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Contents: Volume 21, Suppl 1 June 2005   [Index by Author]   
 
ISMB 2005 Proceedings. Thirteenth International Conference on Intelligent Systems for Molecular Biology, Detroit 25-29 June 2005
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H. V. Jagadish, David States, and Burkhard Rost
ISMB 2005
Bioinformatics 2005 21: i1-i2; doi:10.1093/bioinformatics/bti1057 [Print PDF] [Request Permissions]  

ISMB 2005 Organization
Bioinformatics 2005 21: i3-i6; doi:10.1093/bioinformatics/bti1056 [Print PDF] [Request Permissions]  

Alberto Apostolico, Matteo Comin, and Laxmi Parida
Conservative extraction of over-represented extensible motifs
Bioinformatics 2005 21: i9-i18; doi:10.1093/bioinformatics/bti1051 [Abstract] [Print PDF] [Request Permissions]  

Grégory Batt, Delphine Ropers, Hidde de Jong, Johannes Geiselmann, Radu Mateescu, Michel Page, and Dominique Schneider
Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli
Bioinformatics 2005 21: i19-i28; doi:10.1093/bioinformatics/bti1048 [Abstract] [Print PDF] [Request Permissions]  

Tim Beißbarth, Jason A. Tye-Din, Gordon K. Smyth, Terence P. Speed, and Robert P. Anderson
A systematic approach for comprehensive T-cell epitope discovery using peptide libraries
Bioinformatics 2005 21: i29-i37; doi:10.1093/bioinformatics/bti1013 [Abstract] [Print PDF] [Request Permissions]  

Asa Ben-Hur and William Stafford Noble
Kernel methods for predicting protein–protein interactions
Bioinformatics 2005 21: i38-i46; doi:10.1093/bioinformatics/bti1016 [Abstract] [Print PDF] [Request Permissions]  

Karsten M. Borgwardt, Cheng Soon Ong, Stefan Schönauer, S. V. N. Vishwanathan, Alex J. Smola, and Hans-Peter Kriegel
Protein function prediction via graph kernels
Bioinformatics 2005 21: i47-i56; doi:10.1093/bioinformatics/bti1007 [Abstract] [Print PDF] [Request Permissions]  

Brona Brejová, Daniel G. Brown, Ming Li, and Tomás Vinar
ExonHunter: a comprehensive approach to gene finding
Bioinformatics 2005 21: i57-i65; doi:10.1093/bioinformatics/bti1040 [Abstract] [Print PDF] [Request Permissions]  

T J Brunette and Oliver Brock
Improving protein structure prediction with model-based search
Bioinformatics 2005 21: i66-i74; doi:10.1093/bioinformatics/bti1029 [Abstract] [Print PDF] [Request Permissions]  

Jianlin Cheng and Pierre Baldi
Three-stage prediction of protein ß-sheets by neural networks, alignments and graph algorithms
Bioinformatics 2005 21: i75-i84; doi:10.1093/bioinformatics/bti1004 [Abstract] [Print PDF] [Request Permissions]  

Kei-Hoi Cheung, Kevin Y. Yip, Andrew Smith, Remko deKnikker, Andy Masiar, and Mark Gerstein
YeastHub: a semantic web use case for integrating data in the life sciences domain
Bioinformatics 2005 21: i85-i96; doi:10.1093/bioinformatics/bti1026 [Abstract] [Print PDF] [Request Permissions]  

Benny Chor and Tamir Tuller
Maximum likelihood of evolutionary trees: hardness and approximation
Bioinformatics 2005 21: i97-i106; doi:10.1093/bioinformatics/bti1027 [Abstract] [Print PDF] [Request Permissions]  

Melissa S. Cline, John Blume, Simon Cawley, Tyson A. Clark, Jing-Shan Hu, Gang Lu, Nathan Salomonis, Hui Wang, and Alan Williams
ANOSVA: a statistical method for detecting splice variation from expression data
Bioinformatics 2005 21: i107-i115; doi:10.1093/bioinformatics/bti1010 [Abstract] [Print PDF] [Request Permissions]  

J. Cortés, T. Siméon, V. Ruiz de Angulo, D. Guieysse, M. Remaud-Siméon, and V. Tran
A path planning approach for computing large-amplitude motions of flexible molecules
Bioinformatics 2005 21: i116-i125; doi:10.1093/bioinformatics/bti1017 [Abstract] [Print PDF] [Request Permissions]  

