@article{Bonfield-Staden/02,
AUTHOR = {Bonfield, James K. and Staden, Rodger},
TITLE = {ZTR: A new format for DNA sequence trace data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {3-10},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/3},
PUBLISHER = {Oxford University Press},
}
@article{Althaus-Caprara-Lenhof-Reinert/02,
AUTHOR = {Althaus, Ernst and Caprara, Alberto and Lenhof, Hans-Peter and Reinert, Knut},
TITLE = {Multiple sequence alignment with arbitrary gap costs: Computing an optimal solution using polyhedral combinatorics},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {4-16},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S4},
PUBLISHER = {Oxford University Press},
}
@article{Narayanan-Wu-Yang/02,
AUTHOR = {Narayanan, Ajit and Wu, Xikun and Yang, Z. Rong},
TITLE = {Mining viral protease data to extract cleavage knowledge},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {5-13},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S5},
PUBLISHER = {Oxford University Press},
}
@article{Bo-Jonassen-Eidhammer-Helgesen/02,
AUTHOR = {B{\o}, Trond H. and Jonassen, Inge and Eidhammer, Ingvar and Helgesen, Carsten},
TITLE = {A fast top-down method for constructing reliable radiation hybrid frameworks},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {11-18},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/11},
PUBLISHER = {Oxford University Press},
}
@article{Sasson-Linial-Linial/02,
AUTHOR = {Sasson, Ori and Linial, Nathan and Linial, Michal},
TITLE = {The metric space of proteins --- Comparative study of clustering algorithms},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {14-21},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S14},
PUBLISHER = {Oxford University Press},
}
@article{Andersson-Alsmark-Canback-Davids-Frank-Karlberg-Klasson-Antoine-Legault-Mira-Tamas/02,
AUTHOR = {Andersson, Siv G.E. and Alsmark, Cecilia and Canb{\"a}ck, Bj{\"o}rn and Davids, Wagied and Frank, Carolin and Karlberg, Olof and Klasson, Lisa and Antoine-Legault, Boris and Mira, Alex and Tamas, Ivica},
TITLE = {Comparative genomics of microbial pathogens and symbionts},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {17-17},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S17},
PUBLISHER = {Oxford University Press},
}
@article{Apaydin-Guestrin-Varma-Brutlag-Latombe/02,
AUTHOR = {Apaydin, Mehmet Serkan and Guestrin, Carlos E. and Varma, Chris and Brutlag, Douglas L. and Latombe, Jean-Claude},
TITLE = {Stochastic roadmap simulation for the study of ligand-protein interactions},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {18-26},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S18},
PUBLISHER = {Oxford University Press},
}
@article{Pavlovic-Garg-Kasif/02,
AUTHOR = {Pavlovi{\'c}, Vladimir and Garg, Ashutosh and Kasif, Simon},
TITLE = {A Bayesian framework for combining gene predictions},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {19-27},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/19},
PUBLISHER = {Oxford University Press},
}
@article{Steffen-Murphy-Tolleri-Hatfield-Lathrop/02,
AUTHOR = {Steffen, N.R. and Murphy, S.D. and Tolleri, L. and Hatfield, G.W. and Lathrop, R.H.},
TITLE = {DNA sequence and structure: Direct and indirect recognition in protein-DNA binding},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {22-30},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S22},
PUBLISHER = {Oxford University Press},
}
@article{Arita-Tsuda-Asai/02,
AUTHOR = {Arita, Masanori and Tsuda, Koji and Asai, Kiyoshi},
TITLE = {Modeling splicing sites with pairwise correlations},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {27-34},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S27},
PUBLISHER = {Oxford University Press},
}
@article{Macas-Meszaros-Nouzova/02,
AUTHOR = {Macas, Ji{\v{r}}{\'{i}} and M{\'e}sz{\'a}ros, Tibor and Nouzov{\'a}, Marcela},
TITLE = {PlantSat: A specialized database for plant satellite repeats},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {28-35},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/28},
PUBLISHER = {Oxford University Press},
}
@article{Hauth-Joseph/02,
AUTHOR = {Hauth, Amy M. and Joseph, Deborah A.},
TITLE = {Beyond tandem repeats: Complex pattern structures and distant regions of similarity},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {31-37},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S31},
PUBLISHER = {Oxford University Press},
}
@article{Bazzan-Engel-Schroeder-da_Silva/02,
AUTHOR = {Bazzan, Ana L.C. and Engel, Paulo M. and Schroeder, Luciana F. and da Silva, S{\'e}rgio C.},
TITLE = {Automated annotation of keywords for proteins related to mycoplasmataceae using machine learning techniques},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {35-43},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S35},
PUBLISHER = {Oxford University Press},
}
@article{Haubold-Wiehe/02,
AUTHOR = {Haubold, Bernhard and Wiehe, Thomas},
TITLE = {Calculating the SNP-effective sample size from an alignment},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {36-38},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/36},
PUBLISHER = {Oxford University Press},
}
@article{Nguyen-Rocke/02,
AUTHOR = {Nguyen, Danh V. and Rocke, David M.},
TITLE = {Tumor classification by partial least squares using microarray gene expression data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {39-50},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/39},
PUBLISHER = {Oxford University Press},
}
@article{Benson/02,
AUTHOR = {Benson, Gary},
TITLE = {A new distance measure for comparing sequence profiles based on path lengths along an entropy surface},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {44-53},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S44},
PUBLISHER = {Oxford University Press},
}
@article{Martelli-Fariselli-Krogh-Casadio/02,
AUTHOR = {Martelli, Pier Luigi and Fariselli, Piero and Krogh, Anders and Casadio, Rita},
TITLE = {A sequence-profile-based HMM for predicting and discriminating $\beta$ barrel membrane proteins},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {46-53},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S46},
PUBLISHER = {Oxford University Press},
}
@article{Liebermeister/02,
AUTHOR = {Liebermeister, Wolfram},
TITLE = {Linear modes of gene expression determined by independent component analysis},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {51-60},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/51},
PUBLISHER = {Oxford University Press},
}
@article{Bergeron-Heber-Stoye/02,
AUTHOR = {Bergeron, A. and Heber, S. and Stoye, J.},
TITLE = {Common intervals and sorting by reversals: A marriage of necessity},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {54-63},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S54},
PUBLISHER = {Oxford University Press},
}
@article{Bystroff-Shao/02,
AUTHOR = {Bystroff, Christopher and Shao, Yu},
TITLE = {Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {54-61},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S54},
PUBLISHER = {Oxford University Press},
}
@article{Sasik-Iranfar-Hwa-Loomis/02,
AUTHOR = {{\v{S}}{\'a}{\v{s}}ik, R. and Iranfar, N. and Hwa, T. and Loomis, W.F.},
TITLE = {Extracting transcriptional events from temporal gene expression patterns during Dictyostelium development},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {61-66},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/61},
PUBLISHER = {Oxford University Press},
}
@article{Pollastri-Baldi/02,
AUTHOR = {Pollastri, G. and Baldi, P.},
TITLE = {Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {62-70},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S62},
PUBLISHER = {Oxford University Press},
}
@article{Bork/02,
AUTHOR = {Bork, Peer},
TITLE = {Comparative analysis of protein interaction networks},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {64-64},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S64},
PUBLISHER = {Oxford University Press},
}
@article{Boue-Vingron-Kriventseva-Koch/02,
AUTHOR = {Bou{\'e}, St{\'e}phanie and Vingron, Martin and Kriventseva, Evgenia and Koch, Ina},
TITLE = {Theoretical analysis of alternative splice forms using computational methods},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {65-73},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S65},
PUBLISHER = {Oxford University Press},
}
@article{Siehs-Oberbauer-Mayer-Lukas-Mayer/02,
AUTHOR = {Siehs, Christian and Oberbauer, Rainer and Mayer, Gert and Lukas, Arno and Mayer, Bernd},
TITLE = {Discrete simulation of regulatory homo- and heterodimerization in the apoptosis effector phase},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {67-76},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/67},
PUBLISHER = {Oxford University Press},
}
@article{Pupko-Bell-Mayrose-Glaser-Ben-Tal/02,
AUTHOR = {Pupko, Tal and Bell, Rachel E. and Mayrose, Itay and Glaser, Fabian and Ben-Tal, Nir},
TITLE = {Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {71-77},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S71},
PUBLISHER = {Oxford University Press},
}
@article{Brutlag-Apaydin-Guestrin-Hsu-Varma-Singh-Latombe/02,
AUTHOR = {Brutlag, Douglas and Apaydin, Serkan and Guestrin, Carlos and Hsu, David and Varma, Chris and Singh, Amit and Latombe, Jean-Claude},
TITLE = {Using robotics to fold proteins and dock ligands},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {74-74},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S74},
PUBLISHER = {Oxford University Press},
}
@article{Degroeve-de_Baets-van_de_Peer-Rouze/02,
AUTHOR = {Degroeve, Sven and de Baets, Bernard and van de Peer, Yves and Rouz{\'e}, Pierre},
TITLE = {Feature subset selection for splice site prediction},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {75-83},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S75},
PUBLISHER = {Oxford University Press},
}
@article{Li-Jaroszewski-Godzik/02,
AUTHOR = {Li, Weizhong and Jaroszewski, Lukasz and Godzik, Adam},
TITLE = {Tolerating some redundancy significantly speeds up clustering of large protein databases},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {77-82},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/77},
PUBLISHER = {Oxford University Press},
}
@article{Nair-Rost/02,
AUTHOR = {Nair, Rajesh and Rost, Burkhard},
TITLE = {Inferring sub-cellular localization through automated lexical analysis},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {78-86},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S78},
PUBLISHER = {Oxford University Press},
}
@article{Cotter-Caffrey-Shields/02,
AUTHOR = {Cotter, Philip J. and Caffrey, Daniel R. and Shields, Denis C.},
TITLE = {Improved database searches for orthologous sequences by conditioning on outgroup sequences},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {83-91},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/83},
PUBLISHER = {Oxford University Press},
}
@article{Dieterich-Cusack-Wang-Rateitschak-Krause-Vingron/02,
AUTHOR = {Dieterich, Christoph and Cusack, Brian and Wang, Haiyan and Rateitschak, Katja and Krause, Antje and Vingron, Martin},
TITLE = {Annotating regulatory DNA based on man-mouse genomic comparison},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {84-90},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S84},
PUBLISHER = {Oxford University Press},
}
@article{Myasnikova-Samsonova-Samsonova-Reinitz/02,
AUTHOR = {Myasnikova, E. and Samsonova, A. and Samsonova, M. and Reinitz, J.},
TITLE = {Support vector regression applied to the determination of the developmental age of a Drosophila embryo from its segmentation gene expression patterns},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {87-95},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S87},
PUBLISHER = {Oxford University Press},
}
@article{Duret/02,
AUTHOR = {Duret, Laurent},
TITLE = {Detecting genomic features under weak selective pressure: The example of codon usage in animals and plants},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {91-91},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S91},
PUBLISHER = {Oxford University Press},
}
@article{Elemento-Gascuel/02,
AUTHOR = {Elemento, Olivier and Gascuel, Olivier},
TITLE = {An efficient and accurate distance based algorithm to reconstruct tandem duplication trees},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {92-99},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S92},
PUBLISHER = {Oxford University Press},
}
@article{Storm-Sonnhammer/02,
AUTHOR = {Storm, Christian E.V. and Sonnhammer, Erik L.L.},
TITLE = {Automated ortholog inference from phylogenetic trees and calculation of orthology reliability},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {92-99},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/92},
PUBLISHER = {Oxford University Press},
}
@article{Huber-von_Heydebreck-Sultmann-Poustka-Vingron/02,
AUTHOR = {Huber, Wolfgang and von Heydebreck, Anja and S{\"u}ltmann, Holger and Poustka, Annemarie and Vingron, Martin},
TITLE = {Variance stabilization applied to microarray data calibration and to the quantification of differential expression},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {96-104},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S96},
PUBLISHER = {Oxford University Press},
}
@article{Ellrott-Yang-Sladek-Jiang/02,
AUTHOR = {Ellrott, Kyle and Yang, Chuhu and Sladek, Frances M. and Jiang, Tao},
TITLE = {Identifying transcription factor binding sites through Markov chain optimization},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {100-109},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S100},
PUBLISHER = {Oxford University Press},
