@article{Chen-Gu-Li-Li/12,
AUTHOR = {Chen, Yang and Gu, Jin and Li, Dan and Li, Shao},
TITLE = {Time-course network analysis reveals TNF-$\alpha$ can promote G$_{1}$/S transition of cell cycle in vascular endothelial cells},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {1},
PAGES = {1-4},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr619},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Herbig-Jager-Battke-Nieselt/12,
AUTHOR = {Herbig, A. and J{\"a}ger, G. and Battke, F. and Nieselt, K.},
TITLE = {GenomeRing: Alignment visualization based on SuperGenome coordinates},
BOOKTITLE = {Proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB'2012 (Long Beach, CA, USA, July 15-17, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {7-15},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts217},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Cai-Wang-Huang-Ding/12,
AUTHOR = {Cai, Xiao and Wang, Hua and Huang, Heng and Ding, Chris},
TITLE = {Joint stage recognition and anatomical annotation of drosophila gene expression patterns},
BOOKTITLE = {Proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB'2012 (Long Beach, CA, USA, July 15-17, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {16-24},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts220},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Feng-Zhao-Kim/12,
AUTHOR = {Feng, Linqing and Zhao, Ting and Kim, Jinhyun},
TITLE = {Improved synapse detection for mGRASP-assisted brain connectivity mapping},
BOOKTITLE = {Proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB'2012 (Long Beach, CA, USA, July 15-17, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {25-31},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts221},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Ichinose-Yada-Gotoh/12,
AUTHOR = {Ichinose, Natsuhiro and Yada, Tetsushi and Gotoh, Osamu},
TITLE = {Large-scale motif discovery using DNA Gray code and equiprobable oligomers},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {1},
PAGES = {25-31},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr606},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gusnanto-Wood-Pawitan-Rabbitts-Berri/12,
AUTHOR = {Gusnanto, Arief and Wood, Henry M. and Pawitan, Yudi and Rabbitts, Pamela and Berri, Stefano},
TITLE = {Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {1},
PAGES = {40-47},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr593},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Ames-Money-Ghatge-Whelan-Lovell/12,
AUTHOR = {Ames, Ryan M. and Money, Daniel and Ghatge, Vikramsinh P. and Whelan, Simon and Lovell, Simon C.},
TITLE = {Determining the evolutionary history of gene families},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {1},
PAGES = {48-55},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr592},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Cuellar-Partida-Buske-McLeay-Whitington-Noble-Bailey/12,
AUTHOR = {Cuellar-Partida, Gabriel and Buske, Fabian A. and McLeay, Robert C. and Whitington, Tom and Noble, William Stafford and Bailey, Timothy L.},
TITLE = {Epigenetic priors for identifying active transcription factor binding sites},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {1},
PAGES = {56-62},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr614},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hu-Zhu-Taylor-Liu-Qin/12,
AUTHOR = {Hu, Ming and Zhu, Yu and Taylor, Jeremy M.G. and Liu, Jun S. and Qin, Zhaohui S.},
TITLE = {Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {1},
PAGES = {63-68},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr616},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Frenkel-Morgenstern-Valencia/12,
AUTHOR = {Frenkel-Morgenstern, Milana and Valencia, Alfonso},
TITLE = {Novel domain combinations in proteins encoded by chimeric transcripts},
BOOKTITLE = {Proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB'2012 (Long Beach, CA, USA, July 15-17, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {67-74},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts216},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Disfani-Hsu-Mizianty-Oldfield-Xue-Dunker-Uversky-Kurgan/12,
AUTHOR = {Disfani, Fatemeh Miri and Hsu, Wei-Lun and Mizianty, Marcin J. and Oldfield, Christopher J. and Xue, Bin and Dunker, A. Keith and Uversky, Vladimir N. and Kurgan, Lukasz},
TITLE = {MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins},
BOOKTITLE = {Proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB'2012 (Long Beach, CA, USA, July 15-17, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {75-83},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts209},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Becker-Robisson-Chapple-Guenoche-Brun/12,
AUTHOR = {Becker, Emmanuelle and Robisson, Beno{\^{i}}t and Chapple, Charles E. and Gu{\'e}noche, Alain and Brun, Christine},
TITLE = {Multifunctional proteins revealed by overlapping clustering in protein interaction network},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {1},
PAGES = {84-90},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr621},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Christensen-Enuameh-Noyes-Brodsky-Wolfe-Stormo/12,
AUTHOR = {Christensen, Ryan G. and Enuameh, Metewo Selase and Noyes, Marcus B. and Brodsky, Michael H. and Wolfe, Scot A. and Stormo, Gary D.},
TITLE = {Recognition models to predict DNA-binding specificities of homeodomain proteins},
BOOKTITLE = {Proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB'2012 (Long Beach, CA, USA, July 15-17, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {84-89},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts202},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hayat-Elofsson/12a,
AUTHOR = {Hayat, Sikander and Elofsson, Arne},
TITLE = {Ranking models of transmembrane $\beta$-barrel proteins using Z-coordinate predictions},
BOOKTITLE = {Proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB'2012 (Long Beach, CA, USA, July 15-17, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {90-96},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts233},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chen-Xu-Gordonov-Lim-Perkins-Maayan/12,
AUTHOR = {Chen, Edward Y. and Xu, Huilei and Gordonov, Simon and Lim, Maribel P. and Perkins, Matthew H. and Ma'ayan, Avi},
TITLE = {Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {1},
PAGES = {105-111},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr625},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hochbaum-Hsu-Yang/12,
AUTHOR = {Hochbaum, Dorit S. and Hsu, Chun-Nan and Yang, Yan T.},
TITLE = {Ranking of multidimensional drug profiling data by fractional-adjusted bi-partitional scores},
BOOKTITLE = {Proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB'2012 (Long Beach, CA, USA, July 15-17, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {106-114},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts232},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kalkatawi-Rangkuti-Schramm-Jankovic-Kamau-Chowdhary-Archer-Bajic/12,
AUTHOR = {Kalkatawi, Manal and Rangkuti, Farania and Schramm, Michael and Jankovic, Boris R. and Kamau, Allan and Chowdhary, Rajesh and Archer, John A.C. and Bajic, Vladimir B.},
TITLE = {Dragon PolyA Spotter: Predictor of poly(A) motifs within human genomic DNA sequences},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {1},
PAGES = {127-129},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr602},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bellenguez-Strange-Freeman-Consortium-Donnelly-Spencer/12,
AUTHOR = {Bellenguez, C{\'e}line and Strange, Amy and Freeman, Colin and Consortium, Wellcome Trust Case Control and Donnelly, Peter and Spencer, Chris C.A.},
TITLE = {A robust clustering algorithm for identifying problematic samples in genome-wide association studies},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {1},
PAGES = {134-135},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr599},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Georgescu-Wikswo-Quaranta/12,
AUTHOR = {Georgescu, Walter and Wikswo, John P. and Quaranta, Vito},
TITLE = {cellanimation: An open source MATLAB framework for microscopy assays},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {1},
PAGES = {138-139},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr633},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Canny-Cruz-Southern-Griffin/12,
AUTHOR = {Canny, Stephanie A. and Cruz, Yasel and Southern, Mark R. and Griffin, Patrick R.},
TITLE = {PubChem promiscuity: A web resource for gathering compound promiscuity data from PubChem},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {1},
PAGES = {140-141},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr622},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Dassi-Malossini-Re-Mazza-Tebaldi-Caputi-Quattrone/12,
AUTHOR = {Dassi, E. and Malossini, A. and Re, A. and Mazza, T. and Tebaldi, T. and Caputi, L. and Quattrone, A.},
TITLE = {AURA: Atlas of UTR Regulatory Activity},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {1},
PAGES = {142-144},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr608},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Darnell-Duong-Han-Eskin/12,
AUTHOR = {Darnell, Gregory and Duong, Dat and Han, Buhm and Eskin, Eleazar},
TITLE = {Incorporating prior information into association studies},
