@article{Bock-Lengauer/08,
AUTHOR = {Bock, Christoph and Lengauer, Thomas},
TITLE = {Computational epigenetics},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {1},
PAGES = {1-10},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm546},
PUBLISHER = {Oxford University Press},
}
@article{Dalevi-Ivanova-Mavromatis-Hooper-Szeto-Hugenholtz-Kyrpides-Markowitz/08,
AUTHOR = {Dalevi, Daniel and Ivanova, Natalia N. and Mavromatis, Konstantinos and Hooper, Sean D. and Szeto, Ernest and Hugenholtz, Philip and Kyrpides, Nikos C. and Markowitz, Victor M.},
TITLE = {Annotation of metagenome short reads using proxygenes},
BOOKTITLE = {Proceedings of the 7th European Conference on Computational Biology, ECCB'2008 (Cagliari, Sardinia, Italy, September 22-26, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {7-13},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn276},
PUBLISHER = {Oxford University Press},
}
@article{Abeel-Saeys-Rouze-Van_de_Peer/08,
AUTHOR = {Abeel, Thomas and Saeys, Yvan and Rouz{\'{e}}, Pierre and Van de Peer, Yves},
TITLE = {ProSOM: Core promoter prediction based on unsupervised clustering of DNA physical profiles},
BOOKTITLE = {Proceedings of the 16th International Conference on Intelligent Systems for Molecular Biology, ISMB'2008 (Toronto, Canada, July 19-23, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {24-31},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn172},
PUBLISHER = {Oxford University Press},
}
@article{Hajirasouliha-Hormozdiari-Sahinalp-Birol/08,
AUTHOR = {Hajirasouliha, Iman and Hormozdiari, Fereydoun and Sahinalp, S. Cenk and Birol, Inanc},
TITLE = {Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies},
BOOKTITLE = {Proceedings of the 16th International Conference on Intelligent Systems for Molecular Biology, ISMB'2008 (Toronto, Canada, July 19-23, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {32-40},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn173},
PUBLISHER = {Oxford University Press},
}
@article{Deforche-Camacho-Van_Laethem-Lemey-Rambaut-Moreau-Vandamme/08,
AUTHOR = {Deforche, K. and Camacho, R. and Van Laethem, K. and Lemey, P. and Rambaut, A. and Moreau, Y. and Vandamme, A.-M.},
TITLE = {Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {1},
PAGES = {34-41},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm540},
PUBLISHER = {Oxford University Press},
}
@article{Kall-Storey-Noble/08,
AUTHOR = {K{\"{a}}ll, Lukas and Storey, John D. and Noble, William Stafford},
TITLE = {Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry},
BOOKTITLE = {Proceedings of the 7th European Conference on Computational Biology, ECCB'2008 (Cagliari, Sardinia, Italy, September 22-26, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {42-48},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn294},
PUBLISHER = {Oxford University Press},
}
@article{Bocker-Rasche/08,
AUTHOR = {B{\"{o}}cker, Sebastian and Rasche, Florian},
TITLE = {Towards de novo identification of metabolites by analyzing tandem mass spectra},
BOOKTITLE = {Proceedings of the 7th European Conference on Computational Biology, ECCB'2008 (Cagliari, Sardinia, Italy, September 22-26, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {49-55},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn270},
PUBLISHER = {Oxford University Press},
}
@article{Kastenmuller-Gasteiger-Mewes/08,
AUTHOR = {Kastenm{\"{u}}ller, Gabi and Gasteiger, Johann and Mewes, Hans-Werner},
TITLE = {An environmental perspective on large-scale genome clustering based on metabolic capabilities},
BOOKTITLE = {Proceedings of the 7th European Conference on Computational Biology, ECCB'2008 (Cagliari, Sardinia, Italy, September 22-26, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {56-62},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn302},
PUBLISHER = {Oxford University Press},
}
@article{Do-Foo-Batzoglou/08,
AUTHOR = {Do, Chuong B. and Foo, Chuan-Sheng and Batzoglou, Serafim},
TITLE = {A max-margin model for efficient simultaneous alignment and folding of RNA sequences},
BOOKTITLE = {Proceedings of the 16th International Conference on Intelligent Systems for Molecular Biology, ISMB'2008 (Toronto, Canada, July 19-23, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {68-76},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn177},
PUBLISHER = {Oxford University Press},
}
@article{Gao-Honkela-Rattray-Lawrence/08,
AUTHOR = {Gao, Pei and Honkela, Antti and Rattray, Magnus and Lawrence, Neil D.},
TITLE = {Gaussian process modelling of latent chemical species: Applications to inferring transcription factor activities},
BOOKTITLE = {Proceedings of the 7th European Conference on Computational Biology, ECCB'2008 (Cagliari, Sardinia, Italy, September 22-26, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {70-75},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn278},
PUBLISHER = {Oxford University Press},
}
@article{Kelley-Feizi-Ideker/08,
AUTHOR = {Kelley, Ryan and Feizi, Hoda and Ideker, Trey},
TITLE = {Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {1},
PAGES = {71-77},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm347},
PUBLISHER = {Oxford University Press},
}
@article{Hummel-Meister-Mansmann/08,
AUTHOR = {Hummel, Manuela and Meister, Reinhard and Mansmann, Ulrich},
TITLE = {GlobalANCOVA: Exploration and assessment of gene group effects},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {1},
PAGES = {78-85},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm531},
PUBLISHER = {Oxford University Press},
}
@article{Csaba-Birzele-Zimmer/08,
AUTHOR = {Csaba, Gergely and Birzele, Fabian and Zimmer, Ralf},
TITLE = {Protein structure alignment considering phenotypic plasticity},
BOOKTITLE = {Proceedings of the 7th European Conference on Computational Biology, ECCB'2008 (Cagliari, Sardinia, Italy, September 22-26, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {98-104},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn271},
PUBLISHER = {Oxford University Press},
}
@article{Alves-Arnold-Clemmer-Li-Reilly-Sheng-Tang-Xun-Zeng-Radivojac/08,
AUTHOR = {Alves, Pedro and Arnold, Randy J. and Clemmer, David E. and Li, Yixue and Reilly, James P. and Sheng, Quanhu and Tang, Haixu and Xun, Zhiyin and Zeng, Rong and Radivojac, Predrag},
TITLE = {Fast and accurate identification of semi-tryptic peptides in shotgun proteomics},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {1},
PAGES = {102-109},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm545},
PUBLISHER = {Oxford University Press},
}
@article{Draminski-Rada-Iglesias-Enroth-Wadelius-Koronacki-Komorowski/08,
AUTHOR = {Drami{\'n}ski, Micha{\l} and Rada-Iglesias, Alvaro and Enroth, Stefan and Wadelius, Claes and Koronacki, Jacek and Komorowski, Jan},
TITLE = {Monte Carlo feature selection for supervised classification},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {1},
PAGES = {110-117},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm486},
PUBLISHER = {Oxford University Press},
}
@article{Capriotti-Marti-Renom/08,
AUTHOR = {Capriotti, Emidio and Marti-Renom, Marc A.},
TITLE = {RNA structure alignment by a unit-vector approach},
BOOKTITLE = {Proceedings of the 7th European Conference on Computational Biology, ECCB'2008 (Cagliari, Sardinia, Italy, September 22-26, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {112-118},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn288},
PUBLISHER = {Oxford University Press},
}
@article{Kim-Yoon-Yang/08,
AUTHOR = {Kim, Seonho and Yoon, Juntae and Yang, Jihoon},
TITLE = {Kernel approaches for genic interaction extraction},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {1},
PAGES = {118-126},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm544},
PUBLISHER = {Oxford University Press},
}
@article{Hakenberg-Plake-Leaman-Schroeder-Gonzalez/08,
AUTHOR = {Hakenberg, J{\"{o}}rg and Plake, Conrad and Leaman, Robert and Schroeder, Michael and Gonzalez, Graciela},
TITLE = {Inter-species normalization of gene mentions with GNAT},
BOOKTITLE = {Proceedings of the 7th European Conference on Computational Biology, ECCB'2008 (Cagliari, Sardinia, Italy, September 22-26, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {126-132},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn299},
PUBLISHER = {Oxford University Press},
}
@article{Harmon-Weir-Brock-Glor-Challenger/08,
AUTHOR = {Harmon, Luke J. and Weir, Jason T. and Brock, Chad D. and Glor, Richard E. and Challenger, Wendell},
TITLE = {GEIGER: Investigating evolutionary radiations},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {1},
PAGES = {129-131},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm538},
PUBLISHER = {Oxford University Press},
}
@article{Bansal-Eulenstein/08,
AUTHOR = {Bansal, Mukul S. and Eulenstein, Oliver},
TITLE = {The multiple gene duplication problem revisited},
BOOKTITLE = {Proceedings of the 16th International Conference on Intelligent Systems for Molecular Biology, ISMB'2008 (Toronto, Canada, July 19-23, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {132-138},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn150},
PUBLISHER = {Oxford University Press},
}
@article{Kahn-Raphael/08,
AUTHOR = {Kahn, Crystal L. and Raphael, Benjamin J.},
TITLE = {Analysis of segmental duplications via duplication distance},
BOOKTITLE = {Proceedings of the 7th European Conference on Computational Biology, ECCB'2008 (Cagliari, Sardinia, Italy, September 22-26, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {133-138},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn292},
PUBLISHER = {Oxford University Press},
}
@article{Lama-Girolami/08,
AUTHOR = {Lama, Nicola and Girolami, Mark},
TITLE = {vbmp: Variational Bayesian Multinomial Probit Regression for multi-class classification in R},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {1},
PAGES = {135-136},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm535},
PUBLISHER = {Oxford University Press},
}
@article{Ben-Yaacov-Eldar/08,
AUTHOR = {Ben-Yaacov, Erez and Eldar, Yonina C.},
TITLE = {A fast and flexible method for the segmentation of aCGH data},
BOOKTITLE = {Proceedings of the 7th European Conference on Computational Biology, ECCB'2008 (Cagliari, Sardinia, Italy, September 22-26, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {139-145},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn272},
PUBLISHER = {Oxford University Press},
}
@article{Jourdan-Breitling-Barrett-Gilbert/08,
AUTHOR = {Jourdan, Fabien and Breitling, Rainer and Barrett, Michael P. and Gilbert, David},
TITLE = {MetaNetter: Inference and visualization of high-resolution metabolomic networks},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {1},
PAGES = {143-145},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm536},
PUBLISHER = {Oxford University Press},
}
@article{Bansal-Bafna/08,
AUTHOR = {Bansal, Vikas and Bafna, Vineet},
TITLE = {HapCUT: An efficient and accurate algorithm for the haplotype assembly problem},
BOOKTITLE = {Proceedings of the 7th European Conference on Computational Biology, ECCB'2008 (Cagliari, Sardinia, Italy, September 22-26, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {153-159},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn298},
PUBLISHER = {Oxford University Press},
}
@article{Costa-Roepcke-Hafemeister-Schliep/08,
AUTHOR = {Costa, Ivan G. and Roepcke, Stefan and Hafemeister, Christoph and Schliep, Alexander},
TITLE = {Inferring differentiation pathways from gene expression},
BOOKTITLE = {Proceedings of the 16th International Conference on Intelligent Systems for Molecular Biology, ISMB'2008 (Toronto, Canada, July 19-23, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {156-164},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn153},
PUBLISHER = {Oxford University Press},
}
@article{Hertel-Hofacker-Stadler/08,
AUTHOR = {Hertel, Jana and Hofacker, Ivo L. and Stadler, Peter F.},
TITLE = {SnoReport: Computational identification of snoRNAs with unknown targets},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {2},
PAGES = {158-164},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm464},
PUBLISHER = {Oxford University Press},
}
@article{Hashimoto-Takigawa-Shiga-Kanehisa-Mamitsuka/08,
AUTHOR = {Hashimoto, Kosuke and Takigawa, Ichigaku and Shiga, Motoki and Kanehisa, Minoru and Mamitsuka, Hiroshi},
TITLE = {Mining significant tree patterns in carbohydrate sugar chains},
