@article{Amikam-Galperin/06,
AUTHOR = {Amikam, Dorit and Galperin, Michael Y.},
TITLE = {PilZ domain is part of the bacterial c-di-GMP binding protein},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {1},
PAGES = {3-6},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti739},
PUBLISHER = {Oxford University Press},
}
@article{Alexeyenko-Tamas-Liu-Sonnhammer/06,
AUTHOR = {Alexeyenko, Andrey and Tamas, Ivica and Liu, Gang and Sonnhammer, Erik L.L.},
TITLE = {Automatic clustering of orthologs and inparalogs shared by multiple proteomes},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {9-15},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl213},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Antes-Siu-Lengauer/06,
AUTHOR = {Antes, Iris and Siu, Shirley W.I. and Lengauer, Thomas},
TITLE = {DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {16-24},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl216},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Jensen-Styczynski-Rigoutsos-Stephanopoulos/06,
AUTHOR = {Jensen, Kyle L. and Styczynski, Mark P. and Rigoutsos, Isidore and Stephanopoulos, Gregory N.},
TITLE = {A generic motif discovery algorithm for sequential data},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {1},
PAGES = {21-28},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti745},
PUBLISHER = {Oxford University Press},
}
@article{Aoki-Kinoshita-Ueda-Mamitsuka-Kanehisa/06,
AUTHOR = {Aoki-Kinoshita, Kiyoko F. and Ueda, Nobuhisa and Mamitsuka, Hiroshi and Kanehisa, Minoru},
TITLE = {ProfilePSTMM: Capturing tree-structure motifs in carbohydrate sugar chains},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {25-34},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl244},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Huang-Umbach-Li/06,
AUTHOR = {Huang, Weichun and Umbach, David M. and Li, Leping},
TITLE = {Accurate anchoring alignment of divergent sequences},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {1},
PAGES = {29-34},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti772},
PUBLISHER = {Oxford University Press},
}
@article{Armougom-Moretti-Keduas-Notredame/06,
AUTHOR = {Armougom, Fabrice and Moretti, S{\'{e}}bastien and Keduas, Vladimir and Notredame, Cedric},
TITLE = {The iRMSD: A local measure of sequence alignment accuracy using structural information},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {35-39},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl218},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Asur-Raman-Otey-Parthasarathy/06,
AUTHOR = {Asur, Sitaram and Raman, Pichai and Otey, Matthew Eric and Parthasarathy, Srinivasan},
TITLE = {A model-based approach for mining membrane protein crystallization trials},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {40-48},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl225},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Kim-Koyuturk-Topkara-Grama-Subramaniam/06,
AUTHOR = {Kim, Yohan and Koyut{\"{u}}rk, Mehmet and Topkara, Umut and Grama, Ananth and Subramaniam, Shankar},
TITLE = {Inferring functional information from domain co-evolution},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {1},
PAGES = {40-49},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti723},
PUBLISHER = {Oxford University Press},
}
@article{Borgwardt-Gretton-Rasch-Kriegel-Scholkopf-Smola/06,
AUTHOR = {Borgwardt, Karsten M. and Gretton, Arthur and Rasch, Malte J. and Kriegel, Hans-Peter and Sch{\"{o}}lkopf, Bernhard and Smola, Alex J.},
TITLE = {Integrating structured biological data by Kernel Maximum Mean Discrepancy},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {49-57},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl242},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Blangiardo-Toti-Giusti-Abbate-Magi-Poggi-Rossi-Torricelli-Biggeri/06,
AUTHOR = {Blangiardo, Marta and Toti, Simona and Giusti, Betti and Abbate, Rosanna and Magi, Alberto and Poggi, Filippo and Rossi, Luciana and Torricelli, Francesca and Biggeri, Annibale},
TITLE = {Using a calibration experiment to assess gene-specific information: Full Bayesian and empirical Bayesian models for two-channel microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {1},
PAGES = {50-57},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti750},
PUBLISHER = {Oxford University Press},
}
@article{Bottegoni-Rocchia-Recanatini-Cavalli/06,
AUTHOR = {Bottegoni, Giovanni and Rocchia, Walter and Recanatini, Maurizio and Cavalli, Andrea},
TITLE = {AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {58-65},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl212},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Grotkjar-Winther-Regenberg-Nielsen-Hansen/06,
AUTHOR = {Grotkj{\ae}r, Thomas and Winther, Ole and Regenberg, Birgitte and Nielsen, Jens and Hansen, Lars Kai},
TITLE = {Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {1},
PAGES = {58-67},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti746},
PUBLISHER = {Oxford University Press},
}
@article{Burek-Hoehndorf-Loebe-Visagie-Herre-Kelso/06,
AUTHOR = {Burek, Patryk and Hoehndorf, Robert and Loebe, Frank and Visagie, Johann and Herre, Heinrich and Kelso, Janet},
TITLE = {A top-level ontology of functions and its application in the Open Biomedical Ontologies},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {66-73},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl266},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Contreras-Moreira-Collado-Vides/06,
AUTHOR = {Contreras-Moreira, Bruno and Collado-Vides, Julio},
TITLE = {Comparative footprinting of DNA-binding proteins},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {74-80},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl215},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{DiMaio-Shavlik-Phillips/06,
AUTHOR = {DiMaio, Frank and Shavlik, Jude and Phillips, George N.},
TITLE = {A probabilistic approach to protein backbone tracing in electron density maps},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {81-89},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl252},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Do-Woods-Batzoglou/06,
AUTHOR = {Do, Chuong B. and Woods, Daniel A. and Batzoglou, Serafim},
TITLE = {CONTRAfold: RNA secondary structure prediction without physics-based models},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {90-98},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl246},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Ebbels-Buxton-Jones/06,
AUTHOR = {Ebbels, Timothy M.D. and Buxton, Bernard F. and Jones, David T.},
TITLE = {springScape: Visualisation of microarray and contextual bioinformatic data using spring embedding and an ''information landscape''},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {99-107},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl205},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Edelman-Porrello-Guinney-Balakumaran-Bild-Febbo-Mukherjee/06,
AUTHOR = {Edelman, Elena and Porrello, Alessandro and Guinney, Justin and Balakumaran, Bala and Bild, Andrea and Febbo, Phillip G. and Mukherjee, Sayan},
TITLE = {Analysis of sample set enrichment scores: Assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {108-116},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl231},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Everett-Wang-Hannenhalli/06,
AUTHOR = {Everett, Logan and Wang, Li-San and Hannenhalli, Sridhar},
TITLE = {Dense subgraph computation via stochastic search: Application to detect transcriptional modules},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {117-123},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl260},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Gopalan-Qiu-Chen-Stoltzfus/06,
AUTHOR = {Gopalan, Vivek and Qiu, Wei-Gang and Chen, Michael Z. and Stoltzfus, Arlin},
TITLE = {Nexplorer: Phylogeny-based exploration of sequence family data},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {1},
PAGES = {120-121},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti747},
PUBLISHER = {Oxford University Press},
}
@article{Dabney/06,
AUTHOR = {Dabney, Alan R.},
TITLE = {ClaNC: Point-and-click software for classifying microarrays to nearest centroids},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {1},
PAGES = {122-123},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti756},
PUBLISHER = {Oxford University Press},
}
@article{Faure-Naldi-Chaouiya-Thieffry/06,
AUTHOR = {Faur{\'{e}}, Adrien and Naldi, Aur{\'{e}}lien and Chaouiya, Claudine and Thieffry, Denis},
TITLE = {Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {124-131},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl210},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Ji-Xu/06,
AUTHOR = {Ji, Xinglai and Xu, Ying},
TITLE = {libSRES: A C library for stochastic ranking evolution strategy for parameter estimation},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {1},
PAGES = {124-126},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti753},
PUBLISHER = {Oxford University Press},
}
@article{Gelly-de_Brevern-Hazout/06,
AUTHOR = {Gelly, Jean-Christophe and de Brevern, Alexandre G. and Hazout, Serge},
TITLE = {''Protein Peeling'': An approach for splitting a 3D Protein structure into compact fragments},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {2},
PAGES = {129-133},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti773},
PUBLISHER = {Oxford University Press},
}
@article{Fischer-Grossmann-Roth-Gruissem-Baginsky-Buhmann/06,
AUTHOR = {Fischer, Bernd and Grossmann, Jonas and Roth, Volker and Gruissem, Wilhelm and Baginsky, Sacha and Buhmann, Joachim M.},
TITLE = {Semi-supervised LC/MS alignment for differential proteomics},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {132-140},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl219},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Foat-Morozov-Bussemaker/06,
AUTHOR = {Foat, Barrett C. and Morozov, Alexandre V. and Bussemaker, Harmen J.},
TITLE = {Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {141-149},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl223},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Gordon-Towsey-Hogan-Mathews-Timms/06,
AUTHOR = {Gordon, J.J. and Towsey, M.W. and Hogan, J.M. and Mathews, S.A. and Timms, P.},
TITLE = {Improved prediction of bacterial transcription start sites},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {2},
PAGES = {142-148},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti771},
PUBLISHER = {Oxford University Press},
}
@article{Fratkin-Naughton-Brutlag-Batzoglou/06,
AUTHOR = {Fratkin, Eugene and Naughton, Brian T. and Brutlag, Douglas L. and Batzoglou, Serafim},
TITLE = {MotifCut: Regulatory motifs finding with maximum density subgraphs},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {150-157},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl243},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Fuss-Dubitzky-Downes-Kurth/06,
AUTHOR = {Fu{\ss}, Hendrik and Dubitzky, Werner and Downes, Stephen and Kurth, Mary Jo},
TITLE = {Bistable switching and excitable behaviour in the activation of Src at mitosis},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {158-165},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl201},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Georgi-Schliep/06,
AUTHOR = {Georgi, Benjamin and Schliep, Alexander},
TITLE = {Context-specific independence mixture modeling for positional weight matrices},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {166-173},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl249},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Kamisetty-Bailey-Kellogg-Pandurangan/06,
AUTHOR = {Kamisetty, Hetunandan and Bailey-Kellogg, Chris and Pandurangan, Gopal},
TITLE = {An efficient randomized algorithm for contact-based NMR backbone resonance assignment},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {2},
PAGES = {172-180},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti786},
PUBLISHER = {Oxford University Press},
}
@article{Georgiev-Lilien-Donald/06,
AUTHOR = {Georgiev, Ivelin and Lilien, Ryan H. and Donald, Bruce R.},
TITLE = {Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {174-183},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl220},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Gewehr-Zimmer/06,
AUTHOR = {Gewehr, Jan E. and Zimmer, Ralf},
TITLE = {SSEP-Domain: Protein domain prediction by alignment of secondary structure elements and profiles},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {2},
PAGES = {181-187},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti751},
PUBLISHER = {Oxford University Press},
}
@article{Gevaert-De_Smet-Timmerman-Moreau-De_Moor/06,
AUTHOR = {Gevaert, Olivier and De Smet, Frank and Timmerman, Dirk and Moreau, Yves and De Moor, Bart},
TITLE = {Predicting the prognosis of breast cancer by integrating clinical and microarray data with Bayesian networks},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {184-190},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl230},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Granseth-Viklund-Elofssond/06,
AUTHOR = {Granseth, Erik and Viklund, H{\aa}kan and Elofssond, Arne},
TITLE = {ZPRED: Predicting the distance to the membrane center for residues in $\alpha$-helical membrane proteins},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {191-196},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl206},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Arnold-Bordoli-Kopp-Schwede/06,
AUTHOR = {Arnold, Konstantin and Bordoli, Lorenza and Kopp, J{\"{u}}rgen and Schwede, Torsten},
TITLE = {The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {2},
PAGES = {195-201},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti770},
PUBLISHER = {Oxford University Press},
}
@article{Hertel-Stadler/06,
AUTHOR = {Hertel, Jana and Stadler, Peter F.},
TITLE = {Hairpins in a Haystack: Recognizing microRNA precursors in comparative genomics data},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {197-202},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl257},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Huard-Deane-Wood/06,
AUTHOR = {Huard, Fabien P.E. and Deane, Charlotte M. and Wood, Graham R.},
TITLE = {Modelling sequential protein folding under kinetic control},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {203-210},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl248},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Gupta-Maranas-Albert/06,
