13. ISMB 2005: Detroit, Michigan, USA (Supplement of Bioinformatics)

• H. V. Jagadish, David J. States, Burkhard Rost:
  ISMB 2005. 1-2
  
• H. V. Jagadish, David J. States, Burkhard Rost:
  ISMB 2005 Organization. 3-6
  
• Alberto Apostolico, Matteo Comin, Laxmi Parida:
  Conservative extraction of over-represented extensible motifs. 9-18
  
• Grégory Batt, Delphine Ropers, Hidde de Jong, Johannes Geiselmann, Radu Mateescu, Michel Page, Dominique Schneider:
  Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli. 19-28
  
• Tim Beißbarth, Jason A. Tye-Din, Gordon K. Smyth, Terence P. Speed, Robert P. Anderson:
  A systematic approach for comprehensive T-cell epitope discovery using peptide libraries. 29-37
  
• Asa Ben-Hur, William Stafford Noble:
  Kernel methods for predicting protein-protein interactions. 38-46
  
• Karsten M. Borgwardt, Cheng Soon Ong, Stefan Schönauer, S. V. N. Vishwanathan, Alexander J. Smola, Hans-Peter Kriegel:
  Protein function prediction via graph kernels. 47-56
  
• Brona Brejová, Daniel G. Brown, Ming Li, Tomás Vinar:
  ExonHunter: a comprehensive approach to gene finding. 57-65
  
• T. J. Brunette, Oliver Brock:
  Improving protein structure prediction with model-based search. 66-74
  
• Jianlin Cheng, Pierre Baldi:
  Three-stage prediction of protein ?-sheets by neural networks, alignments and graph algorithms. 75-84
  
• Kei-Hoi Cheung, Kevin Y. Yip, Andrew K. Smith, Remko de Knikker, Andy Masiar, Mark Gerstein:
  YeastHub: a semantic web use case for integrating data in the life sciences domain. 85-96
  
• Benny Chor, Tamir Tuller:
  Maximum likelihood of evolutionary trees: hardness and approximation. 97-106
  
• Melissa S. Cline, John Blume, Simon Cawley, Tyson Clark, Jing-Shan Hu, Gang Lu, Nathan Salomonis, Hui Wang, Alan Williams:
  ANOSVA: a statistical method for detecting splice variation from expression data. 107-115
  
• Juan Cortés, Thierry Siméon, Vicente Ruiz de Angulo, David Guieysse, Magali Remaud-Siméon, Vinh Tran:
  A path planning approach for computing large-amplitude motions of flexible molecules. 116-125
  
• Matthew W. Dimmic, Melissa J. Hubisz, Carlos D. Bustamante, Rasmus Nielsen:
  Detecting coevolving amino acid sites using Bayesian mutational mapping. 126-135
  
• Mary E. Dolan, Li Ni, Evelyn Camon, Judith A. Blake:
  A procedure for assessing GO annotation consistency. 136-143
  
• Delbert Dueck, Quaid Morris, Brendan J. Frey:
  Multi-way clustering of microarray data using probabilistic sparse matrix factorization. 144-151
  
• Robert C. Edgar, Eugene W. Myers:
  PILER: identification and classification of genomic repeats. 152-158
  
• Jason Ernst, Gerard J. Nau, Ziv Bar-Joseph:
  Clustering short time series gene expression data. 159-168
  
• Humberto Miguel Garay-Malpartida, Jõao Marcelo Occhiucci, Juliano Alves, José Ernersto Belizário:
  CaSPredictor: a new computer-based tool for caspase substrate prediction. 169-176
  
• Peddinti V. Gopalacharyulu, Erno Lindfors, Catherine Bounsaythip, Teemu Kivioja, Laxman Yetukuri, Jaakko Hollmén, Matej Oresic:
  Data integration and visualization system for enabling conceptual biology. 177-185
  
• Yoonsoo Hahn, Byungkook Lee:
  Identification of nine human-specific frameshift mutations by comparative analysis of the human and the chimpanzee genome sequences. 186-194
  
• Eran Halperin, Gad Kimmel, Ron Shamir:
  Tag SNP selection in genotype data for maximizing SNP prediction accuracy. 195-203
  
• Sridhar Hannenhalli, Li-San Wang:
  Enhanced position weight matrices using mixture models. 204-212
  
• Haiyan Hu, Xifeng Yan, Yu Huang, Jiawei Han, Xianghong Jasmine Zhou:
  Mining coherent dense subgraphs across massive biological networks for functional discovery. 213-221
  
• Jim C. Huang, Quaid Morris, Timothy R. Hughes, Brendan J. Frey:
  GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data. 222-231
  
• Henrik Jönsson, Marcus Heisler, G. Venugopala Reddy, Vikas Agrawal, Victoria Gor, Bruce E. Shapiro, Eric Mjolsness, Elliot M. Meyerowitz:
  Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem. 232-240
  