}
@article{Stuart-Moffett-Baker/02,
AUTHOR = {Stuart, Gary W. and Moffett, Karen and Baker, Steve},
TITLE = {Integrated gene and species phylogenies from unaligned whole genome protein sequences},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {100-108},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/100},
PUBLISHER = {Oxford University Press},
}
@article{Durbin-Hardin-Hawkins-Rocke/02,
AUTHOR = {Durbin, B.P. and Hardin, J.S. and Hawkins, D.M. and Rocke, D.M.},
TITLE = {A variance-stabilizing transformation for gene-expression microarray data},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {105-110},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S105},
PUBLISHER = {Oxford University Press},
}
@article{Rost-Bornberg-Bauer/02,
AUTHOR = {Rost, Ursula and Bornberg-Bauer, Erich},
TITLE = {TreeWiz: Interactive exploration of huge trees},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {109-114},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/109},
PUBLISHER = {Oxford University Press},
}
@article{Freudenberg-Propping/02,
AUTHOR = {Freudenberg, J. and Propping, P.},
TITLE = {A similarity-based method for genome-wide prediction of disease-relevant human genes},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {110-115},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S110},
PUBLISHER = {Oxford University Press},
}
@article{Seo-Thorne-Hasegawa-Kishino/02,
AUTHOR = {Seo, Tae-Kun and Thorne, Jeffrey L. and Hasegawa, Masami and Kishino, Hirohisa},
TITLE = {A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {115-123},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/115},
PUBLISHER = {Oxford University Press},
}
@article{Gambin-Lasota-Szklarczyk-Tiuryn-Tyszkiewicz/02,
AUTHOR = {Gambin, Anna and Lasota, Slawomir and Szklarczyk, Radoslaw and Tiuryn, Jerzy and Tyszkiewicz, Jerzy},
TITLE = {Contextual alignment of biological sequences},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {116-127},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S116},
PUBLISHER = {Oxford University Press},
}
@article{Park-Tian-Kohane/02,
AUTHOR = {Park, Peter J. and Tian, Lu and Kohane, Isaac S.},
TITLE = {Linking gene expression data with patient survival times using partial least squares},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {120-127},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S120},
PUBLISHER = {Oxford University Press},
}
@article{Goesmann-Haubrock-Meyer-Kalinowski-Giegerich/02,
AUTHOR = {Goesmann, Alexander and Haubrock, Martin and Meyer, Folker and Kalinowski, J{\"o}rn and Giegerich, Robert},
TITLE = {PathFinder: Reconstruction and dynamic visualization of metabolic pathways},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {124-129},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/124},
PUBLISHER = {Oxford University Press},
}
@article{Fernandes-Skiena/02,
AUTHOR = {Fernandes, Rohan J. and Skiena, Steven S.},
TITLE = {Microarray synthesis through multiple-use PCR primer design},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {128-135},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S128},
PUBLISHER = {Oxford University Press},
}
@article{Gramm-Niedermeier/02,
AUTHOR = {Gramm, Jens and Niedermeier, Rolf},
TITLE = {Breakpoint medians and breakpoint phylogenies: A fixed-parameter approach},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {128-139},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S128},
PUBLISHER = {Oxford University Press},
}
@article{Chen-Lin-Liu-Gilson/02,
AUTHOR = {Chen, Xi and Lin, Yuhmei and Liu, Ming and Gilson, Michael K.},
TITLE = {The Binding Database: Data management and interface design},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {130-139},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/130},
PUBLISHER = {Oxford University Press},
}
@article{Hubbard/02,
AUTHOR = {Hubbard, Tim},
TITLE = {Biological information: Making it accessible and integrated (and trying to make sense of it)},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {140-140},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S140},
PUBLISHER = {Oxford University Press},
}
@article{Nagata-Mizushima-Tanaka/02,
AUTHOR = {Nagata, Hiroshi and Mizushima, Hiroshi and Tanaka, Hiroshi},
TITLE = {Concept and prototype of protein-ligand docking simulator with force feedback technology},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {140-146},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/140},
PUBLISHER = {Oxford University Press},
}
@article{Jung-Cho/02,
AUTHOR = {Jung, Ho-Youl and Cho, Hwan-Gue},
TITLE = {An automatic block and spot indexing with $k$-nearest neighbors graph for microarray image analysis},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {141-151},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S141},
PUBLISHER = {Oxford University Press},
}
@article{Hanisch-Zien-Zimmer-Lengauer/02,
AUTHOR = {Hanisch, Daniel and Zien, Alexander and Zimmer, Ralf and Lengauer, Thomas},
TITLE = {Co-clustering of biological networks and gene expression data},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {145-154},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S145},
PUBLISHER = {Oxford University Press},
}
@article{Karchin-Karplus-Haussler/02,
AUTHOR = {Karchin, Rachel and Karplus, Kevin and Haussler, David},
TITLE = {Classifying G-protein coupled receptors with support vector machines},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {147-159},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/147},
PUBLISHER = {Oxford University Press},
}
@article{Metspalu/02,
AUTHOR = {Metspalu, Andres},
TITLE = {Estonian Genome Project --- Before the take-off and take-off},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {152-152},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S152},
PUBLISHER = {Oxford University Press},
}
@article{Muckstein-Hofacker-Stadler/02,
AUTHOR = {M{\"u}ckstein, U. and Hofacker, I.L. and Stadler, P.F.},
TITLE = {Stochastic pairwise alignments},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {153-160},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S153},
PUBLISHER = {Oxford University Press},
}
@article{Model-Konig-Piepenbrock-Adorjan/02,
AUTHOR = {Model, Fabian and K{\"o}nig, Thomas and Piepenbrock, Christian and Adorj{\'a}n, P{\'e}ter},
TITLE = {Statistical process control for large scale microarray experiments},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {155-163},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S155},
PUBLISHER = {Oxford University Press},
}
@article{Clare-King/02,
AUTHOR = {Clare, Amanda and King, Ross D.},
TITLE = {Machine learning of functional class from phenotype data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {160-166},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/160},
PUBLISHER = {Oxford University Press},
}
@article{Nicodeme-Doerks-Vingron/02,
AUTHOR = {Nicod{\`{e}}me, P. and Doerks, T. and Vingron, M.},
TITLE = {Proteome analysis based on motif statistics},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {161-171},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S161},
PUBLISHER = {Oxford University Press},
}
@article{Dietmann-Frommel/02,
AUTHOR = {Dietmann, S. and Fr{\"o}mmel, C.},
TITLE = {Prediction of 3D neighbours of molecular surface patches in proteins by artificial neural networks},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {167-174},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/167},
PUBLISHER = {Oxford University Press},
}
@article{Linhart-Shamir/02,
AUTHOR = {Linhart, Chaim and Shamir, Ron},
TITLE = {The degenerate primer design problem},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {172-181},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S172},
PUBLISHER = {Oxford University Press},
}
@article{Palin-Ukkonen-Brazma-Vilo/02,
AUTHOR = {Palin, Kimmo and Ukkonen, Esko and Brazma, Alvis and Vilo, Jaak},
TITLE = {Correlating gene promoters and expression in gene disruption experiments},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {172-180},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S172},
PUBLISHER = {Oxford University Press},
}
@article{Allcorn-Martin/02,
AUTHOR = {Allcorn, Lee C. and Martin, Andrew C.R.},
TITLE = {SACS --- Self-maintaining database of antibody crystal structure information},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {175-181},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/175},
PUBLISHER = {Oxford University Press},
}
@article{Heber-Alekseyev-Sze-Tang-Pevzner/02,
AUTHOR = {Heber, Steffen and Alekseyev, Max and Sze, Sing-Hoi and Tang, Haixu and Pevzner, Pavel A.},
TITLE = {Splicing graphs and EST assembly problem},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {181-188},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S181},
PUBLISHER = {Oxford University Press},
}
@article{Patterson/02,
AUTHOR = {Patterson, Scott},
TITLE = {Selecting targets for therapeutic validation through differential protein expression using chromatography-mass spectrometry},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {181-181},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S181},
PUBLISHER = {Oxford University Press},
}
@article{Conklin-Jonassen-Aasland-Taylor/02,
AUTHOR = {Conklin, Darrell and Jonassen, Inge and Aasland, Rein and Taylor, William R.},
TITLE = {Association of nucleotide patterns with gene function classes: Application to human 3' untranslated sequences},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {182-189},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/182},
PUBLISHER = {Oxford University Press},
}
@article{Pipenbacher-Schliep-Schneckener-Schonhuth-Schomburg-Schrader/02,
AUTHOR = {Pipenbacher, P. and Schliep, A. and Schneckener, S. and Sch{\"o}nhuth, A. and Schomburg, D. and Schrader, R.},
TITLE = {ProClust: Improved clustering of protein sequences with an extended graph-based approach},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {182-191},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S182},
PUBLISHER = {Oxford University Press},
}
@article{Fishelson-Geiger/02,
AUTHOR = {Fishelson, M. and Geiger, D.},
TITLE = {Exact genetic linkage computations for general pedigrees},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {189-198},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S189},
PUBLISHER = {Oxford University Press},
}
@article{Ponomarenko-Bourne-Shindyalov/02,
AUTHOR = {Ponomarenko, Julia V. and Bourne, Philip E. and Shindyalov, Ilya N.},
TITLE = {Building an automated classification of DNA-binding protein domains},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {192-201},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S192},
PUBLISHER = {Oxford University Press},
}
@article{Bonfield-Beal-Betts-Staden/02,
AUTHOR = {Bonfield, James K. and Beal, Kathryn F. and Betts, Matthew J. and Staden, Rodger},
TITLE = {Trev: A DNA trace editor and viewer},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {194-195},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/194},
PUBLISHER = {Oxford University Press},
}
@article{Issac-Singh-Kaur-Raghava/02,
AUTHOR = {Issac, Biju and Singh, Harpreet and Kaur, Harpreet and Raghava, G.P.S.},
TITLE = {Locating probable genes using Fourier transform approach},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {196-197},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/196},
PUBLISHER = {Oxford University Press},
}
@article{Bajic-Seah-Chong-Zhang-Koh-Brusic/02,
AUTHOR = {Bajic, Vladimir B. and Seah, Seng Hong and Chong, Allen and Zhang, Guanglan and Koh, Judice L.Y. and Brusic, Vladimir},
TITLE = {Dragon Promoter Finder: Recognition of vertebrate RNA polymerase II promoters},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {198-199},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/198},
PUBLISHER = {Oxford University Press},
}
@article{Kivioja-Arvas-Kataja-Penttila-Soderlund-Ukkonen/02,
AUTHOR = {Kivioja, Teemu and Arvas, Mikko and Kataja, Kari and Penttil{\"a}, Merja and S{\"o}derlund, Hans and Ukkonen, Esko},
TITLE = {Assigning probes into a small number of pools separable by electrophoresis},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {199-206},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S199},
PUBLISHER = {Oxford University Press},
}
@article{Stuart-Ilyin-Sali/02,
AUTHOR = {Stuart, Ashley C. and Ilyin, Valentin A. and Sali, Andrej},
TITLE = {LigBase: A database of families of aligned ligand binding sites in known protein sequences and structures},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {200-201},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/200},
PUBLISHER = {Oxford University Press},
}
@article{Chapman-Schenk-Kazan-Manners/02,
AUTHOR = {Chapman, Scott and Schenk, Peer and Kazan, Kemal and Manners, John},
TITLE = {Using biplots to interpret gene expression patterns in plants},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {202-204},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/202},
PUBLISHER = {Oxford University Press},
}
@article{Rung-Schlitt-Brazma-Freivalds-Vilo/02,
AUTHOR = {Rung, J. and Schlitt, T. and Brazma, A. and Freivalds, K. and Vilo, J.},
TITLE = {Building and analysing genome-wide gene disruption networks},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {202-210},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S202},
PUBLISHER = {Oxford University Press},
}
@article{Rhodes-Miller-Haab-Furge/02,
AUTHOR = {Rhodes, Daniel R. and Miller, Jeremy C. and Haab, Brian B. and Furge, Kyle A.},
TITLE = {CIT: Identification of differentially expressed clusters of genes from microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {205-206},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/205},