BOOKTITLE = {Proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB'2012 (Long Beach, CA, USA, July 15-17, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {147-153},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts235},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Brown-Wedge-Goodacre-Kell-Baker-Kenny-Mamas-Neyses-Dunn/12,
AUTHOR = {Brown, Marie and Wedge, David C. and Goodacre, Royston and Kell, Douglas B. and Baker, Philip N. and Kenny, Louise C. and Mamas, Mamas A. and Neyses, Ludwig and Dunn, Warwick B.},
TITLE = {Corrigendum to ``Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets''},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {1},
PAGES = {149-149},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr601},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
NOTE = {Originally in Bioinformatics, Vol. 27, 2011, No. 8, 1108-1112},
}
@article{Hormozdiari-Hach-Sahinalp-Eichler-Alkan/12,
AUTHOR = {Hormozdiari, Farhad and Hach, Faraz and Sahinalp, S. Cenk and Eichler, Evan E. and Alkan, Can},
TITLE = {Corrigendum to ``Sensitive and fast mapping of di-base encoded reads''},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {1},
PAGES = {150-150},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr647},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
NOTE = {Originally in Bioinformatics, Vol. 27, 2011, No. 4, 1915-1921},
}
@article{Aguiar-Halldorsson-Morrow-Istrail/12,
AUTHOR = {Aguiar, Derek and Halld{\'o}rsson, Bjarni V. and Morrow, Eric M. and Istrail, Sorin},
TITLE = {DELISHUS: An efficient and exact algorithm for genome-wide detection of deletion polymorphism in autism},
BOOKTITLE = {Proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB'2012 (Long Beach, CA, USA, July 15-17, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {154-162},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts234},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Ding-Bashashati-Roth-Oloumi-Tse-Zeng-Haffari-Hirst-Marra-Condon-Aparicio-Shah/12,
AUTHOR = {Ding, Jiarui and Bashashati, Ali and Roth, Andrew and Oloumi, Arusha and Tse, Kane and Zeng, Thomas and Haffari, Gholamreza and Hirst, Martin and Marra, Marco A. and Condon, Anne and Aparicio, Samuel and Shah, Sohrab P.},
TITLE = {Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {2},
PAGES = {167-175},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr629},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Conway-Wazny-Bromage-Tymms-Sooraj-Williams-Beresford-Smith/12,
AUTHOR = {Conway, Thomas and Wazny, Jeremy and Bromage, Andrew and Tymms, Martin and Sooraj, Dhanya and Williams, Elizabeth D. and Beresford-Smith, Bryan},
TITLE = {Xenome --- A tool for classifying reads from xenograft samples},
BOOKTITLE = {Proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB'2012 (Long Beach, CA, USA, July 15-17, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {172-178},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts236},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Huang-Golding/12,
AUTHOR = {Huang, Yi-Fei and Golding, G. Brian},
TITLE = {Inferring sequence regions under functional divergence in duplicate genes},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {2},
PAGES = {176-183},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr635},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jones-Buchan-Cozzetto-Pontil/12,
AUTHOR = {Jones, David T. and Buchan, Daniel W.A. and Cozzetto, Domenico and Pontil, Massimiliano},
TITLE = {PSICOV: Precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {2},
PAGES = {184-190},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr638},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Albrecht-Scornavacca-Cenci-Huson/12,
AUTHOR = {Albrecht, Benjamin and Scornavacca, Celine and Cenci, Alberto and Huson, Daniel H.},
TITLE = {Fast computation of minimum hybridization networks},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {2},
PAGES = {191-197},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr618},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Golan-Erlich-Rosset/12,
AUTHOR = {Golan, David and Erlich, Yaniv and Rosset, Saharon},
TITLE = {Weighted pooling --- Practical and cost-effective techniques for pooled high-throughput sequencing},
BOOKTITLE = {Proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB'2012 (Long Beach, CA, USA, July 15-17, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {197-206},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts208},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Geeven-van_Kesteren-Smit-de_Gunst/12,
AUTHOR = {Geeven, Geert and van Kesteren, Ronald E. and Smit, August B. and de Gunst, Mathisca C.M.},
TITLE = {Identification of context-specific gene regulatory networks with GEMULA  --- Gene Expression modeling using LAsso},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {2},
PAGES = {214-221},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr641},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hoinka-Zotenko-Friedman-Sauna-Przytycka/12,
AUTHOR = {Hoinka, Jan and Zotenko, Elena and Friedman, Adam and Sauna, Zuben E. and Przytycka, Teresa M.},
TITLE = {Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers},
BOOKTITLE = {Proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB'2012 (Long Beach, CA, USA, July 15-17, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {215-223},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts210},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Grun-Scharl-Leisch/12,
AUTHOR = {Gr{\"u}n, Bettina and Scharl, Theresa and Leisch, Friedrich},
TITLE = {Modelling time course gene expression data with finite mixtures of linear additive models},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {2},
PAGES = {222-228},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr653},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Heyne-Costa-Rose-Backofen/12,
AUTHOR = {Heyne, Steffen and Costa, Fabrizio and Rose, Dominic and Backofen, Rolf},
TITLE = {GraphClust: Alignment-free structural clustering of local RNA secondary structures},
BOOKTITLE = {Proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB'2012 (Long Beach, CA, USA, July 15-17, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {224-232},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts224},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Caldas-Gehlenborg-Kettunen-Faisal-Ronty-Nicholson-Knuutila-Brazma-Kaski/12,
AUTHOR = {Caldas, Jos{\'e} and Gehlenborg, Nils and Kettunen, Eeva and Faisal, Ali and R{\"o}nty, Mikko and Nicholson, Andrew G. and Knuutila, Sakari and Brazma, Alvis and Kaski, Samuel},
TITLE = {Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {2},
PAGES = {246-253},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr634},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hashimoto-Jaakkola-Sherwood-Mazzoni-Wichterle-Gifford/12,
AUTHOR = {Hashimoto, Tatsunori and Jaakkola, Tommi and Sherwood, Richard and Mazzoni, Esteban O. and Wichterle, Hynek and Gifford, David},
TITLE = {Lineage-based identification of cellular states and expression programs},
BOOKTITLE = {Proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB'2012 (Long Beach, CA, USA, July 15-17, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {250-257},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts204},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Harmston-Filsell-Stumpf/12,
AUTHOR = {Harmston, Nathan and Filsell, Wendy and Stumpf, Michael P.H.},
TITLE = {Which species is it? Species-driven gene name disambiguation using random walks over a mixture of adjacency matrices},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {2},
PAGES = {254-260},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr640},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Carralot-Ogier-Boese-Genovesio-Brodin-Sommer-Dorval/12,
AUTHOR = {Carralot, Jean-Philippe and Ogier, Arnaud and Boese, Annette and Genovesio, Auguste and Brodin, Priscille and Sommer, Peter and Dorval, Thierry},
TITLE = {A novel specific edge effect correction method for RNA interference screenings},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {2},
PAGES = {261-268},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr648},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hufsky-Duhrkop-Rasche-Chimani-Bocker/12,
AUTHOR = {Hufsky, Franziska and D{\"u}hrkop, Kai and Rasche, Florian and Chimani, Markus and B{\"o}cker, Sebastian},
TITLE = {Fast alignment of fragmentation trees},
BOOKTITLE = {Proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB'2012 (Long Beach, CA, USA, July 15-17, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {265-273},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts207},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Asmann-Middha-Hossain-Baheti-Li-Chai-Sun-Duffy-Hadad-Nair-Liu-Zhang-Klee-Kalari-Kocher/12,
AUTHOR = {Asmann, Yan W. and Middha, Sumit and Hossain, Asif and Baheti, Saurabh and Li, Ying and Chai, High-Seng and Sun, Zhifu and Duffy, Patrick H. and Hadad, Ahmed A. and Nair, Asha and Liu, Xiaoyu and Zhang, Yuji and Klee, Eric W. and Kalari, Krishna R. and Kocher, Jean-Pierre A.},
TITLE = {TREAT: A bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {2},
PAGES = {277-278},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr612},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bansal-Alm-Kellis/12,
AUTHOR = {Bansal, Mukul S. and Alm, Eric J. and Kellis, Manolis},
TITLE = {Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss},