AUTHOR = {Gupta, Anshuman and Maranas, Costas D. and Albert, R{\'{e}}ka},
TITLE = {Elucidation of directionality for co-expressed genes: Predicting intra-operon termination sites},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {2},
PAGES = {209-214},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti780},
PUBLISHER = {Oxford University Press},
}
@article{Lee-Shatkay/06,
AUTHOR = {Lee, Phil Hyoun and Shatkay, Hagit},
TITLE = {BNTagger: Improved tagging SNP selection using Bayesian networks},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {211-219},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl233},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Khondoker-Glasbey-Worton/06,
AUTHOR = {Khondoker, Mizanur R. and Glasbey, Chris A. and Worton, Bruce J.},
TITLE = {Statistical estimation of gene expression using multiple laser scans of microarrays},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {2},
PAGES = {215-219},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti790},
PUBLISHER = {Oxford University Press},
}
@article{Jang-Lim-Lim-Park-Lee-Park/06,
AUTHOR = {Jang, Hyunchul and Lim, Jaesoo and Lim, Joon-Ho and Park, Soo-Jun and Lee, Kyu-Chul and Park, Seon-Hee},
TITLE = {Finding the evidence for protein-protein interactions from PubMed abstracts},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {220-226},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl203},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Choudhary-Datta-Bittner-Dougherty/06,
AUTHOR = {Choudhary, Ashish and Datta, Aniruddha and Bittner, Michael L. and Dougherty, Edward R.},
TITLE = {Intervention in a family of Boolean networks},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {2},
PAGES = {226-232},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti765},
PUBLISHER = {Oxford University Press},
}
@article{Jojic-Reyes-Gomez-Heckerman-Kadie-Schueler-Furman/06,
AUTHOR = {Jojic, Nebojsa and Reyes-Gomez, Manuel and Heckerman, David and Kadie, Carl and Schueler-Furman, Ora},
TITLE = {Learning MHC I --- Peptide binding},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {227-235},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl255},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Jones-Pevzner/06,
AUTHOR = {Jones, Neil C. and Pevzner, Pavel A.},
TITLE = {Comparative genomics reveals unusually long motifs in mammalian genomes},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {236-242},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl265},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Lee-Choi-Dalkilic-Kim/06,
AUTHOR = {Lee, DoHoon and Choi, Jeong-Hyeon and Dalkilic, Mehmet M. and Kim, Sun},
TITLE = {COMPAM: Visualization of combining pairwise alignments for multiple genomes},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {2},
PAGES = {242-244},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti759},
PUBLISHER = {Oxford University Press},
}
@article{Karakoc-Cherkasov-Sahinalp/06,
AUTHOR = {Karakoc, Emre and Cherkasov, Artem and Sahinalp, S. Cenk},
TITLE = {Distance based algorithms for small biomolecule classification and structural similarity search},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {243-251},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl259},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Buturovic/06,
AUTHOR = {Buturovi{\'c}, Ljubomir J.},
TITLE = {PCP: A program for supervised classification of gene expression profiles},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {2},
PAGES = {245-247},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti760},
PUBLISHER = {Oxford University Press},
}
@article{Baudot-Martin-Mouren-Chevenet-Guenoche-Jacq-Brun/06,
AUTHOR = {Baudot, Ana{\"{i}}s and Martin, David and Mouren, Pierre and Chevenet, Fran{\c{c}}ois and Gu{\'{e}}noche, Alain and Jacq, Bernard and Brun, Christine},
TITLE = {PRODISTIN Web Site: A tool for the functional classification of proteins from interaction networks},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {2},
PAGES = {248-250},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti757},
PUBLISHER = {Oxford University Press},
}
@article{Criel-Tsiporkova/06,
AUTHOR = {Criel, Jo and Tsiporkova, Elena},
TITLE = {Gene Time E$\chi$pression Warper: A tool for alignment, template matching and visualization of gene expression time series},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {2},
PAGES = {251-252},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti787},
PUBLISHER = {Oxford University Press},
}
@article{Khatib-Weirauch-Rohl/06,
AUTHOR = {Khatib, Firas and Weirauch, Matthew T. and Rohl, Carol A.},
TITLE = {Rapid knot detection and application to protein structure prediction},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {252-259},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl236},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Iyer-Burroughs-Aravind/06,
AUTHOR = {Iyer, Lakshminarayan M. and Burroughs, A. Maxwell and Aravind, L.},
TITLE = {The ASCH superfamily: Novel domains with a fold related to the PUA domain and a potential role in RNA metabolism},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {3},
PAGES = {257-263},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti767},
PUBLISHER = {Oxford University Press},
}
@article{Kirac-Ozsoyoglu-Yang/06,
AUTHOR = {Kirac, Mustafa and Ozsoyoglu, Gultekin and Yang, Jiong},
TITLE = {Annotating proteins by mining protein interaction networks},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {260-270},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl221},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Cordes-Binford/06,
AUTHOR = {Cordes, Matthew H.J. and Binford, Greta J.},
TITLE = {Lateral gene transfer of a dermonecrotic toxin between spiders and bacteria},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {3},
PAGES = {264-268},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti811},
PUBLISHER = {Oxford University Press},
}
@article{Koh-Teong-Clement-Hsu-Thiagarajan/06,
AUTHOR = {Koh, Geoffrey and Teong, Huey Fern Carol and Cl{\'{e}}ment, Marie-V{\'{e}}ronique and Hsu, David and Thiagarajan, P.S.},
TITLE = {A decompositional approach to parameter estimation in pathway modeling: A case study of the Akt and MAPK pathways and their crosstalk},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {271-280},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl264},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Idicula-Thomas-Kulkarni-Kulkarni-Jayaraman-Balaji/06,
AUTHOR = {Idicula-Thomas, Susan and Kulkarni, Abhijit J. and Kulkarni, Bhaskar D. and Jayaraman, Valadi K. and Balaji, Petety V.},
TITLE = {A support vector machine-based method for predicting the propensity of a protein to be soluble or to form inclusion body on overexpression in Escherichia coli},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {3},
PAGES = {278-284},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti810},
PUBLISHER = {Oxford University Press},
}
@article{Krause-Diaz-Bartels-Edwards-Puhler-Rohwer-Meyer-Stoye/06,
AUTHOR = {Krause, Lutz and Diaz, Naryttza N. and Bartels, Daniela and Edwards, Robert A. and P{\"{u}}hler, Alfred and Rohwer, Forest and Meyer, Folker and Stoye, Jens},
TITLE = {Finding novel genes in bacterial communities isolated from the environment},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {281-289},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl247},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Dong-Wang-Lin/06,
AUTHOR = {Dong, Qi-wen and Wang, Xiao-long and Lin, Lei},
TITLE = {Application of latent semantic analysis to protein remote homology detection},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {3},
PAGES = {285-290},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti801},
PUBLISHER = {Oxford University Press},
}
@article{Lasso-Antoniw-Mullins/06,
AUTHOR = {Lasso, Gorka and Antoniw, John F. and Mullins, Jonathan G.L.},
TITLE = {A combinatorial pattern discovery approach for the prediction of membrane dipping (re-entrant) loops},
BOOKTITLE = {Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology, ISMB'2006 (Fortaleza, Brazil, August 6-10, 2006)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {290-297},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl209},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-Cary-Tokyo},
}
@article{Deevi-Martin/06,
AUTHOR = {Deevi, S. Vishnu V. and Martin, Andrew C.R.},
TITLE = {An extensible automated protein annotation tool: Standardizing input and output using validated XML},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {3},
PAGES = {291-296},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti808},
PUBLISHER = {Oxford University Press},
}
@article{Koh-Kim-Cho/06,
AUTHOR = {Koh, Eunhee and Kim, Taehyo and Cho, Hyun-soo},
TITLE = {Mean curvature as a major determinant of $\beta$-sheet propensity},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {3},
PAGES = {297-302},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti775},
PUBLISHER = {Oxford University Press},
}
@article{Cao-Porollo-Adamczak-Jarrell-Meller/06,
AUTHOR = {Cao, Baoqiang and Porollo, Aleksey and Adamczak, Rafal and Jarrell, Mark and Meller, Jaroslaw},
TITLE = {Enhanced recognition of protein transmembrane domains with prediction-based structural profiles},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {3},
PAGES = {303-309},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti784},
PUBLISHER = {Oxford University Press},
}
@article{Glynn-Chen-Mushegian/06,
AUTHOR = {Glynn, Earl F. and Chen, Jie and Mushegian, Arcady R.},
TITLE = {Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {3},
PAGES = {310-316},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti789},
PUBLISHER = {Oxford University Press},
}
@article{Beerli/06,
AUTHOR = {Beerli, Peter},
TITLE = {Comparison of Bayesian and maximum-likelihood inference of population genetic parameters},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {3},
PAGES = {341-345},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti803},
PUBLISHER = {Oxford University Press},
}
@article{Fiers-van_de_Wetering-Peeters-van_Wijk-Nap/06,
AUTHOR = {Fiers, Mark W.E.J. and van de Wetering, Huub and Peeters, Tim H.J.M. and van Wijk, Jarke J. and Nap, Jan-Peter},
TITLE = {DNAVis: Interactive visualization of comparative genome annotations},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {3},
PAGES = {354-355},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti807},
PUBLISHER = {Oxford University Press},
}
@article{Dezulian-Remmert-Palatnik-Weigel-Huson/06,
AUTHOR = {Dezulian, Tobias and Remmert, Michael and Palatnik, Javier F. and Weigel, Detlef and Huson, Daniel H.},
TITLE = {Identification of plant microRNA homologs},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {3},
PAGES = {359-360},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti802},
PUBLISHER = {Oxford University Press},
}
@article{Bortolussi-Durand-Blum-Francois/06,
AUTHOR = {Bortolussi, Nicolas and Durand, Eric and Blum, Michael and Fran{\c{c}}ois, Olivier},
TITLE = {apTreeshape: Statistical analysis of phylogenetic tree shape},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {3},
PAGES = {363-364},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti798},
PUBLISHER = {Oxford University Press},
}
@article{Brinza-Zelikovsky/06,
AUTHOR = {Brinza, Dumitru and Zelikovsky, Alexander},
TITLE = {2SNP: Scalable phasing based on 2-SNP haplotypes},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {3},
PAGES = {371-373},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti785},
PUBLISHER = {Oxford University Press},
}
@article{Dogrusoz-Erson-Giral-Demir-Babur-Cetintas-Colak/06,
AUTHOR = {Dogrusoz, U. and Erson, E.Z. and Giral, E. and Demir, E. and Babur, O. and Cetintas, A. and Colak, R.},
TITLE = {PATIKAweb: A Web interface for analyzing biological pathways through advanced querying and visualization},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {3},
PAGES = {374-375},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti776},
PUBLISHER = {Oxford University Press},
}
@article{Chen-Huang-Sun/06,
AUTHOR = {Chen, Hu and Huang, Ni and Sun, Zhirong},
TITLE = {SubLoc: A server/client suite for protein subcellular location based on SOAP},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {3},
PAGES = {376-377},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti822},
PUBLISHER = {Oxford University Press},
}
@article{Ding-Hughes-Berleant-Fulmer-Wurtele/06,
AUTHOR = {Ding, Jing and Hughes, LaRon M. and Berleant, Daniel and Fulmer, Andy W. and Wurtele, Eve Syrkin},
TITLE = {PubMed Assistant: A biologist-friendly interface for enhanced PubMed search},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {3},
PAGES = {378-380},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti821},
PUBLISHER = {Oxford University Press},
}
@article{Gallo-Li-Hu-Halfon/06,
AUTHOR = {Gallo, Steven M. and Li, Long and Hu, Zihua and Halfon, Marc S.},
TITLE = {REDfly: A Regulatory Element Database for Drosophila},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {3},
PAGES = {381-383},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti794},
PUBLISHER = {Oxford University Press},
}
@article{Guo-Tatsuoka-Liu/06,
AUTHOR = {Guo, Xiang and Tatsuoka, Kay and Liu, Rongxiang},
TITLE = {Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {4},
PAGES = {392-399},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti823},
PUBLISHER = {Oxford University Press},
}
@article{Kocsor-Kertesz-Farkas-Kajan-Pongor/06,
AUTHOR = {Kocsor, Andr{\'{a}}s and Kert{\'{e}}sz-Farkas, Attila and Kaj{\'{a}}n, L{\'{a}}szl{\'{o}} and Pongor, S{\'{a}}ndor},
TITLE = {Application of compression-based distance measures to protein sequence classification: A methodological study},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {4},
PAGES = {407-412},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti806},
PUBLISHER = {Oxford University Press},
}
@article{Huang-Bystroff/06,
AUTHOR = {Huang, Yao-ming and Bystroff, Christopher},
TITLE = {Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {4},
PAGES = {413-422},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti828},
PUBLISHER = {Oxford University Press},
}
@article{Duprat-Lefranc-Gascuel/06,
AUTHOR = {Duprat, Elodie and Lefranc, Marie-Paule and Gascuel, Olivier},
TITLE = {A simple method to predict protein-binding from aligned sequences --- Application to MHC superfamily and $\beta$2-microglobulin},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {4},