PUBLISHER = {Oxford University Press},
}
@article{Rubin-Shafa-Oliver-Hewett-Altman/02,
AUTHOR = {Rubin, Daniel L. and Shafa, Farhad and Oliver, Diane E. and Hewett, Micheal and Altman, Russ B.},
TITLE = {Representing genetic sequence data for pharmacogenomics: An evolutionary approach using ontological and relational models},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {207-215},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S207},
PUBLISHER = {Oxford University Press},
}
@article{Hofmann-Wlodawer/02,
AUTHOR = {Hofmann, A. and Wlodawer, A.},
TITLE = {PCSB --- A program collection for structural biology and biophysical chemistry},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {209-210},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/209},
PUBLISHER = {Oxford University Press},
}
@article{Lobley-Whitmore-Wallace/02,
AUTHOR = {Lobley, A. and Whitmore, L. and Wallace, B.A.},
TITLE = {DICHROWEB: An interactive website for the analysis of protein secondary structure from circular dichroism spectra},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {211-212},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/211},
PUBLISHER = {Oxford University Press},
}
@article{Salmenkivi-Kere-Mannila/02,
AUTHOR = {Salmenkivi, Marko and Kere, Juha and Mannila, Heikki},
TITLE = {Genome segmentation using piecewise constant intensity models and reversible jump MCMC},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {211-218},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S211},
PUBLISHER = {Oxford University Press},
}
@article{Combet-Jambon-Deleage-Geourjon/02,
AUTHOR = {Combet, Christophe and Jambon, Martin and Del{\'e}age, Gilbert and Geourjon, Christophe},
TITLE = {Geno3D: Automatic comparative molecular modelling of protein},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {213-214},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/213},
PUBLISHER = {Oxford University Press},
}
@article{Forsdyke/02,
AUTHOR = {Forsdyke, D.R.},
TITLE = {Symmetry observations in long nucleotide sequences: A commentary on the Discovery Note of Qi and Cuticchia},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {215-217},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/215},
PUBLISHER = {Oxford University Press},
}
@article{Smith-Jarvis-Hartemink/02,
AUTHOR = {Smith, V. Anne and Jarvis, Erich D. and Hartemink, Alexander J.},
TITLE = {Evaluating functional network inference using simulations of complex biological systems},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {216-224},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S216},
PUBLISHER = {Oxford University Press},
}
@article{Moller-Croning-Apweiler/02,
AUTHOR = {M{\"o}ller, Steffen and Croning, Michael D.R. and Apweiler, Rolf},
TITLE = {Erratum to ''Evaluation of methods for the prediction of membrane spanning regions''},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {1},
PAGES = {218-218},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/1/218},
PUBLISHER = {Oxford University Press},
NOTE = {Originally in Bioinformatics, Vol. 17, 2001, No. 7, 646-653},
}
@article{Sirava-Schafer-Eiglsperger-Kaufmann-Kohlbacher-Bornberg-Bauer-Lenhof/02,
AUTHOR = {Sirava, M. and Sch{\"a}fer, T. and Eiglsperger, M. and Kaufmann, M. and Kohlbacher, O. and Bornberg-Bauer, E. and Lenhof, H.P.},
TITLE = {BioMiner --- Modeling, analyzing, and visualizing biochemical pathways and networks},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {219-230},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S219},
PUBLISHER = {Oxford University Press},
}
@article{Karp-Paley-Romero/02,
AUTHOR = {Karp, Peter D. and Paley, Suzanne and Romero, Pedro},
TITLE = {The Pathway Tools software},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {225-232},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S225},
PUBLISHER = {Oxford University Press},
}
@article{Husmeier-Wright/02,
AUTHOR = {Husmeier, Dirk and Wright, Frank},
TITLE = {A Bayesian approach to discriminate between alternative DNA sequence segmentations},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {226-234},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/226},
PUBLISHER = {Oxford University Press},
}
@article{Steuer-Kurths-Daub-Weise-Selbig/02,
AUTHOR = {Steuer, R. and Kurths, J. and Daub, C.O. and Weise, J. and Selbig, J.},
TITLE = {The mutual information: Detecting and evaluating dependencies between variables},
BOOKTITLE = {Proceedings of the European Conference on Computational Biology, ECCB'2002 (Saarbr{\"u}cken, Germany, October 6-9, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S2},
PAGES = {231-240},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_2/S231},
PUBLISHER = {Oxford University Press},
}
@article{Ideker-Ozier-Schwikowski-Siegel/02,
AUTHOR = {Ideker, Trey and Ozier, Owen and Schwikowski, Benno and Siegel, Andrew F.},
TITLE = {Discovering regulatory and signalling circuits in molecular interaction networks},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {233-240},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S233},
PUBLISHER = {Oxford University Press},
}
@article{Sebban-Mokrousov-Rastogi-Sola/02,
AUTHOR = {Sebban, M. and Mokrousov, I. and Rastogi, N. and Sola, C.},
TITLE = {A data-mining approach to spacer oligonucleotide typing of Mycobacterium tuberculosis},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {235-243},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/235},
PUBLISHER = {Oxford University Press},
}
@article{Ong-Glasner-Page/02,
AUTHOR = {Ong, Irene M. and Glasner, Jeremy D. and Page, David},
TITLE = {Modelling regulatory pathways in E. coli from time series expression profiles},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {241-248},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S241},
PUBLISHER = {Oxford University Press},
}
@article{Krauthammer-Kra-Iossifov-Gomez-Hripcsak-Hatzivassiloglou-Friedman-Rzhetsky/02,
AUTHOR = {Krauthammer, Michael and Kra, Pauline and Iossifov, Ivan and Gomez, Shawn M. and Hripcsak, George and Hatzivassiloglou, Vasileios and Friedman, Carol and Rzhetsky, Andrey},
TITLE = {Of truth and pathways: Chasing bits of information through myriads of articles},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {249-257},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S249},
PUBLISHER = {Oxford University Press},
}
@article{Peer-Regev-Tanay/02,
AUTHOR = {Pe'er, Dana and Regev, Aviv and Tanay, Amos},
TITLE = {Minreg: Inferring an active regulator set},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {258-267},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S258},
PUBLISHER = {Oxford University Press},
}
@article{Shmulevich-Dougherty-Kim-Zhang/02,
AUTHOR = {Shmulevich, Ilya and Dougherty, Edward R. and Kim, Seungchan and Zhang, Wei},
TITLE = {Probabilistic Boolean networks: A rule-based uncertainty model for gene regulatory networks},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {261-274},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/261},
PUBLISHER = {Oxford University Press},
}
@article{Ghosh-Chinnaiyan/02,
AUTHOR = {Ghosh, Debashis and Chinnaiyan, Arul M.},
TITLE = {Mixture modelling of gene expression data from microarray experiments},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {275-286},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/275},
PUBLISHER = {Oxford University Press},
}
@article{Stockham-Wang-Warnow/02,
AUTHOR = {Stockham, Cara and Wang, Li-San and Warnow, Tandy},
TITLE = {Statistically based postprocessing of phylogenetic analysis by clustering},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {285-293},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S285},
PUBLISHER = {Oxford University Press},
}
@article{Fasulo-Halpern-Dew-Mobarry/02,
AUTHOR = {Fasulo, Daniel and Halpern, Aaron and Dew, Ian and Mobarry, Clark},
TITLE = {Efficiently detecting polymorphisms during the fragment assembly process},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {294-302},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S294},
PUBLISHER = {Oxford University Press},
}
@article{Bannai-Tamada-Maruyama-Nakai-Miyano/02,
AUTHOR = {Bannai, Hideo and Tamada, Yoshinori and Maruyama, Osamu and Nakai, Kenta and Miyano, Satoru},
TITLE = {Extensive feature detection of N-terminal protein sorting signals},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {298-305},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/298},
PUBLISHER = {Oxford University Press},
}
@article{Korkin-Goldfarb/02,
AUTHOR = {Korkin, Dmitry and Goldfarb, Lev},
TITLE = {Multiple genome rearrangement: A general approach via the evolutionary genome graph},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {303-311},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S303},
PUBLISHER = {Oxford University Press},
}
@article{Cline-Hughey-Karplus/02,
AUTHOR = {Cline, Melissa and Hughey, Richard and Karplus, Kevin},
TITLE = {Predicting reliable regions in protein sequence alignments},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {306-314},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/306},
PUBLISHER = {Oxford University Press},
}
@article{Hohl-Kurtz-Ohlebusch/02,
AUTHOR = {H{\"o}hl, Michael and Kurtz, Stefan and Ohlebusch, Enno},
TITLE = {Efficient multiple genome alignment},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {312-320},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S312},
PUBLISHER = {Oxford University Press},
}
@article{Krieger-Vriend/02,
AUTHOR = {Krieger, Elmar and Vriend, Gert},
TITLE = {Models@Home: Distributed computing in bioinformatics using a screensaver based approach},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {315-318},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/315},
PUBLISHER = {Oxford University Press},
}
@article{Azuaje/02,
AUTHOR = {Azuaje, F.},
TITLE = {A cluster validity framework for genome expression data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {319-320},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/319},
PUBLISHER = {Oxford University Press},
}
@article{Han-Lee-Kim/02,
AUTHOR = {Han, Kyungsook and Lee, Yujin and Kim, Wootaek},
TITLE = {PseudoViewer: Automatic visualization of RNA pseudoknots},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {321-328},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S321},
PUBLISHER = {Oxford University Press},
}
@article{Nielsen-Knudsen/02,
AUTHOR = {Nielsen, H.B. and Knudsen, S.},
TITLE = {Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {321-322},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/321},
PUBLISHER = {Oxford University Press},
}
@article{Bouton-Pevsner/02,
AUTHOR = {Bouton, Christopher M.L.S. and Pevsner, Jonathan},
TITLE = {DRAGON View: Information visualization for annotated microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {323-324},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/323},
PUBLISHER = {Oxford University Press},
}
@article{Bumm-Zheng-Bailey-Zhan-Chiriva-Internati-Eddlemon-Terry-Barlogie-Shaughnessy/02,
AUTHOR = {Bumm, Klaus and Zheng, Mingzhong and Bailey, Clyde and Zhan, Fenghuang and Chiriva-Internati, M. and Eddlemon, Paul and Terry, Julian and Barlogie, Bart and Shaughnessy, and John D., Jr.},
TITLE = {CGO: Utilizing and integrating gene expression microarray data in clinical research and data management},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {327-328},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/327},
PUBLISHER = {Oxford University Press},
}
@article{Collette-Six/02,
AUTHOR = {Collette, A. and Six, A.},
TITLE = {ISEApeaks: An Excel platform for GeneScan and Immunoscope data retrieval, management and analysis},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {329-330},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/329},
PUBLISHER = {Oxford University Press},
}
@article{Moreno-Hagelsieb-Collado-Vides/02,
AUTHOR = {Moreno-Hagelsieb, Gabriel and Collado-Vides, Julio},
TITLE = {A powerful non-homology method for the prediction of operons in prokaryotes},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {329-336},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S329},
PUBLISHER = {Oxford University Press},
}
@article{Messeguer-Escudero-Farre-Nunez-Martinez-Alba/02,
AUTHOR = {Messeguer, Xavier and Escudero, Ruth and Farr{\'e}, Dom{\`e}nec and N{\'u}{\~n}ez, Oscar and Mart{\'{i}}nez, Javier and Alb{\`a}, M. Mar},
TITLE = {PROMO: Detection of known transcription regulatory elements using species-tailored searches},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {333-334},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/333},
PUBLISHER = {Oxford University Press},
}
@article{Kozik-Kochetkova-Michelmore/02,
AUTHOR = {Kozik, A. and Kochetkova, E. and Michelmore, R.},
TITLE = {GenomePixelizer --- A visualization program for comparative genomics within and between species},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {335-336},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/335},
PUBLISHER = {Oxford University Press},
}
@article{Hudson/02,
AUTHOR = {Hudson, Richard R.},
TITLE = {Generating samples under a Wright-Fisher neutral model of genetic variation},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {337-338},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/337},
PUBLISHER = {Oxford University Press},
}
@article{Seaton-Haley-Knott-Kearsey-Visscher/02,
AUTHOR = {Seaton, George and Haley, Chris S. and Knott, Sara A. and Kearsey, Mike and Visscher, Peter M.},
TITLE = {QTL Express: Mapping quantitative trait loci in simple and complex pedigrees},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {339-340},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/339},
