-6 [doi]
• Conservative extraction of over-represented extensible motifsAlberto Apostolico, Matteo Comin, Laxmi Parida. 9-18 [doi]
• Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in ::::Escherichia coli::::Grégory Batt, Delphine Ropers, Hidde de Jong, Johannes Geiselmann, Radu Mateescu, Michel Page, Dominique Schneider. 19-28 [doi]
• A systematic approach for comprehensive T-cell epitope discovery using peptide librariesTim Beißbarth, Jason A. Tye-Din, Gordon K. Smyth, Terence P. Speed, Robert P. Anderson. 29-37 [doi]
• Kernel methods for predicting protein-protein interactionsAsa Ben-Hur, William Stafford Noble. 38-46 [doi]
• Protein function prediction via graph kernelsKarsten M. Borgwardt, Cheng Soon Ong, Stefan Schönauer, S. V. N. Vishwanathan, Alexander J. Smola, Hans-Peter Kriegel. 47-56 [doi]
• ExonHunter: a comprehensive approach to gene findingBrona Brejová, Daniel G. Brown, Ming Li, Tomás Vinar. 57-65 [doi]
• Improving protein structure prediction with model-based searchT. J. Brunette, Oliver Brock. 66-74 [doi]
• Three-stage prediction of protein ?-sheets by neural networks, alignments and graph algorithmsJianlin Cheng, Pierre Baldi. 75-84 [doi]
• YeastHub: a semantic web use case for integrating data in the life sciences domainKei-Hoi Cheung, Kevin Y. Yip, Andrew K. Smith, Remko de Knikker, Andy Masiar, Mark Gerstein. 85-96 [doi]
• Maximum likelihood of evolutionary trees: hardness and approximationBenny Chor, Tamir Tuller. 97-106 [doi]
• ANOSVA: a statistical method for detecting splice variation from expression dataMelissa S. Cline, John Blume, Simon Cawley, Tyson Clark, Jing-Shan Hu, Gang Lu, Nathan Salomonis, Hui Wang, Alan Williams. 107-115 [doi]
• A path planning approach for computing large-amplitude motions of flexible moleculesJuan Cortés, Thierry Siméon, Vicente Ruiz de Angulo, David Guieysse, Magali Remaud-Siméon, Vinh Tran. 116-125 [doi]
• Detecting coevolving amino acid sites using Bayesian mutational mappingMatthew W. Dimmic, Melissa J. Hubisz, Carlos Bustamante, Rasmus Nielsen. 126-135 [doi]
• A procedure for assessing GO annotation consistencyMary E. Dolan, Li Ni, Evelyn Camon, Judith A. Blake. 136-143 [doi]
• Multi-way clustering of microarray data using probabilistic sparse matrix factorizationDelbert Dueck, Quaid Morris, Brendan J. Frey. 144-151 [doi]
• PILER: identification and classification of genomic repeatsRobert C. Edgar, Eugene W. Myers. 152-158 [doi]
• Clustering short time series gene expression dataJason Ernst, Gerard J. Nau, Ziv Bar-Joseph. 159-168 [doi]
• CaSPredictor: a new computer-based tool for caspase substrate predictionHumberto Miguel Garay-Malpartida, Jõao Marcelo Occhiucci, Juliano Alves, José Ernersto Belizário. 169-176 [doi]
• Data integration and visualization system for enabling conceptual biologyPeddinti V. Gopalacharyulu, Erno Lindfors, Catherine Bounsaythip, Teemu Kivioja, Laxman Yetukuri, Jaakko Hollmén, Matej Oresic. 177-185 [doi]
• Identification of nine human-specific frameshift mutations by comparative analysis of the human and the chimpanzee genome sequencesYoonsoo Hahn, Byungkook Lee. 186-194 [doi]
• Tag SNP selection in genotype data for maximizing SNP prediction accuracyEran Halperin, Gad Kimmel, Ron Shamir. 195-203 [doi]
• Enhanced position weight matrices using mixture modelsSridhar Hannenhalli, Li-San Wang. 204-212 [doi]
• Mining coherent dense subgraphs across massive biological networks for functional discoveryHaiyan Hu, Xifeng Yan, Yu Huang 0003, Jiawei Han, Xianghong Jasmine Zhou. 213-221 [doi]
• GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray dataJim C. Huang, Quaid Morris, Timothy R. Hughes, Brendan J. Frey. 222-231 [doi]
• Modeling the organization of the WUSCHEL expression domain in the shoot apical meristemHenrik Jönsson, Marcus Heisler, G. Venugopala Reddy, Vikas Agrawal, Victoria Gor, Bruce E. Shapiro, Eric Mjolsness, Elliot M. Meyerowitz. 232-240 [doi]
• Predicting protein-protein interaction by searching evolutionary tree automorphism spaceRaja Jothi, Maricel G. Kann, Teresa M. Przytycka. 241-250 [doi]