PAGES = {453-459},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti826},
PUBLISHER = {Oxford University Press},
}
@article{Ginzinger-Fischer/06,
AUTHOR = {Ginzinger, Simon W. and Fischer, Johannes},
TITLE = {SimShift: Identifying structural similarities from NMR chemical shifts},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {4},
PAGES = {460-465},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti805},
PUBLISHER = {Oxford University Press},
}
@article{Basu-Bremer-Zhou-Bogenhagen/06,
AUTHOR = {Basu, Siddhartha and Bremer, Erich and Zhou, Chun and Bogenhagen, Daniel F.},
TITLE = {MiGenes: A searchable interspecies database of mitochondrial proteins curated using gene ontology annotation},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {4},
PAGES = {485-492},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk009},
PUBLISHER = {Oxford University Press},
}
@article{Huntley-Baldo-Johri-Sergot/06,
AUTHOR = {Huntley, Derek and Baldo, Angela and Johri, Saurabh and Sergot, Marek},
TITLE = {SEAN: SNP prediction and display program utilizing EST sequence clusters},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {4},
PAGES = {495-496},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk006},
PUBLISHER = {Oxford University Press},
}
@article{Castrignano-DOnorio_De_Meo-Grillo-Liuni-Mignone-Talamo-Pesole/06,
AUTHOR = {Castrignan{\`{o}}, Tiziana and D'Onorio De Meo, Paolo and Grillo, Giorgio and Liuni, Sabino and Mignone, Flavio and Talamo, Ivano Giuseppe and Pesole, Graziano},
TITLE = {GenoMiner: A tool for genome-wide search of coding and non-coding conserved sequence tags},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {4},
PAGES = {497-499},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti754},
PUBLISHER = {Oxford University Press},
}
@article{Eargle-Wright-Luthey-Schulten/06,
AUTHOR = {Eargle, John and Wright, Dan and Luthey-Schulten, Zaida},
TITLE = {Multiple Alignment of protein structures and sequences for VMD},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {4},
PAGES = {504-506},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti825},
PUBLISHER = {Oxford University Press},
}
@article{Leek-Monsen-Dabney-Storey/06,
AUTHOR = {Leek, Jeffrey T. and Monsen, Eva and Dabney, Alan R. and Storey, John D.},
TITLE = {EDGE: Extraction and analysis of differential gene expression},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {4},
PAGES = {507-508},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk005},
PUBLISHER = {Oxford University Press},
NOTE = {see Corrigendum in Bioinformatics, Vol. 22, 2006, No. 11, 1412-1412},
}
@article{Browning/06,
AUTHOR = {Browning, B.L.},
TITLE = {FLOSS: Flexible ordered subset analysis for linkage mapping of complex traits},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {4},
PAGES = {512-513},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk012},
PUBLISHER = {Oxford University Press},
}
@article{Dalevi-Dubhashi-Hermansson/06,
AUTHOR = {Dalevi, Daniel and Dubhashi, Devdatt and Hermansson, Malte},
TITLE = {Bayesian classifiers for detecting HGT using fixed and variable order Markov models of genomic signatures},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {5},
PAGES = {517-522},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk029},
PUBLISHER = {Oxford University Press},
}
@article{DAuria-Pushker-Rodriguez-Valera/06,
AUTHOR = {D'Auria, Giuseppe and Pushker, Ravindra and Rodriguez-Valera, Francisco},
TITLE = {IWoCS: Analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {5},
PAGES = {527-531},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk033},
PUBLISHER = {Oxford University Press},
}
@article{Lehrach-Husmeier-Williams/06,
AUTHOR = {Lehrach, Wolfgang P. and Husmeier, Dirk and Williams, Christopher K.I.},
TITLE = {A regularized discriminative model for the prediction of protein-peptide interactions},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {5},
PAGES = {532-540},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti804},
PUBLISHER = {Oxford University Press},
}
@article{Henschel-Kim-Schroeder/06,
AUTHOR = {Henschel, Andreas and Kim, Wan Kyu and Schroeder, Michael},
TITLE = {Equivalent binding sites reveal convergently evolved interaction motifs},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {5},
PAGES = {550-555},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti782},
PUBLISHER = {Oxford University Press},
}
@article{Amato-Ciaramella-Deniskina-Del_Mondo-di_Bernardo-Donalek-Longo-Mangano-Miele-Raiconi-Staiano-Tagliaferri/06,
AUTHOR = {Amato, R. and Ciaramella, A. and Deniskina, N. and Del Mondo, C. and di Bernardo, D. and Donalek, C. and Longo, G. and Mangano, G. and Miele, G. and Raiconi, G. and Staiano, A. and Tagliaferri, R.},
TITLE = {A multi-step approach to time series analysis and gene expression clustering},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {5},
PAGES = {589-596},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk026},
PUBLISHER = {Oxford University Press},
}
@article{Kim-Zhang-Park-Ng/06,
AUTHOR = {Kim, Jung-jae and Zhang, Zhuo and Park, Jong C. and Ng, See-Kiong},
TITLE = {BioContrasts: Extracting and exploiting protein-protein contrastive relations from biomedical literature},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {5},
PAGES = {597-605},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk016},
PUBLISHER = {Oxford University Press},
}
@article{Bernhart-Hofacker-Stadler/06,
AUTHOR = {Bernhart, Stephan H. and Hofacker, Ivo L. and Stadler, Peter F.},
TITLE = {Local RNA base pairing probabilities in large sequences},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {5},
PAGES = {614-615},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk014},
PUBLISHER = {Oxford University Press},
}
@article{Gront-Kolinski/06,
AUTHOR = {Gront, Dominik and Kolinski, Andrzej},
TITLE = {BioShell --- A package of tools for structural biology computations},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {5},
PAGES = {621-622},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk037},
PUBLISHER = {Oxford University Press},
}
@article{Hemminger-Saelim-Sullivan/06,
AUTHOR = {Hemminger, Bradley M. and Saelim, Billy and Sullivan, Patrick F.},
TITLE = {TAMAL: An integrated approach to choosing SNPs for genetic studies of human complex traits},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {5},
PAGES = {626-627},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk025},
PUBLISHER = {Oxford University Press},
}
@article{Gillespie-Wilkinson-Proctor-Shanley-Boys-Kirkwood/06,
AUTHOR = {Gillespie, Colin S. and Wilkinson, Darren J. and Proctor, Carole J. and Shanley, Daryl P. and Boys, Richard J. and Kirkwood, Thomas B.L.},
TITLE = {Tools for the SBML Community},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {5},
PAGES = {628-629},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk042},
PUBLISHER = {Oxford University Press},
}
@article{Dieterich-Karst-Wehland-Jansch/06,
AUTHOR = {Dieterich, Guido and K{\"{a}}rst, Uwe and Wehland, J{\"{u}}rgen and J{\"{a}}nsch, Lothar},
TITLE = {VIS-O-BAC: Exploratory visualization of functional genome studies from bacteria},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {5},
PAGES = {630-631},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti814},
PUBLISHER = {Oxford University Press},
}
@article{Falkner-Falkner-Andrews/06,
AUTHOR = {Falkner, J.A. and Falkner, J.W. and Andrews, P.C.},
TITLE = {ProteomeCommons.org JAF: Reference information and tools for proteomics},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {5},
PAGES = {632-633},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk015},
PUBLISHER = {Oxford University Press},
}
@article{Katajamaa-Miettinen-Oresic/06,
AUTHOR = {Katajamaa, Mikko and Miettinen, Jarkko and Ore{\v{s}}i{\v{c}}, Matej},
TITLE = {MZmine: Toolbox for processing and visualization of mass spectrometry based molecular profile data},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {5},
PAGES = {634-636},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk039},
PUBLISHER = {Oxford University Press},
}
@article{Lee-Kim-Park/06,
AUTHOR = {Lee, Jin-Bok and Kim, Jung-jae and Park, Jong C.},
TITLE = {Automatic extension of Gene Ontology with flexible identification of candidate terms},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {6},
PAGES = {665-670},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl010},
PUBLISHER = {Oxford University Press},
}
@article{Bab-Dinitz-Shmuely-Maupin-Furlow-Eichler-Shaanan/06,
AUTHOR = {Bab-Dinitz, Elizabeta and Shmuely, Hagay and Maupin-Furlow, Julie and Eichler, Jerry and Shaanan, Boaz},
TITLE = {Haloferax volcanii PitA: An example of functional interaction between the Pfam chlorite dismutase and antibiotic biosynthesis monooxygenase families?},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {6},
PAGES = {671-675},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk043},
PUBLISHER = {Oxford University Press},
}
@article{Boeva-Regnier-Papatsenko-Makeev/06,
AUTHOR = {Boeva, Valentina and Regnier, Mireille and Papatsenko, Dmitri and Makeev, Vsevolod},
TITLE = {Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {6},
PAGES = {676-684},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk032},
PUBLISHER = {Oxford University Press},
}
@article{Chang-Huang-Chao/06,
AUTHOR = {Chang, Chia-Jung and Huang, Yao-Ting and Chao, Kun-Mao},
TITLE = {A greedier approach for finding tag SNPs},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {6},
PAGES = {685-691},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk035},
PUBLISHER = {Oxford University Press},
}
@article{Chiu-Lee-Egan-Sarkar-Coruzzi-DeSalle/06,
AUTHOR = {Chiu, Joanna C. and Lee, Ernest K. and Egan, Mary G. and Sarkar, Indra Neil and Coruzzi, Gloria M. and DeSalle, Rob},
TITLE = {OrthologID: Automation of genome-scale ortholog identification within a parsimony framework},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {6},
PAGES = {699-707},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk040},
PUBLISHER = {Oxford University Press},
}
@article{Catanzaro-Pesenti-Milinkovitch/06,
AUTHOR = {Catanzaro, Daniele and Pesenti, Raffaele and Milinkovitch, Michel C.},
TITLE = {A non-linear optimization procedure to estimate distances and instantaneous substitution rate matrices under the GTR model},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {6},
PAGES = {708-715},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk001},
PUBLISHER = {Oxford University Press},
}
@article{Gesell-von_Haeseler/06,
AUTHOR = {Gesell, Tanja and von Haeseler, Arndt},
TITLE = {In silico sequence evolution with site-specific interactions along phylogenetic trees},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {6},
PAGES = {716-722},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti812},
PUBLISHER = {Oxford University Press},
}
@article{Gerlach-Giegerich/06,
AUTHOR = {Gerlach, Wolfgang and Giegerich, Robert},
TITLE = {GUUGle: A utility for fast exact matching under RNA complementary rules including G-U base pairing},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {6},
PAGES = {762-764},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk041},
PUBLISHER = {Oxford University Press},
}
@article{Blake-Schwager-Kapushesky-Brazma/06,
AUTHOR = {Blake, Jonathon and Schwager, Christian and Kapushesky, Misha and Brazma, Alvis},
TITLE = {ChroCoLoc: An application for calculating the probability of co-localization of microarray gene expression},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {6},
PAGES = {765-767},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk022},
PUBLISHER = {Oxford University Press},
}
@article{Kuhner/06,
AUTHOR = {Kuhner, Mary K.},
TITLE = {LAMARC 2.0: Maximum likelihood and Bayesian estimation of population parameters},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {6},
PAGES = {768-770},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk051},
PUBLISHER = {Oxford University Press},
}
@article{Adie-Adams-Evans-Porteous-Pickard/06,
AUTHOR = {Adie, E.A. and Adams, R.R. and Evans, K.L. and Porteous, D.J. and Pickard, B.S.},
TITLE = {SUSPECTS: Enabling fast and effective prioritization of positional candidates},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {6},
PAGES = {773-774},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk031},
PUBLISHER = {Oxford University Press},
}
@article{Jothi-Zotenko-Tasneem-Przytycka/06,
AUTHOR = {Jothi, Raja and Zotenko, Elena and Tasneem, Asba and Przytycka, Teresa M.},
TITLE = {COCO-CL: Hierarchical clustering of homology relations based on evolutionary correlations},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {7},
PAGES = {779-788},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl009},
PUBLISHER = {Oxford University Press},
}
@article{Irizarry-Wu-Jaffee/06,
AUTHOR = {Irizarry, Rafael A. and Wu, Zhijin and Jaffee, Harris A.},
TITLE = {Comparison of Affymetrix GeneChip expression measures},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {7},
PAGES = {789-794},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk046},
PUBLISHER = {Oxford University Press},
}
@article{Bansal-Della_Gatta-di_Bernardo/06,
AUTHOR = {Bansal, Mukesh and Della Gatta, Giusy and di Bernardo, Diego},
TITLE = {Inference of gene regulatory networks and compound mode of action from time course gene expression profiles},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {7},
PAGES = {815-822},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl003},
PUBLISHER = {Oxford University Press},
}
@article{Barutcuoglu-Schapire-Troyanskaya/06,
AUTHOR = {Barutcuoglu, Zafer and Schapire, Robert E. and Troyanskaya, Olga G.},
TITLE = {Hierarchical multi-label prediction of gene function},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {7},
PAGES = {830-836},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk048},
PUBLISHER = {Oxford University Press},
}
@article{Choudhary-Brun-Hua-Lowey-Suh-Dougherty/06,
AUTHOR = {Choudhary, Ashish and Brun, Marcel and Hua, Jianping and Lowey, James and Suh, Ed and Dougherty, Edward R.},
TITLE = {Genetic test bed for feature selection},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {7},
PAGES = {837-842},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl008},
PUBLISHER = {Oxford University Press},
}
@article{Hakamada-Okamoto-Hanai/06,
AUTHOR = {Hakamada, Kazumi and Okamoto, Masahiro and Hanai, Taizo},
TITLE = {Novel technique for preprocessing high dimensional time-course data from DNA microarray: Mathematical model-based clustering},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {7},
