@article{Coelho-Peng-Murphy/10,
AUTHOR = {Coelho, Luis Pedro and Peng, Tao and Murphy, Robert F.},
TITLE = {Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing},
BOOKTITLE = {Proceedings of the 18th International Conference on Intelligent Systems for Molecular Biology, ISMB'2010 (Boston, MA, USA, July 11-13, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {7-12},
YEAR = {2010},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq220},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jaensch-Decker-Hyman-Myers/10,
AUTHOR = {Jaensch, Steffen and Decker, Markus and Hyman, Anthony A. and Myers, Eugene W.},
TITLE = {Automated tracking and analysis of centrosomes in early Caenorhabditis elegans embryos},
BOOKTITLE = {Proceedings of the 18th International Conference on Intelligent Systems for Molecular Biology, ISMB'2010 (Boston, MA, USA, July 11-13, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {13-20},
YEAR = {2010},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq190},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kockara-Mete-Yip-Lee-Aydin/10,
AUTHOR = {Kockara, Sinan and Mete, Mutlu and Yip, Vincent and Lee, Brendan and Aydin, Kemal},
TITLE = {A soft kinetic data structure for lesion border detection},
BOOKTITLE = {Proceedings of the 18th International Conference on Intelligent Systems for Molecular Biology, ISMB'2010 (Boston, MA, USA, July 11-13, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {21-28},
YEAR = {2010},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq178},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Clement-Snell-Clement-Hollenhorst-Purwar-Graves-Cairns-Johnson/10,
AUTHOR = {Clement, Nathan L. and Snell, Quinn and Clement, Mark J. and Hollenhorst, Peter C. and Purwar, Jahnvi and Graves, Barbara J. and Cairns, Bradley R. and Johnson, W. Evan},
TITLE = {The GNUMAP algorithm: Unbiased probabilistic mapping of oligonucleotides from next-generation sequencing},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {1},
PAGES = {38-45},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp614},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bouvier-Evrard-Todeschi-Girault-Bertho/10,
AUTHOR = {Bouvier, Guillaume and Evrard-Todeschi, Nathalie and Girault, Jean-Pierre and Bertho, Gildas},
TITLE = {Automatic clustering of docking poses in virtual screening process using self-organizing map},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {1},
PAGES = {53-60},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp623},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Forties-Bundschuh/10,
AUTHOR = {Forties, Robert A. and Bundschuh, Ralf},
TITLE = {Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {1},
PAGES = {61-67},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp627},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Holford-Khurana-Cheung-Gerstein/10,
AUTHOR = {Holford, Matthew E. and Khurana, Ekta and Cheung, Kei-Hoi and Gerstein, Mark},
TITLE = {Using semantic web rules to reason on an ontology of pseudogenes},
BOOKTITLE = {Proceedings of the 18th International Conference on Intelligent Systems for Molecular Biology, ISMB'2010 (Boston, MA, USA, July 11-13, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {71-78},
YEAR = {2010},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq173},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kirchner-Renard-Kothe-Pappin-Hamprecht-Steen-Steen/10,
AUTHOR = {Kirchner, Marc and Renard, Bernhard Y. and K{\"{o}}the, Ullrich and Pappin, Darryl J. and Hamprecht, Fred A. and Steen, Hanno and Steen, Judith A.J.},
TITLE = {Computational protein profile similarity screening for quantitative mass spectrometry experiments},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {1},
PAGES = {77-83},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp607},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Carrillo-Yanofsky-Laboissiere-Nadon-Kearney/10,
AUTHOR = {Carrillo, Brian and Yanofsky, Corey and Laboissiere, Sylvie and Nadon, Robert and Kearney, Robert E.},
TITLE = {Methods for combining peptide intensities to estimate relative protein abundance},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {1},
PAGES = {98-103},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp610},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Emde-Grunert-Weese-Reinert-Sperling/10,
AUTHOR = {Emde, Anne-Katrin and Grunert, Marcel and Weese, David and Reinert, Knut and Sperling, Silke R.},
TITLE = {MicroRazerS: Rapid alignment of small RNA reads},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {1},
PAGES = {123-124},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp601},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Arner-Hayashizaki-Daub/10,
AUTHOR = {Arner, Erik and Hayashizaki, Yoshihide and Daub, Carsten O.},
TITLE = {NGSView: An extensible open source editor for next-generation sequencing data},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {1},
PAGES = {125-126},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp611},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Diallo-Makarenkov-Blanchette/10,
AUTHOR = {Diallo, Abdoulaye Banire and Makarenkov, Vladimir and Blanchette, Mathieu},
TITLE = {Ancestors 1.0: A web server for ancestral sequence reconstruction},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {1},
PAGES = {130-131},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp600},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hipp-Escudero/10,
AUTHOR = {Hipp, Andrew L. and Escudero, Marcial},
TITLE = {MATICCE: Mapping transitions in continuous character evolution},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {1},
PAGES = {132-133},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp625},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Buckner-Wilson-Seligman-Athey-Watson-Meng/10,
AUTHOR = {Buckner, Joshua and Wilson, Justin and Seligman, Mark and Athey, Brian and Watson, Stanley and Meng, Fan},
TITLE = {The gputools package enables GPU computing in R},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {1},
PAGES = {134-135},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp608},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gaire-Bailey-Bearfoot-Campbell-Stuckey-Haviv/10,
AUTHOR = {Gaire, Raj K. and Bailey, James and Bearfoot, Jennifer and Campbell, Ian G. and Stuckey, Peter J. and Haviv, Izhak},
TITLE = {MIRAGAA --- A methodology for finding coordinated effects of microRNA expression changes and genome aberrations in cancer},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {2},
PAGES = {161-167},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp654},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bercovici-Meek-Wexler-Geiger/10,
AUTHOR = {Bercovici, Sivan and Meek, Christopher and Wexler, Ydo and Geiger, Dan},
TITLE = {Estimating genome-wide IBD sharing from SNP data via an efficient hidden Markov model of LD with application to gene mapping},
BOOKTITLE = {Proceedings of the 18th International Conference on Intelligent Systems for Molecular Biology, ISMB'2010 (Boston, MA, USA, July 11-13, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {175-182},
YEAR = {2010},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq204},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Huang-Qin-Reidys-Stadler/10,
AUTHOR = {Huang, Fenix W.D. and Qin, Jing and Reidys, Christian M. and Stadler, Peter F.},
TITLE = {Target prediction and a statistical sampling algorithm for RNA-RNA interaction},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {2},
PAGES = {175-181},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp635},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{He-Choi-Pipatsrisawat-Darwiche-Eskin/10,
AUTHOR = {He, Dan and Choi, Arthur and Pipatsrisawat, Knot and Darwiche, Adnan and Eskin, Eleazar},
TITLE = {Optimal algorithms for haplotype assembly from whole-genome sequence data},
BOOKTITLE = {Proceedings of the 18th International Conference on Intelligent Systems for Molecular Biology, ISMB'2010 (Boston, MA, USA, July 11-13, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {183-190},
YEAR = {2010},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq215},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Huang-Zhou-Lafleur-Nevado-Caflisch/10,
AUTHOR = {Huang, Danzhi and Zhou, Ting and Lafleur, Karine and Nevado, Cristina and Caflisch, Amedeo},
TITLE = {Kinase selectivity potential for inhibitors targeting the ATP binding site: A network analysis},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {2},
PAGES = {198-204},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp650},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Ai-Jun-Xin-Yuan/10,
AUTHOR = {Ai-Jun, Yang and Xin-Yuan, Song},
TITLE = {Bayesian variable selection for disease classification using gene expression data},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {2},
PAGES = {215-222},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp638},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jaimovich-Rinott-Schuldiner-Margalit-Friedman/10,
AUTHOR = {Jaimovich, Ariel and Rinott, Ruty and Schuldiner, Maya and Margalit, Hanah and Friedman, Nir},
TITLE = {Modularity and directionality in genetic interaction maps},
BOOKTITLE = {Proceedings of the 18th International Conference on Intelligent Systems for Molecular Biology, ISMB'2010 (Boston, MA, USA, July 11-13, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {228-236},
YEAR = {2010},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq197},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Carvalho-Louis-Irizarry/10,
AUTHOR = {Carvalho, Benilton S. and Louis, Thomas A. and Irizarry, Rafael A.},
TITLE = {Quantifying uncertainty in genotype calls},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {2},
PAGES = {242-249},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp624},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gamazon-Zhang-Konkashbaev-Duan-Kistner-Nicolae-Dolan-Cox/10,
AUTHOR = {Gamazon, Eric R. and Zhang, Wei and Konkashbaev, Anuar and Duan, Shiwei and Kistner, Emily O. and Nicolae, Dan L. and Dolan, M. Eileen and Cox, Nancy J.},
TITLE = {SCAN: SNP and copy number annotation},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {2},
PAGES = {259-262},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp644},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Caporaso-Bittinger-Bushman-DeSantis-Andersen-Knight/10,
AUTHOR = {Caporaso, J. Gregory and Bittinger, Kyle and Bushman, Frederic D. and DeSantis, Todd Z. and Andersen, Gary L. and Knight, Rob},
TITLE = {PyNAST: A flexible tool for aligning sequences to a template alignment},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {2},
PAGES = {266-267},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp636},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chiang-Hsu-Latombe/10,
AUTHOR = {Chiang, Tsung-Han and Hsu, David and Latombe, Jean-Claude},
TITLE = {Markov dynamic models for long-timescale protein motion},
BOOKTITLE = {Proceedings of the 18th International Conference on Intelligent Systems for Molecular Biology, ISMB'2010 (Boston, MA, USA, July 11-13, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {269-277},
YEAR = {2010},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq177},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Duran-Boskovic-Imelfort-Batley-Hamilton-Edwards/10,
AUTHOR = {Duran, Chris and Boskovic, Zoran and Imelfort, Michael and Batley, Jacqueline and Hamilton, Nicholas A. and Edwards, David},
TITLE = {CMap3D: A 3D visualization tool for comparative genetic maps},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {2},
PAGES = {273-274},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp646},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Beagley-Stratton-Webb-Robertson/10,
AUTHOR = {Beagley, Nathaniel and Stratton, Kelly G. and Webb-Robertson, Bobbie-Jo M.},
TITLE = {VIBE 2.0: Visual Integration for Bayesian Evaluation},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {2},
PAGES = {280-282},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp639},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Ikin-Riveros-Moscato-Mendes/10,
AUTHOR = {Ikin, Aaron and Riveros, Carlos and Moscato, Pablo and Mendes, Alexandre},
TITLE = {The Gene Interaction Miner: A new tool for data mining contextual information for protein-protein interaction analysis},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {2},
PAGES = {283-284},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp652},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hooper-Dalevi-Pati-Mavromatis-Ivanova-Kyrpides/10,
AUTHOR = {Hooper, Sean D. and Dalevi, Daniel and Pati, Amrita and Mavromatis, Konstantinos and Ivanova, Natalia N. and Kyrpides, Nikos C.},
TITLE = {Estimating DNA coverage and abundance in metagenomes using a gamma approximation},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {3},
PAGES = {295-301},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp687},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bansal/10,
AUTHOR = {Bansal, Vikas},
TITLE = {A statistical method for the detection of variants from next-generation resequencing of DNA pools},
BOOKTITLE = {Proceedings of the 18th International Conference on Intelligent Systems for Molecular Biology, ISMB'2010 (Boston, MA, USA, July 11-13, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {318-324},
YEAR = {2010},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq214},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Barash-Blencowe-Frey/10,
AUTHOR = {Barash, Yoseph and Blencowe, Benjamin J. and Frey, Brendan J.},
TITLE = {Model-based detection of alternative splicing signals},
BOOKTITLE = {Proceedings of the 18th International Conference on Intelligent Systems for Molecular Biology, ISMB'2010 (Boston, MA, USA, July 11-13, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {325-333},
YEAR = {2010},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq200},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Garbuzynskiy-Lobanov-Galzitskaya/10,
AUTHOR = {Garbuzynskiy, Sergiy O. and Lobanov, Michail Yu. and Galzitskaya, Oxana V.},
TITLE = {FoldAmyloid: A method of prediction of amyloidogenic regions from protein sequence},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {3},
PAGES = {326-332},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp691},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chen-Hoffman-Bilmes-Hesselberth-Noble/10,
AUTHOR = {Chen, Xiaoyu and Hoffman, Michael M. and Bilmes, Jeff A. and Hesselberth, Jay R. and Noble, William S.},
TITLE = {A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data},
BOOKTITLE = {Proceedings of the 18th International Conference on Intelligent Systems for Molecular Biology, ISMB'2010 (Boston, MA, USA, July 11-13, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {334-342},
YEAR = {2010},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq175},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Dalca-Rumble-Levy-Brudno/10,
AUTHOR = {Dalca, Adrian V. and Rumble, Stephen M. and Levy, Samuel and Brudno, Michael},
TITLE = {VARiD: A variation detection framework for color-space and letter-space platforms},