BOOKTITLE = {Proceedings of the 7th European Conference on Computational Biology, ECCB'2008 (Cagliari, Sardinia, Italy, September 22-26, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {167-173},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn293},
PUBLISHER = {Oxford University Press},
}
@article{Knijnenburg-Wessels-Reinders/08,
AUTHOR = {Knijnenburg, T.A. and Wessels, L.F.A. and Reinders, M.J.T.},
TITLE = {Combinatorial influence of environmental parameters on transcription factor activity},
BOOKTITLE = {Proceedings of the 16th International Conference on Intelligent Systems for Molecular Biology, ISMB'2008 (Toronto, Canada, July 19-23, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {172-181},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn155},
PUBLISHER = {Oxford University Press},
}
@article{De_Bona-Ossowski-Schneeberger-Ratsch/08,
AUTHOR = {De Bona, Fabio and Ossowski, Stephan and Schneeberger, Korbinian and R{\"{a}}tsch, Gunnar},
TITLE = {Optimal spliced alignments of short sequence reads},
BOOKTITLE = {Proceedings of the 7th European Conference on Computational Biology, ECCB'2008 (Cagliari, Sardinia, Italy, September 22-26, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {174-180},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn300},
PUBLISHER = {Oxford University Press},
}
@article{Joshi-Van_de_Peer-Michoel/08,
AUTHOR = {Joshi, Anagha and Van de Peer, Yves and Michoel, Tom},
TITLE = {Analysis of a Gibbs sampler method for model-based clustering of gene expression data},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {2},
PAGES = {176-183},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm562},
PUBLISHER = {Oxford University Press},
}
@article{Kim-Kim/08,
AUTHOR = {Kim, Jaehee and Kim, Haseong},
TITLE = {Clustering of change patterns using Fourier coefficients},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {2},
PAGES = {184-191},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm568},
PUBLISHER = {Oxford University Press},
}
@article{Georgiev-Keedy-Richardson-Richardson-Donald/08,
AUTHOR = {Georgiev, Ivelin and Keedy, Daniel and Richardson, Jane S. and Richardson, David C. and Donald, Bruce R.},
TITLE = {Algorithm for backrub motions in protein design},
BOOKTITLE = {Proceedings of the 16th International Conference on Intelligent Systems for Molecular Biology, ISMB'2008 (Toronto, Canada, July 19-23, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {196-204},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn169},
PUBLISHER = {Oxford University Press},
}
@article{Bromberg-Rost/08,
AUTHOR = {Bromberg, Yana and Rost, Burkhard},
TITLE = {Comprehensive in silico mutagenesis highlights functionally important residues in proteins},
BOOKTITLE = {Proceedings of the 7th European Conference on Computational Biology, ECCB'2008 (Cagliari, Sardinia, Italy, September 22-26, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {207-212},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn268},
PUBLISHER = {Oxford University Press},
}
@article{Hardy-Robillard/08,
AUTHOR = {Hardy, Simon and Robillard, Pierre N.},
TITLE = {Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {2},
PAGES = {209-217},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm560},
PUBLISHER = {Oxford University Press},
}
@article{Fromer-Yanover/08,
AUTHOR = {Fromer, Menachem and Yanover, Chen},
TITLE = {A computational framework to empower probabilistic protein design},
BOOKTITLE = {Proceedings of the 16th International Conference on Intelligent Systems for Molecular Biology, ISMB'2008 (Toronto, Canada, July 19-23, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {214-222},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn168},
PUBLISHER = {Oxford University Press},
}
@article{Dittrich-Klau-Rosenwald-Dandekar-Muller/08,
AUTHOR = {Dittrich, Marcus T. and Klau, Gunnar W. and Rosenwald, Andreas and Dandekar, Thomas and M{\"{u}}ller, Tobias},
TITLE = {Identifying functional modules in protein-protein interaction networks: An integrated exact approach},
BOOKTITLE = {Proceedings of the 16th International Conference on Intelligent Systems for Molecular Biology, ISMB'2008 (Toronto, Canada, July 19-23, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {223-231},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn161},
PUBLISHER = {Oxford University Press},
}
@article{Faulon-Misra-Martin-Sale-Sapra/08,
AUTHOR = {Faulon, Jean-Loup and Misra, Milind and Martin, Shawn and Sale, Ken and Sapra, Rajat},
TITLE = {Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {2},
PAGES = {225-233},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm580},
PUBLISHER = {Oxford University Press},
}
@article{Gonzalez-Chaouiya-Thieffry/08,
AUTHOR = {Gonz{\'{a}}lez, Aitor and Chaouiya, Claudine and Thieffry, Denis},
TITLE = {Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc},
BOOKTITLE = {Proceedings of the 7th European Conference on Computational Biology, ECCB'2008 (Cagliari, Sardinia, Italy, September 22-26, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {234-240},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn266},
PUBLISHER = {Oxford University Press},
}
@article{Alon-Dao-Hajirasouliha-Hormozdiari-Sahinalp/08,
AUTHOR = {Alon, Noga and Dao, Phuong and Hajirasouliha, Iman and Hormozdiari, Fereydoun and Sahinalp, S. Cenk},
TITLE = {Biomolecular network motif counting and discovery by color coding},
BOOKTITLE = {Proceedings of the 16th International Conference on Intelligent Systems for Molecular Biology, ISMB'2008 (Toronto, Canada, July 19-23, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {241-249},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn163},
PUBLISHER = {Oxford University Press},
}
@article{Errami-Hicks-Fisher-Trusty-Wren-Long-Garner/08,
AUTHOR = {Errami, Mounir and Hicks, Justin M. and Fisher, Wayne and Trusty, David and Wren, Jonathan D. and Long, Tara C. and Garner, Harold R.},
TITLE = {D{\'{e}}j{\`{a}} vu --- A study of duplicate citations in Medline},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {2},
PAGES = {243-249},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm574},
PUBLISHER = {Oxford University Press},
}
@article{Kronek-Reddy/08,
AUTHOR = {Kronek, Louis-Philippe and Reddy, Anupama},
TITLE = {Logical analysis of survival data: Prognostic survival models by detecting high-degree interactions in right-censored data},
BOOKTITLE = {Proceedings of the 7th European Conference on Computational Biology, ECCB'2008 (Cagliari, Sardinia, Italy, September 22-26, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {248-253},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn265},
PUBLISHER = {Oxford University Press},
}
@article{Jurman-Merler-Barla-Paoli-Galea-Furlanello/08,
AUTHOR = {Jurman, Giuseppe and Merler, Stefano and Barla, Annalisa and Paoli, Silvano and Galea, Antonio and Furlanello, Cesare},
TITLE = {Algebraic stability indicators for ranked lists in molecular profiling},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {2},
PAGES = {258-264},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm550},
PUBLISHER = {Oxford University Press},
}
@article{Klinger-Kolarik-Fluck-Hofmann-Apitius-Friedrich/08,
AUTHOR = {Klinger, Roman and Kol{\'{a}}rik, Corinna and Fluck, Juliane and Hofmann-Apitius, Martin and Friedrich, Christoph M.},
TITLE = {Detection of IUPAC and IUPAC-like chemical names},
BOOKTITLE = {Proceedings of the 16th International Conference on Intelligent Systems for Molecular Biology, ISMB'2008 (Toronto, Canada, July 19-23, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {268-276},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn181},
PUBLISHER = {Oxford University Press},
}
@article{Angyan-Perczel-Pongor-Gaspari/08,
AUTHOR = {{\'{A}}ngy{\'{a}}n, Annam{\'{a}}ria F. and Perczel, Andr{\'{a}}s and Pongor, S{\'{a}}ndor and G{\'{a}}sp{\'{a}}ri, Zolt{\'{a}}n},
TITLE = {Fast protein fold estimation from NMR-derived distance restraints},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {2},
PAGES = {272-275},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm564},
PUBLISHER = {Oxford University Press},
}
@article{Fuchsberger-Falchi-Forer-Pramstaller/08,
AUTHOR = {Fuchsberger, Christian and Falchi, Mario and Forer, Lukas and Pramstaller, Peter P.},
TITLE = {PedVizApi: A Java API for the interactive, visual analysis of extended pedigrees},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {2},
PAGES = {279-281},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm577},
PUBLISHER = {Oxford University Press},
}
@article{Assenov-Ramirez-Schelhorn-Lengauer-Albrecht/08,
AUTHOR = {Assenov, Yassen and Ram{\'{i}}rez, Fidel and Schelhorn, Sven-Eric and Lengauer, Thomas and Albrecht, Mario},
TITLE = {Computing topological parameters of biological networks},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {2},
PAGES = {282-284},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm554},
PUBLISHER = {Oxford University Press},
}
@article{Evans-Gillespie-Wilkinson/08,
AUTHOR = {Evans, Thomas W. and Gillespie, Colin S. and Wilkinson, Darren J.},
TITLE = {The SBML discrete stochastic models test suite},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {2},
PAGES = {285-286},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm566},
PUBLISHER = {Oxford University Press},
}
@article{Hsu-Chang-Kuo-Lin-Huang-Chung/08,
AUTHOR = {Hsu, Chun-Nan and Chang, Yu-Ming and Kuo, Cheng-Ju and Lin, Yu-Shi and Huang, Han-Shen and Chung, I-Fang},
TITLE = {Integrating high dimensional bi-directional parsing models for gene mention tagging},
BOOKTITLE = {Proceedings of the 16th International Conference on Intelligent Systems for Molecular Biology, ISMB'2008 (Toronto, Canada, July 19-23, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {286-294},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn183},
PUBLISHER = {Oxford University Press},
}
@article{Kachalo-Zhang-Sontag-Albert-DasGupta/08,
AUTHOR = {Kachalo, Sema and Zhang, Ranran and Sontag, Eduardo and Albert, R{\'{e}}ka and DasGupta, Bhaskar},
TITLE = {NET-SYNTHESIS: A software for synthesis, inference and simplification of signal transduction networks},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {2},
PAGES = {293-295},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm571},
PUBLISHER = {Oxford University Press},
}
@article{Fujita-Iba/08,
AUTHOR = {Fujita, Shuji and Iba, Hideo},
TITLE = {Putative promoter regions of miRNA genes involved in evolutionarily conserved regulatory systems among vertebrates},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {3},
PAGES = {303-308},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm589},
PUBLISHER = {Oxford University Press},
}
@article{Huttenhower-Troyanskaya/08,
AUTHOR = {Huttenhower, C. and Troyanskaya, O.G.},
TITLE = {Assessing the functional structure of genomic data},
BOOKTITLE = {Proceedings of the 16th International Conference on Intelligent Systems for Molecular Biology, ISMB'2008 (Toronto, Canada, July 19-23, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {330-338},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn160},
PUBLISHER = {Oxford University Press},
}
@article{Dunn-Wahl-Gloor/08,
AUTHOR = {Dunn, S.D. and Wahl, L.M. and Gloor, G.B.},
TITLE = {Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {3},
PAGES = {333-340},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm604},
PUBLISHER = {Oxford University Press},
}
@article{Chan-Leung-Lee/08,
AUTHOR = {Chan, Tak-Ming and Leung, Kwong-Sak and Lee, Kin-Hong},
TITLE = {TFBS identification based on genetic algorithm with combined representations and adaptive post-processing},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {3},
PAGES = {341-349},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm606},
PUBLISHER = {Oxford University Press},
}
@article{Klammer-Reynolds-Bilmes-MacCoss-Noble/08,
AUTHOR = {Klammer, Aaron A. and Reynolds, Sheila M. and Bilmes, Jeff A. and MacCoss, Michael J. and Noble, William Stafford},
TITLE = {Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification},
BOOKTITLE = {Proceedings of the 16th International Conference on Intelligent Systems for Molecular Biology, ISMB'2008 (Toronto, Canada, July 19-23, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {348-356},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn189},
PUBLISHER = {Oxford University Press},
}
@article{Baldi-Benz/08,
AUTHOR = {Baldi, Pierre and Benz, Ryan W.},
TITLE = {BLASTing small molecules --- Statistics and extreme statistics of chemical similarity scores},