BOOKTITLE = {Proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB'2012 (Long Beach, CA, USA, July 15-17, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {283-291},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts225},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Brouwer-van_den_Hout-Grosveld-van_IJcken/12,
AUTHOR = {Brouwer, R.W.W. and van den Hout, M.C.G.N. and Grosveld, F.G. and van IJcken, W.F.J.},
TITLE = {NARWHAL, a primary analysis pipeline for NGS data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {2},
PAGES = {284-285},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr613},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gatto-Lilley/12,
AUTHOR = {Gatto, Laurent and Lilley, Kathryn S.},
TITLE = {MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {2},
PAGES = {288-289},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr645},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chu-Zabet-von_der_Haar/12,
AUTHOR = {Chu, Dominique and Zabet, Nicolae and von der Haar, Tobias},
TITLE = {A novel and versatile computational tool to model translation},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {2},
PAGES = {292-293},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr650},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Fabian-Wachter-Schroeder/12,
AUTHOR = {Fabian, G{\"o}tz and W{\"a}chter, Thomas and Schroeder, Michael},
TITLE = {Extending ontologies by finding siblings using set expansion techniques},
BOOKTITLE = {Proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB'2012 (Long Beach, CA, USA, July 15-17, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {292-300},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts215},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bresler-Sheehan-Chan-Song/12,
AUTHOR = {Bresler, Ma'ayan and Sheehan, Sara and Chan, Andrew H. and Song, Yun S.},
TITLE = {Telescoper: De novo assembly of highly repetitive regions},
BOOKTITLE = {Proceedings of the 11th European Conference on Computational Biology, ECCB'2012 (Basel, Switzerland, September 9-12, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {311-317},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts399},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chen-Mizianty-Kurgan/12,
AUTHOR = {Chen, Ke and Mizianty, Marcin J. and Kurgan, Lukasz},
TITLE = {Prediction and analysis of nucleotide-binding residues using sequence and sequence-derived structural descriptors},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {3},
PAGES = {331-341},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr657},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Goncalves-Almeida-Pires-de_Melo-Minardi-da_Silveira-Meira-Santoro/12,
AUTHOR = {Gon{\c{c}}alves-Almeida, V.M. and Pires, D.E.V. and de Melo-Minardi, R.C. and da Silveira, C.H. and Meira, W. and Santoro, M.M.},
TITLE = {HydroPaCe: Understanding and predicting cross-inhibition in serine proteases through hydrophobic patch centroids},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {3},
PAGES = {342-349},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr680},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Heal-Jimenez-Roldan-Wells-Freedman-Romer/12,
AUTHOR = {Heal, J.W. and Jimenez-Roldan, J.E. and Wells, S.A. and Freedman, R.B. and R{\"o}mer, R.A.},
TITLE = {Inhibition of HIV-1 protease: The rigidity perspective},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {3},
PAGES = {350-357},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr683},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Coin-Cao-Ren-Zuo-Sun-Yang-Zhang-Cui-Li-Jin-Wang/12,
AUTHOR = {Coin, Lachlan J.M. and Cao, Dandan and Ren, Jingjing and Zuo, Xianbo and Sun, Liangdan and Yang, Sen and Zhang, Xuejun and Cui, Yong and Li, Yingrui and Jin, Xin and Wang, Jun},
TITLE = {An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis},
BOOKTITLE = {Proceedings of the 11th European Conference on Computational Biology, ECCB'2012 (Basel, Switzerland, September 9-12, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {370-374},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts379},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Karnovsky-Weymouth-Hull-Tarcea-Scardoni-Laudanna-Sartor-Stringer-Jagadish-Burant-Athey-Omenn/12,
AUTHOR = {Karnovsky, Alla and Weymouth, Terry and Hull, Tim and Tarcea, V. Glenn and Scardoni, Giovanni and Laudanna, Carlo and Sartor, Maureen A. and Stringer, Kathleen A. and Jagadish, H.V. and Burant, Charles and Athey, Brian and Omenn, Gilbert S.},
TITLE = {Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {3},
PAGES = {373-380},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr661},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Ballerstein-von_Kamp-Klamt-Haus/12,
AUTHOR = {Ballerstein, Kathrin and von Kamp, Axel and Klamt, Steffen and Haus, Utz-Uwe},
TITLE = {Minimal cut sets in a metabolic network are elementary modes in a dual network},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {3},
PAGES = {381-387},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr674},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Berard-Gallien-Boussau-Szollosi-Daubin-Tannier/12,
AUTHOR = {B{\'e}rard, S{`e}verine and Gallien, Coralie and Boussau, Bastien and Sz{\"o}ll{\H{o}}si, Gergely J. and Daubin, Vincent and Tannier, Eric},
TITLE = {Evolution of gene neighborhoods within reconciled phylogenies},
BOOKTITLE = {Proceedings of the 11th European Conference on Computational Biology, ECCB'2012 (Basel, Switzerland, September 9-12, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {382-388},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts374},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Cohen-Ashkenazy-Burstein-Pupko/12,
AUTHOR = {Cohen, Ofir and Ashkenazy, Haim and Burstein, David and Pupko, Tal},
TITLE = {Uncovering the co-evolutionary network among prokaryotic genes},
BOOKTITLE = {Proceedings of the 11th European Conference on Computational Biology, ECCB'2012 (Basel, Switzerland, September 9-12, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {389-394},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts396},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Dimitrieva-Bucher/12,
AUTHOR = {Dimitrieva, Slavica and Bucher, Philipp},
TITLE = {Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements},
BOOKTITLE = {Proceedings of the 11th European Conference on Computational Biology, ECCB'2012 (Basel, Switzerland, September 9-12, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {395-401},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts400},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jimenez-Lozano-Segura-Macias-Vega-Carazo/12,
AUTHOR = {Jim{\'e}nez-Lozano, Natalia and Segura, Joan and Mac{\'{i}}as, Jos{\'e} Ram{\'o}n and Vega, Juanjo and Carazo, Jos{\'e} Mar{\'{i}}a},
TITLE = {Integrating human and murine anatomical gene expression data for improved comparisons},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {3},
PAGES = {397-402},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr639},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Dozmorov-Cara-Giles-Wren/12,
AUTHOR = {Dozmorov, Mikhail G. and Cara, Lukas R. and Giles, Cory B. and Wren, Jonathan D.},
TITLE = {GenomeRunner: Automating genome exploration},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {3},
PAGES = {419-420},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr666},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Boeva-Popova-Bleakley-Chiche-Cappo-Schleiermacher-Janoueix-Lerosey-Delattre-Barillot/12,
AUTHOR = {Boeva, Valentina and Popova, Tatiana and Bleakley, Kevin and Chiche, Pierre and Cappo, Julie and Schleiermacher, Gudrun and Janoueix-Lerosey, Isabelle and Delattre, Olivier and Barillot, Emmanuel},
TITLE = {Control-FREEC: A tool for assessing copy number and allelic content using next-generation sequencing data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {3},
PAGES = {423-425},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr670},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gaudreault-Chartier-Najmanovich/12,
AUTHOR = {Gaudreault, Francis and Chartier, Matthieu and Najmanovich, Rafael},
TITLE = {Side-chain rotamer changes upon ligand binding: Common, crucial, correlate with entropy and rearrange hydrogen bonding},
BOOKTITLE = {Proceedings of the 11th European Conference on Computational Biology, ECCB'2012 (Basel, Switzerland, September 9-12, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {423-430},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts395},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kallberg-Bhardwaj-Langlois-Lu/12,
AUTHOR = {K{\"a}llberg, Morten and Bhardwaj, Nitin and Langlois, Robert and Lu, Hui},
TITLE = {A structure-based protocol for learning the family-specific mechanisms of membrane-binding domains},
BOOKTITLE = {Proceedings of the 11th European Conference on Computational Biology, ECCB'2012 (Basel, Switzerland, September 9-12, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {431-437},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts409},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gonzalez-Stombaugh-Lauber-Fierer-Knight/12,
AUTHOR = {Gonzalez, Antonio and Stombaugh, Jesse and Lauber, Christian L. and Fierer, Noah and Knight, Rob},
TITLE = {SitePainter: A tool for exploring biogeographical patterns},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {3},
PAGES = {436-438},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr685},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Fuchsberger-Taliun-Pramstaller-Pattaro-consortium/12,