Matthew W. Dimmic, Melissa J. Hubisz, Carlos D. Bustamante, and Rasmus Nielsen
Detecting coevolving amino acid sites using Bayesian mutational mapping
Bioinformatics 2005 21: i126-i135; doi:10.1093/bioinformatics/bti1032 [Abstract] [Print PDF] [Request Permissions]  

Mary E. Dolan, Li Ni, Evelyn Camon, and Judith A. Blake
A procedure for assessing GO annotation consistency
Bioinformatics 2005 21: i136-i143; doi:10.1093/bioinformatics/bti1019 [Abstract] [Print PDF] [Request Permissions]  

Delbert Dueck, Quaid D. Morris, and Brendan J. Frey
Multi-way clustering of microarray data using probabilistic sparse matrix factorization
Bioinformatics 2005 21: i144-i151; doi:10.1093/bioinformatics/bti1041 [Abstract] [Print PDF] [Request Permissions]  

Robert C. Edgar and Eugene W. Myers
PILER: identification and classification of genomic repeats
Bioinformatics 2005 21: i152-i158; doi:10.1093/bioinformatics/bti1003 [Abstract] [Print PDF] [Request Permissions]  

Jason Ernst, Gerard J. Nau, and Ziv Bar-Joseph
Clustering short time series gene expression data
Bioinformatics 2005 21: i159-i168; doi:10.1093/bioinformatics/bti1022 [Abstract] [Print PDF] [Request Permissions]  

H. M. Garay-Malpartida, J. M. Occhiucci, J. Alves, and J. E. Belizário
CaSPredictor: a new computer-based tool for caspase substrate prediction
Bioinformatics 2005 21: i169-i176; doi:10.1093/bioinformatics/bti1034 [Abstract] [Print PDF] [Request Permissions]  

Peddinti V. Gopalacharyulu, Erno Lindfors, Catherine Bounsaythip, Teemu Kivioja, Laxman Yetukuri, Jaakko Hollmén, and Matej Oresic
Data integration and visualization system for enabling conceptual biology
Bioinformatics 2005 21: i177-i185; doi:10.1093/bioinformatics/bti1015 [Abstract] [Print PDF] [Request Permissions]  

Yoonsoo Hahn and Byungkook Lee
Identification of nine human-specific frameshift mutations by comparative analysis of the human and the chimpanzee genome sequences
Bioinformatics 2005 21: i186-i194; doi:10.1093/bioinformatics/bti1000 [Abstract] [Print PDF] [Request Permissions]  

Eran Halperin, Gad Kimmel, and Ron Shamir
Tag SNP selection in genotype data for maximizing SNP prediction accuracy
Bioinformatics 2005 21: i195-i203; doi:10.1093/bioinformatics/bti1021 [Abstract] [Print PDF] [Request Permissions]  

Sridhar Hannenhalli and Li-San Wang
Enhanced position weight matrices using mixture models
Bioinformatics 2005 21: i204-i212; doi:10.1093/bioinformatics/bti1001 [Abstract] [Print PDF] [Request Permissions]  

Haiyan Hu, Xifeng Yan, Yu Huang, Jiawei Han, and Xianghong Jasmine Zhou
Mining coherent dense subgraphs across massive biological networks for functional discovery
Bioinformatics 2005 21: i213-i221; doi:10.1093/bioinformatics/bti1049 [Abstract] [Print PDF] [Request Permissions]  

Jim C. Huang, Quaid D. Morris, Timothy R. Hughes, and Brendan J. Frey
GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data
Bioinformatics 2005 21: i222-i231; doi:10.1093/bioinformatics/bti1045 [Abstract] [Print PDF] [Request Permissions]  

Henrik Jönsson, Marcus Heisler, G. Venugopala Reddy, Vikas Agrawal, Victoria Gor, Bruce E. Shapiro, Eric Mjolsness, and Elliot M. Meyerowitz
Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem
Bioinformatics 2005 21: i232-i240; doi:10.1093/bioinformatics/bti1036 [Abstract] [Print PDF] [Request Permissions]  

Raja Jothi, Maricel G. Kann, and Teresa M. Przytycka
Predicting protein–protein interaction by searching evolutionary tree automorphism space
Bioinformatics 2005 21: i241-i250; doi:10.1093/bioinformatics/bti1009 [Abstract] [Print PDF] [Request Permissions]  