PAGES = {843-848},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl016},
PUBLISHER = {Oxford University Press},
}
@article{Canaran-Stein-Ware/06,
AUTHOR = {Canaran, Payan and Stein, Lincoln and Ware, Doreen},
TITLE = {Look-Align: An interactive web-based multiple sequence alignment viewer with polymorphism analysis support},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {7},
PAGES = {885-886},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl028},
PUBLISHER = {Oxford University Press},
}
@article{Carrere-Gouzy/06,
AUTHOR = {Carrere, S{\'{e}}bastien and Gouzy, J{\'{e}}r{\^{o}}me},
TITLE = {REMORA: A pilot in the ocean of BioMoby web-services},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {7},
PAGES = {900-901},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl001},
PUBLISHER = {Oxford University Press},
}
@article{Feijao-Neiva-de_Azeredo-Espin-Lessinger/06,
AUTHOR = {Feij{\~{a}}o, Pedro Cipriano and Neiva, Lissiene Silva and de Azeredo-Espin, Ana Maria Lima and Lessinger, Ana Cl{\'{a}}udia},
TITLE = {AMiGA: The arthropodan mitochondrial genomes accessible database},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {7},
PAGES = {902-903},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl021},
PUBLISHER = {Oxford University Press},
}
@article{Broet-Richardson/06,
AUTHOR = {Bro{\"{e}}t, Philippe and Richardson, Sylvia},
TITLE = {Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {8},
PAGES = {911-918},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl035},
PUBLISHER = {Oxford University Press},
}
@article{Jefferys-Kelley-Sergot-Fox-Sternberg/06,
AUTHOR = {Jefferys, Benjamin R. and Kelley, Lawrence A. and Sergot, Marek J. and Fox, John and Sternberg, Michael J.E.},
TITLE = {Capturing expert knowledge with argumentation: A case study in bioinformatics},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {8},
PAGES = {924-933},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl018},
PUBLISHER = {Oxford University Press},
}
@article{Hochreiter-Clevert-Obermayer/06,
AUTHOR = {Hochreiter, Sepp and Clevert, Djork-Arn{\'{e}} and Obermayer, Klaus},
TITLE = {A new summarization method for affymetrix probe level data},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {8},
PAGES = {943-949},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl033},
PUBLISHER = {Oxford University Press},
}
@article{Koo-Sohn-Kim-Lee/06,
AUTHOR = {Koo, Ja-Yong and Sohn, Insuk and Kim, Sujong and Lee, Jae Won},
TITLE = {Structured polychotomous machine diagnosis of multiple cancer types using gene expression},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {8},
PAGES = {950-958},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl029},
PUBLISHER = {Oxford University Press},
}
@article{Guo-Liu-Shriver-Hu-Liebman/06,
AUTHOR = {Guo, Xiang and Liu, Rongxiang and Shriver, Craig D. and Hu, Hai and Liebman, Michael N.},
TITLE = {Assessing semantic similarity measures for the characterization of human regulatory pathways},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {8},
PAGES = {967-973},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl042},
PUBLISHER = {Oxford University Press},
}
@article{Eisenacher-de_Braaf-Konig/06,
AUTHOR = {Eisenacher, Martin and de Braaf, J{\"{u}}rgen and K{\"{o}}nig, Simone},
TITLE = {Mass Analysis Peptide Sequence Prediction (MAPSP)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {8},
PAGES = {1002-1003},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl052},
PUBLISHER = {Oxford University Press},
}
@article{Dixit-Beveridge/06,
AUTHOR = {Dixit, Surjit B. and Beveridge, David L.},
TITLE = {Structural bioinformatics of DNA: A web-based tool for the analysis of molecular dynamics results and structure prediction},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {8},
PAGES = {1007-1009},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl059},
PUBLISHER = {Oxford University Press},
}
@article{Dietzsch-Gehlenborg-Nieselt/06,
AUTHOR = {Dietzsch, Janko and Gehlenborg, Nils and Nieselt, Kay},
TITLE = {Mayday-a microarray data analysis workbench},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {8},
PAGES = {1010-1012},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl070},
PUBLISHER = {Oxford University Press},
}
@article{Aragues-Jaeggi-Oliva/06,
AUTHOR = {Aragues, Ramon and Jaeggi, Daniel and Oliva, Baldo},
TITLE = {PIANA: Protein interactions and network analysis},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {8},
PAGES = {1015-1017},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl072},
PUBLISHER = {Oxford University Press},
}
@article{Adamcsek-Palla-Farkas-Derenyi-Vicsek/06,
AUTHOR = {Adamcsek, Bal{\'{a}}zs and Palla, Gergely and Farkas, Ill{\'{e}}s J. and Der{\'{e}}nyi, Imre and Vicsek, Tam{\'{a}}s},
TITLE = {CFinder: Locating cliques and overlapping modules in biological networks},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {8},
PAGES = {1021-1023},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl039},
PUBLISHER = {Oxford University Press},
}
@article{Ameur-Yankovski-Enroth-Spjuth-Komorowski/06,
AUTHOR = {Ameur, Adam and Yankovski, Vladimir and Enroth, Stefan and Spjuth, Ola and Komorowski, Jan},
TITLE = {The LCB Data Warehouse},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {8},
PAGES = {1024-1026},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl036},
PUBLISHER = {Oxford University Press},
}
@article{Hsu-Kent-Clawson-Kuhn-Diekhans-Haussler/06,
AUTHOR = {Hsu, Fan and Kent, W. James and Clawson, Hiram and Kuhn, Robert M. and Diekhans, Mark and Haussler, David},
TITLE = {The UCSC Known Genes},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {9},
PAGES = {1036-1046},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl048},
PUBLISHER = {Oxford University Press},
}
@article{Hon-Jain/06,
AUTHOR = {Hon, Lawrence S. and Jain, Ajay N.},
TITLE = {A deterministic motif finding algorithm with application to the human genome},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {9},
PAGES = {1047-1054},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl037},
PUBLISHER = {Oxford University Press},
}
@article{Kuznetsov-Hwang/06,
AUTHOR = {Kuznetsov, Igor B. and Hwang, Seungwoo},
TITLE = {A novel sensitive method for the detection of user-defined compositional bias in biological sequences},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {9},
PAGES = {1055-1063},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl049},
PUBLISHER = {Oxford University Press},
}
@article{Collyn-Guy-Marceau-Simonet-Roten/06,
AUTHOR = {Collyn, F. and Guy, L. and Marceau, M. and Simonet, M. and Roten, C.-A.H.},
TITLE = {Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {9},
PAGES = {1072-1079},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti793},
PUBLISHER = {Oxford University Press},
}
@article{Ebert-Brutlag/06,
AUTHOR = {Ebert, Jessica and Brutlag, Douglas},
TITLE = {Development and validation of a consistency based multiple structure alignment algorithm},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {9},
PAGES = {1080-1087},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl046},
PUBLISHER = {Oxford University Press},
}
@article{Conesa-Nueda-Ferrer-Talon/06,
AUTHOR = {Conesa, Ana and Nueda, Mar{\'{i}}a Jos{\'{e}} and Ferrer, Alberto and Tal{\'{o}}n, Manuel},
TITLE = {maSigPro: A method to identify significantly differential expression profiles in time-course microarray experiments},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {9},
PAGES = {1096-1102},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl056},
PUBLISHER = {Oxford University Press},
}
@article{Clare-Karwath-Ougham-King/06,
AUTHOR = {Clare, A. and Karwath, A. and Ougham, H. and King, R.D.},
TITLE = {Functional bioinformatics for Arabidopsis thaliana},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {9},
PAGES = {1130-1136},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl051},
PUBLISHER = {Oxford University Press},
NOTE = {see Corrigendum in Bioinformatics, Vol. 22, 2006, No. 13, 1674-1674},
}
@article{Lee-Yun-Cho-Hou-Park-Lee/06,
AUTHOR = {Lee, Dong-Yup and Yun, Choamun and Cho, Ayoun and Hou, Bo Kyeng and Park, Sunwon and Lee, Sang Yup},
TITLE = {WebCell: A web-based environment for kinetic modeling and dynamic simulation of cellular networks},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {9},
PAGES = {1150-1151},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl091},
PUBLISHER = {Oxford University Press},
}
@article{Hoglund-Donnes-Blum-Adolph-Kohlbacher/06,
AUTHOR = {H{\"{o}}glund, Annette and D{\"{o}}nnes, Pierre and Blum, Torsten and Adolph, Hans-Werner and Kohlbacher, Oliver},
TITLE = {MultiLoc: Prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {10},
PAGES = {1158-1165},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl002},
PUBLISHER = {Oxford University Press},
}
@article{Hofacker-Stadler/06,
AUTHOR = {Hofacker, Ivo L. and Stadler, Peter F.},
TITLE = {Memory efficient folding algorithms for circular RNA secondary structures},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {10},
PAGES = {1172-1176},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl023},
PUBLISHER = {Oxford University Press},
}
@article{Kel-Konovalova-Waleev-Cheremushkin-Kel-Margoulis-Wingender/06,
AUTHOR = {Kel, A. and Konovalova, T. and Waleev, T. and Cheremushkin, E. and Kel-Margoulis, O. and Wingender, E.},
TITLE = {Composite Module Analyst: A fitness-based tool for identification of transcription factor binding site combinations},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {10},
PAGES = {1190-1197},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl041},
PUBLISHER = {Oxford University Press},
}
@article{Ababneh-Jermiin-Ma-Robinson/06,
AUTHOR = {Ababneh, Faisal and Jermiin, Lars S. and Ma, Chunsheng and Robinson, John},
TITLE = {Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {10},
PAGES = {1225-1231},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl064},
PUBLISHER = {Oxford University Press},
}
@article{Agrawal-Stormo/06,
AUTHOR = {Agrawal, Ritesh and Stormo, Gary D.},
TITLE = {Using mRNAs lengths to accurately predict the alternatively spliced gene products in Caenorhabditis elegans},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {10},
PAGES = {1239-1244},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl076},
PUBLISHER = {Oxford University Press},
}
@article{Berrar-Bradbury-Dubitzky/06,
AUTHOR = {Berrar, Daniel and Bradbury, Ian and Dubitzky, Werner},
TITLE = {Avoiding model selection bias in small-sample genomic datasets},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {10},
PAGES = {1245-1250},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl066},
PUBLISHER = {Oxford University Press},
NOTE = {see Corrigendum in Bioinformatics, Vol. 22, 2006, No. 19, 2453-2453},
}
@article{Engelen-Naudts-De_Moor-Marchal/06,
AUTHOR = {Engelen, Kristof and Naudts, Bart and De Moor, Bart and Marchal, Kathleen},
TITLE = {A calibration method for estimating absolute expression levels from microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {10},
PAGES = {1251-1258},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl068},
PUBLISHER = {Oxford University Press},
}
@article{Huang-Pan/06,
AUTHOR = {Huang, Desheng and Pan, Wei},
TITLE = {Incorporating biological knowledge into distance-based clustering analysis of microarray gene expression data},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {10},
PAGES = {1259-1268},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl065},
PUBLISHER = {Oxford University Press},
}
@article{De_Bie-Cristianini-Demuth-Hahn/06,
AUTHOR = {De Bie, Tijl and Cristianini, Nello and Demuth, Jeffery P. and Hahn, Matthew W.},
TITLE = {CAFE: A computational tool for the study of gene family evolution},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {10},
PAGES = {1269-1271},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl097},
PUBLISHER = {Oxford University Press},
}
@article{Kennedy-Kerns-Kong-Archer-Miles/06,
AUTHOR = {Kennedy, Richard E. and Kerns, Robnet T. and Kong, Xiangrong and Archer, Kellie J. and Miles, Michael F.},
TITLE = {SScore: An R package for detecting differential gene expression without gene expression summaries},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {10},
PAGES = {1272-1274},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl108},
PUBLISHER = {Oxford University Press},
}
@article{Keating-Bornstein-Finney-Hucka/06,
AUTHOR = {Keating, Sarah M. and Bornstein, Benjamin J. and Finney, Andrew and Hucka, Michael},
TITLE = {SBMLToolbox: An SBML toolbox for MATLAB users},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {10},
PAGES = {1275-1277},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl111},
PUBLISHER = {Oxford University Press},
}
@article{Barkow-Bleuler-Prelic-Zimmermann-Zitzler/06,
AUTHOR = {Barkow, Simon and Bleuler, Stefan and Prelic, Amela and Zimmermann, Philip and Zitzler, Eckart},
TITLE = {BicAT: A biclustering analysis toolbox},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {10},
PAGES = {1282-1283},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl099},
PUBLISHER = {Oxford University Press},
}
@article{Leinonen-Nardone-Zhu-Apweiler/06,
AUTHOR = {Leinonen, Rasko and Nardone, Francesco and Zhu, Weimin and Apweiler, Rolf},
TITLE = {UniSave: The UniProtKB Sequence/Annotation Version database},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {10},
PAGES = {1284-1285},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl105},
PUBLISHER = {Oxford University Press},
}
@article{Gao-Zhong-Guo-Zhu-Tang-Zheng-Gu-Wei-Luo/06,
AUTHOR = {Gao, Ge and Zhong, Yingfu and Guo, Anyuan and Zhu, Qihui and Tang, Wen and Zheng, Weimou and Gu, Xiaocheng and Wei, Liping and Luo, Jingchu},
TITLE = {DRTF: A database of rice transcription factors},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {10},
PAGES = {1286-1287},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl107},
PUBLISHER = {Oxford University Press},
}
@article{Becker-Meyer-Madaoui-Guerois/06,
AUTHOR = {Becker, Emmanuelle and Meyer, Vincent and Madaoui, Hocine and Guerois, Rapha{\"{e}}l},
TITLE = {Detection of a tandem BRCT in Nbs1 and Xrs2 with functional implications in the DNA damage response},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {11},
PAGES = {1289-1292},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl075},
PUBLISHER = {Oxford University Press},
}
@article{Burgoyne-Jackson/06,
AUTHOR = {Burgoyne, Nicholas J. and Jackson, Richard M.},