• Raja Jothi, Maricel G. Kann, Teresa M. Przytycka:
  Predicting protein-protein interaction by searching evolutionary tree automorphism space. 241-250
  
• Lukas Käll, Anders Krogh, Erik L. L. Sonnhammer:
  An HMM posterior decoder for sequence feature prediction that includes homology information. 251-257
  
• Jaeju Ko, Leonel F. Murga, Ying Wei, Mary Jo Ondrechen:
  Prediction of active sites for protein structures from computed chemical properties. 258-265
  
• Zhenzhen Kou, William W. Cohen, Robert F. Murphy:
  High-recall protein entity recognition using a dictionary. 266-273
  
• Wei Li, Clifford A. Meyer, X. Shirley Liu:
  A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. 274-282
  
• Shaun Mahony, Aaron Golden, Terry J. Smith, Panayiotis V. Benos:
  Improved detection of DNA motifs using a self-organized clustering of familial binding profiles. 283-291
  
• Ramgopal R. Mettu, Ryan H. Lilien, Bruce Randall Donald:
  High-throughput inference of protein-protein interfaces from unassigned NMR data. 292-301
  
• Elena Nabieva, Kam Jim, Amit Agarwal, Bernard Chazelle, Mona Singh:
  Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. 302-310
  
• Niranjan Nagarajan, Neil Jones, Uri Keich:
  Computing the P-value of the information content from an alignment of multiple sequences. 311-318
  
• Meenakshi Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker:
  Beyond the clause: extraction of phosphorylation information from medline abstracts. 319-327
  
• Guy Nimrod, Fabian Glaser, David Steinberg, Nir Ben-Tal, Tal Pupko:
  In silico identification of functional regions in proteins. 328-337
  
• William Stafford Noble, Scott Kuehn, Robert E. Thurman, Man Yu, John A. Stamatoyannopoulos:
  Predicting the in vivo signature of human gene regulatory sequence. 328-343
  
• Amol Prakash, Martin Tompa:
  Statistics of local multiple alignments. 344-350
  
• Alkes L. Price, Neil C. Jones, Pavel A. Pevzner:
  De novo identification of repeat families in large genomes. 351-358
  
• Sanjay Joshua Swamidass, Jonathan H. Chen, Jocelyne Bruand, Peter Phung, Liva Ralaivola, Pierre Baldi:
  Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity. 359-368
  
• Gunnar Rätsch, Sören Sonnenburg, Bernhard Schölkopf:
  RASE: recognition of alternatively spliced exons in C.elegans. 369-377
  
• Tali Sadka, Michal Linial:
  Families of membranous proteins can be characterized by the amino acid composition of their transmembrane domains. 378-386
  
• Roded Sharan, Eugene W. Myers:
  A motif-based framework for recognizing sequence families. 387-393
  
• Alena Shmygelska:
  Search for folding nuclei in native protein structures. 394-402
  
• Andrew D. Smith, Pavel Sumazin, Debopriya Das, Michael Q. Zhang:
  Mining ChIP-chip data for transcription factor and cofactor binding sites. 403-412
  
• Yun S. Song, Yufeng Wu, Dan Gusfield:
  Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. 413-422
  
• Mat Soukup, HyungJun Cho, Jae K. Lee:
  Robust classification modeling on microarray data using misclassification penalized posterior. 423-430
  
• Haixu Tang, Yehia Mechref, Milos V. Novotny:
  Automated interpretation of MS/MS spectra of oligosaccharides. 431-439
  
• Kannan Tharakaraman, Leonardo Mariño-Ramírez, Sergey Sheetlin, David Landsman, John L. Spouge:
  Alignments anchored on genomic landmarks can aid in the identification of regulatory elements. 440-448
  
• Henry F. Winstanley, Sanne Abeln, Charlotte M. Deane:
  How old is your fold? 449-458
  
• Yong Woo, Winfried Krueger, Anupinder Kaur, Gary A. Churchill:
  Experimental design for three-color and four-color gene expression microarrays. 459-467
  
• Yoshihiro Yamanishi, Jean-Philippe Vert, Minoru Kanehisa:
  Supervised enzyme network inference from the integration of genomic data and chemical information. 468-477
  
• Yuzhen Ye, Andrei Osterman, Ross A. Overbeek, Adam Godzik:
  Automatic detection of subsystem/pathway variants in genome analysis. 478-486
  
• Jiangsheng Yu, Xue-wen Chen:
  Bayesian neural network approaches to ovarian cancer identification from high-resolution mass spectrometry data. 487-494
  
• Chenggang Yu, Nela Zavaljevski, Fred J. Stevens, Kelly Yackovich, Jaques Reifman:
  Classifying noisy protein sequence data: a case study of immunoglobulin light chains. 495-501
  
• Chunfang Zheng, Aleksander Lenert, David Sankoff:
  Reversal distance for partially ordered genomes. 502-508
  

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