PUBLISHER = {Oxford University Press},
}
@article{Signorovitch-Nielsen/02,
AUTHOR = {Signorovitch, J. and Nielsen, R.},
TITLE = {PATRI --- Paternity inference using genetic data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {341-342},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/341},
PUBLISHER = {Oxford University Press},
}
@article{Hatzigeorgiou/02,
AUTHOR = {Hatzigeorgiou, Artemis G.},
TITLE = {Translation initiation start prediciton in human cDNAs with high accurcy},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {343-350},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/343},
PUBLISHER = {Oxford University Press},
}
@article{Husmeier-McGuire/02,
AUTHOR = {Husmeier, Dirk and McGuire, Gr{\'a}inne},
TITLE = {Detecting recombination with MCMC},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {345-353},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S345},
PUBLISHER = {Oxford University Press},
}
@article{Schuster-Pfeiffer-Moldenhauer-Koch-Dandekar/02,
AUTHOR = {Schuster, S. and Pfeiffer, T. and Moldenhauer, F. and Koch, I. and Dandekar, T.},
TITLE = {Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {351-361},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/351},
PUBLISHER = {Oxford University Press},
}
@article{Eskin-Pevzner/02,
AUTHOR = {Eskin, Eleazar and Pevzner, Pavel A.},
TITLE = {Finding composite regulatory patterns in DNA sequences},
BOOKTITLE = {Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology, ISMB'2002 (Edmonton, Canada, August 3-7, 2002)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {S1},
PAGES = {354-363},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/suppl_1/S354},
PUBLISHER = {Oxford University Press},
}
@article{Jonassen-Eidhammer-Conklin-Taylor/02,
AUTHOR = {Jonassen, Inge and Eidhammer, Ingvar and Conklin, Darrell and Taylor, William R.},
TITLE = {Structure motif discovery and mining the PDB},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {362-367},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/362},
PUBLISHER = {Oxford University Press},
}
@article{Kanapin-Apweiler-Biswas-Fleischmann-Karavidopoulou-Kersey-Kriventseva-Mittard-Mulder-Oinn-Phan-Servant-Zdobnov/02,
AUTHOR = {Kanapin, A. and Apweiler, R. and Biswas, M. and Fleischmann, W. and Karavidopoulou, Y. and Kersey, P. and Kriventseva, E.V. and Mittard, V. and Mulder, N. and Oinn, T. and Phan, I. and Servant, F. and Zdobnov, E.},
TITLE = {Interactive InterPro-based comparisons of proteins in whole genomes},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {2},
PAGES = {374-375},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/2/374},
PUBLISHER = {Oxford University Press},
}
@article{Ball-Mian-Holding-Allibone-Lowe-Ali-Li-McCardle-Ellis-Creaser-Rees/02,
AUTHOR = {Ball, G. and Mian, S. and Holding, F. and Allibone, R.O. and Lowe, J. and Ali, S. and Li, G. and McCardle, S. and Ellis, I.O. and Creaser, C. and Rees, R.C.},
TITLE = {An integrated approach utilizing artificial neural networks and SELDI mass spectrometry for the classification of human tumours and rapid identification of potential biomarkers},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {3},
PAGES = {395-404},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/395},
PUBLISHER = {Oxford University Press},
}
@article{Kuo-Jenssen-Butte-Ohno-Machado-Kohane/02,
AUTHOR = {Kuo, Winston Patrick and Jenssen, Tor-Kristian and Butte, Atul J. and Ohno-Machado, Lucila and Kohane, Isaac S.},
TITLE = {Analysis of matched mRNA measurements from two different microarray technologies},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {3},
PAGES = {405-412},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/405},
PUBLISHER = {Oxford University Press},
}
@article{McLachlan-Bean-Peel/02,
AUTHOR = {McLachlan, G.J. and Bean, R.W. and Peel, D.},
TITLE = {A mixture model-based approach to the clustering of microarray expression data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {3},
PAGES = {413-422},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/413},
PUBLISHER = {Oxford University Press},
}
@article{Fellenberg-Hauser-Brors-Hoheisel-Vingron/02,
AUTHOR = {Fellenberg, Kurt and Hauser, Nicole C. and Brors, Benedikt and Hoheisel, J{\"o}rg D. and Vingron, Martin},
TITLE = {Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {3},
PAGES = {423-433},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/423},
PUBLISHER = {Oxford University Press},
}
@article{Blythe-Doytchinova-Flower/02,
AUTHOR = {Blythe, Martin J. and Doytchinova, Irini A. and Flower, Darren R.},
TITLE = {JenPep: A database of quantitative functional peptide data for immunology},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {3},
PAGES = {434-439},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/434},
PUBLISHER = {Oxford University Press},
}
@article{Ma-Tromp-Li/02,
AUTHOR = {Ma, Bin and Tromp, John and Li, Ming},
TITLE = {PatternHunter: Faster and more sensitive homology search},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {3},
PAGES = {440-445},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/440},
PUBLISHER = {Oxford University Press},
}
@article{Lee-Grasso-Sharlow/02,
AUTHOR = {Lee, Christopher and Grasso, Catherine and Sharlow, Mark F.},
TITLE = {Multiple sequence alignment using partial order graphs},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {3},
PAGES = {452-464},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/452},
PUBLISHER = {Oxford University Press},
}
@article{Ettinger/02,
AUTHOR = {Ettinger, Mark},
TITLE = {The complexity of comparing reaction systems},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {3},
PAGES = {465-469},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/465},
PUBLISHER = {Oxford University Press},
}
@article{Kierzek/02,
AUTHOR = {Kierzek, Andrzej M.},
TITLE = {STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {3},
PAGES = {470-481},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/470},
PUBLISHER = {Oxford University Press},
}
@article{Mannila-Patrikainen-Seppanen-Kere/02,
AUTHOR = {Mannila, Heikki and Patrikainen, Anne and Sepp{\"a}nen, Jouni K. and Kere, Juha},
TITLE = {Long-range control of expression in yeast},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {3},
PAGES = {482-483},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/482},
PUBLISHER = {Oxford University Press},
}
@article{Ness-Terpstra-Krzywinski-Marra-Jones/02,
AUTHOR = {Ness, S.R. and Terpstra, W. and Krzywinski, M. and Marra, M.A. and Jones, S.J.M.},
TITLE = {Assembly of fingerprint contigs: Parallelized FPC},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {3},
PAGES = {484-485},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/484},
PUBLISHER = {Oxford University Press},
}
@article{Rouillard-Herbert-Zuker/02,
AUTHOR = {Rouillard, Jean-Marie and Herbert, Christopher J. and Zuker, Michael},
TITLE = {OligoArray: Genome-scale oligonucleotide design for microarrays},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {3},
PAGES = {486-487},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/486},
PUBLISHER = {Oxford University Press},
}
@article{Didier-Brezellec-Remy-Henaut/02,
AUTHOR = {Didier, G. and Br{\'e}zellec, P. and Remy, E. and H{\'e}naut, A.},
TITLE = {GeneANOVA --- Gene expression analysis of variance},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {3},
PAGES = {490-491},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/490},
PUBLISHER = {Oxford University Press},
}
@article{Leplae-Hubbard/02,
AUTHOR = {Leplae, Raphael and Hubbard, Tim J.P.},
TITLE = {MaxBench: Evaluation of sequence and structure comparison methods},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {3},
PAGES = {494-495},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/494},
PUBLISHER = {Oxford University Press},
}
@article{Kahsay-Wang-Dongre-Gao-Dunbrack/02,
AUTHOR = {Kahsay, Robel Y. and Wang, Guoli and Dongre, Nataraj and Gao, Guang and Dunbrack, and Roland L., Jr.},
TITLE = {CASA: A server for the critical assessment of protein sequence alignment accuracy},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {3},
PAGES = {496-497},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/496},
PUBLISHER = {Oxford University Press},
}
@article{Kaur-Raghava/02,
AUTHOR = {Kaur, Harpreet and Raghava, G.P.S.},
TITLE = {BetaTPred: Prediction of $\beta$-TURNS in a protein using statistical algorithms},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {3},
PAGES = {498-499},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/498},
PUBLISHER = {Oxford University Press},
}
@article{Gu-Velden/02,
AUTHOR = {Gu, Xun and Velden, Kent Vander},
TITLE = {DIVERGE: Phylogeny-based analysis for functional-structural divergence of a protein family},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {3},
PAGES = {500-501},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/500},
PUBLISHER = {Oxford University Press},
}
@article{Schmidt-Strimmer-Vingron-von_Haeseler/02,
AUTHOR = {Schmidt, Heiko A. and Strimmer, Korbinian and Vingron, Martin and von Haeseler, Arndt},
TITLE = {TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {3},
PAGES = {502-504},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/502},
PUBLISHER = {Oxford University Press},
}
@article{Schreiber-Brown/02,
AUTHOR = {Schreiber, Mark and Brown, Chris},
TITLE = {Compensation for nucleotide bias in a genome by representation as a discrete channel with noise},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {4},
PAGES = {507-512},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/507},
PUBLISHER = {Oxford University Press},
}
@article{Hampson-Kibler-Baldi/02,
AUTHOR = {Hampson, Steven and Kibler, Dennis and Baldi, Pierre},
TITLE = {Distribution patterns of over-represented $k$-mers in non-coding yeast DNA},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {4},
PAGES = {513-528},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/513},
PUBLISHER = {Oxford University Press},
}
@article{Colbourn-Ling-Tompa/02,
AUTHOR = {Colbourn, Charles J. and Ling, Alan C.H. and Tompa, Martin},
TITLE = {Construction of optimal quality control for oligo arrays},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {4},
PAGES = {529-535},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/529},
PUBLISHER = {Oxford University Press},
}
@article{Pan/02,
AUTHOR = {Pan, Wei},
TITLE = {A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {4},
PAGES = {546-554},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/546},
PUBLISHER = {Oxford University Press},
}
@article{Shmulevich-Zhang/02,
AUTHOR = {Shmulevich, Ilya and Zhang, Wei},
TITLE = {Binary analysis and optimization-based normalization of gene expression data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {4},
PAGES = {555-565},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/555},
PUBLISHER = {Oxford University Press},
}
@article{Moloshok-Klevecz-Grant-Manion-Speier-Ochs/02,
AUTHOR = {Moloshok, T.D. and Klevecz, R.R. and Grant, J.D. and Manion, F.J. and Speier IV, W.F. and Ochs, M.F.},
TITLE = {Application of Bayesian Decomposition for analysing microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {4},
PAGES = {566-575},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/566},
PUBLISHER = {Oxford University Press},
}
@article{Hoyle-Rattray-Jupp-Brass/02,
AUTHOR = {Hoyle, David C. and Rattray, Magnus and Jupp, Ray and Brass, Andrew},
TITLE = {Making sense of microarray data distributions},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {4},
PAGES = {576-584},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/576},
PUBLISHER = {Oxford University Press},
}
@article{Greenbaum-Jansen-Gerstein/02,
AUTHOR = {Greenbaum, Dov and Jansen, Ronald and Gerstein, Mark},
TITLE = {Analysis of mRNA expression and protein abundance data: An approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {4},
PAGES = {585-596},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/585},
PUBLISHER = {Oxford University Press},
}
@article{Aguilar-Oliva-Aviles-Querol/02,
AUTHOR = {Aguilar, Daniel and Oliva, Baldomero and Aviles, Francesc X. and Querol, Enrique},
TITLE = {TranScout: Prediction of gene expression regulatory proteins from their sequences},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {4},
PAGES = {597-607},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/597},
PUBLISHER = {Oxford University Press},
}
@article{Mitaku-Hirokawa-Tsuji/02,
AUTHOR = {Mitaku, Shigeki and Hirokawa, Takatsugu and Tsuji, Toshiyuki},
TITLE = {Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {4},
PAGES = {608-616},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/608},
PUBLISHER = {Oxford University Press},
}
@article{Delorenzi-Speed/02,
AUTHOR = {Delorenzi, Mauro and Speed, Terry},
TITLE = {An HMM model for coiled-coil domains and a comparison with PSSM-based predictions},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {4},
PAGES = {617-625},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/617},
PUBLISHER = {Oxford University Press},
}
@article{Bennett-Lovsey-Hart-Shirai-Mizuguchi/02,
AUTHOR = {Bennett-Lovsey, Riccardo and Hart, Sarah E. and Shirai, Hiroki and Mizuguchi, Kenji},
TITLE = {The SWIB and the MDM2 domains are homologous and share a common fold},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {4},
PAGES = {626-630},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/626},
PUBLISHER = {Oxford University Press},
}
@article{Ponger-Mouchiroud/02,
AUTHOR = {Ponger, Lo{\"{i}} and Mouchiroud, Dominique},