BOOKTITLE = {Proceedings of the 16th International Conference on Intelligent Systems for Molecular Biology, ISMB'2008 (Toronto, Canada, July 19-23, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {357-365},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn187},
PUBLISHER = {Oxford University Press},
}
@article{Jacob-Vert/08,
AUTHOR = {Jacob, Laurent and Vert, Jean-Philippe},
TITLE = {Efficient peptide-MHC-I binding prediction for alleles with few known binders},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {3},
PAGES = {358-366},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm611},
PUBLISHER = {Oxford University Press},
}
@article{Cao-Jiang-Girke/08,
AUTHOR = {Cao, Yiqun and Jiang, Tao and Girke, Thomas},
TITLE = {A maximum common substructure-based algorithm for searching and predicting drug-like compounds},
BOOKTITLE = {Proceedings of the 16th International Conference on Intelligent Systems for Molecular Biology, ISMB'2008 (Toronto, Canada, July 19-23, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {366-374},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn186},
PUBLISHER = {Oxford University Press},
}
@article{Kiryu-Kin-Asai/08,
AUTHOR = {Kiryu, Hisanori and Kin, Taishin and Asai, Kiyoshi},
TITLE = {Rfold: An exact algorithm for computing local base pairing probabilities},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {3},
PAGES = {367-373},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm591},
PUBLISHER = {Oxford University Press},
}
@article{Hong-Breitling/08,
AUTHOR = {Hong, Fangxin and Breitling, Rainer},
TITLE = {A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {3},
PAGES = {374-382},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm620},
PUBLISHER = {Oxford University Press},
}
@article{Ho-Stefani-dos_Remedios-Charleston/08,
AUTHOR = {Ho, Joshua W.K. and Stefani, Maurizio and dos Remedios, Cristobal G. and Charleston, Michael A.},
TITLE = {Differential variability analysis of gene expression and its application to human diseases},
BOOKTITLE = {Proceedings of the 16th International Conference on Intelligent Systems for Molecular Biology, ISMB'2008 (Toronto, Canada, July 19-23, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {390-398},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn142},
PUBLISHER = {Oxford University Press},
}
@article{Bandeira-Olsen-Mann-Pevzner/08,
AUTHOR = {Bandeira, Nuno and Olsen, Jesper V. and Mann, Matthias and Pevzner, Pavel A.},
TITLE = {Multi-spectra peptide sequencing and its applications to multistage mass spectrometry},
BOOKTITLE = {Proceedings of the 16th International Conference on Intelligent Systems for Molecular Biology, ISMB'2008 (Toronto, Canada, July 19-23, 2008)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {416-423},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn184},
PUBLISHER = {Oxford University Press},
}
@article{Kim-Jung-Rhyu-Jung-Chung/08,
AUTHOR = {Kim, Tae-Min and Jung, Yu-Chae and Rhyu, Mun-Gan and Jung, Myeong Ho and Chung, Yeun-Jun},
TITLE = {GEAR: Genomic enrichment analysis of regional DNA copy number changes},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {3},
PAGES = {420-421},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm582},
PUBLISHER = {Oxford University Press},
}
@article{Alberts-Vera-Jansen/08,
AUTHOR = {Alberts, Rudi and Vera, Gonzalo and Jansen, Ritsert C.},
TITLE = {affyGG: Computational protocols for genetical genomics with Affymetrix arrays},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {3},
PAGES = {433-434},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm614},
PUBLISHER = {Oxford University Press},
}
@article{Aitken-Chen-Bard/08,
AUTHOR = {Aitken, Stuart and Chen, Yin and Bard, Jonathan},
TITLE = {OBO Explorer: An editor for open biomedical ontologies in OWL},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {3},
PAGES = {443-444},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm593},
PUBLISHER = {Oxford University Press},
}
@article{Kaas-Westermann-Halai-Wang-Craik/08,
AUTHOR = {Kaas, Quentin and Westermann, Jan-C. and Halai, Reena and Wang, Conan K.L. and Craik, David J.},
TITLE = {ConoServer, a database for conopeptide sequences and structures},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {3},
PAGES = {445-446},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm596},
PUBLISHER = {Oxford University Press},
}
@article{Alterovitz-Jiwaji-Ramoni/08,
AUTHOR = {Alterovitz, Gil and Jiwaji, Adnaan and Ramoni, Marco F.},
TITLE = {Automated programming for bioinformatics algorithm deployment},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {3},
PAGES = {450-451},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm602},
PUBLISHER = {Oxford University Press},
}
@article{Chua-Sung-Wong/08,
AUTHOR = {Chua, Hon Nian and Sung, Wing-Kin and Wong, Limsoon},
TITLE = {Erratum to ``Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions''},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {3},
PAGES = {452-452},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm609},
PUBLISHER = {Oxford University Press},
NOTE = {Originally in Bioinformatics Vol. 22, 2006, No. 13, 1623-1630},
}
@article{Abhiman-Iyer-Aravind/08,
AUTHOR = {Abhiman, Saraswathi and Iyer, Lakshminarayan M. and Aravind, L.},
TITLE = {BEN: A novel domain in chromatin factors and DNA viral proteins},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {4},
PAGES = {458-461},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn007},
PUBLISHER = {Oxford University Press},
}
@article{Ginodi-Vider-Shalit-Tsaban-Louzoun/08,
AUTHOR = {Ginodi, Ido and Vider-Shalit, Tal and Tsaban, Lea and Louzoun, Yoram},
TITLE = {Precise score for the prediction of peptides cleaved by the proteasome},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {4},
PAGES = {477-483},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm616},
PUBLISHER = {Oxford University Press},
}
@article{Gunewardena-Zhang/08,
AUTHOR = {Gunewardena, Sumedha and Zhang, Zhaolei},
TITLE = {A hybrid model for robust detection of transcription factor binding sites},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {4},
PAGES = {484-491},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm629},
PUBLISHER = {Oxford University Press},
}
@article{Hinsen/08,
AUTHOR = {Hinsen, Konrad},
TITLE = {Structural flexibility in proteins: Impact of the crystal environment},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {4},
PAGES = {521-528},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm625},
PUBLISHER = {Oxford University Press},
}
@article{Goeman-Mansmann/08,
AUTHOR = {Goeman, Jelle J. and Mansmann, Ulrich},
TITLE = {Multiple testing on the directed acyclic graph of gene ontology},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {4},
PAGES = {537-544},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm628},
PUBLISHER = {Oxford University Press},
}
@article{Datta-Zhao/08,
AUTHOR = {Datta, Debayan and Zhao, Hongyu},
TITLE = {Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {4},
PAGES = {545-552},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm523},
PUBLISHER = {Oxford University Press},
}
@article{Bendana-Holmes/08,
AUTHOR = {Benda{\~{n}}a, Yuri R. and Holmes, Ian H.},
TITLE = {Colorstock, SScolor, Rat{\'{o}}n: RNA alignment visualization tools},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {4},
PAGES = {579-580},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm635},
PUBLISHER = {Oxford University Press},
}
@article{Gront-Kolinski/08,
AUTHOR = {Gront, Dominik and Kolinski, Andrzej},
TITLE = {Utility library for structural bioinformatics},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {4},
PAGES = {584-585},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm627},
PUBLISHER = {Oxford University Press},
}
@article{Adler-Reimand-Janes-Kolde-Peterson-Vilo/08,
AUTHOR = {Adler, Priit and Reimand, J{\"{u}}ri and J{\"{a}}nes, J{\"{u}}rgen and Kolde, Raivo and Peterson, Hedi and Vilo, Jaak},
TITLE = {KEGGanim: Pathway animations for high-throughput data},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {4},
PAGES = {588-590},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm581},
PUBLISHER = {Oxford University Press},
}
@article{Bocker-Liptak-Martin-Pervukhin-Sudek/08,
AUTHOR = {B{\"{o}}cker, Sebastian and Lipt{\'{a}}k, Zsuzsanna and Martin, Marcel and Pervukhin, Anton and Sudek, Henner},
TITLE = {DECOMP --- From interpreting Mass Spectrometry peaks to solving the Money Changing Problem},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {4},
PAGES = {591-593},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm631},
PUBLISHER = {Oxford University Press},
}
@article{Kalaev-Smoot-Ideker-Sharan/08,
AUTHOR = {Kalaev, Maxim and Smoot, Mike and Ideker, Trey and Sharan, Roded},
TITLE = {NetworkBLAST: Comparative analysis of protein networks},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {4},
PAGES = {594-596},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm630},
PUBLISHER = {Oxford University Press},
}
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AUTHOR = {Fischer, J.D. and Mayer, C.E. and S{\"{o}}ding, J.},
TITLE = {Prediction of protein functional residues from sequence by probability density estimation},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {5},
PAGES = {613-620},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm626},
PUBLISHER = {Oxford University Press},
}
@article{Konagurthu-Stuckey-Lesk/08,
AUTHOR = {Konagurthu, Arun S. and Stuckey, Peter J. and Lesk, Arthur M.},
TITLE = {Structural search and retrieval using a tableau representation of protein folding patterns},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {5},
PAGES = {645-651},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm641},
PUBLISHER = {Oxford University Press},
}
@article{Bernauer-Bahadur-Rodier-Janin-Poupon/08,
AUTHOR = {Bernauer, Julie and Bahadur, Ranjit Prasad and Rodier, Francis and Janin, Jo{\"{e}}l and Poupon, Anne},
TITLE = {DiMoVo: A Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {5},
PAGES = {652-658},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn022},
PUBLISHER = {Oxford University Press},
}
@article{Chen-Xiao/08,
AUTHOR = {Chen, Changjun and Xiao, Yi},
TITLE = {Observation of multiple folding pathways of $\beta$-hairpin trpzip2 from independent continuous folding trajectories},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {5},
PAGES = {659-665},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn029},
PUBLISHER = {Oxford University Press},
}
@article{Lai/08,
AUTHOR = {Lai, Yinglei},
TITLE = {Genome-wide co-expression based prediction of differential expressions},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {5},
PAGES = {666-673},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm507},
PUBLISHER = {Oxford University Press},
}
@article{Khatun-Hamlett-Giddings/08,
AUTHOR = {Khatun, Jainab and Hamlett, Eric and Giddings, Morgan C.},
TITLE = {Incorporating sequence information into the scoring function: A hidden Markov model for improved peptide identification},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {5},
PAGES = {674-681},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn011},
PUBLISHER = {Oxford University Press},
}
@article{Brehelin-Gascuel-Martin/08,
AUTHOR = {Br{\'{e}}h{\'{e}}lin, Laurent and Gascuel, Olivier and Martin, Olivier},
TITLE = {Using repeated measurements to validate hierarchical gene clusters},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {5},
PAGES = {682-688},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn017},
PUBLISHER = {Oxford University Press},
}
@article{Kremling-Bettenbrock-Gilles/08,
AUTHOR = {Kremling, A. and Bettenbrock, K. and Gilles, E.D.},
TITLE = {A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {5},
PAGES = {704-710},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn010},
PUBLISHER = {Oxford University Press},
}
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AUTHOR = {Gog, Simon and Bader, Martin and Ohlebusch, Enno},
TITLE = {GENESIS: Genome evolution scenarios},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {5},
PAGES = {711-712},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn026},
PUBLISHER = {Oxford University Press},
}
@article{Langfelder-Zhang-Horvath/08,
AUTHOR = {Langfelder, Peter and Zhang, Bin and Horvath, Steve},
TITLE = {Defining clusters from a hierarchical cluster tree: The Dynamic Tree Cut package for R},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {5},