TITLE = {Predicting protein interaction sites: Binding hot-spots in protein-protein and protein-ligand interfaces},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {11},
PAGES = {1335-1342},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl079},
PUBLISHER = {Oxford University Press},
}
@article{Lelandais-Vincens-Badel-Chagnon-Vialette-Jacq-Hazout/06,
AUTHOR = {Lelandais, Ga{\"{e}}lle and Vincens, Pierre and Badel-Chagnon, Anne and Vialette, St{\'{e}}phane and Jacq, Claude and Hazout, Serge},
TITLE = {Comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {11},
PAGES = {1359-1366},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl087},
PUBLISHER = {Oxford University Press},
}
@article{Chen-Anantha-Wang/06,
AUTHOR = {Chen, Xue-wen and Anantha, Gopalakrishna and Wang, Xinkun},
TITLE = {An effective structure learning method for constructing gene networks},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {11},
PAGES = {1367-1374},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl090},
PUBLISHER = {Oxford University Press},
}
@article{Hsu-Lee-Chang-Lee/06,
AUTHOR = {Hsu, Chao-Ping and Lee, Pei-Hsuan and Chang, Ching-Wei and Lee, Cheng-Tsung},
TITLE = {Constructing quantitative models from qualitative mutant phenotypes: Preferences in selecting sensory organ precursors},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {11},
PAGES = {1375-1382},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl082},
PUBLISHER = {Oxford University Press},
}
@article{Kohler-Baumbach-Taubert-Specht-Skusa-Ruegg-Rawlings-Verrier-Philippi/06,
AUTHOR = {K{\"{o}}hler, Jacob and Baumbach, Jan and Taubert, Jan and Specht, Michael and Skusa, Andre and R{\"{u}}egg, Alexander and Rawlings, Chris and Verrier, Paul and Philippi, Stephan},
TITLE = {Graph-based analysis and visualization of experimental results with ONDEX},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {11},
PAGES = {1383-1390},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl081},
PUBLISHER = {Oxford University Press},
}
@article{De_Souza-Saunders-McConville-Likic/06,
AUTHOR = {De Souza, David P. and Saunders, Eleanor C. and McConville, Malcolm J. and Liki{\'c}, Vladimir A.},
TITLE = {Progressive peak clustering in GC-MS Metabolomic experiments applied to Leishmania parasites},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {11},
PAGES = {1391-1396},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl085},
PUBLISHER = {Oxford University Press},
}
@article{Aylor-Price-Carbone/06,
AUTHOR = {Aylor, David L. and Price, Eric W. and Carbone, Ignazio},
TITLE = {SNAP: Combine and Map modules for multilocus population genetic analysis},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {11},
PAGES = {1399-1401},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl136},
PUBLISHER = {Oxford University Press},
}
@article{Bardel-Danjean-Genin/06,
AUTHOR = {Bardel, Claire and Danjean, Vincent and G{\'{e}}nin, Emmanuelle},
TITLE = {ALTree: Association detection and localization of susceptibility sites using haplotype phylogenetic trees},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {11},
PAGES = {1402-1403},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl131},
PUBLISHER = {Oxford University Press},
}
@article{Falchi-Borlino/06,
AUTHOR = {Falchi, Mario and Borlino, Cesare Cappio},
TITLE = {PowQ: A user-friendly package for the design of variance component multipoint linkage analysis studies},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {11},
PAGES = {1404-1405},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl124},
PUBLISHER = {Oxford University Press},
}
@article{Kim-Golub-Park/06,
AUTHOR = {Kim, Hyunsoo and Golub, Gene H. and Park, Haesun},
TITLE = {Corrigendum to ''Missing value estimation for DNA microarray gene expression data: Local least squares imputation''},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {11},
PAGES = {1410-1411},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btk053},
PUBLISHER = {Oxford University Press},
NOTE = {Originally in Bioinformatics, Vol. 21, 2005, No. 2, 187-198},
}
@article{Leek-Monsen-Dabney-Storey/06a,
AUTHOR = {Leek, Jeffrey T. and Monsen, Eva and Dabney, Alan R. and Storey, John D.},
TITLE = {Corrigendum to ''EDGE: Extraction and analysis of differential gene expression''},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {11},
PAGES = {1412-1412},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl149},
PUBLISHER = {Oxford University Press},
NOTE = {Originally in Bioinformatics, Vol. 22, 2006, No. 4, 507-508},
}
@article{Grigorov/06,
AUTHOR = {Grigorov, Martin G.},
TITLE = {Global dynamics of biological systems from time-resolved omics experiments},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {12},
PAGES = {1424-1430},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl119},
PUBLISHER = {Oxford University Press},
}
@article{Cheng-Baldi/06,
AUTHOR = {Cheng, Jianlin and Baldi, Pierre},
TITLE = {A machine learning information retrieval approach to protein fold recognition},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {12},
PAGES = {1456-1463},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl102},
PUBLISHER = {Oxford University Press},
}
@article{Cuff-Janes-Martin/06,
AUTHOR = {Cuff, Alison L. and Janes, Robert W. and Martin, Andrew C.R.},
TITLE = {Analysing the ability to retain sidechain hydrogen-bonds in mutant proteins},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {12},
PAGES = {1464-1470},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl120},
PUBLISHER = {Oxford University Press},
}
@article{Ahnert-Willbrand-Brown-Fink/06,
AUTHOR = {Ahnert, S.E. and Willbrand, K. and Brown, F.C.S. and Fink, T.M.A.},
TITLE = {Unbiased pattern detection in microarray data series},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {12},
PAGES = {1471-1476},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl121},
PUBLISHER = {Oxford University Press},
}
@article{Broet-Kuznetsov-Bergh-Liu-Miller/06,
AUTHOR = {Bro{\"{e}}t, Philippe and Kuznetsov, Vladimir A. and Bergh, Jonas and Liu, Edison T. and Miller, Lance D.},
TITLE = {Identifying gene expression changes in breast cancer that distinguish early and late relapse among uncured patients},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {12},
PAGES = {1477-1485},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl110},
PUBLISHER = {Oxford University Press},
}
@article{Gao/06,
AUTHOR = {Gao, Xin},
TITLE = {Construction of null statistics in permutation-based multiple testing for multi-factorial microarray experiments},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {12},
PAGES = {1486-1494},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl109},
PUBLISHER = {Oxford University Press},
}
@article{Kaderali-Zander-Faigle-Wolf-Schultze-Schrader/06,
AUTHOR = {Kaderali, Lars and Zander, Thomas and Faigle, Ulrich and Wolf, J{\"{u}}rgen and Schultze, Joachim L. and Schrader, Rainer},
TITLE = {CASPAR: A hierarchical Bayesian approach to predict survival times in cancer from gene expression data},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {12},
PAGES = {1495-1502},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl103},
PUBLISHER = {Oxford University Press},
NOTE = {see Erratum in Bioinformatics, Vol. 23, 2007, No. 2, 266-266},
}
@article{Adryan-Teichmann/06,
AUTHOR = {Adryan, Boris and Teichmann, Sarah A.},
TITLE = {FlyTF: A systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {12},
PAGES = {1532-1533},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl143},
PUBLISHER = {Oxford University Press},
}
@article{Heil-Ludwig-Lichtenberg-Frate-Lengauer/06,
AUTHOR = {Heil, Burkhard and Ludwig, Jost and Lichtenberg-Frat{\'{e}}, Hella and Lengauer, Thomas},
TITLE = {Computational recognition of potassium channel sequences},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {13},
PAGES = {1562-1568},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl132},
PUBLISHER = {Oxford University Press},
}
@article{Bhasi-Zhang-Brazeau-Zhang-Ramanathan/06,
AUTHOR = {Bhasi, Kavitha and Zhang, Li and Brazeau, Daniel and Zhang, Aidong and Ramanathan, Murali},
TITLE = {VizStruct for visualization of genome-wide SNP analyses},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {13},
PAGES = {1569-1576},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl144},
PUBLISHER = {Oxford University Press},
}
@article{Camoglu-Can-Singh/06,
AUTHOR = {Camoglu, Orhan and Can, Tolga and Singh, Ambuj K.},
TITLE = {Integrating multi-attribute similarity networks for robust representation of the protein space},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {13},
PAGES = {1585-1592},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl130},
PUBLISHER = {Oxford University Press},
}
@article{Dalli-Wilm-Mainz-Steger/06,
AUTHOR = {Dalli, Deniz and Wilm, Andreas and Mainz, Indra and Steger, Gerhard},
TITLE = {STRAL: Progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {13},
PAGES = {1593-1599},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl142},
PUBLISHER = {Oxford University Press},
}
@article{Alexa-Rahnenfuhrer-Lengauer/06,
AUTHOR = {Alexa, Adrian and Rahnenf{\"{u}}hrer, J{\"{o}}rg and Lengauer, Thomas},
TITLE = {Improved scoring of functional groups from gene expression data by decorrelating GO graph structure},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {13},
PAGES = {1600-1607},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl140},
PUBLISHER = {Oxford University Press},
}
@article{Chua-Sung-Wong/06,
AUTHOR = {Chua, Hon Nian and Sung, Wing-Kin and Wong, Limsoon},
TITLE = {Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {13},
PAGES = {1623-1630},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl145},
PUBLISHER = {Oxford University Press},
NOTE = {see Erratum in Bioinformatics, Vol. 24, 2008, No. 3, 452-452},
}
@article{Cho-Cho-Zhang/06,
AUTHOR = {Cho, Dong-Yeon and Cho, Kwang-Hyun and Zhang, Byoung-Tak},
TITLE = {Identification of biochemical networks by S-tree based genetic programming},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {13},
PAGES = {1631-1640},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl122},
PUBLISHER = {Oxford University Press},
}
@article{Kirillova-Minor/06,
AUTHOR = {Kirillova, Olga and Minor, Wladek},
TITLE = {Map2mod --- A server for evaluation of crystallographic models and their agreement with electron density maps},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {13},
PAGES = {1660-1661},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl152},
PUBLISHER = {Oxford University Press},
}
@article{Klekota-Roth-Schreiber/06,
AUTHOR = {Klekota, Justin and Roth, Frederick P. and Schreiber, Stuart L.},
TITLE = {Query Chem: A Google-powered web search combining text and chemical structures},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {13},
PAGES = {1670-1673},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl155},
PUBLISHER = {Oxford University Press},
}
@article{Clare-Karwath-Ougham-King/06a,
AUTHOR = {Clare, A. and Karwath, A. and Ougham, H. and King, R.D.},
TITLE = {Corrigendum to ''Functional bioinformatics for Arabidopsis thaliana''},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {13},
PAGES = {1674-1674},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl169},
PUBLISHER = {Oxford University Press},
NOTE = {Originally in Bioinformatics, Vol. 22, 2006, No. 9, 1130-1136},
}
@article{Chu-Li-Qi/06,
AUTHOR = {Chu, K.H. and Li, C.P. and Qi, J.},
TITLE = {Ribosomal RNA as molecular barcodes: A simple correlation analysis without sequence alignment},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {1690-1701},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl146},
PUBLISHER = {Oxford University Press},
}
@article{Gerega-Downard/06,
AUTHOR = {Gerega, Sebastien K. and Downard, Kevin M.},
TITLE = {PROXIMO --- A new docking algorithm to model protein complexes using data from radical probe mass spectrometry (RP-MS)},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {1702-1709},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl178},
PUBLISHER = {Oxford University Press},
}
@article{Jung-Jang/06,
AUTHOR = {Jung, Sin-Ho and Jang, Woncheol},
TITLE = {How accurately can we control the FDR in analyzing microarray data?},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {1730-1736},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl161},
PUBLISHER = {Oxford University Press},
}
@article{Engels-Yu-Burge-Mesirov-DeCaprio-Galagan/06,
AUTHOR = {Engels, Reinhard and Yu, Tamara and Burge, Chris and Mesirov, Jill P. and DeCaprio, David and Galagan, James E.},
TITLE = {Combo: A whole genome comparative browser},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {1782-1783},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl193},
PUBLISHER = {Oxford University Press},
}
@article{Guo-Lin/06,
AUTHOR = {Guo, Jian and Lin, Yuanlie},
TITLE = {TSSub: Eukaryotic protein subcellular localization by extracting features from profiles},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {1784-1785},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl180},
PUBLISHER = {Oxford University Press},
}
@article{Arigon-Perriere-Gouy/06,
AUTHOR = {Arigon, Anne-Muriel and Perri{\`{e}}re, Guy and Gouy, Manolo},
TITLE = {HoSeql: Automated homologous sequence identification in gene family databases},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {1786-1787},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl179},
PUBLISHER = {Oxford University Press},
}
@article{Darcy-Scharein/06,
AUTHOR = {Darcy, Isabel K. and Scharein, Robert G.},
TITLE = {TopoICE-R: 3D visualization modeling the topology of DNA recombination},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {1790-1791},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl164},
PUBLISHER = {Oxford University Press},
}
@article{Garcia-Serna-Opatowski-Mestres/06,
AUTHOR = {Garc{\'{i}}a-Serna, Ricard and Opatowski, Lulla and Mestres, Jordi},
TITLE = {FCP: Functional coverage of the proteome by structures},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {1792-1793},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl188},
PUBLISHER = {Oxford University Press},
}
@article{Kwasigroch-Rooman/06,
AUTHOR = {Kwasigroch, Jean Marc and Rooman, Marianne},
TITLE = {Prelude\&Fugue, predicting local protein structure, early folding regions and structural weaknesses},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {1800-1802},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl176},
PUBLISHER = {Oxford University Press},
}
@article{Calzone-Fages-Soliman/06,
AUTHOR = {Calzone, Laurence and Fages, Fran{\c{c}}ois and Soliman, Sylvain},