BOOKTITLE = {Proceedings of the 18th International Conference on Intelligent Systems for Molecular Biology, ISMB'2010 (Boston, MA, USA, July 11-13, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {343-349},
YEAR = {2010},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq184},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hu-Qiu-Glazko/10,
AUTHOR = {Hu, Rui and Qiu, Xing and Glazko, Galina},
TITLE = {A new gene selection procedure based on the covariance distance},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {3},
PAGES = {348-354},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp672},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hormozdiari-Hajirasouliha-Dao-Hach-Yorukoglu-Alkan-Eichler-Sahinalp/10,
AUTHOR = {Hormozdiari, Fereydoun and Hajirasouliha, Iman and Dao, Phuong and Hach, Faraz and Yorukoglu, Deniz and Alkan, Can and Eichler, Evan E. and Sahinalp, S. Cenk},
TITLE = {Next-generation VariationHunter: Combinatorial algorithms for transposon insertion discovery},
BOOKTITLE = {Proceedings of the 18th International Conference on Intelligent Systems for Molecular Biology, ISMB'2010 (Boston, MA, USA, July 11-13, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {350-357},
YEAR = {2010},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq216},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kiddle-Windram-McHattie-Mead-Beynon-Buchanan-Wollaston-Denby-Mukherjee/10,
AUTHOR = {Kiddle, Steven J. and Windram, Oliver P.F. and McHattie, Stuart and Mead, Andrew and Beynon, Jim and Buchanan-Wollaston, Vicky and Denby, Katherine J. and Mukherjee, Sach},
TITLE = {Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {3},
PAGES = {355-362},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp673},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kemper-Matsuzaki-Matsuoka-Tsuruoka-Kitano-Ananiadou-Tsujii/10,
AUTHOR = {Kemper, Brian and Matsuzaki, Takuya and Matsuoka, Yukiko and Tsuruoka, Yoshimasa and Kitano, Hiroaki and Ananiadou, Sophia and Tsujii, Jun'ichi},
TITLE = {PathText: A text mining integrator for biological pathway visualizations},
BOOKTITLE = {Proceedings of the 18th International Conference on Intelligent Systems for Molecular Biology, ISMB'2010 (Boston, MA, USA, July 11-13, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {374-381},
YEAR = {2010},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq221},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chagoyen-Pazos/10,
AUTHOR = {Chagoyen, Monica and Pazos, Florencio},
TITLE = {Quantifying the biological significance of gene ontology biological processes --- Implications for the analysis of systems-wide data},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {3},
PAGES = {378-384},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp663},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bjorne-Ginter-Pyysalo-Tsujii-Salakoski/10,
AUTHOR = {Bj{\"{o}}rne, Jari and Ginter, Filip and Pyysalo, Sampo and Tsujii, Jun'ichi and Salakoski, Tapio},
TITLE = {Complex event extraction at PubMed scale},
BOOKTITLE = {Proceedings of the 18th International Conference on Intelligent Systems for Molecular Biology, ISMB'2010 (Boston, MA, USA, July 11-13, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {382-390},
YEAR = {2010},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq180},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jung-Hyun-Jang-Hur-Han/10,
AUTHOR = {Jung, Suk Hoon and Hyun, Bora and Jang, Woo-Hyuk and Hur, Hee-Young and Han, Dong-Soo},
TITLE = {Protein complex prediction based on simultaneous protein interaction network},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {3},
PAGES = {385-391},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp668},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Huopaniemi-Suvitaival-Nikkila-Oresic-Kaski/10,
AUTHOR = {Huopaniemi, Ilkka and Suvitaival, Tommi and Nikkil{\"{a}}, Janne and Ore{\v{s}}i{\v{c}}, Matej and Kaski, Samuel},
TITLE = {Multivariate multi-way analysis of multi-source data},
BOOKTITLE = {Proceedings of the 18th International Conference on Intelligent Systems for Molecular Biology, ISMB'2010 (Boston, MA, USA, July 11-13, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {391-398},
YEAR = {2010},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq174},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Abeel-Helleputte-Van_de_Peer-Dupont-Saeys/10,
AUTHOR = {Abeel, Thomas and Helleputte, Thibault and Van de Peer, Yves and Dupont, Pierre and Saeys, Yvan},
TITLE = {Robust biomarker identification for cancer diagnosis with ensemble feature selection methods},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {3},
PAGES = {392-398},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp630},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hanada-Akiyama-Sakurai-Toyoda-Shinozaki-Shiu/10,
AUTHOR = {Hanada, Kousuke and Akiyama, Kenji and Sakurai, Tetsuya and Toyoda, Tetsuro and Shinozaki, Kazuo and Shiu, Shin-Han},
TITLE = {sORF finder: A program package to identify small open reading frames with high coding potential},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {3},
PAGES = {399-400},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp688},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Balzer-Malde-Lanzen-Sharma-Jonassen/10,
AUTHOR = {Balzer, Susanne and Malde, Ketil and Lanz{\'{e}}n, Anders and Sharma, Animesh and Jonassen, Inge},
TITLE = {Characteristics of 454 pyrosequencing data --- Enabling realistic simulation with flowsim},
BOOKTITLE = {Proceedings of the 8th European Conference on Computational Biology, ECCB'2010 (Ghent, Belgium, September 26-29, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {420-425},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq365},
PUBLISHER = {Oxford University Press},
NOTE = {see Corrigendum in Bioinformatics, Vol. 27, 2011, No. 15, 2117-2117},
}
@article{Krause-Uhlendorf-Lubitz-Schulz-Klipp-Liebermeister/10,
AUTHOR = {Krause, Falko and Uhlendorf, Jannis and Lubitz, Timo and Schulz, Marvin and Klipp, Edda and Liebermeister, Wolfram},
TITLE = {Annotation and merging of SBML models with semanticSBML},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {3},
PAGES = {421-422},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp642},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Clement-Gustafson-Berbert-Carroll-Merris-Olsen-Clement-Snell-Allen-Roper/10,
AUTHOR = {Clement, Kendell and Gustafson, Nathaniel and Berbert, Amanda and Carroll, Hyrum and Merris, Christopher and Olsen, Ammon and Clement, Mark and Snell, Quinn and Allen, Jared and Roper, Randall J.},
TITLE = {PathGen: A transitive gene pathway generator},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {3},
PAGES = {423-425},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp661},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Caulfield-Hellander/10,
AUTHOR = {Caulfield, Emmet and Hellander, Andreas},
TITLE = {CellMC --- A multiplatform model compiler for the Cell Broadband Engine and x86},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {3},
PAGES = {426-428},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp662},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Erhard-Zimmer/10,
AUTHOR = {Erhard, Florian and Zimmer, Ralf},
TITLE = {Classification of ncRNAs using position and size information in deep sequencing data},
BOOKTITLE = {Proceedings of the 8th European Conference on Computational Biology, ECCB'2010 (Ghent, Belgium, September 26-29, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {426-432},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq363},
PUBLISHER = {Oxford University Press},
}
@article{Babur-Dogrusoz-Demir-Sander/10,
AUTHOR = {Babur, Ozgun and Dogrusoz, Ugur and Demir, Emek and Sander, Chris},
TITLE = {ChiBE: Interactive visualization and manipulation of BioPAX pathway models},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {3},
PAGES = {429-431},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp665},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hendriks-Espelin/10,
AUTHOR = {Hendriks, Bart S. and Espelin, Christopher W.},
TITLE = {DataPflex: A MATLAB-based tool for the manipulation and visualization of multidimensional datasets},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {3},
PAGES = {432-433},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp667},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Andorf-Lawrence-Harper-Schaeffer-Campbell-Sen/10,
AUTHOR = {Andorf, Carson M. and Lawrence, Carolyn J. and Harper, Lisa C. and Schaeffer, Mary L. and Campbell, Darwin A. and Sen, Taner Z.},
TITLE = {The Locus Lookup tool at MaizeGDB: Identification of genomic regions in maize by integrating sequence information with and genetic maps},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {3},
PAGES = {434-436},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp556},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Boulesteix/10,
AUTHOR = {Boulesteix, Anne-Laure},
TITLE = {Over-optimism in bioinformatics research},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {3},
PAGES = {437-439},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp648},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kahn-Hristov-Raphael/10,
AUTHOR = {Kahn, Crystal L. and Hristov, Borislav H. and Raphael, Benjamin J.},
TITLE = {Parsimony and likelihood reconstruction of human segmental duplications},
BOOKTITLE = {Proceedings of the 8th European Conference on Computational Biology, ECCB'2010 (Ghent, Belgium, September 26-29, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {446-452},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq368},
PUBLISHER = {Oxford University Press},
}
@article{Honer_zu_Siederdissen-Hofacker/10,
AUTHOR = {H{\"{o}}ner zu Siederdissen, Christian and Hofacker, Ivo L.},
TITLE = {Discriminatory power of RNA family models},
BOOKTITLE = {Proceedings of the 8th European Conference on Computational Biology, ECCB'2010 (Ghent, Belgium, September 26-29, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {453-459},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq370},
PUBLISHER = {Oxford University Press},
}
@article{Kato-Sato-Hamada-Watanabe-Asai-Akutsu/10,
AUTHOR = {Kato, Yuki and Sato, Kengo and Hamada, Michiaki and Watanabe, Yoshihide and Asai, Kiyoshi and Akutsu, Tatsuya},
TITLE = {RactIP: Fast and accurate prediction of RNA-RNA interaction using integer programming},
BOOKTITLE = {Proceedings of the 8th European Conference on Computational Biology, ECCB'2010 (Ghent, Belgium, September 26-29, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {460-466},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq372},
PUBLISHER = {Oxford University Press},
}
@article{Csaba-Zimmer/10,
AUTHOR = {Csaba, Gergely and Zimmer, Ralf},
TITLE = {Vorescore --- Fold recognition improved by rescoring of protein structure models},
BOOKTITLE = {Proceedings of the 8th European Conference on Computational Biology, ECCB'2010 (Ghent, Belgium, September 26-29, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {474-481},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq369},
PUBLISHER = {Oxford University Press},
}
@article{Kim-Cho-Kim/10,
AUTHOR = {Kim, Mingoo and Cho, Sung Bum and Kim, Ju Han},
TITLE = {Mixture-model based estimation of gene expression variance from public database improves identification of differentially expressed genes in small sized microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {4},
PAGES = {486-492},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp685},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Goncearenco-Berezovsky/10,
AUTHOR = {Goncearenco, Alexander and Berezovsky, Igor N.},
TITLE = {Prototypes of elementary functional loops unravel evolutionary connections between protein functions},
BOOKTITLE = {Proceedings of the 8th European Conference on Computational Biology, ECCB'2010 (Ghent, Belgium, September 26-29, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {497-503},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq374},
PUBLISHER = {Oxford University Press},
}
@article{Chen-Zhang/10,
AUTHOR = {Chen, Kuan-Bei and Zhang, Yu},
TITLE = {A varying threshold method for ChIP peak-calling using multiple sources of information},
BOOKTITLE = {Proceedings of the 8th European Conference on Computational Biology, ECCB'2010 (Ghent, Belgium, September 26-29, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {504-510},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq379},
PUBLISHER = {Oxford University Press},
}
@article{Dewal-Freedman-LaFramboise-Peer/10,
AUTHOR = {Dewal, Ninad and Freedman, Matthew L. and LaFramboise, Thomas and Pe'er, Itsik},
TITLE = {Power to detect selective allelic amplification in genome-wide scans of tumor data},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {4},
PAGES = {518-528},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp694},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Cannistraci-Ravasi-Montevecchi-Ideker-Alessio/10,
AUTHOR = {Cannistraci, Carlo Vittorio and Ravasi, Timothy and Montevecchi, Franco Maria and Ideker, Trey and Alessio, Massimo},
TITLE = {Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes},
BOOKTITLE = {Proceedings of the 8th European Conference on Computational Biology, ECCB'2010 (Ghent, Belgium, September 26-29, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {531-539},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq376},
PUBLISHER = {Oxford University Press},
}
@article{Kalas-Puntervoll-Joseph-Bartaseviciute-Topfer-Venkataraman-Pettifer-Bryne-Ison-Blanchet-Rapacki-Jonassen/10,
AUTHOR = {Kala{\v{s}}, Mat{\'u}{\v{s}} and Puntervoll, P{\aa}l and Joseph, Alexandre and Barta{\v{s}}evi{\v{c}}i{\=u}t{\.e}, Edita and T{\"{o}}pfer, Armin and Venkataraman, Prabakar and Pettifer, Steve and Bryne, Jan Christian and Ison, Jon and Blanchet, Christophe and Rapacki, Kristoffer and Jonassen, Inge},
TITLE = {BioXSD: The common data-exchange format for everyday bioinformatics web services},
BOOKTITLE = {Proceedings of the 8th European Conference on Computational Biology, ECCB'2010 (Ghent, Belgium, September 26-29, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {540-546},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq391},
PUBLISHER = {Oxford University Press},
}
@article{Fong-Ko-Wasnick-Radey-Miller-Brittnacher/10,
AUTHOR = {Fong, Christine and Ko, Dennis C. and Wasnick, Michael and Radey, Matthew and Miller, Samuel I. and Brittnacher, Mitchell},
TITLE = {GWAS Analyzer: Integrating genotype, phenotype and public annotation data for genome-wide association study analysis},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {4},
PAGES = {560-564},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp714},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Attwood-Kell-McDermott-Marsh-Pettifer-Thorne/10,
AUTHOR = {Attwood, T.K. and Kell, D.B. and McDermott, P. and Marsh, J. and Pettifer, S.R. and Thorne, D.},
TITLE = {Utopia documents: Linking scholarly literature with research data},
BOOKTITLE = {Proceedings of the 8th European Conference on Computational Biology, ECCB'2010 (Ghent, Belgium, September 26-29, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {568-574},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq383},