• An HMM posterior decoder for sequence feature prediction that includes homology informationLukas Käll, Anders Krogh, Erik L. L. Sonnhammer. 251-257 [doi]
• Prediction of active sites for protein structures from computed chemical propertiesJaeju Ko, Leonel F. Murga, Ying Wei, Mary Jo Ondrechen. 258-265 [doi]
• High-recall protein entity recognition using a dictionaryZhenzhen Kou, William W. Cohen, Robert F. Murphy. 266-273 [doi]
• A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequencesWei Li, Clifford A. Meyer, X. Shirley Liu. 274-282 [doi]
• Improved detection of DNA motifs using a self-organized clustering of familial binding profilesShaun Mahony, Aaron Golden, Terry J. Smith, Panayiotis V. Benos. 283-291 [doi]
• High-throughput inference of protein-protein interfaces from unassigned NMR dataRamgopal R. Mettu, Ryan H. Lilien, Bruce Randall Donald. 292-301 [doi]
• Whole-proteome prediction of protein function via graph-theoretic analysis of interaction mapsElena Nabieva, Kam Jim, Amit Agarwal, Bernard Chazelle, Mona Singh. 302-310 [doi]
• Beyond the clause: extraction of phosphorylation information from medline abstractsMeenakshi Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker. 319-327 [doi]
• Predicting the ::::in vivo:::: signature of human gene regulatory sequenceWilliam Stafford Noble, Scott Kuehn, Robert Thurman, Man Yu, John A. Stamatoyannopoulos. 328-343 [doi]
• ::::In silico:::: identification of functional regions in proteinsGuy Nimrod, Fabian Glaser, David Steinberg, Nir Ben-Tal, Tal Pupko. 328-337 [doi]
• Statistics of local multiple alignmentsAmol Prakash, Martin Tompa. 344-350 [doi]
• ::::De novo:::: identification of repeat families in large genomesAlkes L. Price, Neil C. Jones, Pavel A. Pevzner. 351-358 [doi]
• Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activitySanjay Joshua Swamidass, Jonathan H. Chen, Jocelyne Bruand, Peter Phung, Liva Ralaivola, Pierre Baldi. 359-368 [doi]
• RASE: recognition of alternatively spliced exons in ::::C.elegans::::Gunnar Rätsch, Sören Sonnenburg, Bernhard Schölkopf. 369-377 [doi]
• Families of membranous proteins can be characterized by the amino acid composition of their transmembrane domainsTali Sadka, Michal Linial. 378-386 [doi]
• A motif-based framework for recognizing sequence familiesRoded Sharan, Eugene W. Myers. 387-393 [doi]
• Search for folding nuclei in native protein structuresAlena Shmygelska. 394-402 [doi]
• Mining ChIP-chip data for transcription factor and cofactor binding sitesAndrew D. Smith, Pavel Sumazin, Debopriya Das, Michael Q. Zhang. 403-412 [doi]
• Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolutionYun S. Song, Yufeng Wu, Dan Gusfield. 413-422 [doi]
• Robust classification modeling on microarray data using misclassification penalized posteriorMat Soukup, HyungJun Cho, Jae K. Lee. 423-430 [doi]
• Automated interpretation of MS/MS spectra of oligosaccharidesHaixu Tang, Yehia Mechref, Milos V. Novotny. 431-439 [doi]
• Alignments anchored on genomic landmarks can aid in the identification of regulatory elementsKannan Tharakaraman, Leonardo Mariño-Ramírez, Sergey Sheetlin, David Landsman, John L. Spouge. 440-448 [doi]
• How old is your fold?Henry F. Winstanley, Sanne Abeln, Charlotte M. Deane. 449-458 [doi]
• Experimental design for three-color and four-color gene expression microarraysYong Woo, Winfried Krueger, Anupinder Kaur, Gary A. Churchill. 459-467 [doi]
• Supervised enzyme network inference from the integration of genomic data and chemical informationYoshihiro Yamanishi, Jean-Philippe Vert, Minoru Kanehisa. 468-477 [doi]
• Automatic detection of subsystem/pathway variants in genome analysisYuzhen Ye, Andrei Osterman, Ross A. Overbeek, Adam Godzik. 478-486 [doi]
• Bayesian neural network approaches to ovarian cancer identification from high-resolution mass spectrometry dataJiangsheng Yu, Xue-wen Chen. 487-494 [doi]
• Classifying noisy protein sequence data: a case study of immunoglobulin light chainsChenggang Yu, Nela Zavaljevski, Fred J. Stevens, Kelly Yackovich, Jaques Reifman. 495-501 [doi]
• Reversal distance for partially ordered genomesChunfang Zheng, Aleksander Lenert, David Sankoff. 502-508 [doi]