TITLE = {BIOCHAM: An environment for modeling biological systems and formalizing experimental knowledge},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {14},
PAGES = {1805-1807},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl172},
PUBLISHER = {Oxford University Press},
}
@article{Boden-Bailey/06,
AUTHOR = {Bod{\'{e}}n, Mikael and Bailey, Timothy L.},
TITLE = {Identifying sequence regions undergoing conformational change via predicted continuum secondary structure},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {15},
PAGES = {1809-1814},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl198},
PUBLISHER = {Oxford University Press},
}
@article{Dupanloup-Kaessmann/06,
AUTHOR = {Dupanloup, Isabelle and Kaessmann, Henrik},
TITLE = {Evolutionary simulations to detect functional lineage-specific genes},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {15},
PAGES = {1815-1822},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl280},
PUBLISHER = {Oxford University Press},
}
@article{Busch-Backofen/06,
AUTHOR = {Busch, Anke and Backofen, Rolf},
TITLE = {INFO-RNA --- A fast approach to inverse RNA folding},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {15},
PAGES = {1823-1831},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl194},
PUBLISHER = {Oxford University Press},
}
@article{Huang-Zheng/06,
AUTHOR = {Huang, De-Shuang and Zheng, Chun-Hou},
TITLE = {Independent component analysis-based penalized discriminant method for tumor classification using gene expression data},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {15},
PAGES = {1855-1862},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl190},
PUBLISHER = {Oxford University Press},
}
@article{Carroll-Pavlovic/06,
AUTHOR = {Carroll, Steven and Pavlovic, Vladimir},
TITLE = {Protein classification using probabilistic chain graphs and the Gene Ontology Structure},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {15},
PAGES = {1871-1878},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl187},
PUBLISHER = {Oxford University Press},
}
@article{Gauges-Rost-Sahle-Wegner/06,
AUTHOR = {Gauges, Ralph and Rost, Ursula and Sahle, Sven and Wegner, Katja},
TITLE = {A model diagram layout extension for SBML},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {15},
PAGES = {1879-1885},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl195},
PUBLISHER = {Oxford University Press},
}
@article{Galbraith-Tran-Liao/06,
AUTHOR = {Galbraith, Simon J. and Tran, Linh M. and Liao, James C.},
TITLE = {Transcriptome network component analysis with limited microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {15},
PAGES = {1886-1894},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl279},
PUBLISHER = {Oxford University Press},
}
@article{Bellew-Coram-Fitzgibbon-Igra-Randolph-Wang-May-Eng-Fang-Lin-Chen-Goodlett-Whiteaker-Paulovich-McIntosh/06,
AUTHOR = {Bellew, Matthew and Coram, Marc and Fitzgibbon, Matthew and Igra, Mark and Randolph, Tim and Wang, Pei and May, Damon and Eng, Jimmy and Fang, Ruihua and Lin, ChenWei and Chen, Jinzhi and Goodlett, David and Whiteaker, Jeffrey and Paulovich, Amanda and McIntosh, Martin},
TITLE = {A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {15},
PAGES = {1902-1909},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl276},
PUBLISHER = {Oxford University Press},
}
@article{Gould-Getz-Monti-Reich-Mesirov/06,
AUTHOR = {Gould, Joshua and Getz, Gad and Monti, Stefano and Reich, Michael and Mesirov, Jill P.},
TITLE = {Comparative gene marker selection suite},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {15},
PAGES = {1924-1925},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl196},
PUBLISHER = {Oxford University Press},
}
@article{Abad-Grau-Montes-Sebastiani/06,
AUTHOR = {Abad-Grau, Mar{\'{i}}a M. and Montes, Rosana and Sebastiani, Paola},
TITLE = {Building chromosome-wide LD maps},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {16},
PAGES = {1933-1934},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl288},
PUBLISHER = {Oxford University Press},
}
@article{Brezellec-Hoebeke-Hiet-Pasek-Ferat/06,
AUTHOR = {Br{\'{e}}zellec, Pierre and Hoebeke, Mark and Hiet, Marie-Sophie and Pasek, Sophie and Ferat, Jean-Luc},
TITLE = {DomainSieve: A protein domain-based screen that led to the identification of dam-associated genes with potential link to DNA maintenance},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {16},
PAGES = {1935-1941},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl336},
PUBLISHER = {Oxford University Press},
}
@article{Lees-Miles-Wien-Wallace/06,
AUTHOR = {Lees, Jonathan G. and Miles, Andrew J. and Wien, Frank and Wallace, B.A.},
TITLE = {A reference database for circular dichroism spectroscopy covering fold and secondary structure space},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {16},
PAGES = {1955-1962},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl327},
PUBLISHER = {Oxford University Press},
}
@article{Huber-Toedling-Steinmetz/06,
AUTHOR = {Huber, Wolfgang and Toedling, Joern and Steinmetz, Lars M.},
TITLE = {Transcript mapping with high-density oligonucleotide tiling arrays},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {16},
PAGES = {1963-1970},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl289},
PUBLISHER = {Oxford University Press},
}
@article{Chen-Hsu-Lee-Ng/06,
AUTHOR = {Chen, Jin and Hsu, Wynne and Lee, Mong Li and Ng, See-Kiong},
TITLE = {Increasing confidence of protein interactomes using network topological metrics},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {16},
PAGES = {1998-2004},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl335},
PUBLISHER = {Oxford University Press},
}
@article{Joung-Shin-Seong-Zhang/06,
AUTHOR = {Joung, Je-Gun and Shin, Dongho and Seong, Rho Hyun and Zhang, Byoung-Tak},
TITLE = {Identification of regulatory modules by co-clustering latent variable models: Stem cell differentiation},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {16},
PAGES = {2005-2011},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl343},
PUBLISHER = {Oxford University Press},
}
@article{DeLuca-Wu-Pu-Monaghan-Peshkin-Singh-Wall/06,
AUTHOR = {DeLuca, Todd F. and Wu, I-Hsien and Pu, Jian and Monaghan, Thomas and Peshkin, Leonid and Singh, Saurav and Wall, Dennis P.},
TITLE = {Roundup: A multi-genome repository of orthologs and evolutionary distances},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {16},
PAGES = {2044-2046},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl286},
PUBLISHER = {Oxford University Press},
}
@article{Hong-Rho-Yeom-Kim/06,
AUTHOR = {Hong, Seong-Eui and Rho, Seong-Hwan and Yeom, Young Il and Kim, Do Han},
TITLE = {HCNet: A database of heart and calcium functional network},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {16},
PAGES = {2053-2054},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl331},
PUBLISHER = {Oxford University Press},
}
@article{Grimes-Wen-Mewissen-Baxter-Moodie-Beattie-Ghazal/06,
AUTHOR = {Grimes, G.R. and Wen, T.Q. and Mewissen, M. and Baxter, R.M. and Moodie, S. and Beattie, J.S. and Ghazal, P.},
TITLE = {PDQ Wizard: Automated prioritization and characterization of gene and protein lists using biomedical literature},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {16},
PAGES = {2055-2057},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl342},
PUBLISHER = {Oxford University Press},
}
@article{Du-Kibbe-Lin/06,
AUTHOR = {Du, Pan and Kibbe, Warren A. and Lin, Simon M.},
TITLE = {Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {17},
PAGES = {2059-2065},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl355},
PUBLISHER = {Oxford University Press},
}
@article{La_Rosa-Viara-Hupe-Pierron-Liva-Neuvial-Brito-Lair-Servant-Robine-Manie-Brennetot-Janoueix-Lerosey-Raynal-Gruel-Rouveirol-Stransky-Stern-Delattre-Aurias-Radvanyi-Barillot/06,
AUTHOR = {La Rosa, Philippe and Viara, Eric and Hup{\'{e}}, Philippe and Pierron, Ga{\"{e}}lle and Liva, St{\'{e}}phane and Neuvial, Pierre and Brito, Isabel and Lair, S{\'{e}}verine and Servant, Nicolas and Robine, Nicolas and Mani{\'{e}}, Elodie and Brennetot, Caroline and Janoueix-Lerosey, Isabelle and Raynal, Virginie and Gruel, Nad{\`{e}}ge and Rouveirol, C{\'{e}}line and Stransky, Nicolas and Stern, Marc-Henri and Delattre, Olivier and Aurias, Alain and Radvanyi, Fran{\c{c}}ois and Barillot, Emmanuel},
TITLE = {VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {17},
PAGES = {2066-2073},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl359},
PUBLISHER = {Oxford University Press},
}
@article{Chen-Crippen/06,
AUTHOR = {Chen, Yu and Crippen, Gordon M.},
TITLE = {An iterative refinement algorithm for consistency based multiple structural alignment methods},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {17},
PAGES = {2087-2093},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl351},
PUBLISHER = {Oxford University Press},
}
@article{Han-Obradovic-Hu-Wu-Vucetic/06,
AUTHOR = {Han, Bo and Obradovic, Zoran and Hu, Zhang-Zhi and Wu, Cathy H. and Vucetic, Slobodan},
TITLE = {Substring selection for biomedical document classification},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {17},
PAGES = {2136-2142},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl350},
PUBLISHER = {Oxford University Press},
}
@article{Bejerano/06,
AUTHOR = {Bejerano, Gill},
TITLE = {Branch and bound computation of exact $p$-values},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {17},
PAGES = {2158-2159},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl357},
PUBLISHER = {Oxford University Press},
}
@article{Jarman/06,
AUTHOR = {Jarman, Simon N.},
TITLE = {Cleaver: Software for identifying taxon specific restriction endonuclease recognition sites},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {17},
PAGES = {2160-2161},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl330},
PUBLISHER = {Oxford University Press},
}
@article{Ho-Adams-Lew-Matthews-Ng-Shahabi-Sirjani-Tan-Zhao-Easteal-Wilson-Jermiin/06,
AUTHOR = {Ho, Joshua W.K. and Adams, Cameron E. and Lew, Jie Bin and Matthews, Timothy J. and Ng, Chiu Chin and Shahabi-Sirjani, Arash and Tan, Leng Hong and Zhao, Yu and Easteal, Simon and Wilson, Susan R. and Jermiin, Lars S.},
TITLE = {SeqVis: Visualization of compositional heterogeneity in large alignments of nucleotides},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {17},
PAGES = {2162-2163},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl283},
PUBLISHER = {Oxford University Press},
}
@article{Garnier-Friedrich-Bolze-Bettler-Moulinier-Geourjon-Thompson-Deleage-Poch/06,
AUTHOR = {Garnier, N. and Friedrich, A. and Bolze, R. and Bettler, E. and Moulinier, L. and Geourjon, C. and Thompson, J.D. and Del{\'{e}}age, G. and Poch, O.},
TITLE = {MAGOS: Multiple alignment and modelling server},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {17},
PAGES = {2164-2165},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl349},
PUBLISHER = {Oxford University Press},
}
@article{Kolodny-Honig/06,
AUTHOR = {Kolodny, Rachel and Honig, Barry},
TITLE = {VISTAL --- A new 2D visualization tool of protein 3D structural alignments},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {17},
PAGES = {2166-2167},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl353},
PUBLISHER = {Oxford University Press},
}
@article{Bush-Dudek-Ritchie/06,
AUTHOR = {Bush, William S. and Dudek, Scott M. and Ritchie, Marylyn D.},
TITLE = {Parallel multifactor dimensionality reduction: A tool for the large-scale analysis of gene-gene interactions},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {17},
PAGES = {2173-2174},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl347},
PUBLISHER = {Oxford University Press},
}
@article{Chen-Hsiao-Lin-Hu-Hwang-Ho/06,
AUTHOR = {Chen, Yun-Ching and Hsiao, Chung-Der and Lin, Wen-Dar and Hu, Chung-Ming and Hwang, Pung-Pung and Ho, Jan-Ming},
TITLE = {ZooDDD: A cross-species database for digital differential display analysis},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {17},
PAGES = {2180-2182},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl358},
PUBLISHER = {Oxford University Press},
}
@article{He-Liu-Li-Studholme-Li-Liang/06,
AUTHOR = {He, Quan-yuan and Liu, Xiang-hua and Li, Qiang and Studholme, David J. and Li, Xuan-wen and Liang, Song-ping},
TITLE = {G8: A novel domain associated with polycystic kidney disease and non-syndromic hearing loss},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {18},
PAGES = {2189-2191},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl123},
PUBLISHER = {Oxford University Press},
}
@article{Arthur-Sanchez-Perez-Cook/06,
AUTHOR = {Arthur, Jonathan W. and Sanchez-Perez, Angeles and Cook, David I.},
TITLE = {Scoring of predicted GRK2 phosphorylation sites in Nedd4-2},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {18},
PAGES = {2192-2195},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl381},
PUBLISHER = {Oxford University Press},
}
@article{Fang-Fan-Zhang-Zhang/06,
AUTHOR = {Fang, Fang and Fan, Shicai and Zhang, Xuegong and Zhang, Michael Q.},
TITLE = {Predicting methylation status of CpG islands in the human brain},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {18},
PAGES = {2204-2209},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl377},
PUBLISHER = {Oxford University Press},
}
@article{Espadaler-Querol-Aviles-Oliva/06,
AUTHOR = {Espadaler, Jordi and Querol, Enrique and Aviles, Francesc X. and Oliva, Baldo},
TITLE = {Identification of function-associated loop motifs and application to protein function prediction},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {18},
PAGES = {2237-2243},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl382},
PUBLISHER = {Oxford University Press},
}
@article{Huang-Xu-Calian-Hsu/06,
AUTHOR = {Huang, Yifan and Xu, Haiyan and Calian, Violeta and Hsu, Jason C.},
TITLE = {To permute or not to permute},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {18},
PAGES = {2244-2248},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl383},
PUBLISHER = {Oxford University Press},
}
@article{Chang-Wang-Chen/06,
AUTHOR = {Chang, Yu-Hsiang and Wang, Yu-Chao and Chen, Bor-Sen},
TITLE = {Identification of transcription factor cooperativity via stochastic system model},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {18},
PAGES = {2276-2282},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl380},
PUBLISHER = {Oxford University Press},
}
@article{Chen-Yuan/06,
AUTHOR = {Chen, Jingchun and Yuan, Bo},