PUBLISHER = {Oxford University Press},
}
@article{Horton-Bodenhausen-Bergelson/10,
AUTHOR = {Horton, Matthew and Bodenhausen, Natacha and Bergelson, Joy},
TITLE = {MARTA: A suite of Java-based tools for assigning taxonomic status to DNA sequences},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {4},
PAGES = {568-569},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp682},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Husemann-Stoye/10,
AUTHOR = {Husemann, Peter and Stoye, Jens},
TITLE = {r2cat: Synteny plots and comparative assembly},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {4},
PAGES = {570-571},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp690},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Harris-Ponts-Levchuk-Le_Roch-Lonardi/10,
AUTHOR = {Harris, Elena Y. and Ponts, Nadia and Levchuk, Aleksandr and Le Roch, Karine and Lonardi, Stefano},
TITLE = {BRAT: Bisulfite-treated reads analysis tool},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {4},
PAGES = {572-573},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp706},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
NOTE = {see Corrigendum in Bioinformatics, Vol. 26, 2010, No. 19, 2499-2499},
}
@article{Frank-Gruber-Sippl/10,
AUTHOR = {Frank, Karl and Gruber, Markus and Sippl, Manfred J.},
TITLE = {COPS Benchmark: Interactive analysis of database search methods},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {4},
PAGES = {574-575},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp712},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gay-Soliman-Fages/10,
AUTHOR = {Gay, Steven and Soliman, Sylvain and Fages, Fran{\c{c}}ois},
TITLE = {A graphical method for reducing and relating models in systems biology},
BOOKTITLE = {Proceedings of the 8th European Conference on Computational Biology, ECCB'2010 (Ghent, Belgium, September 26-29, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {575-581},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq388},
PUBLISHER = {Oxford University Press},
}
@article{Bush-Dudek-Ritchie/10,
AUTHOR = {Bush, William S. and Dudek, Scott M. and Ritchie, Marylyn D.},
TITLE = {Visualizing SNP statistics in the context of linkage disequilibrium using LD-Plus},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {4},
PAGES = {578-579},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp678},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chen-Yang/10,
AUTHOR = {Chen, Ming-Huei and Yang, Qiong},
TITLE = {GWAF: An R package for genome-wide association analyses with family data},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {4},
PAGES = {580-581},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp710},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chuang-Wu-Cheng-Shieh/10,
AUTHOR = {Chuang, Cheng-Long and Wu, Jia-Hong and Cheng, Chi-Sheng and Shieh, Grace S.},
TITLE = {WebPARE: Web-computing for inferring genetic or transcriptional interactions},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {4},
PAGES = {582-584},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp684},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bender-Henjes-Frohlich-Wiemann-Korf-Beissbarth/10,
AUTHOR = {Bender, Christian and Henjes, Frauke and Fr{\"{o}}hlich, Holger and Wiemann, Stefan and Korf, Ulrike and Bei{\ss}barth, Tim},
TITLE = {Dynamic deterministic effects propagation networks: Learning signalling pathways from longitudinal protein array data},
BOOKTITLE = {Proceedings of the 8th European Conference on Computational Biology, ECCB'2010 (Ghent, Belgium, September 26-29, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {596-602},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq385},
PUBLISHER = {Oxford University Press},
}
@article{Batt-Page-Cantone-Goessler-Monteiro-de_Jong/10,
AUTHOR = {Batt, Gregory and Page, Michel and Cantone, Irene and Goessler, Gregor and Monteiro, Pedro and de Jong, Hidde},
TITLE = {Efficient parameter search for qualitative models of regulatory networks using symbolic model checking},
BOOKTITLE = {Proceedings of the 8th European Conference on Computational Biology, ECCB'2010 (Ghent, Belgium, September 26-29, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {603-610},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq387},
PUBLISHER = {Oxford University Press},
}
@article{Demir-Kavuk-Riedesel-Knapp/10,
AUTHOR = {Demir-Kavuk, Ozgur and Riedesel, Henning and Knapp, Ernst-Walter},
TITLE = {Exploring classification strategies with the CoEPrA 2006 contest},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {5},
PAGES = {603-609},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq021},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Dao-Colak-Salari-Moser-Davicioni-Schonhuth-Ester/10,
AUTHOR = {Dao, Phuong and Colak, Recep and Salari, Raheleh and Moser, Flavia and Davicioni, Elai and Sch{\"{o}}nhuth, Alexander and Ester, Martin},
TITLE = {Inferring cancer subnetwork markers using density-constrained biclustering},
BOOKTITLE = {Proceedings of the 8th European Conference on Computational Biology, ECCB'2010 (Ghent, Belgium, September 26-29, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {625-631},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq393},
PUBLISHER = {Oxford University Press},
}
@article{Janssen-Giegerich/10,
AUTHOR = {Janssen, Stefan and Giegerich, Robert},
TITLE = {Faster computation of exact RNA shape probabilities},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {5},
PAGES = {632-639},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq014},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bonnet-Michoel-Van_de_Peer/10,
AUTHOR = {Bonnet, Eric and Michoel, Tom and Van de Peer, Yves},
TITLE = {Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data},
BOOKTITLE = {Proceedings of the 8th European Conference on Computational Biology, ECCB'2010 (Ghent, Belgium, September 26-29, 2010)},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {638-644},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq395},
PUBLISHER = {Oxford University Press},
}
@article{Itzhack-Louzoun/10,
AUTHOR = {Itzhack, Royi and Louzoun, Yoram},
TITLE = {Random distance dependent attachment as a model for neural network generation in the Caenorhabditis elegans},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {5},
PAGES = {647-652},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq015},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Binsl-Alders-Heringa-Groeneveld-van_Beek/10,
AUTHOR = {Binsl, Thomas W. and Alders, David J.C. and Heringa, Jaap and Groeneveld, A.B. Johan and van Beek, Johannes H.G.M.},
TITLE = {Computational quantification of metabolic fluxes from a single isotope snapshot: Application to an animal biopsy},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {5},
PAGES = {653-660},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq018},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gopalakrishnan-Lustgarten-Visweswaran-Cooper/10,
AUTHOR = {Gopalakrishnan, Vanathi and Lustgarten, Jonathan L. and Visweswaran, Shyam and Cooper, Gregory F.},
TITLE = {Bayesian rule learning for biomedical data mining},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {5},
PAGES = {668-675},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq005},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Carver-Bohme-Otto-Parkhill-Berriman/10,
AUTHOR = {Carver, Tim and B{\"{o}}hme, Ulrike and Otto, Thomas D. and Parkhill, Julian and Berriman, Matthew},
TITLE = {BamView: Viewing mapped read alignment data in the context of the reference sequence},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {5},
PAGES = {676-677},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq010},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Droit-Cheung-Gottardo/10,
AUTHOR = {Droit, Arnaud and Cheung, Charles and Gottardo, Raphael},
TITLE = {rMAT --- An R/Bioconductor package for analyzing ChIP-chip experiments},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {5},
PAGES = {678-679},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq023},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Huang-Niu-Gao-Fu-Li/10,
AUTHOR = {Huang, Ying and Niu, Beifang and Gao, Ying and Fu, Limin and Li, Weizhong},
TITLE = {CD-HIT Suite: A web server for clustering and comparing biological sequences},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {5},
PAGES = {680-682},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq003},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Galvez-Diaz-Hernandez-Esteban-Caballero-Dorado/10,
AUTHOR = {G{\'{a}}lvez, Sergio and D{\'{i}}az, David and Hern{\'{a}}ndez, Pilar and Esteban, Francisco J. and Caballero, Juan A. and Dorado, Gabriel},
TITLE = {Next-generation bioinformatics: Using many-core processor architecture to develop a web service for sequence alignment},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {5},
PAGES = {683-686},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq017},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chaudhury-Lyskov-Gray/10,
AUTHOR = {Chaudhury, Sidhartha and Lyskov, Sergey and Gray, Jeffrey J.},
TITLE = {PyRosetta: A script-based interface for implementing molecular modeling algorithms using Rosetta},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {5},
PAGES = {689-691},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq007},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Greene-Sinnott-Armstrong-Himmelstein-Park-Moore-Harris/10,
AUTHOR = {Greene, Casey S. and Sinnott-Armstrong, Nicholas A. and Himmelstein, Daniel S. and Park, Paul J. and Moore, Jason H. and Harris, Brent T.},
TITLE = {Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {5},
PAGES = {694-695},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq009},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Iannuccelli-Mompart-Gellin-Lahbib-Mansais-Yerle-Boudier/10,
AUTHOR = {Iannuccelli, E. and Mompart, F. and Gellin, J. and Lahbib-Mansais, Y. and Yerle, M. and Boudier, T.},
TITLE = {NEMO: A tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {5},
PAGES = {696-697},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq013},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Cammer-Carter/10,
AUTHOR = {Cammer, Stephen and Carter, Charles W., Jr.},
TITLE = {Six Rossmannoid folds, including the Class I aminoacyl-tRNA synthetases, share a partial core with the anti-codon-binding domain of a Class II aminoacyl-tRNA synthetase},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {6},
PAGES = {709-714},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq039},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Krawitz-Rodelsperger-Jager-Jostins-Bauer-Robinson/10,
AUTHOR = {Krawitz, Peter and R{\"{o}}delsperger, Christian and J{\"{a}}ger, Marten and Jostins, Luke and Bauer, Sebastian and Robinson, Peter N.},
TITLE = {Microindel detection in short-read sequence data},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {6},
PAGES = {722-729},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq027},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Goya-Sun-Morin-Leung-Ha-Wiegand-Senz-Crisan-Marra-Hirst-Huntsman-Murphy-Aparicio-Shah/10,
AUTHOR = {Goya, Rodrigo and Sun, Mark G.F. and Morin, Ryan D. and Leung, Gillian and Ha, Gavin and Wiegand, Kimberley C. and Senz, Janine and Crisan, Anamaria and Marra, Marco A. and Hirst, Martin and Huntsman, David and Murphy, Kevin P. and Aparicio, Sam and Shah, Sohrab P.},
TITLE = {SNVMix: Predicting single nucleotide variants from next-generation sequencing of tumors},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {6},
PAGES = {730-736},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq040},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Dunkler-Schemper-Heinze/10,
AUTHOR = {Dunkler, Daniela and Schemper, Michael and Heinze, Georg},
TITLE = {Gene selection in microarray survival studies under possibly non-proportional hazards},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {6},
PAGES = {784-790},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq035},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kirchner-Timm-Fong-Wangemann-Steen/10,
AUTHOR = {Kirchner, Marc and Timm, Wiebke and Fong, Peying and Wangemann, Philine and Steen, Hanno},
TITLE = {Non-linear classification for on-the-fly fractional mass filtering and targeted precursor fragmentation in mass spectrometry experiments},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {6},
PAGES = {791-797},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq036},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hanczar-Hua-Sima-Weinstein-Bittner-Dougherty/10,
AUTHOR = {Hanczar, Blaise and Hua, Jianping and Sima, Chao and Weinstein, John and Bittner, Michael and Dougherty, Edward R.},
TITLE = {Small-sample precision of ROC-related estimates},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {6},
PAGES = {822-830},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq037},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gabdank-Barash-Trifonov/10,
AUTHOR = {Gabdank, Idan and Barash, Danny and Trifonov, Edward N.},
TITLE = {FineStr: A web server for single-base-resolution nucleosome positioning},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {6},
PAGES = {845-846},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq030},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Carvalho-Han-Xu-Cociorva-Carvalho-Barbosa-Yates/10,
AUTHOR = {Carvalho, Paulo C. and Han, Xuemei and Xu, Tao and Cociorva, Daniel and Carvalho, Maria da Gloria and Barbosa, Valmir C. and Yates III, John R.},
TITLE = {XDIA: Improving on the label-free data-independent analysis},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {6},
PAGES = {847-848},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq031},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chen/10,
AUTHOR = {Chen, Liang},
TITLE = {A link between H3K27me3 mark and exon length in the gene promoters of pluripotent and differentiated cells},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {7},
PAGES = {855-859},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq047},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Buske-Boden-Bauer-Bailey/10,
AUTHOR = {Buske, Fabian A. and Bod{\'{e}}n, Mikael and Bauer, Denis C. and Bailey, Timothy L.},
TITLE = {Assigning roles to DNA regulatory motifs using comparative genomics},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {7},
PAGES = {860-866},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq049},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Cooling-Rouilly-Misirli-Lawson-Yu-Hallinan-Wipat/10,
AUTHOR = {Cooling, M.T. and Rouilly, V. and Misirli, G. and Lawson, J. and Yu, T. and Hallinan, J. and Wipat, A.},
TITLE = {Standard virtual biological parts: A repository of modular modeling components for synthetic biology},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {7},
PAGES = {925-931},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq063},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Dada-Spasic-Paton-Mendes/10,
AUTHOR = {Dada, Joseph O. and Spasi{\'c}, Irena and Paton, Norman W. and Mendes, Pedro},