PAGES = {719-720},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm563},
PUBLISHER = {Oxford University Press},
}
@article{Falchi-Fuchsberger/08,
AUTHOR = {Falchi, Mario and Fuchsberger, Christian},
TITLE = {Jenti: An efficient tool for mining complex inbred genealogies},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {5},
PAGES = {724-726},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm617},
PUBLISHER = {Oxford University Press},
}
@article{Draghici-Tarca-Yu-Ethier-Romero/08,
AUTHOR = {Draghici, Sorin and Tarca, Adi L. and Yu, Longfei and Ethier, Stephen and Romero, Roberto},
TITLE = {KUTE-BASE: Storing, downloading and exporting MIAME-compliant microarray experiments in minutes rather than hours},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {5},
PAGES = {738-740},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm559},
PUBLISHER = {Oxford University Press},
}
@article{Grandison-Morris/08,
AUTHOR = {Grandison, Scott and Morris, Richard J.},
TITLE = {Biological pathway kinetic rate constants are scale-invariant},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {6},
PAGES = {741-743},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn041},
PUBLISHER = {Oxford University Press},
}
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AUTHOR = {Choi, Jeong-Hyeon and Kim, Sun and Tang, Haixu and Andrews, Justen and Gilbert, Don G. and Colbourne, John K.},
TITLE = {A machine-learning approach to combined evidence validation of genome assemblies},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {6},
PAGES = {744-750},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm608},
PUBLISHER = {Oxford University Press},
}
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AUTHOR = {Andersson, Robin and Bruder, Carl E.G. and Piotrowski, Arkadiusz and Menzel, Uwe and Nord, Helena and Sandgren, Johanna and Hvidsten, Torgeir R. and Diaz de St{\aa}hl, Teresita and Dumanski, Jan P. and Komorowski, Jan},
TITLE = {A segmental maximum a posteriori approach to genome-wide copy number profiling},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {6},
PAGES = {751-758},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn003},
PUBLISHER = {Oxford University Press},
}
@article{Bengtsson-Irizarry-Carvalho-Speed/08,
AUTHOR = {Bengtsson, H. and Irizarry, R. and Carvalho, B. and Speed, T.P.},
TITLE = {Estimation and assessment of raw copy numbers at the single locus level},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {6},
PAGES = {759-767},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn016},
PUBLISHER = {Oxford University Press},
}
@article{Lam-Sung-Tam-Wong-Yiu/08,
AUTHOR = {Lam, T.W. and Sung, W.K. and Tam, S.L. and Wong, C.K. and Yiu, S.M.},
TITLE = {Compressed indexing and local alignment of DNA},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {6},
PAGES = {791-797},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn032},
PUBLISHER = {Oxford University Press},
}
@article{Biegert-Soding/08,
AUTHOR = {Biegert, A. and S{\"{o}}ding, J.},
TITLE = {De novo identification of highly diverged protein repeats by probabilistic consistency},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {6},
PAGES = {807-814},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn039},
PUBLISHER = {Oxford University Press},
}
@article{Birin-Gal-Or-Elias-Tuller/08,
AUTHOR = {Birin, Hadas and Gal-Or, Zohar and Elias, Isaac and Tuller, Tamir},
TITLE = {Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {6},
PAGES = {826-832},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn024},
PUBLISHER = {Oxford University Press},
}
@article{Graziano-Kettoola-Munshower-Stapleton-Towfic/08,
AUTHOR = {Graziano, Frank M. and Kettoola, Samira Y. and Munshower, Judy M. and Stapleton, Jack T. and Towfic, George J.},
TITLE = {Effect of spatial distribution of T-Cells and HIV load on HIV progression},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {6},
PAGES = {855-860},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn008},
PUBLISHER = {Oxford University Press},
}
@article{Conant-Wolfe/08,
AUTHOR = {Conant, Gavin C. and Wolfe, Kenneth H.},
TITLE = {GenomeVx: Simple web-based creation of editable circular chromosome maps},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {6},
PAGES = {861-862},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm598},
PUBLISHER = {Oxford University Press},
}
@article{Derthick/08,
AUTHOR = {Derthick, Mark},
TITLE = {Interactive visualization software for exploring phylogenetic trees and clades},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {6},
PAGES = {868-869},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn038},
PUBLISHER = {Oxford University Press},
}
@article{Joo-Booth-Namkoong-Casella/08,
AUTHOR = {Joo, Yongsung and Booth, James G. and Namkoong, Younghwan and Casella, George},
TITLE = {Model-based Bayesian clustering (MBBC)},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {6},
PAGES = {874-875},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn030},
PUBLISHER = {Oxford University Press},
}
@article{Bornstein-Keating-Jouraku-Hucka/08,
AUTHOR = {Bornstein, Benjamin J. and Keating, Sarah M. and Jouraku, Akiya and Hucka, Michael},
TITLE = {LibSBML: An API Library for SBML},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {6},
PAGES = {880-881},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn051},
PUBLISHER = {Oxford University Press},
}
@article{Cho-Kim-Jung-Lee-Lee/08,
AUTHOR = {Cho, HyungJun and Kim, Yang-jin and Jung, Hee Jung and Lee, Sang-Won and Lee, Jae Won},
TITLE = {OutlierD: An R package for outlier detection using quantile regression on mass spectrometry data},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {6},
PAGES = {882-884},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn012},
PUBLISHER = {Oxford University Press},
}
@article{Antezana-Egana-De_Baets-Kuiper-Mironov/08,
AUTHOR = {Antezana, Erick and Ega{\~{n}}a, Mikel and De Baets, Bernard and Kuiper, Martin and Mironov, Vladimir},
TITLE = {ONTO-PERL: An API for supporting the development and analysis of bio-ontologies},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {6},
PAGES = {885-887},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn042},
PUBLISHER = {Oxford University Press},
}
@article{Hirose-Yoshida-Imoto-Yamaguchi-Higuchi-Charnock-Jones-Print-Miyano/08,
AUTHOR = {Hirose, Osamu and Yoshida, Ryo and Imoto, Seiya and Yamaguchi, Rui and Higuchi, Tomoyuki and Charnock-Jones, D. Stephen and Print, Cristin and Miyano, Satoru},
TITLE = {Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {7},
PAGES = {932-942},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm639},
PUBLISHER = {Oxford University Press},
}
@article{Ji-Lu-Mills/08,
AUTHOR = {Ji, Yuan and Lu, Yiling and Mills, Gordon B.},
TITLE = {Bayesian models based on test statistics for multiple hypothesis testing problems},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {7},
PAGES = {943-949},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn049},
PUBLISHER = {Oxford University Press},
}
@article{Dowsey-Dunn-Yang/08,
AUTHOR = {Dowsey, Andrew W. and Dunn, Michael J. and Yang, Guang-Zhong},
TITLE = {Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {7},
PAGES = {950-957},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn059},
PUBLISHER = {Oxford University Press},
}
@article{Kwon-Cho/08,
AUTHOR = {Kwon, Yung-Keun and Cho, Kwang-Hyun},
TITLE = {Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {7},
PAGES = {987-994},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn060},
PUBLISHER = {Oxford University Press},
}
@article{Jacob-Jentsch-Kostka-Bentink-Spang/08,
AUTHOR = {Jacob, Juby and Jentsch, Marcel and Kostka, Dennis and Bentink, Stefan and Spang, Rainer},
TITLE = {Detecting hierarchical structure in molecular characteristics of disease using transitive approximations of directed graphs},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {7},
PAGES = {995-1001},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn056},
PUBLISHER = {Oxford University Press},
}
@article{Kobayashi-Toyoda/08,
AUTHOR = {Kobayashi, Norio and Toyoda, Tetsuro},
TITLE = {Statistical search on the Semantic Web},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {7},
PAGES = {1002-1010},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn054},
PUBLISHER = {Oxford University Press},
}
@article{Lai-Choudhary-Park/08,
AUTHOR = {Lai, Weil and Choudhary, Vidhu and Park, Peter J.},
TITLE = {CGHweb: A tool for comparing DNA copy number segmentations from multiple algorithms},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {7},
PAGES = {1014-1015},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn067},
PUBLISHER = {Oxford University Press},
}
@article{He-Parkinson/08,
AUTHOR = {He, David and Parkinson, John},
TITLE = {SubSeqer: A graph-based approach for the detection and identification of repetitive elements in low-complexity sequences},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {7},
PAGES = {1016-1017},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn073},
PUBLISHER = {Oxford University Press},
}
@article{Denisov-Walenz-Halpern-Miller-Axelrod-Levy-Sutton/08,
AUTHOR = {Denisov, Gennady and Walenz, Brian and Halpern, Aaron L. and Miller, Jason and Axelrod, Nelson and Levy, Samuel and Sutton, Granger},
TITLE = {Consensus generation and variant detection by Celera Assembler},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {8},
PAGES = {1035-1040},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn074},
PUBLISHER = {Oxford University Press},
}
@article{Kliger-Gofer-Wool-Toporik-Apatoff-Olshansky/08,
AUTHOR = {Kliger, Yossef and Gofer, Eyal and Wool, Assaf and Toporik, Amir and Apatoff, Avihay and Olshansky, Moshe},
TITLE = {Predicting proteolytic sites in extracellular proteins: Only halfway there},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {8},
PAGES = {1049-1055},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn084},
PUBLISHER = {Oxford University Press},
}
@article{Futschik-Herzel/08,
AUTHOR = {Futschik, Matthias E. and Herzel, Hanspeter},
TITLE = {Are we overestimating the number of cell-cycling genes? The impact of background models on time-series analysis},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {8},
PAGES = {1063-1069},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn072},
PUBLISHER = {Oxford University Press},
}
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AUTHOR = {Du, Peicheng and Stolovitzky, Gustavo and Horvatovich, Peter and Bischoff, Rainer and Lim, Jihyeon and Suits, Frank},
TITLE = {A noise model for mass spectrometry based proteomics},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {8},
PAGES = {1070-1077},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn078},
PUBLISHER = {Oxford University Press},
}
@article{Higham-Rasajski-Przulj/08,
AUTHOR = {Higham, Desmond J. and Ra{\v{s}}ajski, Marija and Pr{\v{z}}ulj, Nata{\v{s}}a},
TITLE = {Fitting a geometric graph to a protein-protein interaction network},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {8},
PAGES = {1093-1099},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn079},
PUBLISHER = {Oxford University Press},
}
@article{Chiang-Li-Orchard-Kerrien-Hermjakob-Gentleman-Huber/08,
AUTHOR = {Chiang, Tony and Li, Nianhua and Orchard, Sandra and Kerrien, Samuel and Hermjakob, Henning and Gentleman, Robert and Huber, Wolfgang},
TITLE = {Rintact: Enabling computational analysis of molecular interaction data from the IntAct repository},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {8},
PAGES = {1100-1101},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm518},
PUBLISHER = {Oxford University Press},
}
@article{Douglas-Sandefur/08,
AUTHOR = {Douglas, Julie A. and Sandefur, Conner I.},
TITLE = {PedMine --- A simulated annealing algorithm to identify maximally unrelated individuals in population isolates},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {8},
PAGES = {1106-1108},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn087},
PUBLISHER = {Oxford University Press},
}
@article{Gladki-Siedlecki-Kaczanowski-Zielenkiewicz/08,
AUTHOR = {Gladki, Arek and Siedlecki, Pawel and Kaczanowski, Szymon and Zielenkiewicz, Piotr},
TITLE = {e-LiSe -- An online tool for finding needles in the ``(Medline) haystack''},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {8},
PAGES = {1115-1117},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn086},
PUBLISHER = {Oxford University Press},