TITLE = {CpGProD: Identifying CpG islands associated with transcription start sites in large genomic mammalian sequences},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {4},
PAGES = {631-633},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/631},
PUBLISHER = {Oxford University Press},
}
@article{Castelo-Martins-Gao/02,
AUTHOR = {Castelo, Adalberto T. and Martins, Wellington and Gao, Guang R.},
TITLE = {TROLL --- Tandem Repeat Occurrence Locator},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {4},
PAGES = {634-636},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/634},
PUBLISHER = {Oxford University Press},
}
@article{Ochagavia-Richelle-Wodak/02,
AUTHOR = {Ochagavia, Maria Elena and Richelle, Jean and Wodak, Shoshana J.},
TITLE = {Advanced pairwise structure alignments of proteins and analysis of conformational changes},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {4},
PAGES = {637-640},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/637},
PUBLISHER = {Oxford University Press},
}
@article{Babu-Sankaran/02,
AUTHOR = {Babu, M. Madan and Sankaran, K.},
TITLE = {DOLOP --- Database of bacterial lipoproteins},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {4},
PAGES = {641-643},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/641},
PUBLISHER = {Oxford University Press},
}
@article{Rusconi-Belghazi/02,
AUTHOR = {Rusconi, Filippo and Belghazi, Maya},
TITLE = {Desktop prediction/analysis of mass spectrometric data in proteomic projects by using massXpert},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {4},
PAGES = {644-645},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/644},
PUBLISHER = {Oxford University Press},
}
@article{Qi-Cuticchia/02,
AUTHOR = {Qi, Dong and Cuticchia, A. Jamie},
TITLE = {Erratum to ''Compositional symmetries in complete genomes''},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {4},
PAGES = {648-648},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/4/648},
PUBLISHER = {Oxford University Press},
NOTE = {Originally in Bioinformatics, Vol. 17, 2001, No. 6, 557-559},
}
@article{Blazewicz-Formanowicz-Guinand-Kasprzak/02,
AUTHOR = {B{\l}a{\.z}ewicz, Jacek and Formanowicz, Piotr and Guinand, Frederic and Kasprzak, Marta},
TITLE = {A heuristic managing errors for DNA sequencing},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {5},
PAGES = {652-660},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/5/652},
PUBLISHER = {Oxford University Press},
}
@article{Hao-Tan/02,
AUTHOR = {Hao, Yu-hua and Tan, Zheng},
TITLE = {The generation of long telomere overhangs in human cells: A model and its implication},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {5},
PAGES = {666-671},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/5/666},
PUBLISHER = {Oxford University Press},
NOTE = {see Erratum in Bioinformatics, Vol. 18, 2002, No. 9, 1282-1282},
}
@article{Alba-Laskowski-Hancock/02,
AUTHOR = {Alb{\`a}, M. Mar and Laskowski, Roman A. and Hancock, John M.},
TITLE = {Detecting cryptically simple protein sequences using the SIMPLE algorithm},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {5},
PAGES = {672-678},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/5/672},
PUBLISHER = {Oxford University Press},
}
@article{Estrada/02,
AUTHOR = {Estrada, Ernesto},
TITLE = {Characterization of the folding degree of proteins},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {5},
PAGES = {697-704},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/5/697},
PUBLISHER = {Oxford University Press},
}
@article{Oyama-Kitano-Satou-Ito/02,
AUTHOR = {Oyama, T. and Kitano, K. and Satou, K. and Ito, T.},
TITLE = {Extraction of knowledge on protein-protein interaction by association rule discovery},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {5},
PAGES = {705-714},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/5/705},
PUBLISHER = {Oxford University Press},
NOTE = {see Erratum in Bioinformatics, Vol. 18, 2002, No. 8, 1151-1151},
}
@article{Paley-Karp/02,
AUTHOR = {Paley, Suzanne M. and Karp, Peter D.},
TITLE = {Evaluation of computational metabolic-pathway predictions for Helicobacter pylori},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {5},
PAGES = {715-724},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/5/715},
PUBLISHER = {Oxford University Press},
}
@article{Li-Wong/02,
AUTHOR = {Li, Jinyan and Wong, Limsoon},
TITLE = {Identifying good diagnostic gene groups from gene expression profiles using the concept of emerging patterns},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {5},
PAGES = {725-734},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/5/725},
PUBLISHER = {Oxford University Press},
NOTE = {see Erratum in Bioinformatics, Vol. 18, 2002, No. 10, 1406-1407},
}
@article{Bozinov-Rahnenfuhrer/02,
AUTHOR = {Bozinov, Daniel and Rahnenf{\"u}hrer, J{\"o}rg},
TITLE = {Unsupervised technique for robust target separation and analysis of DNA microarray spots through adaptive pixel clustering},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {5},
PAGES = {747-756},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/5/747},
PUBLISHER = {Oxford University Press},
}
@article{Lombard-Camon-Parkinson-Hingamp-Stoesser-Redaschi/02,
AUTHOR = {Lombard, V. and Camon, E.B. and Parkinson, H.E. and Hingamp, P. and Stoesser, G. and Redaschi, N.},
TITLE = {EMBL-Align: A new public nucleotide and amino acid multiple sequence alignment database},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {5},
PAGES = {763-764},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/5/763},
PUBLISHER = {Oxford University Press},
}
@article{Grant-Dunbrack-Manion-Ochs/02,
AUTHOR = {Grant, J.D. and Dunbrack, R.L. and Manion, F.J. and Ochs, M.F.},
TITLE = {BeoBLAST: Distributed BLAST and PSI-BLAST on a Beowulf cluster},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {5},
PAGES = {765-766},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/5/765},
PUBLISHER = {Oxford University Press},
}
@article{Gouet-Courcelle/02,
AUTHOR = {Gouet, Patrice and Courcelle, Emmanuel},
TITLE = {ENDscript: A workflow to display sequence and structure information},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {5},
PAGES = {767-768},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/5/767},
PUBLISHER = {Oxford University Press},
}
@article{Monigatti-Gasteiger-Bairoch-Jung/02,
AUTHOR = {Monigatti, Flavio and Gasteiger, Elisabeth and Bairoch, Amos and Jung, Eva},
TITLE = {The Sulfinator: Predicting tyrosine sulfation sites in protein sequences},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {5},
PAGES = {769-770},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/5/769},
PUBLISHER = {Oxford University Press},
}
@article{Fielden-Halgren-Dere-Zacharewski/02,
AUTHOR = {Fielden, M.R. and Halgren, R.G. and Dere, E. and Zacharewski, T.R.},
TITLE = {GP3: GenePix post-processing program for automated analysis of raw microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {5},
PAGES = {771-773},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/5/771},
PUBLISHER = {Oxford University Press},
}
@article{Edgerton-Taylor-Powell-Hunter-Simon-Liu/02,
AUTHOR = {Edgerton, Mary E. and Taylor, Ronald and Powell, John I. and Hunter, Lawrence and Simon, Richard and Liu, Edison T.},
TITLE = {A bioinformatics tool to select sequences for microarray studies of mouse models of oncogenesis},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {5},
PAGES = {774-775},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/5/774},
PUBLISHER = {Oxford University Press},
}
@article{Morgenstern-Rinner-Abdeddaim-Haase-Mayer-Dress-Mewes/02,
AUTHOR = {Morgenstern, Burkhard and Rinner, Oliver and Abdedda{\"{i}}m, Sa{\"{i}}d and Haase, Dirk and Mayer, Klaus F.X. and Dress, Andreas W.M. and Mewes, Hans-Werner},
TITLE = {Exon discovery by genomic sequence alignment},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {6},
PAGES = {777-787},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/6/777},
PUBLISHER = {Oxford University Press},
}
@article{Raval-Ghahramani-Wild/02,
AUTHOR = {Raval, A. and Ghahramani, Z. and Wild, D.L.},
TITLE = {A Bayesian network model for protein fold and remote homologue recognition},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {6},
PAGES = {788-801},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/6/788},
PUBLISHER = {Oxford University Press},
}
@article{Sommer-Zien-von_Ohsen-Zimmer-Lengauer/02,
AUTHOR = {Sommer, Ingolf and Zien, Alexander and von {\"O}hsen, Niklas and Zimmer, Ralf and Lengauer, Thomas},
TITLE = {Confidence measures for protein fold recognition},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {6},
PAGES = {802-812},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/6/802},
PUBLISHER = {Oxford University Press},
}
@article{Luyf-de_Gast-van_Kampen/02,
AUTHOR = {Luyf, A.C.M. and de Gast, J. and van Kampen, A.H.C.},
TITLE = {Visualizing metabolic activity on a genome-wide scale},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {6},
PAGES = {813-818},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/6/813},
PUBLISHER = {Oxford University Press},
}
@article{Ahmad-Gromiha/02,
AUTHOR = {Ahmad, Shandar and Gromiha, M. Michael},
TITLE = {NETASA: Neural network based prediction of solvent accessibility},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {6},
PAGES = {819-824},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/6/819},
PUBLISHER = {Oxford University Press},
}
@article{Peleg-Yeh-Altman/02,
AUTHOR = {Peleg, Mor and Yeh, Iwei and Altman, Russ B.},
TITLE = {Modelling biological processes using workflow and Petri Net models},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {6},
PAGES = {825-837},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/6/825},
PUBLISHER = {Oxford University Press},
}
@article{Leontovich-Brodsky-Drachev-Nikolaev/02,
AUTHOR = {Leontovich, A.M. and Brodsky, L.I. and Drachev, V.A. and Nikolaev, V.K.},
TITLE = {Adaptive algorithm of automated annotation},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {6},
PAGES = {838-846},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/6/838},
PUBLISHER = {Oxford University Press},
}
@article{Schlosshauer-Ohlsson/02,
AUTHOR = {Schlosshauer, Maximilian and Ohlsson, Mattias},
TITLE = {A novel approach to local reliability of sequence alignments},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {6},
PAGES = {847-854},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/6/847},
PUBLISHER = {Oxford University Press},
}
@article{Bhalla/02,
AUTHOR = {Bhalla, Upinder S.},
TITLE = {The chemical organization of signaling interactions},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {6},
PAGES = {855-863},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/6/855},
PUBLISHER = {Oxford University Press},
}
@article{Giladi-Walker-Wang-Volkmuth/02,
AUTHOR = {Giladi, Eldar and Walker, Michael G. and Wang, James Z. and Volkmuth, Wayne},
TITLE = {SST: An algorithm for finding near-exact sequence matches in time proportional to the logarithm of the database size},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {6},
PAGES = {873-879},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/6/873},
PUBLISHER = {Oxford University Press},
}
@article{Gazit/02,
AUTHOR = {Gazit, Ehud},
TITLE = {Global analysis of tandem aromatic octapeptide repeats: The significance of the aromatic-glycine motif},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {6},
PAGES = {880-883},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/6/880},
PUBLISHER = {Oxford University Press},
}
@article{Karreman/02,
AUTHOR = {Karreman, Christiaan},
TITLE = {AiO, combining DNA/protein programs and oligo-management},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {6},
PAGES = {884-885},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/6/884},
PUBLISHER = {Oxford University Press},
}
@article{Gonzales-Dugan-Shafer/02,
AUTHOR = {Gonzales, Matthew J. and Dugan, Jonathan M. and Shafer, Robert W.},
TITLE = {Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {6},
PAGES = {886-887},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/6/886},
PUBLISHER = {Oxford University Press},
}
@article{Marc-Jacq/02,
AUTHOR = {Marc, Philippe and Jacq, Claude},
TITLE = {Arrayplot for visualization and normalization of cDNA microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {6},
PAGES = {888-889},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/6/888},
PUBLISHER = {Oxford University Press},
}
@article{Burckhardt/02,
AUTHOR = {Burckhardt, Florian},
TITLE = {MOUSE (Mitochondrial and Other Useful SEquences) a compilation of population genetic markers},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {6},
PAGES = {890-891},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/6/890},
PUBLISHER = {Oxford University Press},
}
@article{Dutheil-Galtier/02,
AUTHOR = {Dutheil, J. and Galtier, N.},
TITLE = {BAOBAB: A Java editor for large phylogenetic trees},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {6},
PAGES = {892-893},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/6/892},
PUBLISHER = {Oxford University Press},
}
@article{Reeve-Rannala/02,
AUTHOR = {Reeve, Jeff P. and Rannala, Bruce},
TITLE = {DMLE+: Bayesian linkage disequilibrium gene mapping},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {6},
PAGES = {894-895},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/6/894},
PUBLISHER = {Oxford University Press},
}
@article{Lessem-Cherny/02,
AUTHOR = {Lessem, J.M. and Cherny, S.S.},
TITLE = {Erratum to ''DeFries-Fulker multiple regression analysis of sibship QTL data: A SAS{\textregistered} macro''},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {6},
PAGES = {896-896},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/6/896},