TITLE = {Detecting functional modules in the yeast protein-protein interaction network},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {18},
PAGES = {2283-2290},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl370},
PUBLISHER = {Oxford University Press},
}
@article{Jonsson-Bates/06,
AUTHOR = {Jonsson, Pall F. and Bates, Paul A.},
TITLE = {Global topological features of cancer proteins in the human interactome},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {18},
PAGES = {2291-2297},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl390},
PUBLISHER = {Oxford University Press},
}
@article{Lee-Yi-Park/06,
AUTHOR = {Lee, Eun-Kyung and Yi, Sung-Gon and Park, Taesung},
TITLE = {arrayQCplot: Software for checking the quality of microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {18},
PAGES = {2305-2307},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl367},
PUBLISHER = {Oxford University Press},
}
@article{Chowdhary-Tan-Ali-Boerlage-Wong-Bajic/06,
AUTHOR = {Chowdhary, Rajesh and Tan, Sin Lam and Ali, R. Ayesha and Boerlage, Brent and Wong, Limsoon and Bajic, Vladimir B.},
TITLE = {Dragon Promoter Mapper (DPM): A Bayesian framework for modelling promoter structures},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {18},
PAGES = {2310-2312},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl125},
PUBLISHER = {Oxford University Press},
}
@article{Buendia-Narasimhan/06,
AUTHOR = {Buendia, Patricia and Narasimhan, Giri},
TITLE = {Serial NetEvolve: A flexible utility for generating serially-sampled sequences along a tree or recombinant network},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {18},
PAGES = {2313-2314},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl387},
PUBLISHER = {Oxford University Press},
}
@article{Cheng-Miura-Tian/06,
AUTHOR = {Cheng, Yiming and Miura, Robert M. and Tian, Bin},
TITLE = {Prediction of mRNA polyadenylation sites by support vector machine},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {19},
PAGES = {2320-2325},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl394},
PUBLISHER = {Oxford University Press},
}
@article{Ferraro-Via-Ausiello-Helmer-Citterich/06,
AUTHOR = {Ferraro, E. and Via, A. and Ausiello, G. and Helmer-Citterich, M.},
TITLE = {A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {19},
PAGES = {2333-2339},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl403},
PUBLISHER = {Oxford University Press},
}
@article{Cawley-Talbot/06,
AUTHOR = {Cawley, Gavin C. and Talbot, Nicola L.C.},
TITLE = {Gene selection in cancer classification using sparse logistic regression with Bayesian regularization},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {19},
PAGES = {2348-2355},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl386},
PUBLISHER = {Oxford University Press},
}
@article{Davis-Gerick-Hintermair-Friedel-Fundel-Kuffner-Zimmer/06,
AUTHOR = {Davis, Chad A. and Gerick, Fabian and Hintermair, Volker and Friedel, Caroline C. and Fundel, Katrin and K{\"u}ffner, Robert and Zimmer, Ralf},
TITLE = {Reliable gene signatures for microarray classification: Assessment of stability and performance},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {19},
PAGES = {2356-2363},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl400},
PUBLISHER = {Oxford University Press},
}
@article{Goldstein/06,
AUTHOR = {Goldstein, Darlene R.},
TITLE = {Partition resampling and extrapolation averaging: Approximation methods for quantifying gene expression in large numbers of short oligonucleotide arrays},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {19},
PAGES = {2364-2372},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl402},
PUBLISHER = {Oxford University Press},
}
@article{Kong-Pu-Park/06,
AUTHOR = {Kong, Sek Won and Pu, William T. and Park, Peter J.},
TITLE = {A multivariate approach for integrating genome-wide expression data and biological knowledge},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {19},
PAGES = {2373-2380},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl401},
PUBLISHER = {Oxford University Press},
}
@article{Friedman-Borlawsky-Shagina-Xing-Lussier/06,
AUTHOR = {Friedman, Carol and Borlawsky, Tara and Shagina, Lyudmila and Xing, H. Rosie and Lussier, Yves A.},
TITLE = {Bio-Ontology and text: Bridging the modeling gap},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {19},
PAGES = {2421-2429},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl405},
PUBLISHER = {Oxford University Press},
}
@article{Armougom-Poirot-Moretti-Higgins-Bucher-Keduas-Notredame/06,
AUTHOR = {Armougom, Fabrice and Poirot, Olivier and Moretti, S{\'{e}}bastien and Higgins, Desmond G. and Bucher, Phillip and Keduas, Vladimir and Notredame, Cedric},
TITLE = {APDB: A web server to evaluate the accuracy of sequence alignments using structural information},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {19},
PAGES = {2439-2440},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl404},
PUBLISHER = {Oxford University Press},
}
@article{Hiller-Grote-Maneck-Munch-Jahn/06,
AUTHOR = {Hiller, Karsten and Grote, Andreas and Maneck, Matthias and M{\"{u}}nch, Richard and Jahn, Dieter},
TITLE = {JVirGel 2.0: Computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {19},
PAGES = {2441-2443},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl409},
PUBLISHER = {Oxford University Press},
}
@article{Cho-Lee/06,
AUTHOR = {Cho, HyungJun and Lee, Jae K.},
TITLE = {Response to comments on ''Bayesian Hierarchical Error Model for Analysis of Gene Expression Data''},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {19},
PAGES = {2452-2452},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl333},
PUBLISHER = {Oxford University Press},
}
@article{Berrar-Bradbury-Dubitzky/06a,
AUTHOR = {Berrar, Daniel and Bradbury, Ian and Dubitzky, Werner},
TITLE = {Corrigendum to ''Avoiding model selection bias in small-sample genomic datasets''},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {19},
PAGES = {2453-2453},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl435},
PUBLISHER = {Oxford University Press},
NOTE = {Originally in Bioinformatics, Vol. 22, 2006, No. 10, 1245-1250},
}
@article{Archak-Nagaraju/06,
AUTHOR = {Archak, Sunil and Nagaraju, Javaregowda},
TITLE = {Eicosapentapeptide repeats (EPRs): Novel repeat proteins specific to flowering plants},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {20},
PAGES = {2455-2458},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl340},
PUBLISHER = {Oxford University Press},
}
@article{Bekaert-Atkins-Baranov/06,
AUTHOR = {Bekaert, Micha{\"e}l and Atkins, John F and Baranov, Pavel V.},
TITLE = {ARFA: A program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {20},
PAGES = {2463-2465},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl430},
PUBLISHER = {Oxford University Press},
}
@article{Ge-Wu-Jung-Chen-Wang/06,
AUTHOR = {Ge, Xijin and Wu, Qingfa and Jung, Yong-Chul and Chen, Jun and Wang, San Ming},
TITLE = {A large quantity of novel human antisense transcripts detected by LongSAGE},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {20},
PAGES = {2475-2479},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl429},
PUBLISHER = {Oxford University Press},
}
@article{Hamada-Tsuda-Kudo-Kin-Asai/06,
AUTHOR = {Hamada, Michiaki and Tsuda, Koji and Kudo, Taku and Kin, Taishin and Asai, Kiyoshi},
TITLE = {Mining frequent stem patterns from unaligned RNA sequences},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {20},
PAGES = {2480-2487},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl431},
PUBLISHER = {Oxford University Press},
}
@article{Bylesjo-Sjodin-Eriksson-Antti-Moritz-Jansson-Trygg/06,
AUTHOR = {Bylesj{\"o}, Max and Sj{\"o}din, Andreas and Eriksson, Daniel and Antti, Henrik and Moritz, Thomas and Jansson, Stefan and Trygg, Johan},
TITLE = {MASQOT-GUI: Spot quality assessment for the two-channel microarray platform},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {20},
PAGES = {2554-2555},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl434},
PUBLISHER = {Oxford University Press},
}
@article{Guillaume-Rougemont/06,
AUTHOR = {Guillaume, Fr{\'e}d{\'e}ric and Rougemont, Jacques},
TITLE = {Nemo: An evolutionary and population genetics programming framework},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {20},
PAGES = {2556-2557},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl415},
PUBLISHER = {Oxford University Press},
}
@article{He-Zelikovsky/06,
AUTHOR = {He, Jingwu and Zelikovsky, Alexander},
TITLE = {MLR-tagging: Informative SNP selection for unphased genotypes based on multiple linear regression},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {20},
PAGES = {2558-2561},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl420},
PUBLISHER = {Oxford University Press},
}
@article{Jarvis-Broadhurst-Johnson-OBoyle-Goodacre/06,
AUTHOR = {Jarvis, Roger M. and Broadhurst, David and Johnson, Helen and O'Boyle, Noel M. and Goodacre, Royston},
TITLE = {PYCHEM: A multivariate analysis package for python},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {20},
PAGES = {2565-2566},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl416},
PUBLISHER = {Oxford University Press},
}
@article{Bonis-Furlong-Sanz/06,
AUTHOR = {Bonis, Julio and Furlong, Laura In{\'e}s and Sanz, Ferran},
TITLE = {OSIRIS: A tool for retrieving literature about sequence variants},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {20},
PAGES = {2567-2569},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl421},
PUBLISHER = {Oxford University Press},
}
@article{Gariev-Varfolomeev/06,
AUTHOR = {Gariev, Igor A. and Varfolomeev, Sergey D.},
TITLE = {Hierarchical classification of hydrolases catalytic sites},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {20},
PAGES = {2574-2576},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl413},
PUBLISHER = {Oxford University Press},
}
@article{Gnad-Parsch/06,
AUTHOR = {Gnad, Florian and Parsch, John},
TITLE = {Sebida: A database for the functional and evolutionary analysis of genes with sex-biased expression},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {20},
PAGES = {2577-2579},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl422},
PUBLISHER = {Oxford University Press},
}
@article{Budagyan-Abagyan/06,
AUTHOR = {Budagyan, Levon and Abagyan, Ruben},
TITLE = {Weighted quality estimates in machine learning},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {21},
PAGES = {2597-2603},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl458},
PUBLISHER = {Oxford University Press},
}
@article{Jin-Nakhleh-Snir-Tuller/06,
AUTHOR = {Jin, Guohua and Nakhleh, Luay and Snir, Sagi and Tuller, Tamir},
TITLE = {Maximum likelihood of phylogenetic networks},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {21},
PAGES = {2604-2611},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl452},
PUBLISHER = {Oxford University Press},
NOTE = {see Erratum in Bioinformatics, Vol. 23, 2007, No. 8, 1046-1047},
}
@article{Douguet-Chen-Tovchigrechko-Vakser/06,
AUTHOR = {Douguet, Dominique and Chen, Huei-Chi and Tovchigrechko, Andrey and Vakser, Ilya A.},
TITLE = {DOCKGROUND resource for studying protein-protein interfaces},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {21},
PAGES = {2612-2618},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl447},
PUBLISHER = {Oxford University Press},
}
@article{Eyal-Yang-Bahar/06,
AUTHOR = {Eyal, Eran and Yang, Lee-Wei and Bahar, Ivet},
TITLE = {Anisotropic network model: Systematic evaluation and a new web interface},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {21},
PAGES = {2619-2627},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl448},
PUBLISHER = {Oxford University Press},
}
@article{Birzele-Kramer/06,
AUTHOR = {Birzele, Fabian and Kramer, Stefan},
TITLE = {A new representation for protein secondary structure prediction based on frequent patterns},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {21},
PAGES = {2628-2634},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl453},
PUBLISHER = {Oxford University Press},
}
@article{Cheng-Ma-Yan-Sun-Li/06,
AUTHOR = {Cheng, Chao and Ma, Xiaotu and Yan, Xiting and Sun, Fengzhu and Li, Lei M.},
TITLE = {MARD: A new method to detect differential gene expression in treatment-control time courses},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {21},
PAGES = {2650-2657},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl451},
PUBLISHER = {Oxford University Press},
}
@article{Callegaro-Basso-Bicciato/06,
AUTHOR = {Callegaro, A. and Basso, D. and Bicciato, S.},
TITLE = {A locally adaptive statistical procedure (LAP) to identify differentially expressed chromosomal regions},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {21},
PAGES = {2658-2666},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl455},
PUBLISHER = {Oxford University Press},
}
@article{Faith-Mintram-Angelova/06,
AUTHOR = {Faith, Joe and Mintram, Robert and Angelova, Maia},
TITLE = {Targeted projection pursuit for visualizing gene expression data classifications},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {21},
PAGES = {2667-2673},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl463},
PUBLISHER = {Oxford University Press},
}
@article{Kadirkamanathan-Yang-Billings-Wright/06,
AUTHOR = {Kadirkamanathan, Visakan and Yang, Jing and Billings, Stephen A. and Wright, Phillip C.},
TITLE = {Markov Chain Monte Carlo Algorithm based metabolic flux distribution analysis on Corynebacterium glutamicum},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {21},
PAGES = {2681-2687},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl445},
PUBLISHER = {Oxford University Press},
}
@article{Grant-Rodrigues-ElSawy-McCammon-Caves/06,
AUTHOR = {Grant, Barry J. and Rodrigues, Ana P.C. and ElSawy, Karim M. and McCammon, J. Andrew and Caves, Leo S.D.},
TITLE = {Bio3d: An R package for the comparative analysis of protein structures},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {21},
PAGES = {2695-2696},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl461},
PUBLISHER = {Oxford University Press},
}
@article{Archer-Guennel/06,
AUTHOR = {Archer, Kellie J. and Guennel, Tobias},
TITLE = {An application for assessing quality of RNA hybridized to Affymetrix GeneChips},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {21},
PAGES = {2699-2701},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl459},
PUBLISHER = {Oxford University Press},
}
@article{Deceliere-Letrillard-Charles-Biemont/06,
AUTHOR = {Deceliere, Gr{\'e}gory and Letrillard, Yann and Charles, Sandrine and Bi{\'e}mont, Christian},