}
@article{Chen-Guo-Fan-Jiang/08,
AUTHOR = {Chen, Xin and Guo, Lingqiong and Fan, Zhaocheng and Jiang, Tao},
TITLE = {W-AlignACE: An improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {9},
PAGES = {1121-1128},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn088},
PUBLISHER = {Oxford University Press},
}
@article{Demissie-Mascialino-Calza-Pawitan/08,
AUTHOR = {Demissie, Meaza and Mascialino, Barbara and Calza, Stefano and Pawitan, Yudi},
TITLE = {Unequal group variances in microarray data analyses},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {9},
PAGES = {1168-1174},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn100},
PUBLISHER = {Oxford University Press},
}
@article{Chuang-Jen-Chen-Shieh/08,
AUTHOR = {Chuang, Cheng-Long and Jen, Chih-Hung and Chen, Chung-Ming and Shieh, Grace S.},
TITLE = {A pattern recognition approach to infer time-lagged genetic interactions},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {9},
PAGES = {1183-1190},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn098},
PUBLISHER = {Oxford University Press},
}
@article{Jayawardhana-Kell-Rattray/08,
AUTHOR = {Jayawardhana, Bayu and Kell, Douglas B. and Rattray, Magnus},
TITLE = {Bayesian inference of the sites of perturbations in metabolic pathways via Markov chain Monte Carlo},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {9},
PAGES = {1191-1197},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn103},
PUBLISHER = {Oxford University Press},
}
@article{Abascal-Carmona-Saez-Carazo-Pascual-Montano/08,
AUTHOR = {Abascal, Federico and Carmona-Saez, Pedro and Carazo, Jose-Maria and Pascual-Montano, Alberto},
TITLE = {ChIPCodis: Mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {9},
PAGES = {1208-1209},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn094},
PUBLISHER = {Oxford University Press},
}
@article{Campbell-Royle-Radcliffe-Dwek-Rudd/08,
AUTHOR = {Campbell, Matthew P. and Royle, Louise and Radcliffe, Catherine M. and Dwek, Raymond A. and Rudd, Pauline M.},
TITLE = {GlycoBase and autoGU: Tools for HPLC-based glycan analysis},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {9},
PAGES = {1214-1216},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn090},
PUBLISHER = {Oxford University Press},
}
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AUTHOR = {Krabbenh{\"{o}}ft, Hajo N. and M{\"{o}}ller, Steffen and Bayer, Daniel},
TITLE = {Integrating ARC grid middleware with Taverna workflows},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {9},
PAGES = {1221-1222},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn095},
PUBLISHER = {Oxford University Press},
}
@article{Fujibuchi-Kiseleva-Taniguchi-Harada-Horton/08,
AUTHOR = {Fujibuchi, Wataru and Kiseleva, Larisa and Taniguchi, Takeaki and Harada, Hajime and Horton, Paul},
TITLE = {Erratum to ``CellMontage: Similar Expression Profile Search Server''},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {9},
PAGES = {1223-1223},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn101},
PUBLISHER = {Oxford University Press},
NOTE = {Originally in Bioinformatics, Vol. 23, 2007, No. 22, 3103-3104},
}
@article{Higdon-van_Belle-Kolker/08,
AUTHOR = {Higdon, Roger and van Belle, Gerald and Kolker, Eugene},
TITLE = {A note on the false discovery rate and inconsistent comparisons between experiments},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {10},
PAGES = {1225-1228},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn120},
PUBLISHER = {Oxford University Press},
}
@article{Gonzalez-Zimmer/08,
AUTHOR = {Gonzalez, Orland and Zimmer, Ralf},
TITLE = {Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {10},
PAGES = {1257-1263},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn106},
PUBLISHER = {Oxford University Press},
}
@article{Damoulas-Girolami/08,
AUTHOR = {Damoulas, Theodoros and Girolami, Mark A.},
TITLE = {Probabilistic multi-class multi-kernel learning: On protein fold recognition and remote homology detection},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {10},
PAGES = {1264-1270},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn112},
PUBLISHER = {Oxford University Press},
}
@article{Kim-Bates-Postlethwaite-Heslop-Harrison-Cho/08,
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TITLE = {Linear time-varying models can reveal non-linear interactions of biomolecular regulatory networks using multiple time-series data},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {10},
PAGES = {1286-1292},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn107},
PUBLISHER = {Oxford University Press},
}
@article{He-Yang-Yu/08,
AUTHOR = {He, Zengyou and Yang, Can and Yu, Weichuan},
TITLE = {Peak bagging for peptide mass fingerprinting},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {10},
PAGES = {1293-1299},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn123},
PUBLISHER = {Oxford University Press},
}
@article{Castrignano-DAntonio-Anselmo-Carrabino-DOnorio_De_Meo-DErchia-Licciulli-Mangiulli-Mignone-Pavesi-Picardi-Riva-Rizzi-Bonizzoni-Pesole/08,
AUTHOR = {Castrignan{\`o}, T. and D'Antonio, M. and Anselmo, A. and Carrabino, D. and D'Onorio De Meo, A. and D'Erchia, A.M. and Licciulli, F. and Mangiulli, M. and Mignone, F. and Pavesi, G. and Picardi, E. and Riva, A. and Rizzi, R. and Bonizzoni, P. and Pesole, G.},
TITLE = {ASPicDB: A database resource for alternative splicing analysis},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {10},
PAGES = {1300-1304},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn113},
PUBLISHER = {Oxford University Press},
}
@article{Albert-Wachi-Jiang-Pugh/08,
AUTHOR = {Albert, Istvan and Wachi, Shinichiro and Jiang, Cizhong and Pugh, B. Franklin},
TITLE = {GeneTrack --- A genomic data processing and visualization framework},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {10},
PAGES = {1305-1306},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn119},
PUBLISHER = {Oxford University Press},
}
@article{Edwards-Davey-Shields/08,
AUTHOR = {Edwards, Richard J. and Davey, Norman E. and Shields, Denis C.},
TITLE = {CompariMotif: Quick and easy comparisons of sequence motifs},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {10},
PAGES = {1307-1309},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn105},
PUBLISHER = {Oxford University Press},
}
@article{Hennig-Hennig-Sunnerhagen/08,
AUTHOR = {Hennig, Janosch and Hennig, Klaus D.M. and Sunnerhagen, Maria},
TITLE = {MTMDAT: Automated analysis and visualization of mass spectrometry data for tertiary and quaternary structure probing of proteins},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {10},
PAGES = {1310-1312},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn116},
PUBLISHER = {Oxford University Press},
}
@article{Chalk-Sonnhammer/08,
AUTHOR = {Chalk, Alistair M. and Sonnhammer, Erik L.L.},
TITLE = {siRNA specificity searching incorporating mismatch tolerance data},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {10},
PAGES = {1316-1317},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn121},
PUBLISHER = {Oxford University Press},
}
@article{Hannenhalli/08,
AUTHOR = {Hannenhalli, Sridhar},
TITLE = {Eukaryotic transcription factor binding sites --- Modeling and integrative search methods},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {11},
PAGES = {1325-1331},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn198},
PUBLISHER = {Oxford University Press},
}
@article{Dalevi-Eriksen/08,
AUTHOR = {Dalevi, Daniel and Eriksen, Niklas},
TITLE = {Expected gene-order distances and model selection in bacteria},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {11},
PAGES = {1332-1338},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn111},
PUBLISHER = {Oxford University Press},
}
@article{Ishida-Kinoshita/08,
AUTHOR = {Ishida, Takashi and Kinoshita, Kengo},
TITLE = {Prediction of disordered regions in proteins based on the meta approach},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {11},
PAGES = {1344-1348},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn195},
PUBLISHER = {Oxford University Press},
}
@article{Chang-Ding-Hung-Fung/08,
AUTHOR = {Chang, Chunqi and Ding, Zhi and Hung, Yeung Sam and Fung, Peter Chin Wan},
TITLE = {Fast network component analysis (FastNCA) for gene regulatory network reconstruction from microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {11},
PAGES = {1349-1358},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn131},
PUBLISHER = {Oxford University Press},
}
@article{Bhattacharya-De/08,
AUTHOR = {Bhattacharya, Anindya and De, Rajat K.},
TITLE = {Divisive Correlation Clustering Algorithm (DCCA) for grouping of genes: Detecting varying patterns in expression profiles},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {11},
PAGES = {1359-1366},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn133},
PUBLISHER = {Oxford University Press},
}
@article{Hackenberg-Matthiesen/08,
AUTHOR = {Hackenberg, Michael and Matthiesen, Rune},
TITLE = {Annotation-Modules: A tool for finding significant combinations of multisource annotations for gene lists},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {11},
PAGES = {1386-1393},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn178},
PUBLISHER = {Oxford University Press},
}
@article{Jombart/08,
AUTHOR = {Jombart, Thibaut},
TITLE = {adegenet: A R package for the multivariate analysis of genetic markers},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {11},
PAGES = {1403-1405},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn129},
PUBLISHER = {Oxford University Press},
}
@article{Guillot-Santos-Estoup/08,
AUTHOR = {Guillot, Gilles and Santos, Filipe and Estoup, Arnaud},
TITLE = {Analysing georeferenced population genetics data with Geneland: A new algorithm to deal with null alleles and a friendly graphical user interface},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {11},
PAGES = {1406-1407},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn136},
PUBLISHER = {Oxford University Press},
}
@article{Kim-Pezik-Rebholz-Schuhmann/08,
AUTHOR = {Kim, Jung-jae and P{\c{e}}zik, Piotr and Rebholz-Schuhmann, Dietrich},
TITLE = {MedEvi: Retrieving textual evidence of relations between biomedical concepts from MEDLINE},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {11},
PAGES = {1410-1412},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn117},
PUBLISHER = {Oxford University Press},
}
@article{Ha-Seo-Kwon-Chang-Han-Yoon/08,
AUTHOR = {Ha, Soyang and Seo, Young-Ju and Kwon, Min-Seok and Chang, Byung-Ha and Han, Cheol-Kyu and Yoon, Jeong-Hyeok},
TITLE = {IDMap: Facilitating the detection of potential leads with therapeutic targets},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {11},
PAGES = {1413-1415},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn138},
PUBLISHER = {Oxford University Press},
}
@article{Kojima-Nagasaki-Miyano/08,
AUTHOR = {Kojima, Kaname and Nagasaki, Masao and Miyano, Satoru},
TITLE = {Fast grid layout algorithm for biological networks with sweep calculation},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {12},
PAGES = {1433-1441},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn196},
PUBLISHER = {Oxford University Press},
}
@article{Bada-Hunter/08,
AUTHOR = {Bada, Michael and Hunter, Lawrence},
TITLE = {Identification of OBO nonalignments and its implications for OBO enrichment},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {12},
PAGES = {1448-1455},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn194},
PUBLISHER = {Oxford University Press},
}
@article{Ashkenazi-Bader-Kuchinsky-Moshelion-States/08,
AUTHOR = {Ashkenazi, Maital and Bader, Gary D. and Kuchinsky, Allan and Moshelion, Menachem and States, David J.},
TITLE = {Cytoscape ESP: Simple search of complex biological networks},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {12},
PAGES = {1465-1466},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn208},
PUBLISHER = {Oxford University Press},
}
@article{Klammer-Roopra-Sonnhammer/08,
AUTHOR = {Klammer, Martin and Roopra, Sanjit and Sonnhammer, Erik L.L.},
TITLE = {jSquid: A Java applet for graphical on-line network exploration},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {12},
PAGES = {1467-1468},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn213},
PUBLISHER = {Oxford University Press},
}
@article{Capra-Singh/08,
AUTHOR = {Capra, John A. and Singh, Mona},