Lukas Käll, Anders Krogh, and Erik L. L. Sonnhammer
An HMM posterior decoder for sequence feature prediction that includes homology information
Bioinformatics 2005 21: i251-i257; doi:10.1093/bioinformatics/bti1014 [Abstract] [Print PDF] [Request Permissions]  

Jaeju Ko, Leonel F. Murga, Ying Wei, and Mary Jo Ondrechen
Prediction of active sites for protein structures from computed chemical properties
Bioinformatics 2005 21: i258-i265; doi:10.1093/bioinformatics/bti1039 [Abstract] [Print PDF] [Request Permissions]  

Zhenzhen Kou, William W. Cohen, and Robert F. Murphy
High-recall protein entity recognition using a dictionary
Bioinformatics 2005 21: i266-i273; doi:10.1093/bioinformatics/bti1006 [Abstract] [Print PDF] [Request Permissions]  

Wei Li, Clifford A. Meyer, and X. Shirley Liu
A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences
Bioinformatics 2005 21: i274-i282; doi:10.1093/bioinformatics/bti1046 [Abstract] [Print PDF] [Request Permissions]  

Shaun Mahony, Aaron Golden, Terry J. Smith, and Panayiotis V. Benos
Improved detection of DNA motifs using a self-organized clustering of familial binding profiles
Bioinformatics 2005 21: i283-i291; doi:10.1093/bioinformatics/bti1025 [Abstract] [Print PDF] [Request Permissions]  

Ramgopal R. Mettu, Ryan H. Lilien, and Bruce Randall Donald
High-throughput inference of protein–protein interfaces from unassigned NMR data
Bioinformatics 2005 21: i292-i301; doi:10.1093/bioinformatics/bti1005 [Abstract] [Print PDF] [Request Permissions]  

Elena Nabieva, Kam Jim, Amit Agarwal, Bernard Chazelle, and Mona Singh
Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
Bioinformatics 2005 21: i302-i310; doi:10.1093/bioinformatics/bti1054 [Abstract] [Print PDF] [Request Permissions]  

Niranjan Nagarajan, Neil Jones, and Uri Keich
Computing the P-value of the information content from an alignment of multiple sequences
Bioinformatics 2005 21: i311-i318; doi:10.1093/bioinformatics/bti1044 [Abstract] [Print PDF] [Request Permissions]  

M. Narayanaswamy, K. E. Ravikumar, and K. Vijay-Shanker
Beyond the clause: extraction of phosphorylation information from medline abstracts
Bioinformatics 2005 21: i319-i327; doi:10.1093/bioinformatics/bti1011 [Abstract] [Print PDF] [Request Permissions]  

Guy Nimrod, Fabian Glaser, David Steinberg, Nir Ben-Tal, and Tal Pupko
In silico identification of functional regions in proteins
Bioinformatics 2005 21: i328-i337; doi:10.1093/bioinformatics/bti1023 [Abstract] [Print PDF] [Request Permissions]  

William Stafford Noble, Scott Kuehn, Robert Thurman, Man Yu, and John Stamatoyannopoulos
Predicting the in vivo signature of human gene regulatory sequences
Bioinformatics 2005 21: i338-i343; doi:10.1093/bioinformatics/bti1047 [Abstract] [Print PDF] [Request Permissions]  

Amol Prakash and Martin Tompa
Statistics of local multiple alignments
Bioinformatics 2005 21: i344-i350; doi:10.1093/bioinformatics/bti1042 [Abstract] [Print PDF] [Request Permissions]  

Alkes L. Price, Neil C. Jones, and Pavel A. Pevzner
De novo identification of repeat families in large genomes
Bioinformatics 2005 21: i351-i358; doi:10.1093/bioinformatics/bti1018 [Abstract] [Print PDF] [Request Permissions]  

S. Joshua Swamidass, Jonathan Chen, Jocelyne Bruand, Peter Phung, Liva Ralaivola, and Pierre Baldi
Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity
Bioinformatics 2005 21: i359-i368; doi:10.1093/bioinformatics/bti1055 [Abstract] [Print PDF] [Request Permissions]  

G. Rätsch, S. Sonnenburg, and B. Schölkopf
RASE: recognition of alternatively spliced exons in C.elegans
Bioinformatics 2005 21: i369-i377; doi:10.1093/bioinformatics/bti1053 [Abstract] [Print PDF] [Request Permissions]  