AUTHOR = {Fuchsberger, Christian and Taliun, Daniel and Pramstaller, Peter P. and Pattaro, Cristian and consortium, on behalf of the CKDGen},
TITLE = {GWAtoolbox: An R package for fast quality control and handling of genome-wide association studies meta-analysis data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {3},
PAGES = {444-445},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr679},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Glaab-Schneider/12,
AUTHOR = {Glaab, Enrico and Schneider, Reinhard},
TITLE = {PathVar: Analysis of gene and protein expression variance in cellular pathways using microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {3},
PAGES = {446-447},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr656},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Glaab-Baudot-Krasnogor-Schneider-Valencia/12,
AUTHOR = {Glaab, Enrico and Baudot, Ana{\"{i}}s and Krasnogor, Natalio and Schneider, Reinhard and Valencia, Alfonso},
TITLE = {EnrichNet: Network-based gene set enrichment analysis},
BOOKTITLE = {Proceedings of the 11th European Conference on Computational Biology, ECCB'2012 (Basel, Switzerland, September 9-12, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {451-457},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts389},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Goh-Oikawa-Sng-Sergot-Wong/12,
AUTHOR = {Goh, Wilson Wen Bin and Oikawa, Hirotaka and Sng, Judy Chia Ghee and Sergot, Marek and Wong, Limsoon},
TITLE = {The role of miRNAs in complex formation and control},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {4},
PAGES = {453-456},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr693},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hardcastle-Kelly-Baulcombe/12,
AUTHOR = {Hardcastle, Thomas J. and Kelly, Krystyna A. and Baulcombe, David C.},
TITLE = {Identifying small interfering RNA loci from high-throughput sequencing data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {4},
PAGES = {457-463},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr687},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Goldberg-Hamp-Rost/12,
AUTHOR = {Goldberg, Tatyana and Hamp, Tobias and Rost, Burkhard},
TITLE = {LocTree2 predicts localization for all domains of life},
BOOKTITLE = {Proceedings of the 11th European Conference on Computational Biology, ECCB'2012 (Basel, Switzerland, September 9-12, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {458-465},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts390},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Carver-Harris-Berriman-Parkhill-McQuillan/12,
AUTHOR = {Carver, Tim and Harris, Simon R. and Berriman, Matthew and Parkhill, Julian and McQuillan, Jacqueline A.},
TITLE = {Artemis: An integrated platform for visualization and analysis of high-throughput sequence-based experimental data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {4},
PAGES = {464-469},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr703},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Arnold-Erb-Pachkov-Molina-van_Nimwegen/12,
AUTHOR = {Arnold, Phil and Erb, Ionas and Pachkov, Mikhail and Molina, Nacho and van Nimwegen, Erik},
TITLE = {MotEvo: Integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {4},
PAGES = {487-494},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr695},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Blackburne-Whelan/12,
AUTHOR = {Blackburne, Benjamin P. and Whelan, Simon},
TITLE = {Measuring the distance between multiple sequence alignments},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {4},
PAGES = {495-502},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr701},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Harder-Borg-Boomsma-Rogen-Hamelryck/12,
AUTHOR = {Harder, Tim and Borg, Mikael and Boomsma, Wouter and R{\o}gen, Peter and Hamelryck, Thomas},
TITLE = {Fast large-scale clustering of protein structures using Gauss integrals},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {4},
PAGES = {510-515},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr692},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hayat-Elofsson/12,
AUTHOR = {Hayat, Sikander and Elofsson, Arne},
TITLE = {BOCTOPUS: Improved topology prediction of transmembrane $\beta$ barrel proteins},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {4},
PAGES = {516-522},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr710},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jager-Battke-Nieselt/12,
AUTHOR = {J{\"a}ger, G{\"u}nter and Battke, Florian and Nieselt, Kay},
TITLE = {{\sc Reveal}  --- Visual eQTL analytics},
BOOKTITLE = {Proceedings of the 11th European Conference on Computational Biology, ECCB'2012 (Basel, Switzerland, September 9-12, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {542-548},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts382},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Acharya-Judeh-Wang-Zhu/12,
AUTHOR = {Acharya, Lipi R. and Judeh, Thair and Wang, Guangdi and Zhu, Dongxiao},
TITLE = {Optimal structural inference of signaling pathways from unordered and overlapping gene sets},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {4},
PAGES = {546-556},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr696},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Klann-Ganguly-Koeppl/12,
AUTHOR = {Klann, Michael and Ganguly, Arnab and Koeppl, Heinz},
TITLE = {Hybrid spatial Gillespie and particle tracking simulation},
BOOKTITLE = {Proceedings of the 11th European Conference on Computational Biology, ECCB'2012 (Basel, Switzerland, September 9-12, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {549-555},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts384},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Handorf-Klipp/12,
AUTHOR = {Handorf, T. and Klipp, E.},
TITLE = {Modeling mechanistic biological networks: An advanced Boolean approach},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {4},
PAGES = {557-563},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr697},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bell-Gillespie-Swan-Lord/12,
AUTHOR = {Bell, Michael J. and Gillespie, Colin S. and Swan, Daniel and Lord, Phillip},
TITLE = {An approach to describing and analysing bulk biological annotation quality: A case study using UniProtKB},
BOOKTITLE = {Proceedings of the 11th European Conference on Computational Biology, ECCB'2012 (Basel, Switzerland, September 9-12, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {562-568},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts372},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Iacucci-Tranchevent-Popovic-Pavlopoulos-De_Moor-Schneider-Moreau/12,
AUTHOR = {Iacucci, Ernesto and Tranchevent, L{\'e}on-Charles and Popovic, Dusan and Pavlopoulos, Georgios A. and De Moor, Bart and Schneider, Reinhard and Moreau, Yves},
TITLE = {ReLiance: A machine learning and literature-based prioritization of receptor --- Ligand pairings},
BOOKTITLE = {Proceedings of the 11th European Conference on Computational Biology, ECCB'2012 (Basel, Switzerland, September 9-12, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {569-574},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts391},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Huang-Renault-Sengenes-Touleimat-Michel-Lathrop-Tost/12,
AUTHOR = {Huang, J. and Renault, V. and Sengen{`e}s, J. and Touleimat, N. and Michel, S. and Lathrop, M. and Tost, J.},
TITLE = {MeQA: A pipeline for MeDIP-seq data quality assessment and analysis},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {4},
PAGES = {587-588},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr699},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Huang-Li-Myers-Marth/12,
AUTHOR = {Huang, Weichun and Li, Leping and Myers, Jason R. and Marth, Gabor T.},
TITLE = {ART: A next-generation sequencing read simulator},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {4},
PAGES = {593-594},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr708},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kim-Kwon-Shin-Wilbur/12,
AUTHOR = {Kim, Sun and Kwon, Dongseop and Shin, Soo-Yong and Wilbur, W. John},
TITLE = {PIE the search: Searching PubMed literature for protein interaction information},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {4},
PAGES = {597-598},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr702},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chikina-Troyanskaya/12,
AUTHOR = {Chikina, Maria D. and Troyanskaya, Olga G.},
TITLE = {An effective statistical evaluation of ChIPseq dataset similarity},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {5},
PAGES = {607-613},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts009},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Emde-Schulz-Weese-Sun-Vingron-Kalscheuer-Haas-Reinert/12,
AUTHOR = {Emde, Anne-Katrin and Schulz, Marcel H. and Weese, David and Sun, Ruping and Vingron, Martin and Kalscheuer, Vera M. and Haas, Stefan A. and Reinert, Knut},
TITLE = {Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {5},
PAGES = {619-627},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts019},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Buettner-Theis/12,
AUTHOR = {Buettner, Florian and Theis, Fabian J.},
TITLE = {A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst},