TITLE = {TESD: A transposable element dynamics simulation environment},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {21},
PAGES = {2702-2703},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl454},
PUBLISHER = {Oxford University Press},
}
@article{Dlakic/06,
AUTHOR = {Dlaki{\'c}, Mensur},
TITLE = {DUF283 domain of Dicer proteins has a double-stranded RNA-binding fold},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {22},
PAGES = {2711-2714},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl468},
PUBLISHER = {Oxford University Press},
}
@article{Capriotti-Calabrese-Casadio/06,
AUTHOR = {Capriotti, E. and Calabrese, R. and Casadio, R.},
TITLE = {Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {22},
PAGES = {2729-2734},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl423},
PUBLISHER = {Oxford University Press},
}
@article{Counterman_Burba-Lehnert-Yu-Gerstein/06,
AUTHOR = {Counterman Burba, Anne E. and Lehnert, Ursula and Yu, Eric Z. and Gerstein, Mark},
TITLE = {Helix Interaction Tool (HIT): A web-based tool for analysis of helix-helix interactions in proteins},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {22},
PAGES = {2735-2738},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl274},
PUBLISHER = {Oxford University Press},
}
@article{Eckel-Passow-Oberg-Therneau-Mason-Mahoney-Johnson-Olson-Bergen/06,
AUTHOR = {Eckel-Passow, J.E. and Oberg, A.L. and Therneau, T.M. and Mason, C.J. and Mahoney, D.W. and Johnson, K.L. and Olson, J.E. and Bergen III, H.R.},
TITLE = {Regression analysis for comparing protein samples with $^{16}O/^{18}O$ stable-isotope labeled mass spectrometry},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {22},
PAGES = {2739-2745},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl464},
PUBLISHER = {Oxford University Press},
}
@article{Chang-Ghosh-Kirschner-Linderman/06,
AUTHOR = {Chang, Stewart T. and Ghosh, Debashis and Kirschner, Denise E. and Linderman, Jennifer J.},
TITLE = {Peptide length-based prediction of peptide-MHC class II binding},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {22},
PAGES = {2761-2767},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl479},
PUBLISHER = {Oxford University Press},
}
@article{Griffith-Courtney-Peccoud-Sanders/06,
AUTHOR = {Griffith, Mark and Courtney, Tod and Peccoud, Jean and Sanders, William H.},
TITLE = {Dynamic partitioning for hybrid simulation of the bistable HIV-1 transactivation network},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {22},
PAGES = {2782-2789},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl465},
PUBLISHER = {Oxford University Press},
}
@article{Heinemann-Panke/06,
AUTHOR = {Heinemann, Matthias and Panke, Sven},
TITLE = {Synthetic biology --- Putting engineering into biology},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {22},
PAGES = {2790-2799},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl469},
PUBLISHER = {Oxford University Press},
}
@article{Billion-Ghai-Chakraborty-Hain/06,
AUTHOR = {Billion, A. and Ghai, R. and Chakraborty, T. and Hain, T.},
TITLE = {Augur --- A computational pipeline for whole genome microbial surface protein prediction and classification},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {22},
PAGES = {2819-2820},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl466},
PUBLISHER = {Oxford University Press},
}
@article{Fares-McNally/06,
AUTHOR = {Fares, Mario A. and McNally, David},
TITLE = {CAPS: Coevolution analysis using protein sequences},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {22},
PAGES = {2821-2822},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl493},
PUBLISHER = {Oxford University Press},
}
@article{Hong-Breitling-McEntee-Wittner-Nemhauser-Chory/06,
AUTHOR = {Hong, Fangxin and Breitling, Rainer and McEntee, Connor W. and Wittner, Ben S. and Nemhauser, Jennifer L. and Chory, Joanne},
TITLE = {RankProd: A bioconductor package for detecting differentially expressed genes in meta-analysis},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {22},
PAGES = {2825-2827},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl476},
PUBLISHER = {Oxford University Press},
}
@article{Hothorn-Buhlmann/06,
AUTHOR = {Hothorn, Torsten and B{\"u}hlmann, Peter},
TITLE = {Model-based boosting in high dimensions},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {22},
PAGES = {2828-2829},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl462},
PUBLISHER = {Oxford University Press},
}
@article{Laukens-Matthiesen-Lemiere-Esmans-Van_Onckelen-Jensen-Witters/06,
AUTHOR = {Laukens, Kris and Matthiesen, Rune and Lemi{\`e}re, Filip and Esmans, Eddy and Van Onckelen, Harry and Jensen, Ole N{\o}rregaard and Witters, Erwin},
TITLE = {Integration of gel-based proteome data with pProRep},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {22},
PAGES = {2838-2840},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl487},
PUBLISHER = {Oxford University Press},
}
@article{Birtle-Ponting/06,
AUTHOR = {Birtle, Zo{\"{e}} and Ponting, Chris P.},
TITLE = {Meisetz and the birth of the KRAB motif},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {23},
PAGES = {2841-2845},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl498},
PUBLISHER = {Oxford University Press},
}
@article{Da_Silva-Shen-Tcherepanov-Watson-Upton/06,
AUTHOR = {Da Silva, Melissa and Shen, Ling and Tcherepanov, Vasily and Watson, Cristalle and Upton, Chris},
TITLE = {Predicted function of the vaccinia virus G5R protein},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {23},
PAGES = {2846-2850},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl506},
PUBLISHER = {Oxford University Press},
}
@article{Friedrich-Pils-Dandekar-Schultz-Muller/06,
AUTHOR = {Friedrich, Torben and Pils, Birgit and Dandekar, Thomas and Schultz, J{\"{o}}rg and M{\"{u}}ller, Tobias},
TITLE = {Modelling interaction sites in protein domains with interaction profile hidden Markov models},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {23},
PAGES = {2851-2857},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl486},
PUBLISHER = {Oxford University Press},
}
@article{Kajan-Kertesz-Farkas-Franklin-Ivanova-Kocsor-Pongor/06,
AUTHOR = {Kaj{\'{a}}n, L{\'{a}}szl{\'{o}} and Kert{\'{e}}sz-Farkas, Attila and Franklin, Dino and Ivanova, Neli and Kocsor, Andr{\'{a}}s and Pongor, S{\'{a}}ndor},
TITLE = {Application of a simple likelihood ratio approximant to protein sequence classification},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {23},
PAGES = {2865-2869},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl512},
PUBLISHER = {Oxford University Press},
}
@article{Kim-Tharakaraman-Spouge/06,
AUTHOR = {Kim, Nak-Kyeong and Tharakaraman, Kannan and Spouge, John L.},
TITLE = {Adding sequence context to a Markov background model improves the identification of regulatory elements},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {23},
PAGES = {2870-2875},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl528},
PUBLISHER = {Oxford University Press},
}
@article{Huttenhower-Hibbs-Myers-Troyanskaya/06,
AUTHOR = {Huttenhower, Curtis and Hibbs, Matt and Myers, Chad and Troyanskaya, Olga G.},
TITLE = {A scalable method for integration and functional analysis of multiple microarray datasets},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {23},
PAGES = {2890-2897},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl492},
PUBLISHER = {Oxford University Press},
}
@article{Begun/06,
AUTHOR = {Begun, Alexander},
TITLE = {Robust method for detecting differential gene expression in twin studies},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {23},
PAGES = {2905-2909},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl501},
PUBLISHER = {Oxford University Press},
}
@article{Lehmussola-Ruusuvuori-Yli-Harja/06,
AUTHOR = {Lehmussola, Antti and Ruusuvuori, Pekka and Yli-Harja, Olli},
TITLE = {Evaluating the performance of microarray segmentation algorithms},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {23},
PAGES = {2910-2917},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl502},
PUBLISHER = {Oxford University Press},
}
@article{Chang-Nevins/06,
AUTHOR = {Chang, Jeffrey T. and Nevins, Joseph R.},
TITLE = {GATHER: A systems approach to interpreting genomic signatures},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {23},
PAGES = {2926-2933},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl483},
PUBLISHER = {Oxford University Press},
}
@article{Draghici-Sellamuthu-Khatri/06,
AUTHOR = {Dr{\u{a}}ghici, Sorin and Sellamuthu, Sivakumar and Khatri, Purvesh},
TITLE = {Babel's tower revisited: A universal resource for cross-referencing across annotation databases},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {23},
PAGES = {2934-2939},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl372},
PUBLISHER = {Oxford University Press},
}
@article{Galzitskaya-Garbuzynskiy-Lobanov/06,
AUTHOR = {Galzitskaya, Oxana V. and Garbuzynskiy, Sergiy O. and Lobanov, Michail Yu.},
TITLE = {FoldUnfold: Web server for the prediction of disordered regions in protein chain},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {23},
PAGES = {2948-2949},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl504},
PUBLISHER = {Oxford University Press},
}
@article{Chen-Chen-Ning/06,
AUTHOR = {Chen, Xiaohui and Chen, Ming and Ning, Kaida},
TITLE = {BNArray: An R package for constructing gene regulatory networks from microarray data by using Bayesian network},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {23},
PAGES = {2952-2954},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl491},
PUBLISHER = {Oxford University Press},
}
@article{Goffard-Weiller/06,
AUTHOR = {Goffard, Nicolas and Weiller, Georg},
TITLE = {Extending MapMan: Application to legume genome arrays},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {23},
PAGES = {2958-2959},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl517},
PUBLISHER = {Oxford University Press},
}
@article{Bunk-Kucklick-Jonas-Munch-Schobert-Jahn-Hiller/06,
AUTHOR = {Bunk, Boyke and Kucklick, Martin and Jonas, Rochus and M{\"{u}}nch, Richard and Schobert, Max and Jahn, Dieter and Hiller, Karsten},
TITLE = {MetaQuant: A tool for the automatic quantification of GC/MS-based metabolome data},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {23},
PAGES = {2962-2965},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl526},
PUBLISHER = {Oxford University Press},
}
@article{Deckard-Bergmann-Sauro/06,
AUTHOR = {Deckard, Anastasia and Bergmann, Frank T. and Sauro, Herbert M.},
TITLE = {Supporting the SBML layout extension},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {23},
PAGES = {2966-2967},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl520},
PUBLISHER = {Oxford University Press},
}
@article{Hedges-Dudley-Kumar/06,
AUTHOR = {Hedges, S. Blair and Dudley, Joel and Kumar, Sudhir},
TITLE = {TimeTree: A public knowledge-base of divergence times among organisms},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {23},
PAGES = {2971-2972},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl505},
PUBLISHER = {Oxford University Press},
}
@article{Deforche-Camacho-Grossman-Soares-Van_Laethem-Kantor-Moreau-Workgroup/06,
AUTHOR = {Deforche, K. and Camacho, T. Silander R. and Grossman, Z. and Soares, M.A. and Van Laethem, K. and Kantor, R. and Moreau, Y. and Workgroup, A.-M. Vandamme on behalf of the non-B},
TITLE = {Analysis of HIV-1 pol sequences using Bayesian networks: Implications for drug resistance},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {24},
PAGES = {2975-2979},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl508},
PUBLISHER = {Oxford University Press},
}
@article{Du-Rozowsky-Korbel-Zhang-Royce-Schultz-Snyder-Gerstein/06,
AUTHOR = {Du, Jiang and Rozowsky, Joel S. and Korbel, Jan O. and Zhang, Zhengdong D. and Royce, Thomas E. and Schultz, Martin H. and Snyder, Michael and Gerstein, Mark},
TITLE = {A supervised hidden Markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: Systematically incorporating validated biological knowledge},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {24},
PAGES = {3016-3024},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl515},
PUBLISHER = {Oxford University Press},
}
@article{Brynildsen-Tran-Liao/06,
AUTHOR = {Brynildsen, Mark P. and Tran, Linh M. and Liao, James C.},
TITLE = {A Gibbs sampler for the identification of gene expression and network connectivity consistency},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {24},
PAGES = {3040-3046},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl541},
PUBLISHER = {Oxford University Press},
}
@article{Kelemen-Kertesz-Farkas-Kocsor-Puskas/06,
AUTHOR = {Kelemen, J{\'{a}}nos Z. and Kert{\'{e}}sz-Farkas, Attila and Kocsor, Andr{\'{a}}s and Pusk{\'{a}}s, L{\'{a}}szl{\'{o}} G.},
TITLE = {Kalman filtering for disease-state estimation from microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {24},
PAGES = {3047-3053},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl545},
PUBLISHER = {Oxford University Press},
}
@article{Fearnhead/06,
AUTHOR = {Fearnhead, Paul},
TITLE = {SequenceLDhot: Detecting recombination hotspots},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {24},
PAGES = {3061-3066},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl540},
PUBLISHER = {Oxford University Press},
}
@article{Hoops-Sahle-Gauges-Lee-Pahle-Simus-Singhal-Xu-Mendes-Kummer/06,
AUTHOR = {Hoops, Stefan and Sahle, Sven and Gauges, Ralph and Lee, Christine and Pahle, J{\"{u}}rgen and Simus, Natalia and Singhal, Mudita and Xu, Liang and Mendes, Pedro and Kummer, Ursula},
TITLE = {COPASI --- A COmplex PAthway SImulator},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {24},
PAGES = {3067-3074},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl485},
PUBLISHER = {Oxford University Press},
}
@article{Eccher-Priami/06,
AUTHOR = {Eccher, Claudio and Priami, Corrado},
TITLE = {Design and implementation of a tool for translating SBML into the biochemical stochastic $\pi$-calculus},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {24},
PAGES = {3075-3081},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl516},
PUBLISHER = {Oxford University Press},
}
@article{Hoffmann-Lange/06,
AUTHOR = {Hoffmann, Thomas and Lange, Christoph},
TITLE = {P$^2$BAT: A massive parallel implementation of PBAT for genome-wide association studies in R},
JOURNAL = {Bioinformatics},
VOLUME = {22},
NUMBER = {24},
PAGES = {3103-3105},
YEAR = {2006},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl507},
PUBLISHER = {Oxford University Press},
}