PUBLISHER = {Oxford University Press},
NOTE = {Originally in Bioinformatics, Vol. 17, 2001, No. 4, 371-372},
}
@article{Portugaly-Kifer-Linial/02,
AUTHOR = {Portugaly, Elon and Kifer, Ilona and Linial, Michal},
TITLE = {Selecting targets for structural determination by navigating in a graph of protein families},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {7},
PAGES = {899-907},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/7/899},
PUBLISHER = {Oxford University Press},
}
@article{Abascal-Valencia/02,
AUTHOR = {Abascal, Federico and Valencia, Alfonso},
TITLE = {Clustering of proximal sequence space for the identification of protein families},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {7},
PAGES = {908-921},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/7/908},
PUBLISHER = {Oxford University Press},
}
@article{Liu-Rost/02,
AUTHOR = {Liu, Jinfeng and Rost, Burkhard},
TITLE = {Target space for structural genomics revisited},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {7},
PAGES = {922-933},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/7/922},
PUBLISHER = {Oxford University Press},
}
@article{Peitsch/02,
AUTHOR = {Peitsch, Manuel C.},
TITLE = {About the use of protein models},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {7},
PAGES = {934-938},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/7/934},
PUBLISHER = {Oxford University Press},
}
@article{Fradera-de_la_Cruz-Silva-Gelpi-Luque-Orozco/02,
AUTHOR = {Fradera, Xavier and de la Cruz, Xavier and Silva, Carlos H.T.P. and Gelp{\'{i}}, Jose Luis and Luque, F. Javier and Orozco, Modesto},
TITLE = {Ligand-induced changes in the binding sites of proteins},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {7},
PAGES = {939-948},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/7/939},
PUBLISHER = {Oxford University Press},
}
@article{Ostermeier-Dix-Krawetz/02,
AUTHOR = {Ostermeier, G. Charles and Dix, David J. and Krawetz, Stephen A.},
TITLE = {A bioinformatic strategy to rapidly characterize cDNA libraries},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {7},
PAGES = {949-952},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/7/949},
PUBLISHER = {Oxford University Press},
}
@article{Dodson-Charles-Stenger-Pancrazio/02,
AUTHOR = {Dodson, J.M. and Charles, P.T. and Stenger, D.A. and Pancrazio, J.J.},
TITLE = {Quantitative assessment of filter-based cDNA microarrays: Gene expression profiles of human T-lymphoma cell lines},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {7},
PAGES = {953-960},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/7/953},
PUBLISHER = {Oxford University Press},
}
@article{Olshen-Jain/02,
AUTHOR = {Olshen, Adam B. and Jain, Ajay N.},
TITLE = {Deriving quantitative conclusions from microarray expression data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {7},
PAGES = {961-970},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/7/961},
PUBLISHER = {Oxford University Press},
}
@article{Lillo-Basile-Mantegna/02,
AUTHOR = {Lillo, Fabrizio and Basile, Salvatore and Mantegna, Rosario N.},
TITLE = {Comparative genomics study of inverted repeats in bacteria},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {7},
PAGES = {971-979},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/7/971},
PUBLISHER = {Oxford University Press},
}
@article{Pintar-Carugo-Pongor/02,
AUTHOR = {Pintar, Alessandro and Carugo, Oliviero and Pongor, S{\'a}ndor},
TITLE = {CX, an algorithm that identifies protruding atoms in proteins},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {7},
PAGES = {980-984},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/7/980},
PUBLISHER = {Oxford University Press},
}
@article{Demir-Babur-Dogrusoz-Gursoy-Nisanci-Cetin-Atalay-Ozturk/02,
AUTHOR = {Demir, E. and Babur, O. and Dogrusoz, U. and Gursoy, A. and Nisanci, G. and Cetin-Atalay, R. and Ozturk, M.},
TITLE = {PATIKA: An integrated visual environment for collaborative construction and analysis of cellular pathways},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {7},
PAGES = {996-1003},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/7/996},
PUBLISHER = {Oxford University Press},
}
@article{Saka-Vazquez/02,
AUTHOR = {Saka, Yuki and V{\'a}zquez, Mariel},
TITLE = {TangleSolve: Topological analysis of site-specific recombination},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {7},
PAGES = {1011-1012},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/7/1011},
PUBLISHER = {Oxford University Press},
}
@article{Bober-Wiehe-Yung-Suzek-Lin-Baumgartner-Winslow/02,
AUTHOR = {Bober, Michael and Wiehe, Kevin and Yung, Christina and Suzek, Tugba Onal and Lin, Matthew and Baumgartner, William, Jr. and Winslow, Raimond},
TITLE = {CaGE: Cardiac gene expression knowledgebase},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {7},
PAGES = {1013-1014},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/7/1013},
PUBLISHER = {Oxford University Press},
}
@article{Kolesov-Mewes-Frishman/02,
AUTHOR = {Kolesov, Grigory and Mewes, Hans-Werner and Frishman, Dmitrij},
TITLE = {SNAPper: Gene order predicts gene function},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {7},
PAGES = {1017-1019},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/7/1017},
PUBLISHER = {Oxford University Press},
}
@article{Baisnee-Hampson-Baldi/02,
AUTHOR = {Baisn{\'e}e, Pierre-Fran{\c{c}}ois and Hampson, Steve and Baldi, Pierre},
TITLE = {Why are complementary DNA strands symmetric?},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {8},
PAGES = {1021-1033},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1021},
PUBLISHER = {Oxford University Press},
}
@article{Rogic-Ouellette-Mackworth/02,
AUTHOR = {Rogic, Sanja and Ouellette, B.F. Francis and Mackworth, Alan K.},
TITLE = {Improving gene recognition accuracy by combining predictions from two gene-finding programs},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {8},
PAGES = {1034-1045},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1034},
PUBLISHER = {Oxford University Press},
}
@article{Shah-Giddings-Parvaz-Gesteland-Atkins-Ivanov/02,
AUTHOR = {Shah, Atul A. and Giddings, Michael C. and Parvaz, Jasmin B. and Gesteland, Raymond F. and Atkins, John F. and Ivanov, Ivaylo P.},
TITLE = {Computational identification of putative programmed translational frameshift sites},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {8},
PAGES = {1046-1053},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1046},
PUBLISHER = {Oxford University Press},
}
@article{Stephanopoulos-Hwang-Schmitt-Misra-Stephanopoulos/02,
AUTHOR = {Stephanopoulos, Gregory and Hwang, Daehee and Schmitt, William A. and Misra, Jatin and Stephanopoulos, George},
TITLE = {Mapping physiological states from microarray expression measurements},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {8},
PAGES = {1054-1063},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1054},
PUBLISHER = {Oxford University Press},
}
@article{Love-Rank-Penn-Jenkins-Thomas/02,
AUTHOR = {Love, Brad and Rank, David R. and Penn, Sharron G. and Jenkins, David A. and Thomas, Russell S.},
TITLE = {A conditional density error model for the statistical analysis of microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {8},
PAGES = {1064-1072},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1064},
PUBLISHER = {Oxford University Press},
}
@article{Chang-Halgamuge/02,
AUTHOR = {Chang, Bill C.H. and Halgamuge, Saman K.},
TITLE = {Protein motif extraction with neuro-fuzzy optimization},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {8},
PAGES = {1084-1090},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1084},
PUBLISHER = {Oxford University Press},
}
@article{Gonnet-Lisacek/02,
AUTHOR = {Gonnet, Pedro and Lisacek, Fr{\'e}d{\'e}rique},
TITLE = {Probabilistic alignment of motifs with sequences},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {8},
PAGES = {1091-1101},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1091},
PUBLISHER = {Oxford University Press},
}
@article{Cannata-Toppo-Romualdi-Valle/02,
AUTHOR = {Cannata, Nicola and Toppo, Stefano and Romualdi, Chiara and Valle, Giorgio},
TITLE = {Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {8},
PAGES = {1102-1108},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1102},
PUBLISHER = {Oxford University Press},
}
@article{Pupko-Peer-Hasegawa-Graur-Friedman/02,
AUTHOR = {Pupko, Tal and Pe'er, Itsik and Hasegawa, Masami and Graur, Dan and Friedman, Nir},
TITLE = {A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {8},
PAGES = {1116-1123},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1116},
PUBLISHER = {Oxford University Press},
}
@article{Spicker-Wikman-Lu-Cordon-Cardo-Workman-Orntoft-Brunak-Knudsen/02,
AUTHOR = {Spicker, Jeppe S. and Wikman, Friedrik and Lu, Ming-Lan and Cordon-Cardo, Carlos and Workman, Christopher and {\O}rntoft, Torben F. and Brunak, S{\o}ren and Knudsen, Steen},
TITLE = {Neural network predicts sequence of TP53 gene based on DNA chip},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {8},
PAGES = {1133-1134},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1133},
PUBLISHER = {Oxford University Press},
}
@article{Lenhard-Wasserman/02,
AUTHOR = {Lenhard, Boris and Wasserman, Wyeth W.},
TITLE = {TFBS: Computational framework for transcription factor binding site analysis},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {8},
PAGES = {1135-1136},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1135},
PUBLISHER = {Oxford University Press},
}
@article{Seroussi-Ron-Kedra/02,
AUTHOR = {Seroussi, Eyal and Ron, Micha and Kedra, Darek},
TITLE = {ShiftDetector: Detection of shift mutations},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {8},
PAGES = {1137-1138},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1137},
PUBLISHER = {Oxford University Press},
}
@article{Contreras-Moreira-Bates/02,
AUTHOR = {Contreras-Moreira, B. and Bates, P.A.},
TITLE = {Domain Fishing: A first step in protein comparative modelling},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {8},
PAGES = {1141-1142},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1141},
PUBLISHER = {Oxford University Press},
}
@article{Chetouani-Glaser-Kunst/02,
AUTHOR = {Chetouani, Farid and Glaser, Philippe and Kunst, Frank},
TITLE = {DiffTool: Building, visualizing and querying protein clusters},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {8},
PAGES = {1143-1144},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1143},
PUBLISHER = {Oxford University Press},
}
@article{Hu/02,
AUTHOR = {Hu, Yuh-Jyh},
TITLE = {The NCTU BioInfo Archive of biological data sets for bioinformatics research and experimentation},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {8},
PAGES = {1145-1146},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1145},
PUBLISHER = {Oxford University Press},
}
@article{Oyama-Kitano-Satou-Ito/02a,
AUTHOR = {Oyama, T. and Kitano, K. and Satou, K. and Ito, T.},
TITLE = {Erratum to ''Extraction of knowledge on protein-protein interaction by association rule discovery''},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {8},
PAGES = {1151-1151},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1151},
PUBLISHER = {Oxford University Press},
NOTE = {Originally in Bioinformatics, Vol. 18, 2002, No. 5, 705-714},
}
@article{Nishigaki-Saito/02,
AUTHOR = {Nishigaki, Koichi and Saito, Ayumu},
TITLE = {Genome structures embossed by oligonucleotide-stickiness},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1153-1161},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1153},
PUBLISHER = {Oxford University Press},
}
@article{Gavin-Scheetz-Roberts-OLeary-Braun-Sheffield-Soares-Robinson-Casavant/02,
AUTHOR = {Gavin, A.J. and Scheetz, T.E. and Roberts, C.A. and O'Leary, B. and Braun, T.A. and Sheffield, V.C. and Soares, M.B. and Robinson, J.P. and Casavant, T.L.},
TITLE = {Pooled library tissue tags for EST-based gene discovery},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1162-1166},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1162},
PUBLISHER = {Oxford University Press},
}
@article{Keles-van_der_Laan-Eisen/02,
AUTHOR = {Kele{\c{s}}, S{\"u}nd{\"u}z and van der Laan, Mark and Eisen, Michael B.},
TITLE = {Identification of regulatory elements using a feature selection method},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1167-1175},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1167},
PUBLISHER = {Oxford University Press},
}
@article{Rifkin-Kim/02,
AUTHOR = {Rifkin, S.A. and Kim, J.},
TITLE = {Geometry of gene expression dynamics},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1176-1183},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1176},
PUBLISHER = {Oxford University Press},
}
@article{Hwang-Schmitt-Stephanopoulos-Stephanopoulos/02,
AUTHOR = {Hwang, Daehee and Schmitt, William A. and Stephanopoulos, George and Stephanopoulos, Gregory},
TITLE = {Determination of minimum sample size and discriminatory expression patterns in microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1184-1193},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1184},
PUBLISHER = {Oxford University Press},
}
@article{Medvedovic-Sivaganesan/02,
AUTHOR = {Medvedovic, Mario and Sivaganesan, Siva},
TITLE = {Bayesian infinite mixture model based clustering of gene expression profiles},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1194-1206},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1194},
PUBLISHER = {Oxford University Press},
}
@article{Chen-Kamat-Dougherty-Bittner-Meltzer-Trent/02,