BOOKTITLE = {Proceedings of the 11th European Conference on Computational Biology, ECCB'2012 (Basel, Switzerland, September 9-12, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {626-632},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts385},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hatsuda/12,
AUTHOR = {Hatsuda, Hiroshi},
TITLE = {Finding differentially expressed regions of arbitrary length in quantitative genomic data based on marked point process model},
BOOKTITLE = {Proceedings of the 11th European Conference on Computational Biology, ECCB'2012 (Basel, Switzerland, September 9-12, 2012)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {633-639},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts371},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gumus-Kursun-Sertbas-Ustek/12,
AUTHOR = {Gumus, Ergun and Kursun, Olcay and Sertbas, Ahmet and Ustek, Duran},
TITLE = {Application of canonical correlation analysis for identifying viral integration preferences},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {5},
PAGES = {651-655},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts027},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Goke-Schulz-Lasserre-Vingron/12,
AUTHOR = {G{\"o}ke, Jonathan and Schulz, Marcel H. and Lasserre, Julia and Vingron, Martin},
TITLE = {Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {5},
PAGES = {656-663},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts028},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Garcia-Millat-Carus-Bertucci-Finetti-Birnbaum-Bidaut/12,
AUTHOR = {Garcia, Maxime and Millat-Carus, Raphaelle and Bertucci, Fran{\c{c}}ois and Finetti, Pascal and Birnbaum, Daniel and Bidaut, Ghislain},
TITLE = {Interactome-transcriptome integration for predicting distant metastasis in breast cancer},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {5},
PAGES = {672-678},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts025},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chen-Chou-Hsieh-Lee-Liu-Yu-Oyang-Tsai-Chen/12,
AUTHOR = {Chen, Mei-Ju May and Chou, Lih-Ching and Hsieh, Tsung-Ting and Lee, Ding-Dar and Liu, Kai-Wei and Yu, Chi-Yuan and Oyang, Yen-Jen and Tsai, Huai-Kuang and Chen, Chien-Yu},
TITLE = {De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {5},
PAGES = {701-708},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts002},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{DeLuca-Cui-Jung-Gabriel-Wall/12,
AUTHOR = {DeLuca, Todd F. and Cui, Jike and Jung, Jae-Yoon and Gabriel, Kristian Che St. and Wall, Dennis P.},
TITLE = {Roundup 2.0: Enabling comparative genomics for over 1800 genomes},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {5},
PAGES = {715-716},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts006},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hentrich-Schulze-Emberly-Kobor/12,
AUTHOR = {Hentrich, Thomas and Schulze, Julia M. and Emberly, Eldon and Kobor, Michael S.},
TITLE = {CHROMATRA: A Galaxy tool for visualizing genome-wide chromatin signatures},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {5},
PAGES = {717-718},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts007},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chen/12,
AUTHOR = {Chen, Gary K.},
TITLE = {A scalable and portable framework for massively parallel variable selection in genetic association studies},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {5},
PAGES = {719-720},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts015},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hong-Rhie-Park-Lee-Ju-Kim-Yu-Bleazard-Park-Rhee-Chong-Yang-Lee-Kim-Lee-Kim-Seo/12,
AUTHOR = {Hong, Dongwan and Rhie, Arang and Park, Sung-Soo and Lee, Jongkeun and Ju, Young Seok and Kim, Sujung and Yu, Saet-Byeol and Bleazard, Thomas and Park, Hyun-Seok and Rhee, Hwanseok and Chong, Hyonyong and Yang, Kap-Seok and Lee, Yeon-Su and Kim, In-Hoo and Lee, Jin Soo and Kim, Jong-Il and Seo, Jeong-Sun},
TITLE = {FX: An RNA-Seq analysis tool on the cloud},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {5},
PAGES = {721-723},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts023},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chittenden-Howe-Taylor-Mar-Aryee-Gomez-Sultana-Braisted-Nair-Quackenbush-Holmes/12,
AUTHOR = {Chittenden, Thomas W. and Howe, Eleanor A. and Taylor, Jennifer M. and Mar, Jessica C. and Aryee, Martin J. and G{\'o}mez, Harold and Sultana, Razvan and Braisted, John and Nair, Sarita J. and Quackenbush, John and Holmes, Chris},
TITLE = {nEASE: A method for gene ontology subclassification of high-throughput gene expression data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {5},
PAGES = {726-728},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts011},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Carr-Borenstein/12,
AUTHOR = {Carr, Rogan and Borenstein, Elhanan},
TITLE = {NetSeed: A network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {5},
PAGES = {734-735},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr721},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bueschl-Kluger-Berthiller-Lirk-Winkler-Krska-Schuhmacher/12,
AUTHOR = {Bueschl, Christoph and Kluger, Bernhard and Berthiller, Franz and Lirk, Gerald and Winkler, Stephan and Krska, Rudolf and Schuhmacher, Rainer},
TITLE = {MetEtract: A new software tool for the automated comprehensive extraction of metabolite-derived LC/MS signals in metabolomics research},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {5},
PAGES = {736-738},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts012},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Benton-Holmes-Hill-Chung-Ungar/12,
AUTHOR = {Benton, A. and Holmes, J.H. and Hill, S. and Chung, A. and Ungar, L.},
TITLE = {medpie: An information extraction package for medical message board posts},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {5},
PAGES = {743-744},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts030},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Balaji-Mcclendon-Chowdhary-Liu-Zhang/12,
AUTHOR = {Balaji, Sentil and Mcclendon, Charles and Chowdhary, Rajesh and Liu, Jun S. and Zhang, Jinfeng},
TITLE = {IMID: Integrated molecular interaction database},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {5},
PAGES = {747-749},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts010},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Berry-Gillet-Melamed-Gormley-Bangham-Bushman/12,
AUTHOR = {Berry, Charles C. and Gillet, Nicolas A. and Melamed, Anat and Gormley, Niall and Bangham, Charles R.M. and Bushman, Frederic D.},
TITLE = {Estimating abundances of retroviral insertion sites from DNA fragment length data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {6},
PAGES = {755-762},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts004},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gonzalez-Montserrat-Sentis-Sanchez-Puiggros-Blanco-Ramirez-Torrents/12,
AUTHOR = {Gonz{\'a}lez, Santi and Montserrat-Sent{\'{i}}s, B{\`a}rbara and S{\'a}nchez, Friman and Puiggr{\`o}s, Montserrat and Blanco, Enrique and Ramirez, Alex and Torrents, David},
TITLE = {ReLa, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {6},
PAGES = {763-770},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts024},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chakraborty-Datta-Datta/12,
AUTHOR = {Chakraborty, Sutirtha and Datta, Somnath and Datta, Susmita},
TITLE = {Surrogate variable analysis using partial least squares (SVA-PLS) in gene expression studies},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {6},
PAGES = {799-806},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts022},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kim-Jiang-Teng-Feldman-Huang/12,
AUTHOR = {Kim, Kyungpil and Jiang, Keni and Teng, Siew Leng and Feldman, Lewis J. and Huang, Haiyan},
TITLE = {Using biologically interrelated experiments to identify pathway genes in Arabidopsis},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {6},
PAGES = {815-822},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts038},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Illingworth-Mustonen/12,
AUTHOR = {Illingworth, Christopher J.R. and Mustonen, Ville},
TITLE = {A method to infer positive selection from marker dynamics in an asexual population},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {6},
PAGES = {831-837},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr722},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kang-Marjoram/12,
AUTHOR = {Kang, Chul Joo and Marjoram, Paul},
TITLE = {Exact coalescent simulation of new haplotype data from existing reference haplotypes},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {6},
PAGES = {838-844},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts033},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chojnowski-Bujnicki-Bochtler/12,
AUTHOR = {Chojnowski, Grzegorz and Bujnicki, Janusz M. and Bochtler, Matthias},
TITLE = {RIBER/DIBER: A software suite for crystal content analysis in the studies of protein-nucleic acid complexes},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {6},
PAGES = {880-881},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts003},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chandan-van_Iersel-Aladjem-Kohn-Luna/12,
AUTHOR = {Chandan, Kumar and van Iersel, Martijn P. and Aladjem, Mirit I. and Kohn, Kurt W. and Luna, Augustin},
TITLE = {PathVisio-Validator: A rule-based validation plugin for graphical pathway notations},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {6},