TITLE = {SBRML: A markup language for associating systems biology data with models},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {7},
PAGES = {932-938},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq069},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Cao-Jiang-Girke/10,
AUTHOR = {Cao, Yiqun and Jiang, Tao and Girke, Thomas},
TITLE = {Accelerated similarity searching and clustering of large compound sets by geometric embedding and locality sensitive hashing},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {7},
PAGES = {953-959},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq067},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gao-Tarcea-Karnovsky-Mirel-Weymouth-Beecher-Cavalcoli-Athey-Omenn-Burant-Jagadish/10,
AUTHOR = {Gao, Jing and Tarcea, V. Glenn and Karnovsky, Alla and Mirel, Barbara R. and Weymouth, Terry E. and Beecher, Christopher W. and Cavalcoli, James D. and Athey, Brian D. and Omenn, Gilbert S. and Burant, Charles F. and Jagadish, H.V.},
TITLE = {Metscape: A Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {7},
PAGES = {971-973},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq048},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Garcia-Serna-Ursu-Oprea-Mestres/10,
AUTHOR = {Garcia-Serna, Ricard and Ursu, Oleg and Oprea, Tudor I. and Mestres, Jordi},
TITLE = {iPHACE: Integrative navigation in pharmacological space},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {7},
PAGES = {985-986},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq061},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hollunder-Friedel-Kuiper-Wilhelm/10,
AUTHOR = {Hollunder, Jens and Friedel, Maik and Kuiper, Martin and Wilhelm, Thomas},
TITLE = {DASS-GUI: A user interface for identification and analysis of significant patterns in non-sequential data},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {7},
PAGES = {987-989},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq071},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Golan-Levy-Friedman-Shomron/10,
AUTHOR = {Golan, David and Levy, Carmit and Friedman, Brad and Shomron, Noam},
TITLE = {Biased hosting of intronic microRNA genes},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {8},
PAGES = {992-995},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq077},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Johannes-Wardenaar-Colome-Tatche-Mousson-de_Graaf-Mokry-Guryev-Timmers-Cuppen-Jansen/10,
AUTHOR = {Johannes, Frank and Wardenaar, Ren{\'{e}} and Colom{\'{e}}-Tatch{\'{e}}, Maria and Mousson, Florence and de Graaf, Petra and Mokry, Michal and Guryev, Victor and Timmers, H.Th. Marc and Cuppen, Edwin and Jansen, Ritsert C.},
TITLE = {Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {8},
PAGES = {1000-1006},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq087},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Corel-Pitschi-Morgenstern/10,
AUTHOR = {Corel, Eduardo and Pitschi, Florian and Morgenstern, Burkhard},
TITLE = {A min-cut algorithm for the consistency problem in multiple sequence alignment},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {8},
PAGES = {1015-1021},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq082},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chou-Chou-Pai-Lin-Jiang-Tang-Chang/10,
AUTHOR = {Chou, Wei-Yao and Chou, Wei-I and Pai, Tun-Wen and Lin, Shu-Chuan and Jiang, Ting-Ying and Tang, Chuan-Yi and Chang, Margaret Dah-Tsyr},
TITLE = {Feature-incorporated alignment based ligand-binding residue prediction for carbohydrate-binding modules},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {8},
PAGES = {1022-1028},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq084},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hugo-Song-Aung-Ng-Sung/10,
AUTHOR = {Hugo, Willy and Song, Fushan and Aung, Zeyar and Ng, See-Kiong and Sung, Wing-Kin},
TITLE = {SLiM on Diet: Finding short linear motifs on domain interaction interfaces in Protein Data Bank},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {8},
PAGES = {1036-1042},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq065},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Clarke-Seo-Clarke/10,
AUTHOR = {Clarke, Jennifer and Seo, Pearl and Clarke, Bertrand},
TITLE = {Statistical expression deconvolution from mixed tissue samples},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {8},
PAGES = {1043-1049},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq097},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gholami-Fellenberg/10,
AUTHOR = {Gholami, Amin Moghaddas and Fellenberg, Kurt},
TITLE = {Cross-species common regulatory network inference without requirement for prior gene affiliation},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {8},
PAGES = {1082-1090},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq096},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Dahlmeier-Ng/10,
AUTHOR = {Dahlmeier, Daniel and Ng, Hwee Tou},
TITLE = {Domain adaptation for semantic role labeling in the biomedical domain},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {8},
PAGES = {1098-1104},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq075},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jiang-Singh/10,
AUTHOR = {Jiang, Peng and Singh, Mona},
TITLE = {SPICi: A fast clustering algorithm for large biological networks},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {8},
PAGES = {1105-1111},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq078},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hemmerich-Buechlein-Podicheti-Revanna-Dong/10,
AUTHOR = {Hemmerich, Chris and Buechlein, Aaron and Podicheti, Ram and Revanna, Kashi V. and Dong, Qunfeng},
TITLE = {An Ergatis-based prokaryotic genome annotation web server},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {8},
PAGES = {1122-1124},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq090},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chevenet-Croce-Hebrard-Christen-Berry/10,
AUTHOR = {Chevenet, Fran{\c{c}}ois and Croce, Olivier and Hebrard, Maxime and Christen, Richard and Berry, Vincent},
TITLE = {ScripTree: Scripting phylogenetic graphics},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {8},
PAGES = {1125-1126},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq086},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Beisser-Klau-Dandekar-Muller-Dittrich/10,
AUTHOR = {Beisser, Daniela and Klau, Gunnar W. and Dandekar, Thomas and M{\"{u}}ller, Tobias and Dittrich, Marcus T.},
TITLE = {BioNet: An R-package for the functional analysis of biological networks},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {8},
PAGES = {1129-1130},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq089},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Fernandes-Gloor/10,
AUTHOR = {Fernandes, Andrew D. and Gloor, Gregory B.},
TITLE = {Mutual information is critically dependent on prior assumptions: Would the correct estimate of mutual information please identify itself?},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {9},
PAGES = {1135-1139},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq111},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
NOTE = {see Corrigendum in Bioinformatics, Vol. 26, 2010, No. 19, 2500-2500},
}
@article{Callebaut-Mornon/10,
AUTHOR = {Callebaut, Isabelle and Mornon, Jean-Paul},
TITLE = {LOTUS, a new domain associated with small RNA pathways in the germline},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {9},
PAGES = {1140-1144},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq122},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Grabherr-Russell-Meyer-Mauceli-Alfoldi-Di_Palma-Lindblad-Toh/10,
AUTHOR = {Grabherr, Manfred G. and Russell, Pamela and Meyer, Miriah and Mauceli, Evan and Alf{\"{o}}ldi, Jessica and Di Palma, Federica and Lindblad-Toh, Kerstin},
TITLE = {Genome-wide synteny through highly sensitive sequence alignment: Satsuma},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {9},
PAGES = {1145-1151},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq102},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Konc-Janezic/10,
AUTHOR = {Konc, Janez and Jane{\v{z}}i{\v{c}}, Dusanka},
TITLE = {ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {9},
PAGES = {1160-1168},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq100},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Ballester-Mitchell/10,
AUTHOR = {Ballester, Pedro J. and Mitchell, John B.O.},
TITLE = {A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {9},
PAGES = {1169-1175},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq112},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Cao-Meugnier-McLachlan/10,
AUTHOR = {Cao, Kim-Anh L{\^{e}} and Meugnier, Emmanuelle and McLachlan, Geoffrey J.},
TITLE = {Integrative mixture of experts to combine clinical factors and gene markers},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {9},
PAGES = {1192-1198},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq107},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Denny-Ritchie-Basford-Pulley-Bastarache-Brown-Gentry-Wang-Masys-Roden-Crawford/10,
AUTHOR = {Denny, Joshua C. and Ritchie, Marylyn D. and Basford, Melissa A. and Pulley, Jill M. and Bastarache, Lisa and Brown-Gentry, Kristin and Wang, Deede and Masys, Dan R. and Roden, Dan M. and Crawford, Dana C.},
TITLE = {PheWAS: Demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {9},
PAGES = {1205-1210},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq126},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Faust-Dupont-Callut-van_Helden/10,
AUTHOR = {Faust, Karoline and Dupont, Pierre and Callut, J{\'{e}}r{\^{o}}me and van Helden, Jacques},
TITLE = {Pathway discovery in metabolic networks by subgraph extraction},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {9},
PAGES = {1211-1218},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq105},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Briesemeister-Rahnenfuhrer-Kohlbacher/10,
AUTHOR = {Briesemeister, Sebastian and Rahnenf{\"{u}}hrer, J{\"{o}}rg and Kohlbacher, Oliver},
TITLE = {Going from where to why --- Interpretable prediction of protein subcellular localization},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {9},
PAGES = {1232-1238},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq115},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bayjanov-Siezen-van_Hijum/10,
AUTHOR = {Bayjanov, Jumamurat R. and Siezen, Roland J. and van Hijum, Sacha A.F.T.},
TITLE = {PanCGHweb: A web tool for genotype calling in pangenome CGH data},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {9},
PAGES = {1256-1257},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq103},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Boyer-Besson-Baptist-Izard-Pinel-Ropers-Geiselmann-de_Jong/10,
AUTHOR = {Boyer, Fr{\'{e}}d{\'{e}}ric and Besson, Bruno and Baptist, Guillaume and Izard, J{\'{e}}r{\^{o}}me and Pinel, Corinne and Ropers, Delphine and Geiselmann, Johannes and de Jong, Hidde},
TITLE = {WellReader: A MATLAB program for the analysis of fluorescence and luminescence reporter gene data},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {9},
PAGES = {1262-1263},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq016},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Friedel-Kaufmann-Dolken-Zimmer/10,
AUTHOR = {Friedel, Caroline C. and Kaufmann, Stefanie and D{\"{o}}lken, Lars and Zimmer, Ralf},
TITLE = {HALO --- A Java framework for precise transcript half-life determination},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {9},
PAGES = {1264-1266},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq117},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Glaab-Baudot-Krasnogor-Valencia/10,
AUTHOR = {Glaab, Enrico and Baudot, Ana{\"{i}}s and Krasnogor, Natalio and Valencia, Alfonso},
TITLE = {TopoGSA: Network topological gene set analysis},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {9},
PAGES = {1271-1272},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq131},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hajirasouliha-Hormozdiari-Alkan-Kidd-Birol-Eichler-Sahinalp/10,
AUTHOR = {Hajirasouliha, Iman and Hormozdiari, Fereydoun and Alkan, Can and Kidd, Jeffrey M. and Birol, Inanc and Eichler, Evan E. and Sahinalp, S. Cenk},
TITLE = {Detection and characterization of novel sequence insertions using paired-end next-generation sequencing},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {10},
PAGES = {1277-1283},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq152},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kalman-Ben-Tal/10,
AUTHOR = {Kalman, Matan and Ben-Tal, Nir},
TITLE = {Quality assessment of protein model-structures using evolutionary conservation},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {10},
PAGES = {1299-1307},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq114},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Adiamah-Handl-Schwartz/10,
AUTHOR = {Adiamah, Delali A. and Handl, Julia and Schwartz, Jean-Marc},
TITLE = {Streamlining the construction of large-scale dynamic models using generic kinetic equations},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {10},
PAGES = {1324-1331},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq136},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Banerjee-Maiti-Parashurama-Yarmush/10,
AUTHOR = {Banerjee, Ipsita and Maiti, Spandan and Parashurama, Natesh and Yarmush, Martin},
TITLE = {An integer programming formulation to identify the sparse network architecture governing differentiation of embryonic stem cells},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {10},
PAGES = {1332-1339},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq139},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Altmann-Tolosi-Sander-Lengauer/10,
AUTHOR = {Altmann, Andr{\'{e}} and Tolo{\c{s}}i, Laura and Sander, Oliver and Lengauer, Thomas},
TITLE = {Permutation importance: A corrected feature importance measure},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {10},
PAGES = {1340-1347},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq134},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Frohler-Dieterich/10,
AUTHOR = {Fr{\"{o}}hler, Sebastian and Dieterich, Christoph},
TITLE = {ACCUSA --- Accurate SNP calling on draft genomes},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {10},
PAGES = {1364-1365},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq138},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bouckaert/10,
AUTHOR = {Bouckaert, Remco R.},
TITLE = {DensiTree: Making sense of sets of phylogenetic trees},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {10},
PAGES = {1372-1373},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq110},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Csardi-Kutalik-Bergmann/10,
AUTHOR = {Cs{\'{a}}rdi, G{\'{a}}bor and Kutalik, Zolt{\'{a}}n and Bergmann, Sven},
TITLE = {Modular analysis of gene expression data with R},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {10},
PAGES = {1376-1377},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq130},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kang-Ko-Kim/10,