AUTHOR = {Chen, Yidong and Kamat, Vishnu and Dougherty, Edward R. and Bittner, Michael L. and Meltzer, Paul S. and Trent, Jeffery M.},
TITLE = {Ratio statistics of gene expression levels and applications to microarray data analysis},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1207-1215},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1207},
PUBLISHER = {Oxford University Press},
}
@article{Nguyen-Rocke/02a,
AUTHOR = {Nguyen, Danh V. and Rocke, David M.},
TITLE = {Multi-class cancer classification via partial least squares with gene expression profiles},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1216-1226},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1216},
PUBLISHER = {Oxford University Press},
}
@article{Stengel-Ghigliazza-Kulkarni/02,
AUTHOR = {Stengel, Robert F. and Ghigliazza, Raffaele M. and Kulkarni, Nilesh V.},
TITLE = {Optimal enhancement of immune response},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1227-1235},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1227},
PUBLISHER = {Oxford University Press},
}
@article{Park-Spouge/02,
AUTHOR = {Park, Yonil and Spouge, John L.},
TITLE = {The correlation error and finite-size correction in an ungapped sequence alignment},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1236-1242},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1236},
PUBLISHER = {Oxford University Press},
}
@article{Griffiths-Jones-Bateman/02,
AUTHOR = {Griffiths-Jones, Sam and Bateman, Alex},
TITLE = {The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1243-1249},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1243},
PUBLISHER = {Oxford University Press},
}
@article{Lambert-Leonard-de_Bolle-Depiereux/02,
AUTHOR = {Lambert, Christophe and L{\'e}onard, Nadia and de Bolle, Xavier and Depiereux, Eric},
TITLE = {ESyPred3D: Prediction of proteins 3D structures},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1250-1256},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1250},
PUBLISHER = {Oxford University Press},
}
@article{Rantanen-Gyllenberg-Koski-Johnson/02,
AUTHOR = {Rantanen, Ville-Veikko and Gyllenberg, Mats and Koski, Timo and Johnson, Mark S.},
TITLE = {A dissimilarity matrix between protein atom classes based on Gaussian mixtures},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1257-1263},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1257},
PUBLISHER = {Oxford University Press},
}
@article{Moseyko-Feldman/02,
AUTHOR = {Moseyko, Nick and Feldman, Lewis J.},
TITLE = {VIZARD: Analysis of Affymetrix Arabidopsis GeneChip{\textregistered} data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1264-1265},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1264},
PUBLISHER = {Oxford University Press},
}
@article{Sakharkar-Kangueane-Petrov-Kolaskar-Subbiah/02,
AUTHOR = {Sakharkar, Meena K. and Kangueane, Pandjassarame and Petrov, Dmitri A. and Kolaskar, A.S. and Subbiah, S.},
TITLE = {SEGE: A database on ''intron less/single exonic'' genes from eukaryotes},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1266-1267},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1266},
PUBLISHER = {Oxford University Press},
}
@article{Kleinjung-Douglas-Heringa/02,
AUTHOR = {Kleinjung, Jens and Douglas, Nigel and Heringa, Jaap},
TITLE = {Parallelized multiple alignment},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1270-1271},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1270},
PUBLISHER = {Oxford University Press},
}
@article{Hollich-Storm-Sonnhammer/02,
AUTHOR = {Hollich, Volker and Storm, Christian E.V. and Sonnhammer, Erik L.L.},
TITLE = {OrthoGUI: Graphical presentation of Orthostrapper results},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1272-1273},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1272},
PUBLISHER = {Oxford University Press},
}
@article{Buzko-Shokat/02,
AUTHOR = {Buzko, Oleksandr and Shokat, Kevan M.},
TITLE = {A kinase sequence database: Sequence alignments and family assignment},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1274-1275},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1274},
PUBLISHER = {Oxford University Press},
}
@article{Friedberg-Margalit/02,
AUTHOR = {Friedberg, Iddo and Margalit, Hanah},
TITLE = {PeCoP: Automatic determination of persistently conserved positions in protein families},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1276-1277},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1276},
PUBLISHER = {Oxford University Press},
}
@article{McConnell-Johnson-Lin/02,
AUTHOR = {McConnell, Patrick and Johnson, Kimberly and Lin, Simon},
TITLE = {Applications of Tree-Maps to hierarchical biological data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1278-1279},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1278},
PUBLISHER = {Oxford University Press},
}
@article{Greer-Westbrook-Bourne/02,
AUTHOR = {Greer, Douglas S. and Westbrook, John D. and Bourne, Philip E.},
TITLE = {An ontology driven architecture for derived representations of macromolecular structure},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1280-1281},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1280},
PUBLISHER = {Oxford University Press},
}
@article{Hao-Tan/02a,
AUTHOR = {Hao, Y.H. and Tan, Z.},
TITLE = {Erratum to ''The generation of long telomere overhangs in human cells: A model and its implication''},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {9},
PAGES = {1282-1282},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/9/1282},
PUBLISHER = {Oxford University Press},
NOTE = {Originally in Bioinformatics, Vol. 18, 2002, No. 5, 666-671},
}
@article{Palakal-Mukhopadhyay-Mostafa-Raje-NCho-Mishra/02,
AUTHOR = {Palakal, Mathew and Mukhopadhyay, Snehasis and Mostafa, Javed and Raje, Rajeev and N'Cho, Mathias and Mishra, Santosh},
TITLE = {An intelligent biological information management system},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {10},
PAGES = {1283-1288},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/10/1283},
PUBLISHER = {Oxford University Press},
}
@article{Harrison-DeLisi/02,
AUTHOR = {Harrison, Rhonda and DeLisi, Charles},
TITLE = {Condition specific transcription factor binding site characterization in Saccharomyces cerevisiae},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {10},
PAGES = {1289-1296},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/10/1289},
PUBLISHER = {Oxford University Press},
}
@article{Sankoff/02,
AUTHOR = {Sankoff, David},
TITLE = {Short inversions and conserved gene cluster},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {10},
PAGES = {1305-1308},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/10/1305},
PUBLISHER = {Oxford University Press},
}
@article{Meyer-Durbin/02,
AUTHOR = {Meyer, Irmtraud M. and Durbin, Richard},
TITLE = {Comparative ab initio prediction of gene structures using pair HMMs},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {10},
PAGES = {1309-1318},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/10/1309},
PUBLISHER = {Oxford University Press},
}
@article{Shmulevich-Dougherty-Zhang/02,
AUTHOR = {Shmulevich, Ilya and Dougherty, Edward R. and Zhang, Wei},
TITLE = {Gene perturbation and intervention in probabilistic Boolean networks},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {10},
PAGES = {1319-1331},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/10/1319},
PUBLISHER = {Oxford University Press},
}
@article{Li-Campbell-Tipping/02,
AUTHOR = {Li, Yi and Campbell, Colin and Tipping, Michael},
TITLE = {Bayesian automatic relevance determination algorithms for classifying gene expression data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {10},
PAGES = {1332-1339},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/10/1332},
PUBLISHER = {Oxford University Press},
}
@article{Kaderali-Schliep/02,
AUTHOR = {Kaderali, Lars and Schliep, Alexander},
TITLE = {Selecting signature oligonucleotides to identify organisms using DNA arrays},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {10},
PAGES = {1340-1349},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/10/1340},
PUBLISHER = {Oxford University Press},
}
@article{Lin-May-Taylor/02,
AUTHOR = {Lin, Kuang and May, Alex C.W. and Taylor, William R.},
TITLE = {Threading Using Neural nEtwork (TUNE): The measure of protein sequence-structure compatibility},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {10},
PAGES = {1350-1357},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/10/1350},
PUBLISHER = {Oxford University Press},
}
@article{Ivanciuc-Schein-Braun/02,
AUTHOR = {Ivanciuc, Ovidiu and Schein, Catherine H. and Braun, Werner},
TITLE = {Data mining of sequences and 3D structures of allergenic proteins},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {10},
PAGES = {1358-1364},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/10/1358},
PUBLISHER = {Oxford University Press},
}
@article{McConkey-Sobolev-Edelman/02,
AUTHOR = {McConkey, B.J. and Sobolev, V. and Edelman, M.},
TITLE = {Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {10},
PAGES = {1365-1373},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/10/1365},
PUBLISHER = {Oxford University Press},
}
@article{Keich-Pevzner/02,
AUTHOR = {Keich, U. and Pevzner, P.A.},
TITLE = {Finding motifs in the twilight zone},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {10},
PAGES = {1374-1381},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/10/1374},
PUBLISHER = {Oxford University Press},
}
@article{Keich-Pevzner/02a,
AUTHOR = {Keich, U. and Pevzner, P.A.},
TITLE = {Subtle motifs: Defining the limits of motif finding algorithms},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {10},
PAGES = {1382-1390},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/10/1382},
PUBLISHER = {Oxford University Press},
}
@article{Bujnicki-Rychlewski-Fischer/02,
AUTHOR = {Bujnicki, Janusz and Rychlewski, Leszek and Fischer, Daniel},
TITLE = {Fold-recognition detects an error in the Protein Data Bank},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {10},
PAGES = {1391-1395},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/10/1391},
PUBLISHER = {Oxford University Press},
}
@article{Berezikov-Plasterk-Cuppen/02,
AUTHOR = {Berezikov, Eugene and Plasterk, Ronald H.A. and Cuppen, Edwin},
TITLE = {GENOTRACE: cDNA-based local GENOme assembly from TRACE archives},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {10},
PAGES = {1396-1397},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/10/1396},
PUBLISHER = {Oxford University Press},
}
@article{Lord-Selley-Attwood/02,
AUTHOR = {Lord, P.W. and Selley, J.N. and Attwood, T.K.},
TITLE = {CINEMA-MX: A modular multiple alignment editor},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {10},
PAGES = {1402-1403},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/10/1402},
PUBLISHER = {Oxford University Press},
}
@article{Pybus-Rambaut/02,
AUTHOR = {Pybus, O.G. and Rambaut, A.},
TITLE = {GENIE: Estimating demographic history from molecular phylogenies},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {10},
PAGES = {1404-1405},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/10/1404},
PUBLISHER = {Oxford University Press},
}
@article{Li-Wong/02a,
AUTHOR = {Li, Jinyan and Wong, Limsoon},
TITLE = {Erratum to ''Identifying good diagnostic gene groups from gene expression profiles using the concept of emerging patterns''},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {10},
PAGES = {1406-1407},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/10/1406},
PUBLISHER = {Oxford University Press},
NOTE = {Originally in Bioinformatics, Vol. 18, 2002, No. 5, 725-734},
}
@article{Kulkarni-Williams-Lian-Wren-Mittelman-Pertsemlidis-Garner/02,
AUTHOR = {Kulkarni, Amit V. and Williams, Noelle Sevilir and Lian, Yun and Wren, Jonathan D. and Mittelman, David and Pertsemlidis, Alexander and Garner, Harold R.},
TITLE = {ARROGANT: An application to manipulate large gene collections},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1410-1417},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1410},
PUBLISHER = {Oxford University Press},
}
@article{Stojanovic-Chang-Lehoczky-Zody-Dewar/02,
AUTHOR = {Stojanovic, Nikola and Chang, Jean L. and Lehoczky, Jessica and Zody, Michael C. and Dewar, Ken},
TITLE = {Identification of mixups among DNA sequencing plates},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1418-1426},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1418},
PUBLISHER = {Oxford University Press},
}
@article{Li-Dahiya/02,
AUTHOR = {Li, Long-Cheng and Dahiya, Rajvir},
TITLE = {MethPrimer: Designing primers for methylation PCRs},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1427-1431},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1427},
PUBLISHER = {Oxford University Press},
}
@article{Dobbin-Simon/02,
AUTHOR = {Dobbin, K. and Simon, R.},
TITLE = {Comparison of microarray designs for class comparison and class discovery},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1438-1445},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1438},
PUBLISHER = {Oxford University Press},
}
@article{Mavroudi-Papadimitriou-Bezerianos/02,
AUTHOR = {Mavroudi, Seferina and Papadimitriou, Stergios and Bezerianos, Anastasios},
TITLE = {Gene expression data analysis with a dynamically extended self-organized map that exploits class information},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1446-1453},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1446},
PUBLISHER = {Oxford University Press},
}
@article{McShane-Radmacher-Freidlin-Yu-Li-Simon/02,
AUTHOR = {McShane, Lisa M. and Radmacher, Michael D. and Freidlin, Boris and Yu, Ren and Li, Ming-Chung and Simon, Richard},