PAGES = {889-890},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr694},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{DeJongh-Bockstege-Frybarger-Hazekamp-Kammeraad-McGeehan/12,
AUTHOR = {DeJongh, Matthew and Bockstege, Benjamin and Frybarger, Paul and Hazekamp, Nicholas and Kammeraad, Joshua and McGeehan, Travis},
TITLE = {CytoSEED: A Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {6},
PAGES = {891-892},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/btr719},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hartung-Gross-Rahm/12,
AUTHOR = {Hartung, Michael and Gross, Anika and Rahm, Erhard},
TITLE = {CODEX: Exploration of semantic changes between ontology versions},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {6},
PAGES = {895-896},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts029},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Dessimoz-Gabaldon-Roos-Sonnhammer-Herrero-Consortium/12,
AUTHOR = {Dessimoz, Christophe and Gabald{\'o}n, Toni and Roos, David S. and Sonnhammer, Erik L.L. and Herrero, Javier and Consortium, the Quest for Orthologs},
TITLE = {Toward community standards in the quest for orthologs},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {6},
PAGES = {900-904},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts050},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jones-Ruzzo-Peng-Katze/12,
AUTHOR = {Jones, Daniel C. and Ruzzo, Walter L. and Peng, Xinxia and Katze, Michael G.},
TITLE = {A new approach to bias correction in RNA-Seq},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {7},
PAGES = {921-928},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts055},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kawaguchi-Iida-Harada-Hanada-Matsui-Okamoto-Shinozaki-Seki-Toyoda/12,
AUTHOR = {Kawaguchi, Shuji and Iida, Kei and Harada, Erimi and Hanada, Kousuke and Matsui, Akihiro and Okamoto, Masanori and Shinozaki, Kazuo and Seki, Motoaki and Toyoda, Tetsuro},
TITLE = {Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {7},
PAGES = {929-937},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts065},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{He-Ren-Wang-Ma/12,
AUTHOR = {He, Feng and Ren, Jie and Wang, Wei and Ma, Jun},
TITLE = {Evaluating the Drosophila Bicoid morphogen gradient system through dissecting the noise in transcriptional bursts},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {7},
PAGES = {970-975},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts068},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Karaletsos-Stegle-Dreyer-Winn-Borgwardt/12,
AUTHOR = {Karaletsos, Theofanis and Stegle, Oliver and Dreyer, Christine and Winn, John and Borgwardt, Karsten M.},
TITLE = {ShapePheno: Unsupervised extraction of shape phenotypes from biological image collections},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {7},
PAGES = {1001-1008},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts081},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Aghaeepour-Chattopadhyay-Ganesan-ONeill-Zare-Jalali-Hoos-Roederer-Brinkman/12,
AUTHOR = {Aghaeepour, Nima and Chattopadhyay, Pratip K. and Ganesan, Anuradha and O'Neill, Kieran and Zare, Habil and Jalali, Adrin and Hoos, Holger H. and Roederer, Mario and Brinkman, Ryan R.},
TITLE = {Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {7},
PAGES = {1009-1016},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts082},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chi-Nam/12,
AUTHOR = {Chi, Sang-Mun and Nam, Dougu},
TITLE = {WegoLoc: Accurate prediction of protein subcellular localization using weighted Gene Ontology terms},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {7},
PAGES = {1028-1030},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts062},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bonnal-Aerts-Githinji-Goto-MacLean-Miller-Mishima-Pagani-Ramirez-Gonzalez-Smant-Strozzi-Syme-Vos-Wennblom-Woodcroft-Katayama-Prins/12,
AUTHOR = {Bonnal, Raoul J.P. and Aerts, Jan and Githinji, George and Goto, Naohisa and MacLean, Dan and Miller, Chase A. and Mishima, Hiroyuki and Pagani, Massimiliano and Ramirez-Gonzalez, Ricardo and Smant, Geert and Strozzi, Francesco and Syme, Rob and Vos, Rutger and Wennblom, Trevor J. and Woodcroft, Ben J. and Katayama, Toshiaki and Prins, Pjotr},
TITLE = {Biogem: An effective tool-based approach for scaling up open source software development in bioinformatics},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {7},
PAGES = {1035-1037},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts080},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Barbato-Benkert-Schwede-Tramontano-Kosinski/12,
AUTHOR = {Barbato, Alessandro and Benkert, Pascal and Schwede, Torsten and Tramontano, Anna and Kosinski, Jan},
TITLE = {Improving your target-template alignment with MODalign},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {7},
PAGES = {1038-1039},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts070},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Arends-van_der_Velde-Prins-Broman-Moller-Jansen-Swertz/12,
AUTHOR = {Arends, Danny and van der Velde, K. Joeri and Prins, Pjotr and Broman, Karl W. and M{\"o}ller, Steffen and Jansen, Ritsert C. and Swertz, Morris A.},
TITLE = {xQTL workbench: A scalable web environment for multi-level QTL analysis},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {7},
PAGES = {1042-1044},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts049},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bunge-Woodard-Bohning-Foster-Connolly-Allen/12,
AUTHOR = {Bunge, John and Woodard, Linda and B{\"o}hning, Dankmar and Foster, James A. and Connolly, Sean and Allen, Heather K.},
TITLE = {Estimating population diversity with CatchAll},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {7},
PAGES = {1045-1047},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts075},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Creek-Jankevics-Burgess-Breitling-Barrett/12,
AUTHOR = {Creek, Darren J. and Jankevics, Andris and Burgess, Karl E.V. and Breitling, Rainer and Barrett, Michael P.},
TITLE = {IDEOM: An Excel interface for analysis of LC-MS-based metabolomics data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {7},
PAGES = {1048-1049},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts069},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bald-Barth-Niehues-Specht-Hippler-Fufezan/12,
AUTHOR = {Bald, Till and Barth, Johannes and Niehues, Anna and Specht, Michael and Hippler, Michael and Fufezan, Christian},
TITLE = {pymzML --- Python module for high-throughput bioinformatics on mass spectrometry data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {7},
PAGES = {1052-1053},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts066},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Guignon-Droc-Alaux-Baurens-Garsmeur-Poiron-Carver-Rouard-Bocs/12,
AUTHOR = {Guignon, Valentin and Droc, Ga{\"e}tan and Alaux, Michael and Baurens, Franc-Christophe and Garsmeur, Olivier and Poiron, Claire and Carver, Tim and Rouard, Mathieu and Bocs, St{\'e}phanie},
TITLE = {Chado Controller: Advanced annotation management with a community annotation system},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {7},
PAGES = {1054-1056},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts046},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Beck-Brandl-Boelen-Unnikrishnan-Pimanda-Wong/12,
AUTHOR = {Beck, Dominik and Brandl, Miriam B. and Boelen, Lies and Unnikrishnan, Ashwin and Pimanda, John E. and Wong, Jason W.H.},
TITLE = {Signal analysis for genome-wide maps of histone modifications measured by ChIP-seq},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {8},
PAGES = {1062-1069},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts085},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Galinsky/12,
AUTHOR = {Galinsky, V.L.},
TITLE = {YOABS: Yet other aligner of biological sequences --- An efficient linearly scaling nucleotide aligner},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {8},
PAGES = {1070-1077},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts102},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kiryu-Asai/12,
AUTHOR = {Kiryu, Hisanori and Asai, Kiyoshi},
TITLE = {Rchange: Algorithms for computing energy changes of RNA secondary structures in response to base mutations},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {8},
PAGES = {1093-1101},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts097},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chen-Liu-Nadarajah/12,
AUTHOR = {Chen, Zhongxue and Liu, Qingzhong and Nadarajah, Saralees},
TITLE = {A new statistical approach to detecting differentially methylated loci for case control Illumina array methylation data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {8},
PAGES = {1109-1113},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts093},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chindelevitch-Ziemek-Enayetallah-Randhawa-Sidders-Brockel-Huang/12,
AUTHOR = {Chindelevitch, Leonid and Ziemek, Daniel and Enayetallah, Ahmed and Randhawa, Ranjit and Sidders, Ben and Brockel, Christoph and Huang, Enoch S.},
TITLE = {Causal reasoning on biological networks: Interpreting transcriptional changes},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {8},
PAGES = {1114-1121},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts090},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chang/12,