TITLE = {Characterization and prediction of residues determining protein functional specificity},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {1473-1480},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn214},
PUBLISHER = {Oxford University Press},
}
@article{Cardona-Llabres-Rossello-Valiente/08,
AUTHOR = {Cardona, Gabriel and Llabr{\'{e}}s, Merc{\`{e}} and Rossell{\'{o}}, Francesc and Valiente, Gabriel},
TITLE = {A distance metric for a class of tree-sibling phylogenetic networks},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {1481-1488},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn231},
PUBLISHER = {Oxford University Press},
}
@article{Bogdan-Rivers-Beynon-Coca/08,
AUTHOR = {Bogd{\'{a}}n, Istv{\'{a}}n A. and Rivers, Jenny and Beynon, Robert J. and Coca, Daniel},
TITLE = {High-performance hardware implementation of a parallel database search engine for real-time peptide mass fingerprinting},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {1498-1502},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn216},
PUBLISHER = {Oxford University Press},
}
@article{Kim-Kim-Jung-Kim-Park-Heslop-Harrison-Cho/08,
AUTHOR = {Kim, Junil and Kim, Tae-Geon and Jung, Sung Hoon and Kim, Jeong-Rae and Park, Taesung and Heslop-Harrison, Pat and Cho, Kwang-Hyun},
TITLE = {Evolutionary design principles of modules that control cellular differentiation: Consequences for hysteresis and multistationarity},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {1516-1522},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn229},
PUBLISHER = {Oxford University Press},
}
@article{Kuznetsov/08,
AUTHOR = {Kuznetsov, Igor B.},
TITLE = {ProBias: A web-server for the identification of user-specified types of compositionally biased segments in protein sequences},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {1534-1535},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn233},
PUBLISHER = {Oxford University Press},
}
@article{Abraham-Rocha-Pothier/08,
AUTHOR = {Abraham, Anne-Laure and Rocha, Eduardo P.C. and Pothier, Jo{\"{e}}l},
TITLE = {Swelfe: A detector of internal repeats in sequences and structures},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {1536-1537},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn234},
PUBLISHER = {Oxford University Press},
}
@article{Csuuros/08,
AUTHOR = {Cs{\H{u}}ur{\"{o}}s, Mikl{\'{o}}s},
TITLE = {Malin: Maximum likelihood analysis of intron evolution in eukaryotes},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {1538-1539},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn226},
PUBLISHER = {Oxford University Press},
}
@article{Hazelhurst-Hide-Liptak-Nogueira-Starfield/08,
AUTHOR = {Hazelhurst, Scott and Hide, Winston and Lipt{\'{a}}k, Zsuzsanna and Nogueira, Ramon and Starfield, Richard},
TITLE = {An overview of the wcd EST clustering tool},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {1542-1546},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn203},
PUBLISHER = {Oxford University Press},
}
@article{Du-Kibbe-Lin/08,
AUTHOR = {Du, Pan and Kibbe, Warren A. and Lin, Simon M.},
TITLE = {lumi: A pipeline for processing Illumina microarray},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {1547-1548},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn224},
PUBLISHER = {Oxford University Press},
}
@article{Gilmore-Auberry-Sharp-White-Anderson-Daly/08,
AUTHOR = {Gilmore, Jason M. and Auberry, Deanna L. and Sharp, Julia L. and White, Amanda M. and Anderson, Kevin K. and Daly, Don S.},
TITLE = {A Bayesian estimator of protein-protein association probabilities},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {1554-1555},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn238},
PUBLISHER = {Oxford University Press},
}
@article{Huttenhower-Schroeder-Chikina-Troyanskaya/08,
AUTHOR = {Huttenhower, Curtis and Schroeder, Mark and Chikina, Maria D. and Troyanskaya, Olga G.},
TITLE = {The Sleipnir library for computational functional genomics},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {13},
PAGES = {1559-1561},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn237},
PUBLISHER = {Oxford University Press},
}
@article{Conley-Piriyapongsa-Jordan/08,
AUTHOR = {Conley, Andrew B. and Piriyapongsa, Jittima and Jordan, I. King},
TITLE = {Retroviral promoters in the human genome},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {14},
PAGES = {1563-1567},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn243},
PUBLISHER = {Oxford University Press},
}
@article{Ayers-Lange/08,
AUTHOR = {Ayers, Kristin L. and Lange, Kenneth},
TITLE = {Penalized estimation of haplotype frequencies},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {14},
PAGES = {1596-1602},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn236},
PUBLISHER = {Oxford University Press},
}
@article{Centler-Kaleta-Speroni_di_Fenizio-Dittrich/08,
AUTHOR = {Centler, Florian and Kaleta, Christoph and Speroni di Fenizio, Pietro and Dittrich, Peter},
TITLE = {Computing chemical organizations in biological networks},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {14},
PAGES = {1611-1618},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn228},
PUBLISHER = {Oxford University Press},
}
@article{Cao-Zhao/08,
AUTHOR = {Cao, Jiguo and Zhao, Hongyu},
TITLE = {Estimating dynamic models for gene regulation networks},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {14},
PAGES = {1619-1624},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn246},
PUBLISHER = {Oxford University Press},
}
@article{Evers-Messow/08,
AUTHOR = {Evers, Ludger and Messow, Claudia-Martina},
TITLE = {Sparse kernel methods for high-dimensional survival data},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {14},
PAGES = {1632-1638},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn253},
PUBLISHER = {Oxford University Press},
}
@article{Jordan-Piel/08,
AUTHOR = {Jordan, Gregory E. and Piel, William H.},
TITLE = {PhyloWidget: Web-based visualizations for the tree of life},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {14},
PAGES = {1641-1642},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn235},
PUBLISHER = {Oxford University Press},
}
@article{Kato-Nakamura-Tsunoda/08,
AUTHOR = {Kato, Mamoru and Nakamura, Yusuke and Tsunoda, Tatsuhiko},
TITLE = {MOCSphaser: A haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {14},
PAGES = {1645-1646},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn242},
PUBLISHER = {Oxford University Press},
}
@article{Bauer-Grossmann-Vingron-Robinson/08,
AUTHOR = {Bauer, Sebastian and Grossmann, Steffen and Vingron, Martin and Robinson, Peter N.},
TITLE = {Ontologizer 2.0 --- A multifunctional tool for GO term enrichment analysis and data exploration},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {14},
PAGES = {1650-1651},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn250},
PUBLISHER = {Oxford University Press},
}
@article{Khatun-Giddings/08,
AUTHOR = {Khatun, Jainab and Giddings, Morgan},
TITLE = {In response to ``On $E$-value for tandem MS scoring schemes''},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {14},
PAGES = {1654-1654},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn252},
PUBLISHER = {Oxford University Press},
}
@article{Jiao-Zhang/08,
AUTHOR = {Jiao, Shuo and Zhang, Shunpu},
TITLE = {On correcting the overestimation of the permutation-based false discovery rate estimator},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {15},
PAGES = {1655-1661},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn310},
PUBLISHER = {Oxford University Press},
}
@article{Forslund-Sonnhammer/08,
AUTHOR = {Forslund, Kristoffer and Sonnhammer, Erik L.L.},
TITLE = {Predicting protein function from domain content},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {15},
PAGES = {1681-1687},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn312},
PUBLISHER = {Oxford University Press},
NOTE = {see Erratum in Bioinformatics, Vol. 24, 2008, No. 19, 2275-2275},
}
@article{Boulesteix-Porzelius-Daumer/08,
AUTHOR = {Boulesteix, Anne-Laure and Porzelius, Christine and Daumer, Martin},
TITLE = {Microarray-based classification and clinical predictors: On combined classifiers and additional predictive value},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {15},
PAGES = {1698-1706},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn262},
PUBLISHER = {Oxford University Press},
}
@article{Greene-Cagney-Krogan-Cunningham/08,
AUTHOR = {Greene, Derek and Cagney, Gerard and Krogan, Nevan and Cunningham, P{\'{a}}draig},
TITLE = {Ensemble non-negative matrix factorization methods for clustering protein-protein interactions},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {15},
PAGES = {1722-1728},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn286},
PUBLISHER = {Oxford University Press},
}
@article{Fejes-Robertson-Bilenky-Varhol-Bainbridge-Jones/08,
AUTHOR = {Fejes, Anthony P. and Robertson, Gordon and Bilenky, Mikhail and Varhol, Richard and Bainbridge, Matthew and Jones, Steven J.M.},
TITLE = {FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {15},
PAGES = {1729-1730},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn305},
PUBLISHER = {Oxford University Press},
}
@article{Goni-Fenollosa-Perez-Torrents-Orozco/08,
AUTHOR = {Go{\~{n}}i, J. Ramon and Fenollosa, Carlos and P{\'{e}}rez, Alberto and Torrents, David and Orozco, Modesto},
TITLE = {DNAlive: A tool for the physical analysis of DNA at the genomic scale},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {15},
PAGES = {1731-1732},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn259},
PUBLISHER = {Oxford University Press},
}
@article{Cao-Charisi-Cheng-Jiang-Girke/08,
AUTHOR = {Cao, Yiqun and Charisi, Anna and Cheng, Li-Chang and Jiang, Tao and Girke, Thomas},
TITLE = {ChemmineR: A compound mining framework for R},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {15},
PAGES = {1733-1734},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn307},
PUBLISHER = {Oxford University Press},
}
@article{Goll-Rajagopala-Shiau-Wu-Lamb-Uetz/08,
AUTHOR = {Goll, Johannes and Rajagopala, Seesandra V. and Shiau, Shen C. and Wu, Hank and Lamb, Brian T. and Uetz, Peter},
TITLE = {MPIDP: The microbial protein interaction database},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {15},
PAGES = {1743-1744},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn285},
PUBLISHER = {Oxford University Press},
}
@article{Chen-Hsu-Jiang-Tsai-Yang-Meltzer-Chuang-Chen/08,
AUTHOR = {Chen, Hung-I Harry and Hsu, Fang-Han and Jiang, Yuan and Tsai, Mong-Hsun and Yang, Pan-Chyr and Meltzer, Paul S. and Chuang, Eric Y. and Chen, Yidong},
TITLE = {A probe-density-based analysis method for array CGH data: Simulation, normalization and centralization},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {1749-1756},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn321},
PUBLISHER = {Oxford University Press},
NOTE = {see Erratum in Bioinformatics, Vol. 24, 2008, No. 19, 2276-2276},
}
@article{Brown/08,
AUTHOR = {Brown, Duncan P.},
TITLE = {Efficient functional clustering of protein sequences using the Dirichlet process},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {1765-1771},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn244},
PUBLISHER = {Oxford University Press},
}
@article{Lambert-Terwilliger-Weiss/08,
AUTHOR = {Lambert, Brian W. and Terwilliger, Joseph D. and Weiss, Kenneth M.},
TITLE = {ForSim: A tool for exploring the genetic architecture of complex traits with controlled truth},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {1821-1822},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn317},
PUBLISHER = {Oxford University Press},
}
@article{Filangi-Beausse-Assi-Legrand-Larre-Martin-Collin-Caron-Leroy-Allouche/08,
AUTHOR = {Filangi, Olivier and Beausse, Yoann and Assi, Anthony and Legrand, Ludovic and Larr{\'{e}}, Jean-Marc and Martin, V{\'{e}}ronique and Collin, Olivier and Caron, Christophe and Leroy, Hugues and Allouche, David},
TITLE = {BioMAJ: A flexible framework for databanks synchronization and processing},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {16},
PAGES = {1823-1825},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn325},
PUBLISHER = {Oxford University Press},
}
@article{Ji-Sun-Jin-Kumar-Ye/08,
AUTHOR = {Ji, Shuiwang and Sun, Liang and Jin, Rong and Kumar, Sudhir and Ye, Jieping},
TITLE = {Automated annotation of Drosophila gene expression patterns using a controlled vocabulary},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {17},