AUTHOR = {Kang, Bo-Yeong and Ko, Song and Kim, Dae-Won},
TITLE = {SICAGO: Semi-supervised cluster analysis using semantic distance between gene pairs in Gene Ontology},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {10},
PAGES = {1384-1385},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq133},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Johnson/10,
AUTHOR = {Johnson, Andrew D.},
TITLE = {An extended IUPAC nomenclature code for polymorphic nucleic acids},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {10},
PAGES = {1386-1389},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq098},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chen-Meng-Ma-Mao-Bai-Cao-Gu-Wu-Chen/10,
AUTHOR = {Chen, Dijun and Meng, Yijun and Ma, Xiaoxia and Mao, Chuanzao and Bai, Youhuang and Cao, Junjie and Gu, Haibin and Wu, Ping and Chen, Ming},
TITLE = {Small RNAs in angiosperms: Sequence characteristics, distribution and generation},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {11},
PAGES = {1391-1394},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq150},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Ivakhno-Tavare/10,
AUTHOR = {Ivakhno, Sergii and Tavar{\'{e}}, Simon},
TITLE = {CNAnova: A new approach for finding recurrent copy number abnormalities in cancer SNP microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {11},
PAGES = {1395-1402},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq145},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bulla-Schultz-Schreiber-Zhang-Leitner-Korber-Morgenstern-Stanke/10,
AUTHOR = {Bulla, Ingo and Schultz, Anne-Kathrin and Schreiber, Fabian and Zhang, Ming and Leitner, Thomas and Korber, Bette and Morgenstern, Burkhard and Stanke, Mario},
TITLE = {HIV classification using the coalescent theory},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {11},
PAGES = {1409-1415},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq159},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chen-Xuan-Riggins-Wang-Hoffman-Clarke/10,
AUTHOR = {Chen, Li and Xuan, Jianhua and Riggins, Rebecca B. and Wang, Yue and Hoffman, Eric P. and Clarke, Robert},
TITLE = {Multilevel support vector regression analysis to identify condition-specific regulatory networks},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {11},
PAGES = {1416-1422},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq144},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Errami-Sun-George-Long-Skinner-Wren-Garner/10,
AUTHOR = {Errami, Mounir and Sun, Zhaohui and George, Angela C. and Long, Tara C. and Skinner, Michael A. and Wren, Jonathan D. and Garner, Harold R.},
TITLE = {Identifying duplicate content using statistically improbable phrases},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {11},
PAGES = {1453-1457},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq146},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hoffman-Buske-Noble/10,
AUTHOR = {Hoffman, Michael M. and Buske, Orion J. and Noble, William Stafford},
TITLE = {The Genomedata format for storing large-scale functional genomics data},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {11},
PAGES = {1458-1459},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq164},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kembel-Cowan-Helmus-Cornwell-Morlon-Ackerly-Blomberg-Webb/10,
AUTHOR = {Kembel, Steven W. and Cowan, Peter D. and Helmus, Matthew R. and Cornwell, William K. and Morlon, Helene and Ackerly, David D. and Blomberg, Simon P. and Webb, Campbell O.},
TITLE = {Picante: R tools for integrating phylogenies and ecology},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {11},
PAGES = {1463-1464},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq166},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Dibrova-Galperin-Mulkidjanian/10,
AUTHOR = {Dibrova, Daria V. and Galperin, Michael Y. and Mulkidjanian, Armen Y.},
TITLE = {Characterization of the N-ATPase, a distinct, laterally transferred Na$^+$-translocating form of the bacterial F-type membrane ATPase},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {1473-1476},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq234},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kasahara-Kinoshita-Takagi/10,
AUTHOR = {Kasahara, Kota and Kinoshita, Kengo and Takagi, Toshihisa},
TITLE = {Ligand-binding site prediction of proteins based on known fragment-fragment interactions},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {1493-1499},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq232},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bryant-Shen-Priest-Wong-Mockler/10,
AUTHOR = {Bryant, Douglas W., Jr. and Shen, Rongkun and Priest, Henry D. and Wong, Weng-Keen and Mockler, Todd C.},
TITLE = {Supersplat --- Spliced RNA-seq alignment},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {1500-1505},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq206},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Iam-on-Boongoen-Garrett/10,
AUTHOR = {Iam-on, Natthakan and Boongoen, Tossapon and Garrett, Simon},
TITLE = {LCE: A link-based cluster ensemble method for improved gene expression data analysis},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {1513-1519},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq226},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hochreiter-Bodenhofer-Heusel-Mayr-Mitterecker-Kasim-Khamiakova-Van_Sanden-Lin-Talloen-Bijnens-Gohlmann-Shkedy-Clevert/10,
AUTHOR = {Hochreiter, Sepp and Bodenhofer, Ulrich and Heusel, Martin and Mayr, Andreas and Mitterecker, Andreas and Kasim, Adetayo and Khamiakova, Tatsiana and Van Sanden, Suzy and Lin, Dan and Talloen, Willem and Bijnens, Luc and G{\"{o}}hlmann, Hinrich W.H. and Shkedy, Ziv and Clevert, Djork-Arn{\'{e}}},
TITLE = {FABIA: Factor analysis for bicluster acquisition},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {1520-1527},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq227},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Heath-Bennett-Kavraki/10,
AUTHOR = {Heath, Allison P. and Bennett, George N. and Kavraki, Lydia E.},
TITLE = {Finding metabolic pathways using atom tracking},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {1548-1555},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq223},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Ghaffari-Ivanov-Qian-Dougherty/10,
AUTHOR = {Ghaffari, Noushin and Ivanov, Ivan and Qian, Xiaoning and Dougherty, Edward R.},
TITLE = {A CoD-based reduction algorithm for designing stationary control policies on Boolean networks},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {1556-1563},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq225},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kim-Cong-Grishin/10,
AUTHOR = {Kim, Bong-Hyun and Cong, Qian and Grishin, Nick V.},
TITLE = {HangOut: Generating clean PSI-BLAST profiles for domains with long insertions},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {1564-1565},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq208},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bonnet-He-Billiau-Van_de_Peer/10,
AUTHOR = {Bonnet, Eric and He, Ying and Billiau, Kenny and Van de Peer, Yves},
TITLE = {TAPIR, a web server for the prediction of plant microRNA targets, including target mimics},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {1566-1568},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq233},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Heinecke-Pratt-Vaisar-Becker/10,
AUTHOR = {Heinecke, N.L. and Pratt, B.S. and Vaisar, T. and Becker, L.},
TITLE = {PepC: Proteomics software for identifying differentially expressed proteins based on spectral counting},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {12},
PAGES = {1574-1575},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq171},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Firpi-Ucar-Tan/10,
AUTHOR = {Firpi, Hiram A. and Ucar, Duygu and Tan, Kai},
TITLE = {Discover regulatory DNA elements using chromatin signatures and artificial neural network},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {13},
PAGES = {1579-1586},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq248},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hu-Osuna-Highley-Hua-Nowicki-Stolz-McKayle-Murphy/10,
AUTHOR = {Hu, Yanhua and Osuna-Highley, Elvira and Hua, Juchang and Nowicki, Theodore Scott and Stolz, Robert and McKayle, Camille and Murphy, Robert F.},
TITLE = {Automated analysis of protein subcellular location in time series images},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {13},
PAGES = {1630-1636},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq239},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Baitaluk-Ponomarenko/10,
AUTHOR = {Baitaluk, Michael and Ponomarenko, Julia},
TITLE = {Semantic integration of data on transcriptional regulation},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {13},
PAGES = {1651-1661},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq231},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Ibarra-Melo/10,
AUTHOR = {Ibarra, Ignacio L. and Melo, Francisco},
TITLE = {Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {13},
PAGES = {1664-1665},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq252},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gnad-Ren-Choudhary-Cox-Mann/10,
AUTHOR = {Gnad, Florian and Ren, Shubin and Choudhary, Chunaram and Cox, J{\"{u}}rgen and Mann, Matthias},
TITLE = {Predicting post-translational lysine acetylation using support vector machines},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {13},
PAGES = {1666-1668},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq260},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Junier-Zdobnov/10,
AUTHOR = {Junier, Thomas and Zdobnov, Evgeny M.},
TITLE = {The Newick utilities: High-throughput phylogenetic tree processing in the UNIX shell},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {13},
PAGES = {1669-1670},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq243},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hung-Wasmuth-Sanford-Parkinson/10,
AUTHOR = {Hung, Stacy S. and Wasmuth, James and Sanford, Christopher and Parkinson, John},
TITLE = {DETECT --- A Density Estimation Tool for Enzyme ClassificaTion and its application to Plasmodium falciparum},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {14},
PAGES = {1690-1698},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq266},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bonfield-Whitwham/10,
AUTHOR = {Bonfield, James K. and Whitwham, Andrew},
TITLE = {Gap5 --- Editing the billion fragment sequence assembly},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {14},
PAGES = {1699-1703},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq268},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Carroll-Kann-Sheetlin-Spouge/10,
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TITLE = {Threshold Average Precision (TAP-$k$): A measure of retrieval designed for bioinformatics},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {14},
PAGES = {1708-1713},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq270},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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TITLE = {Prediction of protease substrates using sequence and structure features},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {14},
PAGES = {1714-1722},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq267},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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TITLE = {Global analysis of microarray data reveals intrinsic properties in gene expression and tissue selectivity},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {14},
PAGES = {1723-1730},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq279},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Altay-Emmert-Streib/10,
AUTHOR = {Altay, G{\"{o}}kmen and Emmert-Streib, Frank},
TITLE = {Revealing differences in gene network inference algorithms on the network level by ensemble methods},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {14},
PAGES = {1738-1744},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq259},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Baumgartner-Lewis-Netzer-Pfeifer-Gerszten/10,
AUTHOR = {Baumgartner, Christian and Lewis, Gregory D. and Netzer, Michael and Pfeifer, Bernhard and Gerszten, Robert E.},
TITLE = {A new data mining approach for profiling and categorizing kinetic patterns of metabolic biomarkers after myocardial injury},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {14},
PAGES = {1745-1751},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq254},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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AUTHOR = {Kiran, Anmol and Baranov, Pavel V.},
TITLE = {DARNED: A DAtabase of RNa EDiting in humans},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {14},
PAGES = {1772-1776},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq285},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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AUTHOR = {Floratos, Aris and Smith, Kenneth and Ji, Zhou and Watkinson, John and Califano, Andrea},
TITLE = {geWorkbench: An open source platform for integrative genomics},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {14},
PAGES = {1779-1780},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq282},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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TITLE = {CisGenome Browser: A flexible tool for genomic data visualization},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {14},
PAGES = {1781-1782},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq286},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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TITLE = {Manipulation of FASTQ data with Galaxy},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {14},
PAGES = {1783-1785},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq281},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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TITLE = {A parallel algorithm to compute chemical organizations in biological networks},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {14},
PAGES = {1788-1789},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq263},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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AUTHOR = {Bozdag, Serdar and Li, Aiguo and Wuchty, Stefan and Fine, Howard A.},
TITLE = {FastMEDUSA: A parallelized tool to infer gene regulatory networks},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {14},
PAGES = {1792-1793},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq275},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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TITLE = {DA 1.0: Parameter estimation of biological pathways using data assimilation approach},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {14},