Tali Sadka and Michal Linial
Families of membranous proteins can be characterized by the amino acid composition of their transmembrane domains
Bioinformatics 2005 21: i378-i386; doi:10.1093/bioinformatics/bti1035 [Abstract] [Print PDF] [Request Permissions]  

Roded Sharan and Eugene W. Myers
A motif-based framework for recognizing sequence families
Bioinformatics 2005 21: i387-i393; doi:10.1093/bioinformatics/bti1002 [Abstract] [Print PDF] [Request Permissions]  

Alena Shmygelska
Search for folding nuclei in native protein structures
Bioinformatics 2005 21: i394-i402; doi:10.1093/bioinformatics/bti1050 [Abstract] [Print PDF] [Request Permissions]  

Andrew D. Smith, Pavel Sumazin, Debopriya Das, and Michael Q. Zhang
Mining ChIP-chip data for transcription factor and cofactor binding sites
Bioinformatics 2005 21: i403-i412; doi:10.1093/bioinformatics/bti1043 [Abstract] [Print PDF] [Request Permissions]  

Yun S. Song, Yufeng Wu, and Dan Gusfield
Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution
Bioinformatics 2005 21: i413-i422; doi:10.1093/bioinformatics/bti1033 [Abstract] [Print PDF] [Request Permissions]  

Mat Soukup, HyungJun Cho, and Jae K. Lee
Robust classification modeling on microarray data using misclassification penalized posterior
Bioinformatics 2005 21: i423-i430; doi:10.1093/bioinformatics/bti1020 [Abstract] [Print PDF] [Request Permissions]  

Haixu Tang, Yehia Mechref, and Milos V. Novotny
Automated interpretation of MS/MS spectra of oligosaccharides
Bioinformatics 2005 21: i431-i439; doi:10.1093/bioinformatics/bti1038 [Abstract] [Print PDF] [Request Permissions]  

Kannan Tharakaraman, Leonardo Mariño-Ramírez, Sergey Sheetlin, David Landsman, and John L. Spouge
Alignments anchored on genomic landmarks can aid in the identification of regulatory elements
Bioinformatics 2005 21: i440-i448; doi:10.1093/bioinformatics/bti1028 [Abstract] [Print PDF] [Request Permissions]  

Henry F. Winstanley, Sanne Abeln, and Charlotte M. Deane
How old is your fold?
Bioinformatics 2005 21: i449-i458; doi:10.1093/bioinformatics/bti1008 [Abstract] [Print PDF] [Request Permissions]  

Yong Woo, Winfried Krueger, Anupinder Kaur, and Gary Churchill
Experimental design for three-color and four-color gene expression microarrays
Bioinformatics 2005 21: i459-i467; doi:10.1093/bioinformatics/bti1031 [Abstract] [Print PDF] [Request Permissions]  

Yoshihiro Yamanishi, Jean-Philippe Vert, and Minoru Kanehisa
Supervised enzyme network inference from the integration of genomic data and chemical information
Bioinformatics 2005 21: i468-i477; doi:10.1093/bioinformatics/bti1012 [Abstract] [Print PDF] [Request Permissions]  

Yuzhen Ye, Andrei Osterman, Ross Overbeek, and Adam Godzik
Automatic detection of subsystem/pathway variants in genome analysis
Bioinformatics 2005 21: i478-i486; doi:10.1093/bioinformatics/bti1052 [Abstract] [Print PDF] [Request Permissions]  

Jiangsheng Yu and Xue-Wen Chen
Bayesian neural network approaches to ovarian cancer identification from high-resolution mass spectrometry data
Bioinformatics 2005 21: i487-i494; doi:10.1093/bioinformatics/bti1030 [Abstract] [Print PDF] [Request Permissions]  

Chenggang Yu, Nela Zavaljevski, Fred J. Stevens, Kelly Yackovich, and Jaques Reifman
Classifying noisy protein sequence data: a case study of immunoglobulin light chains
Bioinformatics 2005 21: i495-i501; doi:10.1093/bioinformatics/bti1024 [Abstract] [Print PDF] [Request Permissions]  

Chunfang Zheng, Aleksander Lenert, and David Sankoff
Reversal distance for partially ordered genomes
Bioinformatics 2005 21: i502-i508; doi:10.1093/bioinformatics/bti1037 [Abstract] [Print PDF] [Request Permissions]  

Author Index
Bioinformatics 2005 21: i509-i510; doi:10.1093/bioinformatics/bti1058 [Print PDF] [Request Permissions]  

To see an article, click its [Full Text] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.