PAGES = {1881-1888},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn347},
PUBLISHER = {Oxford University Press},
}
@article{Hanczar-Dougherty/08,
AUTHOR = {Hanczar, Blaise and Dougherty, Edward R.},
TITLE = {Classification with reject option in gene expression data},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {17},
PAGES = {1889-1895},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn349},
PUBLISHER = {Oxford University Press},
}
@article{Homer-Tembe-Szelinger-Redman-Stephan-Pearson-Nelson-Craig/08,
AUTHOR = {Homer, Nils and Tembe, Waibhav D. and Szelinger, Szabolcs and Redman, Margot and Stephan, Dietrich A. and Pearson, John V. and Nelson, Stanley F. and Craig, David},
TITLE = {Multimarker analysis and imputation of multiple platform pooling-based genome-wide association studies},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {17},
PAGES = {1896-1902},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn333},
PUBLISHER = {Oxford University Press},
}
@article{Garg-Di_Cara-Xenarios-Mendoza-De_Micheli/08,
AUTHOR = {Garg, Abhishek and Di Cara, Alessandro and Xenarios, Ioannis and Mendoza, Luis and De Micheli, Giovanni},
TITLE = {Synchronous versus asynchronous modeling of gene regulatory networks},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {17},
PAGES = {1917-1925},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn336},
PUBLISHER = {Oxford University Press},
}
@article{Kwon-Cho/08a,
AUTHOR = {Kwon, Yung-Keun and Cho, Kwang-Hyun},
TITLE = {Coherent coupling of feedback loops: A design principle of cell signaling networks},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {17},
PAGES = {1926-1932},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn337},
PUBLISHER = {Oxford University Press},
}
@article{Kim-Yim-Jeong-Jung-Chung/08,
AUTHOR = {Kim, Tae-Min and Yim, Seon-Hee and Jeong, Yong-Bok and Jung, Yu-Chae and Chung, Yeun-Jun},
TITLE = {PathCluster: A framework for gene set-based hierarchical clustering},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {17},
PAGES = {1957-1958},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn357},
PUBLISHER = {Oxford University Press},
}
@article{Harrington-Bork/08,
AUTHOR = {Harrington, Eoghan D. and Bork, Peer},
TITLE = {Sircah: A tool for the detection and visualization of alternative transcripts},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {17},
PAGES = {1959-1960},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn361},
PUBLISHER = {Oxford University Press},
}
@article{Heider-Kessler-Barnekow/08,
AUTHOR = {Heider, Dominik and Kessler, Daniel and Barnekow, Angelika},
TITLE = {Watermarking sexually reproducing diploid organisms},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {17},
PAGES = {1961-1962},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn342},
PUBLISHER = {Oxford University Press},
}
@article{Bergmann-Sauro/08,
AUTHOR = {Bergmann, Frank T. and Sauro, Herbert M.},
TITLE = {Comparing simulation results of SBML capable simulators},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {17},
PAGES = {1963-1965},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn319},
PUBLISHER = {Oxford University Press},
}
@article{Dancik-Dorman/08,
AUTHOR = {Dancik, Garrett M. and Dorman, Karin S.},
TITLE = {mlegp: Statistical analysis for computer models of biological systems using R},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {17},
PAGES = {1966-1967},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn329},
PUBLISHER = {Oxford University Press},
}
@article{Fan-Friedman/08,
AUTHOR = {Fan, Jung-Wei and Friedman, Carol},
TITLE = {Semantic reclassification of the UMLS concepts},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {17},
PAGES = {1971-1973},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn343},
PUBLISHER = {Oxford University Press},
}
@article{Kalari-Casavant-Scheetz/08,
AUTHOR = {Kalari, Krishna R. and Casavant, Thomas L. and Scheetz, Todd E.},
TITLE = {A knowledge-based approach to predict intragenic deletions or duplications},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {18},
PAGES = {1975-1979},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn370},
PUBLISHER = {Oxford University Press},
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PUBLISHER = {Oxford University Press},
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YEAR = {2008},
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JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {20},
PAGES = {2405-2406},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn442},
PUBLISHER = {Oxford University Press},
}
@article{Jadeau-Bechet-Cozzone-Deleage-Grangeasse-Combet/08,
AUTHOR = {Jadeau, Fanny and Bechet, Emmanuelle and Cozzone, Alain J. and Del{\'{e}}age, Gilbert and Grangeasse, Christophe and Combet, Christophe},
TITLE = {Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {21},
PAGES = {2427-2430},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn462},
PUBLISHER = {Oxford University Press},
}
@article{Gotoh/08,
AUTHOR = {Gotoh, Osamu},
TITLE = {Direct mapping and alignment of protein sequences onto genomic sequence},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {21},
PAGES = {2438-2444},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn460},
PUBLISHER = {Oxford University Press},
}
@article{Katzman-Barrett-Thiltgen-Karchin-Karplus/08,
AUTHOR = {Katzman, Sol and Barrett, Christian and Thiltgen, Grant and Karchin, Rachel and Karplus, Kevin},
TITLE = {PREDICT-2ND: A tool for generalized protein local structure prediction},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {21},
PAGES = {2453-2459},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn438},
PUBLISHER = {Oxford University Press},
}
@article{Chen-Wang-Smith-Zhang/08,
AUTHOR = {Chen, Xi and Wang, Lily and Smith, Jonathan D. and Zhang, Bing},
TITLE = {Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {21},
PAGES = {2474-2481},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn458},
PUBLISHER = {Oxford University Press},
}
@article{Cosgrove-Zhou-Gardner-Kolaczyk/08,
AUTHOR = {Cosgrove, Elissa J. and Zhou, Yingchun and Gardner, Timothy S. and Kolaczyk, Eric D.},
TITLE = {Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {21},
PAGES = {2482-2490},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn476},
PUBLISHER = {Oxford University Press},
}
@article{Goel-Chou-Voit/08,
AUTHOR = {Goel, Gautam and Chou, I-Chun and Voit, Eberhard O.},
TITLE = {System estimation from metabolic time-series data},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {21},
PAGES = {2505-2511},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn470},
PUBLISHER = {Oxford University Press},
}
@article{Fyshe-Liu-Szafron-Greiner-Lu/08,
AUTHOR = {Fyshe, Alona and Liu, Yifeng and Szafron, Duane and Greiner, Russ and Lu, Paul},
TITLE = {Improving subcellular localization prediction using text classification and the gene ontology},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {21},
PAGES = {2512-2517},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn463},
PUBLISHER = {Oxford University Press},
}
@article{Klekota-Roth/08,
AUTHOR = {Klekota, Justin and Roth, Frederick P.},
TITLE = {Chemical substructures that enrich for biological activity},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {21},
PAGES = {2518-2525},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn479},
PUBLISHER = {Oxford University Press},
}
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TITLE = {PathCase: Pathways database system},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {21},
PAGES = {2526-2533},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn459},
PUBLISHER = {Oxford University Press},
}
@article{Kessner-Chambers-Burke-Agus-Mallick/08,
AUTHOR = {Kessner, Darren and Chambers, Matt and Burke, Robert and Agus, David and Mallick, Parag},
TITLE = {ProteoWizard: Open source software for rapid proteomics tools development},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {21},
PAGES = {2534-2536},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn323},
PUBLISHER = {Oxford University Press},
}
@article{Boyle-Guinney-Crawford-Furey/08,
AUTHOR = {Boyle, Alan P. and Guinney, Justin and Crawford, Gregory E. and Furey, Terrence S.},
TITLE = {F-Seq: A feature density estimator for high-throughput sequence tags},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {21},
PAGES = {2537-2538},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn480},
PUBLISHER = {Oxford University Press},
}
@article{Bauer-Bailey/08,
AUTHOR = {Bauer, Denis C. and Bailey, Timothy L.},
TITLE = {STREAM: Static Thermodynamic REgulAtory Model of transcription},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {21},
PAGES = {2544-2545},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn467},
PUBLISHER = {Oxford University Press},
}
@article{Emig-Cline-Lengauer-Albrecht/08,
AUTHOR = {Emig, Dorothea and Cline, Melissa S. and Lengauer, Thomas and Albrecht, Mario},
TITLE = {Integrating expression data with domain interaction networks},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {21},
PAGES = {2546-2548},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn437},
PUBLISHER = {Oxford University Press},
}
@article{Frohlich-Beissbarth-Tresch-Kostka-Jacob-Spang-Markowetz/08,
AUTHOR = {Fr{\"{o}}hlich, Holger and Bei{\ss}barth, Tim and Tresch, Achim and Kostka, Dennis and Jacob, Juby and Spang, Rainer and Markowetz, F.},
TITLE = {Analyzing gene perturbation screens with nested effects models in R and bioconductor},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {21},
PAGES = {2549-2550},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn446},
PUBLISHER = {Oxford University Press},
}
@article{Hill-Tomshine-Weeding-Sotiropoulos-Kaznessis/08,
AUTHOR = {Hill, Anthony D. and Tomshine, Jonathan R. and Weeding, Emma M.B. and Sotiropoulos, Vassilios and Kaznessis, Yiannis N.},
TITLE = {SynBioSS: The synthetic biology modeling suite},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {21},
PAGES = {2551-2553},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn468},
PUBLISHER = {Oxford University Press},
}
@article{Hayes-Diez-Joannin-Honda-Kanehisa-Wahlgren-Wheelock-Goto/08,
AUTHOR = {Hayes, C. Nelson and Diez, Diego and Joannin, Nicolas and Honda, Wataru and Kanehisa, Minoru and Wahlgren, Mats and Wheelock, Craig E. and Goto, Susumu},
TITLE = {varDB: A pathogen-specific sequence database of protein families involved in antigenic variation},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {21},
PAGES = {2564-2565},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn477},
PUBLISHER = {Oxford University Press},
}
@article{Binder-Schumacher/08,
AUTHOR = {Binder, Harald and Schumacher, Martin},
TITLE = {Comment on ``Network-constrained regularization and variable selection for analysis of genomic data''},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {21},
PAGES = {2566-2568},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn412},
PUBLISHER = {Oxford University Press},
}
@article{Beargie-Liu-Corriveau-Lee-Gott-Bundschuh/08,
AUTHOR = {Beargie, Christina and Liu, Tsunglin and Corriveau, Mark and Lee, Ha Youn and Gott, Jonatha and Bundschuh, Ralf},
TITLE = {Genome annotation in the presence of insertional RNA editing},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {22},
PAGES = {2571-2578},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn487},
PUBLISHER = {Oxford University Press},
}
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AUTHOR = {Jones, Craig E. and Schwerdt, Julian and Bretag, Tessa Arwen and Baumann, Ute and Brown, Alfred L.},
TITLE = {GOSLING: A rule-based protein annotator using BLAST and GO},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {22},
PAGES = {2628-2629},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn486},
PUBLISHER = {Oxford University Press},
}
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TITLE = {MS-BID: A Java package for label-free LC-MS-based comparative proteomic analysis},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {22},
PAGES = {2641-2642},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn491},
PUBLISHER = {Oxford University Press},
}
@article{Khouangsathiene-Pearson-Street-Ferguson-Dubay/08,
AUTHOR = {Khouangsathiene, Samone and Pearson, Carlo and Street, Summer and Ferguson, Betsy and Dubay, Christopher},
TITLE = {MonkeySNP: A web portal for non-human primate single nucleotide polymorphisms},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {22},