PAGES = {1794-1796},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq276},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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TITLE = {GPCR-OKB: The G Protein Coupled Receptor Oligomer Knowledge Base},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {14},
PAGES = {1804-1805},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq264},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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TITLE = {FuncBase: A resource for quantitative gene function annotation},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {14},
PAGES = {1806-1807},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq265},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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TITLE = {MISS: A non-linear methodology based on mutual information for genetic association studies in both population and sib-pairs analysis},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {15},
PAGES = {1811-1818},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq273},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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TITLE = {A computational genomics pipeline for prokaryotic sequencing projects},
JOURNAL = {Bioinformatics},
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NUMBER = {15},
PAGES = {1819-1826},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq284},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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JOURNAL = {Bioinformatics},
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NUMBER = {15},
PAGES = {1871-1878},
YEAR = {2010},
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URL = {http://dx.doi.org/10.1093/bioinformatics/btq290},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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TITLE = {Cassis: Detection of genomic rearrangement breakpoints},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {15},
PAGES = {1897-1898},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq301},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {15},
PAGES = {1899-1900},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq224},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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TITLE = {Cloud-Coffee: Implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {15},
PAGES = {1903-1904},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq304},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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TITLE = {adephylo: New tools for investigating the phylogenetic signal in biological traits},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {15},
PAGES = {1907-1909},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq292},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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AUTHOR = {Cs{\H{u}}r{\"o}s, Mikl{\'{o}}s},
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JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {15},
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YEAR = {2010},
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URL = {http://dx.doi.org/10.1093/bioinformatics/btq315},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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JOURNAL = {Bioinformatics},
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YEAR = {2010},
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URL = {http://dx.doi.org/10.1093/bioinformatics/btq288},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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URL = {http://dx.doi.org/10.1093/bioinformatics/btq298},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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YEAR = {2010},
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PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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JOURNAL = {Bioinformatics},
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URL = {http://dx.doi.org/10.1093/bioinformatics/btq326},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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YEAR = {2010},
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URL = {http://dx.doi.org/10.1093/bioinformatics/btq332},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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YEAR = {2010},
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PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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YEAR = {2010},
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URL = {http://dx.doi.org/10.1093/bioinformatics/btq336},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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YEAR = {2010},
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PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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NUMBER = {16},
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YEAR = {2010},
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URL = {http://dx.doi.org/10.1093/bioinformatics/btq316},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
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PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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TITLE = {Molecular signatures-based prediction of enzyme promiscuity},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {16},
PAGES = {2012-2019},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq317},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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TITLE = {Uniformly curated signaling pathways reveal tissue-specific cross-talks and support drug target discovery},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {16},
PAGES = {2042-2050},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq310},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
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TITLE = {A new method for designing degenerate primers and its use in the identification of sequences in Brachiaria showing similarity to apomixis-associated genes},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {16},
PAGES = {2053-2054},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq312},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kondrashov-Assis/10,
AUTHOR = {Kondrashov, Alexey S. and Assis, Raquel},
TITLE = {Bridges: A tool for identifying local similarities in long sequences},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {16},
PAGES = {2055-2056},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq320},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jossinet-Ludwig-Westhof/10,
AUTHOR = {Jossinet, Fabrice and Ludwig, Thomas E. and Westhof, Eric},
TITLE = {Assemble: An interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {16},
PAGES = {2057-2059},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq321},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Ewing-Hermisson/10,
AUTHOR = {Ewing, Gregory and Hermisson, Joachim},
TITLE = {MSMS: A coalescent simulation program including recombination, demographic structure and selection at a single locus},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {16},
PAGES = {2064-2065},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq322},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Dimitrov-Garnev-Flower-Doytchinova/10,
AUTHOR = {Dimitrov, Ivan and Garnev, Panayot and Flower, Darren R. and Doytchinova, Irini},
TITLE = {EpiTOP --- A proteochemometric tool for MCH class II binding prediction},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {16},
PAGES = {2066-2068},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq324},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bogojeska-Bickel-Altmann-Lengauer/10,
AUTHOR = {Bogojeska, Jasmina and Bickel, Steffen and Altmann, Andr{\'{e}} and Lengauer, Thomas},
TITLE = {Dealing with sparse data in predicting outcomes of HIV combination therapies},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {17},
PAGES = {2085-2092},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq361},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Arunachalam-Jayasurya-Tomancak-Ohler/10,
AUTHOR = {Arunachalam, Manonmani and Jayasurya, Karthik and Tomancak, Pavel and Ohler, Uwe},
TITLE = {An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {17},
PAGES = {2109-2115},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq358},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Huang-Gromiha/10,
AUTHOR = {Huang, Liang-Tsung and Gromiha, M. Michael},
TITLE = {First insight into the prediction of protein folding rate change upon point mutation},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {17},
PAGES = {2121-2127},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq350},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hancock-Takigawa-Mamitsuka/10,
AUTHOR = {Hancock, Timothy and Takigawa, Ichigaku and Mamitsuka, Hiroshi},
TITLE = {Mining metabolic pathways through gene expression},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {17},
PAGES = {2128-2135},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq344},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Johannes-Brase-Frohlich-Gade-Gehrmann-Falth-Sultmann-Beissbarth/10,
AUTHOR = {Johannes, Marc and Brase, Jan C. and Fr{\"{o}}hlich, Holger and Gade, Stephan and Gehrmann, Mathias and F{\"{a}}lth, Maria and S{\"{u}}ltmann, Holger and Bei{\ss}barth, Tim},
TITLE = {Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {17},
PAGES = {2136-2144},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq345},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Klamt-Flassig-Sundmacher/10,
AUTHOR = {Klamt, Steffen and Flassig, Robert J. and Sundmacher, Kai},
TITLE = {TRANSWESD: Inferring cellular networks with transitive reduction},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {17},
PAGES = {2160-2168},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq342},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gim-Kim-Kim-Choi-Kim-Chung-Cho/10,
AUTHOR = {Gim, Jungsoo and Kim, Ho-Shik and Kim, Junil and Choi, Minsoo and Kim, Jeong-Rae and Chung, Yeun Jun and Cho, Kwang-Hyun},
TITLE = {A system-level investigation into the cellular toxic response mechanism mediated by AhR signal transduction pathway},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {17},
PAGES = {2169-2175},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq400},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Klepper-Drablos/10,
AUTHOR = {Klepper, Kjetil and Drabl{\o}s, Finn},
TITLE = {PriorsEditor: A tool for the creation and use of positional priors in motif discovery},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {17},
PAGES = {2195-2197},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq357},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Calle-Urrea-Malats-Van_Steen/10,
AUTHOR = {Calle, M. Luz and Urrea, V{\'{i}}ctor and Malats, N{\'u}ria and Van Steen, Kristel},
TITLE = {mbmdr: An R package for exploring gene-gene interactions associated with binary or quantitative traits},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {17},
PAGES = {2198-2199},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq352},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kent-Zweig-Barber-Hinrichs-Karolchik/10,
AUTHOR = {Kent, W.J. and Zweig, A.S. and Barber, G. and Hinrichs, A.S. and Karolchik, D.},
TITLE = {BigWig and BigBed: Enabling browsing of large distributed datasets},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {17},
PAGES = {2204-2207},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq351},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Brohee-Barriot-Moreau/10,
AUTHOR = {Broh{\'{e}}e, Sylvain and Barriot, Roland and Moreau, Yves},
TITLE = {Biological knowledge bases using Wikis: Combining the flexibility of Wikis with the structure of databases},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {17},
PAGES = {2210-2211},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq348},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Good/10,
AUTHOR = {Good, Phillip},
TITLE = {Exchangeable random variables},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {17},
PAGES = {2214-2214},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq297},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Calian-Hsu/10,
AUTHOR = {Calian, Violeta and Hsu, Jason C.},
TITLE = {Response to Letter to the Editor by Philip Good on To Permute or Not to Permute},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {17},
PAGES = {2215-2215},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq313},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Geraci/10,
AUTHOR = {Geraci, Filippo},
TITLE = {A comparison of several algorithms for the single individual SNP haplotyping reconstruction problem},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {2217-2225},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq411},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kotamarti-Hahsler-Raiford-McGee-Dunham/10,
AUTHOR = {Kotamarti, Rao M. and Hahsler, Michael and Raiford, Douglas and McGee, Monnie and Dunham, Margaret H.},
TITLE = {Analyzing taxonomic classification using extensible Markov models},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {2235-2241},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq349},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Di_Lena-Fariselli-Margara-Vassura-Casadio/10,
AUTHOR = {Di Lena, Pietro and Fariselli, Piero and Margara, Luciano and Vassura, Marco and Casadio, Rita},
TITLE = {Fast overlapping of protein contact maps by alignment of eigenvectors},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {2250-2258},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq402},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gao-Skolnick/10,
AUTHOR = {Gao, Mu and Skolnick, Jeffrey},
TITLE = {iAlign: A method for the structural comparison of protein-protein interfaces},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {2259-2265},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq404},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Fromer-Linial/10,
AUTHOR = {Fromer, Menachem and Linial, Michal},
TITLE = {Exposing the co-adaptive potential of protein-protein interfaces through computational sequence design},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {2266-2272},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq412},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hu-Wan-Hackler-Zack-Qian/10,
AUTHOR = {Hu, Jianfei and Wan, Jun and Hackler, Laszlo, Jr. and Zack, Donald J. and Qian, Jiang},
TITLE = {Computational analysis of tissue-specific gene networks: Application to murine retinal functional studies},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {2289-2297},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq408},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gellert-Jenniches-Braun-Uchida/10,
AUTHOR = {Gellert, Pascal and Jenniches, Katharina and Braun, Thomas and Uchida, Shizuka},