AUTHOR = {Chang, Jeffrey T.},
TITLE = {Deriving transcriptional programs and functional processes from gene expression databases},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {8},
PAGES = {1122-1129},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts112},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kim-Koo-Wei-Zhang/12,
AUTHOR = {Kim, Seongho and Koo, Imhoi and Wei, Xiaoli and Zhang, Xiang},
TITLE = {A method of finding optimal weight factors for compound identification in gas chromatography-mass spectrometry},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {8},
PAGES = {1158-1163},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts083},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bhaduri-Qu-Lee-Ungewickell-Khavari/12,
AUTHOR = {Bhaduri, Aparna and Qu, Kun and Lee, Carolyn S. and Ungewickell, Alexander and Khavari, Paul A.},
TITLE = {Rapid identification of non-human sequences in high-throughput sequencing datasets},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {8},
PAGES = {1174-1175},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts100},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gautier-Vitalis/12,
AUTHOR = {Gautier, Mathieu and Vitalis, Renaud},
TITLE = {rehh: An R package to detect footprints of selection in genome-wide SNP data from haplotype structure},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {8},
PAGES = {1176-1177},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts115},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Grassler-Koschutzki-Schreiber/12,
AUTHOR = {Gr{\"a}{\ss}ler, Johannes and Kosch{\"u}tzki, Dirk and Schreiber, Falk},
TITLE = {CentiLib: Comprehensive analysis and exploration of network centralities},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {8},
PAGES = {1178-1179},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts106},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Adams/12,
AUTHOR = {Adams, Richard R.},
TITLE = {SED-ED, a workflow editor for computational biology experiments written in SED-ML},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {8},
PAGES = {1180-1181},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts101},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Huang-Lu-Liu-Haaland-Marron/12,
AUTHOR = {Huang, Hanwen and Lu, Xiaosun and Liu, Yufeng and Haaland, Perry and Marron, J.S.},
TITLE = {R/DWD: Distance-weighted discrimination for classification, visualization and batch adjustment},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {8},
PAGES = {1182-1183},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts096},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Collier-Doan/12,
AUTHOR = {Collier, Nigel and Doan, Son},
TITLE = {GENI-DB: A database of global events for epidemic intelligence},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {8},
PAGES = {1186-1188},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts099},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hajirasouliha-Schonhuth-de_Juan-Valencia-Sahinalp/12,
AUTHOR = {Hajirasouliha, Iman and Sch{\"o}nhuth, Alexander and de Juan, David and Valencia, Alfonso and Sahinalp, S. Cenk},
TITLE = {Mirroring co-evolving trees in the light of their topologies},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {9},
PAGES = {1202-1208},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts109},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Daniels-Hosur-Berger-Cowen/12,
AUTHOR = {Daniels, Noah M. and Hosur, Raghavendra and Berger, Bonnie and Cowen, Lenore J.},
TITLE = {SMURFLite: Combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {9},
PAGES = {1216-1222},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts110},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Campos-Matos-Lewin-Oliveira-Rebholz-Schuhmann/12,
AUTHOR = {Campos, David and Matos, S{\'e}rgio and Lewin, Ian and Oliveira, Jos{\'e} Lu{\'{i}}s and Rebholz-Schuhmann, Dietrich},
TITLE = {Harmonization of gene/protein annotations: Towards a gold standard MEDLINE},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {9},
PAGES = {1253-1261},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts125},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hospital-Andrio-Fenollosa-Cicin-Sain-Orozco-Gelpi/12,
AUTHOR = {Hospital, Adam and Andrio, Pau and Fenollosa, Carles and Cicin-Sain, Damjan and Orozco, Modesto and Gelp{\'{i}}, Josep Llu{\'{i}}s},
TITLE = {MDWeb and MDMoby: An integrated web-based platform for molecular dynamics simulations},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {9},
PAGES = {1278-1279},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts139},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Barfield-Kilaru-Smith-Conneely/12,
AUTHOR = {Barfield, Richard T. and Kilaru, Varun and Smith, Alicia K. and Conneely, Karen N.},
TITLE = {CpGassoc: An R function for analysis of DNA methylation microarray data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {9},
PAGES = {1280-1281},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts124},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gnad-Estrada-Gunawardena/12,
AUTHOR = {Gnad, Florian and Estrada, Javier and Gunawardena, Jeremy},
TITLE = {Proteus: A web-based, context-specific modelling tool for molecular networks},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {9},
PAGES = {1284-1286},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts126},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Barnett-Yang-Cai-Zhang-Wan/12,
AUTHOR = {Barnett, J. Lamar and Yang, Jialiang and Cai, Zhipeng and Zhang, Tong and Wan, Xiu-Feng},
TITLE = {AntigenMap 3D: An online antigenic cartography resource},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {9},
PAGES = {1292-1293},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts105},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Joshi-Christiansen-Fitz-Cao-Lipzen-Martin-Smith-Moritz-Pennacchio-Schackwitz-Weigel-Heazlewood/12,
AUTHOR = {Joshi, Hiren J. and Christiansen, Katy M. and Fitz, Joffrey and Cao, Jun and Lipzen, Anna and Martin, Joel and Smith-Moritz, A. Michelle and Pennacchio, Len A. and Schackwitz, Wendy S. and Weigel, Detlef and Heazlewood, Joshua L.},
TITLE = {1001 Proteomes: A functional proteomics portal for the analysis of Arabidopsis thaliana accessions},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {10},
PAGES = {1303-1306},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts133},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Burriesci-Lehnert-Pringle/12,
AUTHOR = {Burriesci, Matthew S. and Lehnert, Erik M. and Pringle, John R.},
TITLE = {Fulcrum: Condensing redundant reads from high-throughput sequencing studies},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {10},
PAGES = {1324-1327},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts123},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Baran-Pasaniuc-Sankararaman-Torgerson-Gignoux-Eng-Rodriguez-Cintron-Chapela-Ford-Avila-Rodriguez-Santana-Burchard-Halperin/12,
AUTHOR = {Baran, Yael and Pasaniuc, Bogdan and Sankararaman, Sriram and Torgerson, Dara G. and Gignoux, Christopher and Eng, Celeste and Rodriguez-Cintron, William and Chapela, Rocio and Ford, Jean G. and Avila, Pedro C. and Rodriguez-Santana, Jose and Burchard, Esteban Gonz{\`a}lez and Halperin, Eran},
TITLE = {Fast and accurate inference of local ancestry in Latino populations},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {10},
PAGES = {1359-1367},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts144},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Fawal-Savelli-Dunand-Mathe/12,
AUTHOR = {Fawal, Nizar and Savelli, Bruno and Dunand, Christophe and Math{\'e}, Catherine},
TITLE = {GECA: A fast tool for gene evolution and conservation analysis in eukaryotic protein families},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {10},
PAGES = {1398-1399},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts153},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Comoglio-Rinaldi/12,
AUTHOR = {Comoglio, Federico and Rinaldi, Maurizio},
TITLE = {Rknots: Topological analysis of knotted biopolymers with R},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {10},
PAGES = {1400-1401},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts160},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Feng-Sales-Kepler/12,
AUTHOR = {Feng, Feng and Sales, Ana Paula and Kepler, Thomas B.},
TITLE = {Corrigendum to ``A Bayesian approach for estimating calibration curves and unknown concentrations in immunoassays''},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {10},
PAGES = {1413-1413},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts136},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
NOTE = {Originally in Bioinformatics, Vol. 27, 2011, No. 5, 707-712},
}
@article{Cox-Bauer-Jakobi-Rosone/12,
AUTHOR = {Cox, Anthony J. and Bauer, Markus J. and Jakobi, Tobias and Rosone, Giovanna},
TITLE = {Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {11},
PAGES = {1415-1419},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts173},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gritsenko-Nijkamp-Reinders-de_Ridder/12,
AUTHOR = {Gritsenko, Alexey A. and Nijkamp, Jurgen F. and Reinders, Marcel J.T. and de Ridder, Dick},
TITLE = {GRASS: A generic algorithm for scaffolding next-generation sequencing assemblies},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {11},