TITLE = {Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1462-1469},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1462},
PUBLISHER = {Oxford University Press},
}
@article{Lemon-Palatini-Krahe-Wright/02,
AUTHOR = {Lemon, William J. and Palatini, Jeffrey J.T. and Krahe, Ralf and Wright, Fred A.},
TITLE = {Theoretical and experimental comparisons of gene expression indexes for oligonucleotide arrays},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1470-1476},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1470},
PUBLISHER = {Oxford University Press},
}
@article{Bhan-Galas-Dewey/02,
AUTHOR = {Bhan, Ashish and Galas, David J. and Dewey, T. Gregory},
TITLE = {A duplication growth model of gene expression networks},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1486-1493},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1486},
PUBLISHER = {Oxford University Press},
}
@article{Keith-Adams-Bryant-Kroese-Mitchelson-Cochran-Lala/02,
AUTHOR = {Keith, Jonathan M. and Adams, Peter and Bryant, Darryn and Kroese, Dirk P. and Mitchelson, Keith R. and Cochran, Duncan A.E. and Lala, Gita H.},
TITLE = {A simulated annealing algorithm for finding consensus sequences},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1494-1499},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1494},
PUBLISHER = {Oxford University Press},
}
@article{Reese-Pearson/02,
AUTHOR = {Reese, J.T. and Pearson, W.R.},
TITLE = {Empirical determination of effective gap penalties for sequence comparison},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1500-1507},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1500},
PUBLISHER = {Oxford University Press},
}
@article{Kaur-Raghava/02a,
AUTHOR = {Kaur, Harpreet and Raghava, G.P.S.},
TITLE = {An evaluation of $\beta$-turn prediction methods},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1508-1514},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1508},
PUBLISHER = {Oxford University Press},
}
@article{Leonard-Colombe-Levy/02,
AUTHOR = {Leonard, Julie E. and Colombe, Jeffrey B. and Levy, Joshua L.},
TITLE = {Finding relevant references to genes and proteins in Medline using a Bayesian approach},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1515-1522},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1515},
PUBLISHER = {Oxford University Press},
}
@article{Grishin-Grishin/02,
AUTHOR = {Grishin, Vyacheslav N. and Grishin, Nick V.},
TITLE = {Euclidian space and grouping of biological objects},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1523-1533},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1523},
PUBLISHER = {Oxford University Press},
}
@article{Janecek/02,
AUTHOR = {Jane{\v{c}}ek, {\v{S}}tefan},
TITLE = {A motif of a microbial starch-binding domain found in human genethonin},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1534-1537},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1534},
PUBLISHER = {Oxford University Press},
}
@article{McKay-Jones/02,
AUTHOR = {McKay, Sheldon J. and Jones, Steven J.M.},
TITLE = {AcePrimer: Automation of PCR primer design based on gene structure},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1538-1539},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1538},
PUBLISHER = {Oxford University Press},
}
@article{Colantuoni-Henry-Zeger-Pevsner/02,
AUTHOR = {Colantuoni, Carlo and Henry, George and Zeger, Scott and Pevsner, Jonathan},
TITLE = {SNOMAD (Standardization and NOrmalization of MicroArray Data): Web-accessible gene expression data analysis},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1540-1541},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1540},
PUBLISHER = {Oxford University Press},
}
@article{Safran-Solomon-Shmueli-Lapidot-Shen-Orr-Adato-Ben-Dor-Esterman-Rosen-Peter-Olender-Chalifa-Caspi-Lancet/02,
AUTHOR = {Safran, Marilyn and Solomon, Irina and Shmueli, Orit and Lapidot, Michal and Shen-Orr, Shai and Adato, Avital and Ben-Dor, Uri and Esterman, Nir and Rosen, Naomi and Peter, Inga and Olender, Tsviya and Chalifa-Caspi, Vered and Lancet, Doron},
TITLE = {GeneCards{\texttrademark} 2002: Towards a complete, object-oriented, human gene compendium},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1542-1543},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1542},
PUBLISHER = {Oxford University Press},
}
@article{Ehlers-Osborne-Slack-Roper-Upton/02,
AUTHOR = {Ehlers, Angelika and Osborne, John and Slack, Stephanie and Roper, Rachel L. and Upton, Chris},
TITLE = {Poxvirus Orthologous Clusters (POCs)},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1544-1545},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1544},
PUBLISHER = {Oxford University Press},
}
@article{Howe-Bateman-Durbin/02,
AUTHOR = {Howe, Kevin and Bateman, Alex and Durbin, Richard},
TITLE = {QuickTree: Building huge Neighbour-Joining trees of protein sequences},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1546-1547},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1546},
PUBLISHER = {Oxford University Press},
}
@article{Sheik-Sundararajan-Hussain-Sekar/02,
AUTHOR = {Sheik, S.S. and Sundararajan, P. and Hussain, A.S.Z. and Sekar, K.},
TITLE = {Ramachandran plot on the web},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {11},
PAGES = {1548-1549},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1548},
PUBLISHER = {Oxford University Press},
}
@article{Hirschman-Park-Tsujii-Wong-Wu/02,
AUTHOR = {Hirschman, Lynette and Park, Jong C. and Tsujii, Junichi and Wong, Limsoon and Wu, Cathy H.},
TITLE = {Accomplishments and challenges in literature data mining for biology},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1553-1561},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1553},
PUBLISHER = {Oxford University Press},
}
@article{Lao-Arai-Ikeda-Shimizu/02,
AUTHOR = {Lao, Demelo M. and Arai, Masafumi and Ikeda, Masami and Shimizu, Toshio},
TITLE = {The presence of signal peptide significantly affects transmembrane topology prediction},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1562-1566},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1562},
PUBLISHER = {Oxford University Press},
}
@article{Chalk-Sonnhammer/02,
AUTHOR = {Chalk, Alistair M. and Sonnhammer, Erik L.L.},
TITLE = {Computational antisense oligo prediction with a neural network model},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1567-1575},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1567},
PUBLISHER = {Oxford University Press},
}
@article{Park-Butte-Kohane/02,
AUTHOR = {Park, Peter J. and Butte, Atul J. and Kohane, Isaac S.},
TITLE = {Comparing expression profiles of genes with similar promoter regions},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1576-1584},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1576},
PUBLISHER = {Oxford University Press},
}
@article{Hubbell-Liu-Mei/02,
AUTHOR = {Hubbell, Earl and Liu, Wei-Min and Mei, Rui},
TITLE = {Robust estimators for expression analysis},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1585-1592},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1585},
PUBLISHER = {Oxford University Press},
}
@article{Liu-Mei-Di-Ryder-Hubbell-Dee-Webster-Harrington-Ho-Baid-Smeekens/02,
AUTHOR = {Liu, W.-m. and Mei, R. and Di, X. and Ryder, T.B. and Hubbell, E. and Dee, S. and Webster, T.A. and Harrington, C.A. and Ho, M.-h. and Baid, J. and Smeekens, S.P.},
TITLE = {Analysis of high density expression microarrays with signed-rank call algorithms},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1593-1599},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1593},
PUBLISHER = {Oxford University Press},
}
@article{Culhane-Perriere-Considine-Cotter-Higgins/02,
AUTHOR = {Culhane, Aed{\'{i}}n C. and Perri{\`e}re, Guy and Considine, Elizabeth C. and Cotter, Thomas G. and Higgins, Desmond G.},
TITLE = {Between-group analysis of microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1600-1608},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1600},
PUBLISHER = {Oxford University Press},
}
@article{Black-Doerge/02,
AUTHOR = {Black, Michael A. and Doerge, R.W.},
TITLE = {Calculation of the minimum number of replicate spots required for detection of significant gene expression fold change in microarray experiments},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1609-1616},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1609},
PUBLISHER = {Oxford University Press},
}
@article{Martoglio-Miskin-Smith-MacKay/02,
AUTHOR = {Martoglio, Ann-Marie and Miskin, James W. and Smith, Stephen K. and MacKay, David J.C.},
TITLE = {A decomposition model to track gene expression signatures: Preview on observer-independent classification of ovarian cancer},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1617-1624},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1617},
PUBLISHER = {Oxford University Press},
}
@article{Nguyen-Rocke/02b,
AUTHOR = {Nguyen, Danh V. and Rocke, David M.},
TITLE = {Partial least squares proportional hazard regression for application to DNA microarray survival data},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1625-1632},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1625},
PUBLISHER = {Oxford University Press},
}
@article{Sasik-Calvo-Corbeil/02,
AUTHOR = {{\v{S}}{\'a}{\v{s}}ik, R. and Calvo, E. and Corbeil, J.},
TITLE = {Statistical analysis of high-density oligonucleotide arrays: A multiplicative noise model},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1633-1640},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1633},
PUBLISHER = {Oxford University Press},
}
@article{Gilks-Audit-de_Angelis-Tsoka-Ouzounis/02,
AUTHOR = {Gilks, Walter R. and Audit, Benjamin and de Angelis, Daniela and Tsoka, Sophia and Ouzounis, Christos A.},
TITLE = {Modeling the percolation of annotation errors in a database of protein sequences},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1641-1649},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1641},
PUBLISHER = {Oxford University Press},
}
@article{Shepherd-Martin-Johnson-Kellam-Orengo/02,
AUTHOR = {Shepherd, Adrian J. and Martin, Nigel J. and Johnson, Roger G. and Kellam, Paul and Orengo, Christine A.},
TITLE = {PFDB: A generic protein family database integrating the CATH domain structure database with sequence based protein family resources},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1666-1672},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1666},
PUBLISHER = {Oxford University Press},
}
@article{Roytberg-Ogurtsov-Shabalina-Kondrashov/02,
AUTHOR = {Roytberg, Mikhail A. and Ogurtsov, Aleksey Y. and Shabalina, Svetlana A. and Kondrashov, Alexey S.},
TITLE = {A hierarchical approach to aligning collinear regions of genomes},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1673-1680},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1673},
PUBLISHER = {Oxford University Press},
}
@article{Riva-Kohane/02,
AUTHOR = {Riva, A. and Kohane, I.S.},
TITLE = {SNPper: Retrieval and analysis of human SNPs},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1681-1685},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1681},
PUBLISHER = {Oxford University Press},
}
@article{Mrowka-Schuchhardt-Gille/02,
AUTHOR = {Mrowka, Ralf and Schuchhardt, Johannes and Gille, Christoph},
TITLE = {Oligodb --- Interactive design of oligo DNA for transcription profiling of human genes},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1686-1687},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1686},
PUBLISHER = {Oxford University Press},
}
@article{Ke-Collins-Ye/02,
AUTHOR = {Ke, Xiayi and Collins, Andrew and Ye, Shu},
TITLE = {PCR designer for restriction analysis of various types of sequence mutation},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1688-1689},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1688},
PUBLISHER = {Oxford University Press},
}
@article{Hou/02,
AUTHOR = {Hou, Jianghui},
TITLE = {Design of endonuclease restriction sites into primers for PCR cloning},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1690-1691},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1690},
PUBLISHER = {Oxford University Press},
}
@article{Everitt-Minnema-Wride-Koster-Hance-Mansergh-Rancourt/02,
AUTHOR = {Everitt, R. and Minnema, S.E. and Wride, M.A. and Koster, C.S. and Hance, J.E. and Mansergh, F.C. and Rancourt, D.E.},
TITLE = {RED: The analysis, management and dissemination of expressed sequence tags},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1692-1693},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1692},
PUBLISHER = {Oxford University Press},
}
@article{Chen-Li-Ma-Tromp/02,
AUTHOR = {Chen, Xin and Li, Ming and Ma, Bin and Tromp, John},
TITLE = {DNACompress: Fast and effective DNA sequence compression},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1696-1698},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1696},
PUBLISHER = {Oxford University Press},
}
@article{Kwasigroch-Gilis-Dehouck-Rooman/02,
AUTHOR = {Kwasigroch, J.M. and Gilis, D. and Dehouck, Y. and Rooman, M.},
TITLE = {PoPMuSIC, rationally designing point mutations in protein structures},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1701-1702},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1701},
PUBLISHER = {Oxford University Press},
}
@article{Ogurtsov-Roytberg-Shabalina-Kondrashov/02,
AUTHOR = {Ogurtsov, Aleksey Y. and Roytberg, Mikhail A. and Shabalina, Svetlana A. and Kondrashov, Alexey S.},
TITLE = {OWEN: Aligning long collinear regions of genomes},
JOURNAL = {Bioinformatics},
VOLUME = {18},
NUMBER = {12},
PAGES = {1703-1704},
YEAR = {2002},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/12/1703},
PUBLISHER = {Oxford University Press},
}