TITLE = {C-It: A knowledge database for tissue-enriched genes},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {2328-2333},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq417},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Guy-Kultima-Andersson/10,
AUTHOR = {Guy, Lionel and Kultima, Jens Roat and Andersson, Siv G.E.},
TITLE = {genoPlotR: Comparative gene and genome visualization in R},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {2334-2335},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq413},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Czauderna-Klukas-Schreiber/10,
AUTHOR = {Czauderna, Tobias and Klukas, Christian and Schreiber, Falk},
TITLE = {Editing, validating and translating of SBGN maps},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {2340-2341},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq407},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Fujita-Kojima-Patriota-Sato-Severino-Miyano/10,
AUTHOR = {Fujita, Andr{\'{e}} and Kojima, Kaname and Patriota, Alexandre G. and Sato, Jo{\~{a}}o R. and Severino, Patricia and Miyano, Satoru},
TITLE = {A fast and robust statistical test based on likelihood ratio with Bartlett correction to identify Granger causality between gene sets},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {2349-2351},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq427},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Forth-McConkey-Westhead/10,
AUTHOR = {Forth, Thomas and McConkey, Glenn A. and Westhead, David R.},
TITLE = {MetNetMaker: A free and open-source tool for the creation of novel metabolic networks in SBML format},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {2352-2353},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq425},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kawas-Wilkinson/10,
AUTHOR = {Kawas, Edward and Wilkinson, Mark D.},
TITLE = {OWL:2Perl: Creating Perl modules from OWL class definitions},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {2357-2358},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq416},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jang-Kim-Kim-Kim-Bae-Kim-Eom-Song/10,
AUTHOR = {Jang, Hyunchul and Kim, Jinhyun and Kim, Sang-Kyun and Kim, Chul and Bae, Soon-Hee and Kim, Anna and Eom, Dong-Myung and Song, Mi-Young},
TITLE = {Ontology for medicinal materials based on traditional Korean medicine},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {2359-2360},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq424},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gonzalez-Pearson/10,
AUTHOR = {Gonzalez, Mileidy W. and Pearson, William R.},
TITLE = {RefProtDom: A protein database with improved domain boundaries and homology relationships},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {18},
PAGES = {2361-2362},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq426},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Carvalho-Irizarry/10,
AUTHOR = {Carvalho, Benilton S. and Irizarry, Rafael A.},
TITLE = {A framework for oligonucleotide microarray preprocessing},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {19},
PAGES = {2363-2367},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq431},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Askitis-Sinha/10,
AUTHOR = {Askitis, Nikolas and Sinha, Ranjan},
TITLE = {RepMaestro: Scalable repeat detection on disk-based genome sequences},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {19},
PAGES = {2368-2374},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq433},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Koohy-Dyer-Reid-Koentges-Ott/10,
AUTHOR = {Koohy, Hashem and Dyer, Nigel P. and Reid, John E. and Koentges, Georgy and Ott, Sascha},
TITLE = {An alignment-free model for comparison of regulatory sequences},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {19},
PAGES = {2391-2397},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq453},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jaitly-Brubaker-Rubinstein-Lilien/10,
AUTHOR = {Jaitly, Navdeep and Brubaker, Marcus A. and Rubinstein, John L. and Lilien, Ryan H.},
TITLE = {A Bayesian method for 3D macromolecular structure inference using class average images from single particle electron microscopy},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {19},
PAGES = {2406-2415},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq456},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Dzyubachyk-Essers-van_Cappellen-Baldeyron-Inagaki-Niessen-Meijering/10,
AUTHOR = {Dzyubachyk, Oleh and Essers, Jeroen and van Cappellen, Wiggert A. and Baldeyron, C{\'{e}}line and Inagaki, Akiko and Niessen, Wiro J. and Meijering, Erik},
TITLE = {Automated analysis of time-lapse fluorescence microscopy images: From live cell images to intracellular foci},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {19},
PAGES = {2424-2430},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq434},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jin-Lu/10,
AUTHOR = {Jin, Bo and Lu, Xinghua},
TITLE = {Identifying informative subsets of the Gene Ontology with information bottleneck methods},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {19},
PAGES = {2445-2451},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq449},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Darzentas-Bousios-Apostolidou-Tsaftaris/10,
AUTHOR = {Darzentas, N. and Bousios, A. and Apostolidou, V. and Tsaftaris, A.S.},
TITLE = {MASiVE: Mapping and Analysis of SireVirus Elements in plant genome sequences},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {19},
PAGES = {2452-2454},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq454},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Delport-Poon-Frost-Pond/10,
AUTHOR = {Delport, Wayne and Poon, Art F.Y. and Frost, Simon D.W. and Pond, Sergei L. Kosakovsky},
TITLE = {Datamonkey 2010: A suite of phylogenetic analysis tools for evolutionary biology},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {19},
PAGES = {2455-2457},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq429},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Edgar/10,
AUTHOR = {Edgar, Robert C.},
TITLE = {Search and clustering orders of magnitude faster than BLAST},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {19},
PAGES = {2460-2461},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq461},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chou-Yin-Xu/10,
AUTHOR = {Chou, Wen-Chi and Yin, Yanbin and Xu, Ying},
TITLE = {GolgiP: Prediction of Golgi-resident proteins in plants},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {19},
PAGES = {2464-2465},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq446},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Fromer-Yanover-Harel-Shachar-Weiss-Linial/10,
AUTHOR = {Fromer, Menachem and Yanover, Chen and Harel, Amir and Shachar, Ori and Weiss, Yair and Linial, Michal},
TITLE = {SPRINT: Side-chain prediction inference toolbox for multistate protein design},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {19},
PAGES = {2466-2467},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq445},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Dorff-Chambwe-Srdanovic-Campagne/10,
AUTHOR = {Dorff, Kevin C. and Chambwe, Nyasha and Srdanovic, Marko and Campagne, Fabien},
TITLE = {BDVal: Reproducible large-scale predictive model development and validation in high-throughput datasets},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {19},
PAGES = {2472-2473},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq463},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jocker-Sonntag-Henjes-Gotschel-Tresch-Beissbarth-Wiemann-Korf/10,
AUTHOR = {J{\"{o}}cker, Anika and Sonntag, Johanna and Henjes, Frauke and G{\"{o}}tschel, Frank and Tresch, Achim and Bei{\ss}barth, Tim and Wiemann, Stefan and Korf, Ulrike},
TITLE = {QuantProReloaded: Quantitative analysis of microspot immunoassays},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {19},
PAGES = {2480-2481},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq443},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kano-Dobson-Nakanishi-Tsujii-Ananiadou/10,
AUTHOR = {Kano, Yoshinobu and Dobson, Paul and Nakanishi, Mio and Tsujii, Jun'ichi and Ananiadou, Sophia},
TITLE = {Text mining meets workflow: Linking U-Compare with Taverna},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {19},
PAGES = {2486-2487},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq464},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Benton-Want-Ebbels/10,
AUTHOR = {Benton, H. Paul and Want, Elizabeth J. and Ebbels, Timothy M.D.},
TITLE = {Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {19},
PAGES = {2488-2489},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq441},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bai-Wang-Xue-Li-Bu-Hu-Xu-Bao-Zhao-Ding-Yan-Wu/10,
AUTHOR = {Bai, Jie and Wang, Junrong and Xue, Feng and Li, Jingsong and Bu, Lijing and Hu, Junming and Xu, Gang and Bao, Qiyu and Zhao, Guoping and Ding, Xiaoming and Yan, Jie and Wu, Jinyu},
TITLE = {proTF: A comprehensive data and phylogenomics resource for prokaryotic transcription factors},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {19},
PAGES = {2493-2495},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq432},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Fischer-Holliday-Thornton/10,
AUTHOR = {Fischer, Julia D. and Holliday, Gemma L. and Thornton, Janet M.},
TITLE = {The CoFactor database: Organic cofactors in enzyme catalysis},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {19},
PAGES = {2496-2497},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq442},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Harris-Ponts-Levchuk-Le_Roch-Lonardi/10a,
AUTHOR = {Harris, Elena Y. and Ponts, Nadia and Levchuk, Aleksandr and Le Roch, Karine and Lonardi, Stefano},
TITLE = {Corrigendum to ``BRAT: Bisulfite-treated reads analysis tool''},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {19},
PAGES = {2499-2499},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq494},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
NOTE = {Originally in Bioinformatics, Vol. 26, 2010, No. 4, 572-573},
}
@article{Fernandes-Gloor/10a,
AUTHOR = {Fernandes, Andrew D. and Gloor, Gregory B.},
TITLE = {Corrigendum to ``Mutual information is critically dependent on prior assumptions: Would the correct estimate of mutual information please identify itself?''},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {19},
PAGES = {2500-2500},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq497},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
NOTE = {Originally in Bioinformatics, Vol. 26, 2010, No. 9, 1135-1139},
}
@article{Itzhaki-Akiva-Margalit/10,
AUTHOR = {Itzhaki, Zohar and Akiva, Eyal and Margalit, Hanah},
TITLE = {Preferential use of protein domain pairs as interaction mediators: Order and transitivity},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {20},
PAGES = {2564-2570},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq495},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Erkkila-Lehmusvaara-Ruusuvuori-Visakorpi-Shmulevich-Lahdesmaki/10,
AUTHOR = {Erkkil{\"{a}}, Timo and Lehmusvaara, Saara and Ruusuvuori, Pekka and Visakorpi, Tapio and Shmulevich, Ilya and L{\"{a}}hdesm{\"{a}}ki, Harri},
TITLE = {Probabilistic analysis of gene expression measurements from heterogeneous tissues},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {20},
PAGES = {2571-2577},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq406},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Koestler-Marsit-Christensen-Karagas-Bueno-Sugarbaker-Kelsey-Houseman/10,
AUTHOR = {Koestler, Devin C. and Marsit, Carmen J. and Christensen, Brock C. and Karagas, Margaret R. and Bueno, Raphael and Sugarbaker, David J. and Kelsey, Karl T. and Houseman, E. Andres},
TITLE = {Semi-supervised recursively partitioned mixture models for identifying cancer subtypes},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {20},
PAGES = {2578-2585},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq470},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Erten-Sozdinler/10,
AUTHOR = {Erten, Cesim and S{\"{o}}zdinler, Melih},
TITLE = {Improving performances of suboptimal greedy iterative biclustering heuristics via localization},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {20},
PAGES = {2594-2600},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq473},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Fasani-Savageau/10,
AUTHOR = {Fasani, Rick A. and Savageau, Michael A.},
TITLE = {Automated construction and analysis of the design space for biochemical systems},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {20},
PAGES = {2601-2609},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq479},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Goto-Prins-Nakao-Bonnal-Aerts-Katayama/10,
AUTHOR = {Goto, Naohisa and Prins, Pjotr and Nakao, Mitsuteru and Bonnal, Raoul and Aerts, Jan and Katayama, Toshiaki},
TITLE = {BioRuby: Bioinformatics software for the Ruby programming language},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {20},
PAGES = {2617-2619},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq475},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Darzentas/10,
AUTHOR = {Darzentas, Nikos},
TITLE = {Circoletto: Visualizing sequence similarity with Circos},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {20},
PAGES = {2620-2621},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq484},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Klose-Wallace-Janes/10,
AUTHOR = {Klose, D.P. and Wallace, B.A. and Janes, Robert W.},
TITLE = {2Struc: The secondary structure server},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {20},
PAGES = {2624-2625},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq480},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Biasini-Mariani-Haas-Scheuber-Schenk-Schwede-Philippsen/10,
AUTHOR = {Biasini, Marco and Mariani, Valerio and Haas, J{\"{u}}rgen and Scheuber, Stefan and Schenk, Andreas D. and Schwede, Torsten and Philippsen, Ansgar},
TITLE = {OpenStructure: A flexible software framework for computational structural biology},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {20},
PAGES = {2626-2628},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq481},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Goll-Rusch-Tanenbaum-Thiagarajan-Li-Methe-Yooseph/10,
AUTHOR = {Goll, Johannes and Rusch, Douglas B. and Tanenbaum, David M. and Thiagarajan, Mathangi and Li, Kelvin and Meth{\'{e}}, Barbara A. and Yooseph, Shibu},
TITLE = {METAREP: JCVI metagenomics reports --- An open source tool for high-performance comparative metagenomics},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {20},
PAGES = {2631-2632},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq455},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Asif-Rolfe-Green-Lawrence-Rattray-Sanguinetti/10,
AUTHOR = {Asif, H.M. Shahzad and Rolfe, Matthew D. and Green, Jeff and Lawrence, Neil D. and Rattray, Magnus and Sanguinetti, Guido},
TITLE = {TFInfer: A tool for probabilistic inference of transcription factor activities},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {20},