PAGES = {2645-2646},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn493},
PUBLISHER = {Oxford University Press},
}
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AUTHOR = {Belhajjame, Khalid and Jones, Andrew R. and Paton, Norman W.},
TITLE = {A toolkit for capturing and sharing FuGE experiments},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {22},
PAGES = {2647-2649},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn496},
PUBLISHER = {Oxford University Press},
}
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AUTHOR = {Fr{\"{o}}hlich, Holger and Fellmann, Mark and S{\"{u}}ltmann, Holger and Poustka, Annemarie and Beissbarth, Tim},
TITLE = {Estimating large-scale signaling networks through nested effect models with intervention effects from microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {22},
PAGES = {2650-2656},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm634},
PUBLISHER = {Oxford University Press},
}
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TITLE = {Artemis and ACT: Viewing, annotating and comparing sequences stored in a relational database},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {23},
PAGES = {2672-2676},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn529},
PUBLISHER = {Oxford University Press},
}
@article{Bradley-Pachter-Holmes/08,
AUTHOR = {Bradley, Robert K. and Pachter, Lior and Holmes, Ian},
TITLE = {Specific alignment of structured RNA: Stochastic grammars and sequence annealing},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {23},
PAGES = {2677-2683},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn495},
PUBLISHER = {Oxford University Press},
}
@article{Hutchins-Murphy-Singh-Graber/08,
AUTHOR = {Hutchins, Lucie N. and Murphy, Sean M. and Singh, Priyam and Graber, Joel H.},
TITLE = {Position-dependent motif characterization using non-negative matrix factorization},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {23},
PAGES = {2684-2690},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn526},
PUBLISHER = {Oxford University Press},
}
@article{Chen-Yang-Hsu-Sun-Hsu-Yang/08,
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TITLE = {Protease substrate site predictors derived from machine learning on multilevel substrate phage display data},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {23},
PAGES = {2691-2697},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn538},
PUBLISHER = {Oxford University Press},
}
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TITLE = {Improving 2D-DIGE protein expression analysis by two-stage linear mixed models: Assessing experimental effects in a melanoma cell study},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {23},
PAGES = {2706-2712},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn508},
PUBLISHER = {Oxford University Press},
}
@article{Cornuet-Santos-Beaumont-Robert-Marin-Balding-Guillemaud-Estoup/08,
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TITLE = {Inferring population history with DIY ABC: A user-friendly approach to approximate Bayesian computation},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {23},
PAGES = {2713-2719},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn514},
PUBLISHER = {Oxford University Press},
}
@article{Casey-Cagney-Krogan-Shields/08,
AUTHOR = {Casey, Fergal P. and Cagney, Gerard and Krogan, Nevan J. and Shields, Denis C.},
TITLE = {Optimal stepwise experimental design for pairwise functional interaction studies},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {23},
PAGES = {2733-2739},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn472},
PUBLISHER = {Oxford University Press},
}
@article{Cinquemani-Milias-Argeitis-Summers-Lygeros/08,
AUTHOR = {Cinquemani, Eugenio and Milias-Argeitis, Andreas and Summers, Sean and Lygeros, John},
TITLE = {Stochastic dynamics of genetic networks: Modelling and parameter identification},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {23},
PAGES = {2748-2754},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn527},
PUBLISHER = {Oxford University Press},
}
@article{Jablonsky-Susila-Lazar/08,
AUTHOR = {Jablonsky, Jiri and Susila, Petr and Lazar, Dusan},
TITLE = {Impact of dimeric organization of enzyme on its function: The case of photosynthetic water splitting},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {23},
PAGES = {2755-2759},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn530},
PUBLISHER = {Oxford University Press},
}
@article{Chen-Liu-Chao/08,
AUTHOR = {Chen, Peng-An and Liu, Hsiao-Fei and Chao, Kun-Mao},
TITLE = {CNVDetector: Locating copy number variations using array CGH data},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {23},
PAGES = {2773-2775},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn517},
PUBLISHER = {Oxford University Press},
}
@article{Juliusdottir-Pettersson-Copley/08,
AUTHOR = {Juliusdottir, Thorhildur and Pettersson, Fredrik and Copley, Richard R.},
TITLE = {POPE --- A tool to aid high-throughput phylogenetic analysis},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {23},
PAGES = {2778-2779},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn533},
PUBLISHER = {Oxford University Press},
}
@article{Holm-Kaariainen-Rosenstrom-Schenkel/08,
AUTHOR = {Holm, L. and K{\"{a}}{\"{a}}ri{\"{a}}inen, S. and Rosenstr{\"{o}}m, P. and Schenkel, A.},
TITLE = {Searching protein structure databases with DaliLite v.3},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {23},
PAGES = {2780-2781},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn507},
PUBLISHER = {Oxford University Press},
}
@article{Heymann-Paramelle-Subra-Forest-Martinez-Geourjon-Deleage/08,
AUTHOR = {Heymann, Micha{\"{e}}l and Paramelle, David and Subra, Gilles and Forest, Eric and Martinez, Jean and Geourjon, Christophe and Del{\'{e}}age, Gilbert},
TITLE = {MSX-3D: A tool to validate 3D protein models using mass spectrometry},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {23},
PAGES = {2782-2783},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn510},
PUBLISHER = {Oxford University Press},
}
@article{Holden-Deng-Wojnowski-Kulle/08,
AUTHOR = {Holden, Marit and Deng, Shiwei and Wojnowski, Leszek and Kulle, Bettina},
TITLE = {GSEA-SNP: Applying gene set enrichment analysis to SNP data from genome-wide association studies},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {23},
PAGES = {2784-2785},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn516},
PUBLISHER = {Oxford University Press},
}
@article{Hernandez/08,
AUTHOR = {Hernandez, Ryan D.},
TITLE = {A flexible forward simulator for populations subject to selection and demography},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {23},
PAGES = {2786-2787},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn522},
PUBLISHER = {Oxford University Press},
}
@article{Joehanes-Nelson/08,
AUTHOR = {Joehanes, Roby and Nelson, James C.},
TITLE = {QGene 4.0, an extensible Java QTL-analysis platform},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {23},
PAGES = {2788-2789},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn523},
PUBLISHER = {Oxford University Press},
}
@article{Demey-Vicente-Villardon-Galindo-Villardon-Zambrano/08,
AUTHOR = {Demey, J.R. and Vicente-Villard{\'{o}}n, J.L. and Galindo-Villard{\'{o}}n, M.P. and Zambrano, A.Y.},
TITLE = {Identifying molecular markers associated with classification of genotypes by External Logistic Biplots},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {24},
PAGES = {2832-2838},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn552},
PUBLISHER = {Oxford University Press},
}
@article{Busch-Richter-Backofen/08,
AUTHOR = {Busch, Anke and Richter, Andreas S. and Backofen, Rolf},
TITLE = {IntaRNA: Efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {24},
PAGES = {2849-2856},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn544},
PUBLISHER = {Oxford University Press},
}
@article{Dang-Van_Leemput-Verschoren-Laukens/08,
AUTHOR = {Dang, Thanh Hai and Van Leemput, Koenraad and Verschoren, Alain and Laukens, Kris},
TITLE = {Prediction of kinase-specific phosphorylation sites using conditional random fields},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {24},
PAGES = {2857-2864},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn546},
PUBLISHER = {Oxford University Press},
}
@article{Bordner/08,
AUTHOR = {Bordner, Andrew J.},
TITLE = {Predicting small ligand binding sites in proteins using backbone structure},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {24},
PAGES = {2865-2871},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn543},
PUBLISHER = {Oxford University Press},
}
@article{Kapur-Jiang-Xing-Wong/08,
AUTHOR = {Kapur, Karen and Jiang, Hui and Xing, Yi and Wong, Wing Hung},
TITLE = {Cross-hybridization modeling on Affymetrix exon arrays},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {24},
PAGES = {2887-2893},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn571},
PUBLISHER = {Oxford University Press},
}
@article{Finkenstadt-Heron-Komorowski-Edwards-Tang-Harper-Davis-White-Millar-Rand/08,
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TITLE = {Reconstruction of transcriptional dynamics from gene reporter data using differential equations},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {24},
PAGES = {2901-2907},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn562},
PUBLISHER = {Oxford University Press},
}
@article{Cesaroni-Cittaro-Brozzi-Pelicci-Luzi/08,
AUTHOR = {Cesaroni, Matteo and Cittaro, Davide and Brozzi, Alessandro and Pelicci, Pier Giuseppe and Luzi, Lucilla},
TITLE = {CARPET: A web-based package for the analysis of ChIP-chip and expression tiling data},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {24},
PAGES = {2918-2920},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn542},
PUBLISHER = {Oxford University Press},
}
@article{Cairns-Dunning-Ritchie-Russell-Lynch/08,
AUTHOR = {Cairns, J.M. and Dunning, M.J. and Ritchie, M.E. and Russell, R. and Lynch, A.G.},
TITLE = {BASH: A tool for managing BeadArray spatial artefacts},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {24},
PAGES = {2921-2922},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn557},
PUBLISHER = {Oxford University Press},
}
@article{Kong-Zhu-Stalker-Adams/08,
AUTHOR = {Kong, Jun and Zhu, Fei and Stalker, Jim and Adams, David J.},
TITLE = {iMapper: A web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {24},
PAGES = {2923-2925},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn541},
PUBLISHER = {Oxford University Press},
}
@article{Ho-Kuiper-Kotagiri/08,
AUTHOR = {Ho, Hui Kian and Kuiper, Michael J. and Kotagiri, Ramamohanarao},
TITLE = {PConPy --- A Python module for generating 2D protein maps},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {24},
PAGES = {2934-2935},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn566},
PUBLISHER = {Oxford University Press},
}
@article{Jobin-Mountain/08,
AUTHOR = {Jobin, Matthew J. and Mountain, Joanna L.},
TITLE = {REJECTOR: Software for population history inference from genetic data via a rejection algorithm},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {24},
PAGES = {2936-2937},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn540},
PUBLISHER = {Oxford University Press},
}
@article{Johnson-Handsaker-Pulit-Nizzari-ODonnell-de_Bakker/08,
AUTHOR = {Johnson, Andrew D. and Handsaker, Robert E. and Pulit, Sara L. and Nizzari, Marcia M. and O'Donnell, Christopher J. and de Bakker, Paul I.W.},
TITLE = {SNAP: A web-based tool for identification and annotation of proxy SNPs using HapMap},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {24},
PAGES = {2938-2939},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn564},
PUBLISHER = {Oxford University Press},
}
@article{Collier-Doan-Kawazoe-Goodwin-Conway-Tateno-Ngo-Dien-Kawtrakul-Takeuchi-Shigematsu-Taniguchi/08,
AUTHOR = {Collier, Nigel and Doan, Son and Kawazoe, Ai and Goodwin, Reiko Matsuda and Conway, Mike and Tateno, Yoshio and Ngo, Quoc-Hung and Dien, Dinh and Kawtrakul, Asanee and Takeuchi, Koichi and Shigematsu, Mika and Taniguchi, Kiyosu},
TITLE = {BioCaster: Detecting public health rumors with a Web-based text mining system},
JOURNAL = {Bioinformatics},
VOLUME = {24},
NUMBER = {24},
PAGES = {2940-2941},
YEAR = {2008},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn534},
PUBLISHER = {Oxford University Press},
}