PAGES = {2635-2636},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq469},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Biswas-Mynampati-Umashankar-Reuben-Parab-Rao-Kannan-Swarup/10,
AUTHOR = {Biswas, Ambarish and Mynampati, Kalyan C. and Umashankar, Shivshankar and Reuben, Sheela and Parab, Gauri and Rao, Raghuraj and Kannan, Velayutham S. and Swarup, Sanjay},
TITLE = {MetDAT: A modular and workflow-based free online pipeline for mass spectrometry data processing, analysis and interpretation},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {20},
PAGES = {2639-2640},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq436},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hoehme-Drasdo/10,
AUTHOR = {Hoehme, Stefan and Drasdo, Dirk},
TITLE = {A cell-based simulation software for multi-cellular systems},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {20},
PAGES = {2641-2642},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq437},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chubb-Jefferys-Sternberg-Kelley/10,
AUTHOR = {Chubb, Daniel and Jefferys, Benjamin R. and Sternberg, Michael J.E. and Kelley, Lawrence A.},
TITLE = {Sequencing delivers diminishing returns for homology detection: Implications for mapping the protein universe},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {21},
PAGES = {2664-2671},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq527},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Abel-Duncavage-Becker-Armstrong-Magrini-Pfeifer/10,
AUTHOR = {Abel, Haley J. and Duncavage, Eric J. and Becker, Nils and Armstrong, Jon R. and Magrini, Vincent J. and Pfeifer, John D.},
TITLE = {SLOPE: A quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {21},
PAGES = {2684-2688},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq528},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kato-Nagano/10,
AUTHOR = {Kato, Tsuyoshi and Nagano, Nozomi},
TITLE = {Metric learning for enzyme active-site search},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {21},
PAGES = {2698-2704},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq519},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Dogan-Lu/10,
AUTHOR = {Do{\u{g}}an, Rezarta Islamaj and Lu, Zhiyong},
TITLE = {Click-words: Learning to predict document keywords from a user perspective},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {21},
PAGES = {2767-2775},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq459},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Goodstadt/10,
AUTHOR = {Goodstadt, Leo},
TITLE = {Ruffus: A lightweight Python library for computational pipelines},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {21},
PAGES = {2778-2779},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq524},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bilbao-Castro-Sorzano-Garcia-Fernandez/10,
AUTHOR = {Bilbao-Castro, J.R. and Sorzano, C.O.S. and Garc{\'{i}}a, I. and Fern{\'{a}}ndez, J.J.},
TITLE = {XMSF: Structure-preserving noise reduction and pre-segmentation in microscope tomography},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {21},
PAGES = {2786-2787},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq496},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Fertig-Ding-Favorov-Parmigiani-Ochs/10,
AUTHOR = {Fertig, Elana J. and Ding, Jie and Favorov, Alexander V. and Parmigiani, Giovanni and Ochs, Michael F.},
TITLE = {CoGAPS: An R/C++ package to identify patterns and biological process activity in transcriptomic data},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {21},
PAGES = {2792-2793},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq503},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Garcia-Remesal-Cuevas-Perez-Rey-Martin-Anguita-de_la_Iglesia-de_la_Calle-Crespo-Maojo/10,
AUTHOR = {Garc{\'{i}}a-Remesal, Miguel and Cuevas, Alejandro and P{\'{e}}rez-Rey, David and Mart{\'{i}}n, Luis and Anguita, Alberto and de la Iglesia, Diana and de la Calle, Guillermo and Crespo, Jos{\'{e}} and Maojo, V{\'{i}}ctor},
TITLE = {PubDNA Finder: A web database linking full-text articles to sequences of nucleic acids},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {21},
PAGES = {2801-2802},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq520},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bagos-Nikolaou-Liakopoulos-Tsirigos/10,
AUTHOR = {Bagos, Pantelis G. and Nikolaou, Elisanthi P. and Liakopoulos, Theodore D. and Tsirigos, Konstantinos D.},
TITLE = {Combined prediction of Tat and Sec signal peptides with hidden Markov models},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {22},
PAGES = {2811-2817},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq530},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Datta-Prado-Rodriguez-Escalante/10,
AUTHOR = {Datta, Saheli and Prado, Raquel and Rodr{\'{i}}guez, Abel and Escalante, Anan{\'{i}}as A.},
TITLE = {Characterizing molecular adaptation: A hierarchical approach to assess the selective influence of amino acid properties},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {22},
PAGES = {2818-2825},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq532},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kelm-Shi-Deane/10,
AUTHOR = {Kelm, Sebastian and Shi, Jiye and Deane, Charlotte M.},
TITLE = {MEDELLER: Homology-based coordinate generation for membrane proteins},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {22},
PAGES = {2833-2840},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq554},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Brinza-Schultz-Tesler-Bafna/10,
AUTHOR = {Brinza, Dumitru and Schultz, Matthew and Tesler, Glenn and Bafna, Vineet},
TITLE = {RAPID detection of gene-gene interactions in genome-wide association studies},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {22},
PAGES = {2856-2862},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq529},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chu-Bunce-Hogge-Peters/10,
AUTHOR = {Chu, Tianjiao and Bunce, Kimberly and Hogge, W. Allen and Peters, David G.},
TITLE = {Statistical considerations for digital approaches to non-invasive fetal genotyping},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {22},
PAGES = {2863-2866},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq544},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Cheng-Wang-Bryant/10,
AUTHOR = {Cheng, Tiejun and Wang, Yanli and Bryant, Stephen H.},
TITLE = {Investigating the correlations among the chemical structures, bioactivity profiles and molecular targets of small molecules},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {22},
PAGES = {2881-2888},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq550},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Agirre-Soroa-Stevenson/10,
AUTHOR = {Agirre, Eneko and Soroa, Aitor and Stevenson, Mark},
TITLE = {Graph-based Word Sense Disambiguation of biomedical documents},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {22},
PAGES = {2889-2896},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq555},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bartonicek-Enright/10,
AUTHOR = {Bartonicek, Nenad and Enright, Anton J.},
TITLE = {SylArray: A web server for automated detection of miRNA effects from expression data},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {22},
PAGES = {2900-2901},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq545},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Davey-James-Dicks-Roberts/10,
AUTHOR = {Davey, Robert P. and James, Stephen A. and Dicks, Jo and Roberts, Ian N.},
TITLE = {TURNIP: Tracking unresolved nucleotide polymorphisms in large hard-to-assemble regions of repetitive DNA sequence},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {22},
PAGES = {2908-2909},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq557},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chen-Wang/10,
AUTHOR = {Chen, Zhi-Zhong and Wang, Lusheng},
TITLE = {HybridNET: A tool for constructing hybridization networks},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {22},
PAGES = {2912-2913},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq548},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Cohen-Ashkenazy-Belinky-Huchon-Pupko/10,
AUTHOR = {Cohen, Ofir and Ashkenazy, Haim and Belinky, Frida and Huchon, Doroth{\'{e}}e and Pupko, Tal},
TITLE = {GLOOME: Gain loss mapping engine},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {22},
PAGES = {2914-2915},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq549},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Berenger-Coti-Zhang/10,
AUTHOR = {Berenger, Francois and Coti, Camille and Zhang, Kam Y.J.},
TITLE = {PAR: A PARallel and distributed job crusher},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {22},
PAGES = {2918-2919},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq542},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bauer-Mehren-Rautschka-Sanz-Furlong/10,
AUTHOR = {Bauer-Mehren, Anna and Rautschka, Michael and Sanz, Ferran and Furlong, Laura I.},
TITLE = {DisGeNET: A Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {22},
PAGES = {2924-2926},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq538},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Eitner-Koch-Gaweda-Marciniak/10,
AUTHOR = {Eitner, Krystian and Koch, Uwe and Gaw{\c{e}}da, Tomasz and Marciniak, J{\c{e}}drzej},
TITLE = {Statistical distribution of amino acid sequences: A proof of Darwinian evolution},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {23},
PAGES = {2933-2935},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq571},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Huang-Cao-Zhong/10,
AUTHOR = {Huang, Wei and Cao, Xiaoyi and Zhong, Sheng},
TITLE = {Network-based comparison of temporal gene expression patterns},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {23},
PAGES = {2944-2951},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq561},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Aggio-Ruggiero-Villas-Boas/10,
AUTHOR = {Aggio, Raphael B.M. and Ruggiero, Katya and Villas-B{\^o}as, Silas Granato},
TITLE = {Pathway Activity Profiling (PAPi): From the metabolite profile to the metabolic pathway activity},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {23},
PAGES = {2969-2976},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq567},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Arumugam-Harrington-Foerstner-Raes-Bork/10,
AUTHOR = {Arumugam, Manimozhiyan and Harrington, Eoghan D. and Foerstner, Konrad U. and Raes, Jeroen and Bork, Peer},
TITLE = {SmashCommunity: A metagenomic annotation and analysis tool},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {23},
PAGES = {2977-2978},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq536},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Harrington-Arumugam-Raes-Bork-Relman/10,
AUTHOR = {Harrington, Eoghan D. and Arumugam, Manimozhiyan and Raes, Jeroen and Bork, Peer and Relman, David A.},
TITLE = {SmashCell: A software framework for the analysis of single-cell amplified genome sequences},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {23},
PAGES = {2979-2980},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq564},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gajda-Tuszynska-Kaczor-Bakulina-Bujnicki/10,
AUTHOR = {Gajda, Michal J. and Tuszynska, Irina and Kaczor, Marta and Bakulina, Anastasia Yu. and Bujnicki, Janusz M.},
TITLE = {FILTREST3D: Discrimination of structural models using restraints from experimental data},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {23},
PAGES = {2986-2987},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq582},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Arends-Prins-Jansen-Broman/10,
AUTHOR = {Arends, Danny and Prins, Pjotr and Jansen, Ritsert C. and Broman, Karl W.},
TITLE = {R/qtl: High-throughput multiple QTL mapping},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {23},
PAGES = {2990-2992},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq565},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Florez-Lammers-Michna-Stulke/10,
AUTHOR = {Fl{\'{o}}rez, Lope A. and Lammers, Christoph R. and Michna, Raphael and St{\"{u}}lke, J{\"{o}}rg},
TITLE = {CellPublisher: A web platform for the intuitive visualization and sharing of metabolic, signalling and regulatory pathways},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {23},
PAGES = {2997-2999},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq585},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Guo-Papachristoudis-Altshuler-Gerber-Jaakkola-Gifford-Mahony/10,
AUTHOR = {Guo, Yuchun and Papachristoudis, Georgios and Altshuler, Robert C. and Gerber, Georg K. and Jaakkola, Tommi S. and Gifford, David K. and Mahony, Shaun},
TITLE = {Discovering homotypic binding events at high spatial resolution},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {24},
PAGES = {3028-3034},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq590},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Ivakhno-Royce-Cox-Evers-Cheetham-Tavare/10,
AUTHOR = {Ivakhno, Sergii and Royce, Tom and Cox, Anthony J. and Evers, Dirk J. and Cheetham, R. Keira and Tavar{\'{e}}, Simon},
TITLE = {CNAseg --- A novel framework for identification of copy number changes in cancer from second-generation sequencing data},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {24},
PAGES = {3051-3058},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq587},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Day-Lennox-Dahl-Vannucci-Tsai/10,
AUTHOR = {Day, Ryan and Lennox, Kristin P. and Dahl, David B. and Vannucci, Marina and Tsai, Jerry W.},
TITLE = {Characterizing the regularity of tetrahedral packing motifs in protein tertiary structure},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {24},
PAGES = {3059-3066},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq573},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hoehndorf-Oellrich-Rebholz-Schuhmann/10,
AUTHOR = {Hoehndorf, Robert and Oellrich, Anika and Rebholz-Schuhmann, Dietrich},
TITLE = {Interoperability between phenotype and anatomy ontologies},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {24},
PAGES = {3112-3118},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq578},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chuang-Tsai-Yang/10,
AUTHOR = {Chuang, Li-Yeh and Tsai, Jui-Hung and Yang, Cheng-Hong},
TITLE = {PPO: Predictor for Prokaryotic Operons},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {24},
PAGES = {3127-3128},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq601},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jackson-Boyd-Gaeta-Collins/10,
AUTHOR = {Jackson, Katherine J.L. and Boyd, Scott and Ga{\"{e}}ta, Bruno A. and Collins, Andrew M.},
TITLE = {Benchmarking the performance of human antibody gene alignment utilities using a 454 sequence dataset},
JOURNAL = {Bioinformatics},
VOLUME = {26},
NUMBER = {24},
PAGES = {3129-3130},
YEAR = {2010},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq604},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}