PAGES = {1429-1437},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts175},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chartier-Gaudreault-Najmanovich/12,
AUTHOR = {Chartier, Matthieu and Gaudreault, Francis and Najmanovich, Rafael},
TITLE = {Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {11},
PAGES = {1438-1445},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts149},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Aboukhalil-Bulyk/12,
AUTHOR = {Aboukhalil, Anton and Bulyk, Martha L.},
TITLE = {LOESS correction for length variation in gene set-based genomic sequence analysis},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {11},
PAGES = {1446-1454},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts155},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{DeLuca-Levin-Sivachenko-Fennell-Nazaire-Williams-Reich-Winckler-Getz/12,
AUTHOR = {DeLuca, David S. and Levin, Joshua Z. and Sivachenko, Andrey and Fennell, Timothy and Nazaire, Marc-Danie and Williams, Chris and Reich, Michael and Winckler, Wendy and Getz, Gad},
TITLE = {RNA-SeQC: RNA-seq metrics for quality control and process optimization},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {11},
PAGES = {1530-1532},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts196},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hu-Yuan-Shi-Lu-Liu-Li-Chen-Mu-Zhang-Li-Yue-Bai-Li-Fan/12,
AUTHOR = {Hu, Xuesong and Yuan, Jianying and Shi, Yujian and Lu, Jianliang and Liu, Binghang and Li, Zhenyu and Chen, Yanxiang and Mu, Desheng and Zhang, Hao and Li, Nan and Yue, Zhen and Bai, Fan and Li, Heng and Fan, Wei},
TITLE = {pIRS: Profile-based Illumina pair-end reads simulator},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {11},
PAGES = {1533-1535},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts187},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jourdren-Bernard-Dillies-Le_Crom/12,
AUTHOR = {Jourdren, Laurent and Bernard, Maria and Dillies, Marie-Agn{`e}s and Le Crom, St{\'e}phane},
TITLE = {Eoulsan: A cloud computing-based framework facilitating high throughput sequencing analyses},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {11},
PAGES = {1542-1543},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts165},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gao-Luo-Zhang/12,
AUTHOR = {Gao, Feng and Luo, Hao and Zhang, Chun-Ting},
TITLE = {DeOri: A database of eukaryotic DNA replication origins},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {11},
PAGES = {1551-1552},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts151},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bernal-Crammer-Pereira/12,
AUTHOR = {Bernal, Axel and Crammer, Koby and Pereira, Fernando},
TITLE = {Automated gene-model curation using global discriminative learning},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {1571-1578},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts176},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Iancu-Kawane-Bottomly-Searles-Hitzemann-McWeeney/12,
AUTHOR = {Iancu, Ovidiu D. and Kawane, Sunita and Bottomly, Daniel and Searles, Robert and Hitzemann, Robert and McWeeney, Shannon},
TITLE = {Utilizing RNA-Seq data for de novo coexpression network inference bioinformatics},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {1592-1597},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts245},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chen-Wu/12,
AUTHOR = {Chen, Bor-Sen and Wu, Chia-Chou},
TITLE = {On the calculation of signal transduction ability of signaling transduction pathways in intracellular communication: Systematic approach},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {1604-1611},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts159},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Egen-Lun/12,
AUTHOR = {Egen, Dennis and Lun, Desmond S.},
TITLE = {Truncated branch and bound achieves efficient constraint-based genetic design},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {1619-1623},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts255},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Anderson-Laegreid-Cerutti-Osorio-Nelson-Christopher-Hennings-Goldberg/12,
AUTHOR = {Anderson, Tavis K. and Laegreid, William W. and Cerutti, Francesco and Osorio, Fernando A. and Nelson, Eric A. and Christopher-Hennings, Jane and Goldberg, Tony L.},
TITLE = {Ranking viruses: Measures of positional importance within networks define core viruses for rational polyvalent vaccine development},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {1624-1632},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts181},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kearse-Moir-Wilson-Stones-Havas-Cheung-Sturrock-Buxton-Cooper-Markowitz-Duran-Thierer-Ashton-Meintjes-Drummond/12,
AUTHOR = {Kearse, Matthew and Moir, Richard and Wilson, Amy and Stones-Havas, Steven and Cheung, Matthew and Sturrock, Shane and Buxton, Simon and Cooper, Alex and Markowitz, Sidney and Duran, Chris and Thierer, Tobias and Ashton, Bruce and Meintjes, Peter and Drummond, Alexei},
TITLE = {Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {1647-1649},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts199},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Carvalho-Yates-Barbosa/12,
AUTHOR = {Carvalho, Paulo C. and Yates III, John R. and Barbosa, Valmir C.},
TITLE = {Improving the TFold test for differential shotgun proteomics},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {1652-1654},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts247},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Andreini-Cavallaro-Lorenzini/12,
AUTHOR = {Andreini, Claudia and Cavallaro, Gabriele and Lorenzini, Serena},
TITLE = {FindGeo: A tool for determining metal coordination geometry},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {1658-1660},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts246},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Cereto-Massague-Guasch-Valls-Mulero-Pujadas-Garcia-Vallve/12,
AUTHOR = {Cereto-Massagu{\'e}, Adri{\`a} and Guasch, Laura and Valls, Cristina and Mulero, Miquel and Pujadas, Gerard and Garcia-Vallv{\'e}, Santiago},
TITLE = {DecoyFinder: An easy-to-use python GUI application for building target-specific decoy sets},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {1661-1662},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts249},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Brandizi-Kurbatova-Sarkans-Rocca-Serra/12,
AUTHOR = {Brandizi, Marco and Kurbatova, Natalja and Sarkans, Ugis and Rocca-Serra, Philippe},
TITLE = {graph2tab, a library to convert experimental workflow graphs into tabular formats},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {12},
PAGES = {1665-1667},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts258},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hayes-Nemes-Karlsson/12,
AUTHOR = {Hayes, Catherine A. and Nemes, Szilard and Karlsson, Niclas G.},
TITLE = {Statistical analysis of glycosylation profiles to compare tissue type and inflammatory disease state},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {13},
PAGES = {1669-1676},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts242},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Das-Vikalo/12,
AUTHOR = {Das, Shreepriya and Vikalo, Haris},
TITLE = {OnlineCall: Fast online parameter estimation and base calling for illumina's next-generation sequencing},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {13},
PAGES = {1677-1683},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts256},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kangas-Metz-Isaac-Schrom-Ginovska-Pangovska-Wang-Tan-Lewis-Miller/12,
AUTHOR = {Kangas, Lars J. and Metz, Thomas O. and Isaac, Giorgis and Schrom, Brian T. and Ginovska-Pangovska, Bojana and Wang, Luning and Tan, Li and Lewis, Robert R. and Miller, John H.},
TITLE = {In silico identification software (ISIS): A machine learning approach to tandem mass spectral identification of lipids},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {13},
PAGES = {1705-1713},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts194},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Glaus-Honkela-Rattray/12,
AUTHOR = {Glaus, Peter and Honkela, Antti and Rattray, Magnus},
TITLE = {Identifying differentially expressed transcripts from RNA-seq data with biological variation},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {13},
PAGES = {1721-1728},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts260},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Huynh-Thu-Saeys-Wehenkel-Geurts/12,
AUTHOR = {Huynh-Thu, V{\^a}n Anh and Saeys, Yvan and Wehenkel, Louis and Geurts, Pierre},
TITLE = {Statistical interpretation of machine learning-based feature importance scores for biomarker discovery},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {13},
PAGES = {1766-1774},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts238},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Dragiev-Nadon-Makarenkov/12,
AUTHOR = {Dragiev, Plamen and Nadon, Robert and Makarenkov, Vladimir},
TITLE = {Two effective methods for correcting experimental high-throughput screening data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {13},
PAGES = {1775-1782},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts262},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hoehndorf-Harris-Herre-Rustici-Gkoutos/12,
AUTHOR = {Hoehndorf, Robert and Harris, Midori A. and Herre, Heinrich and Rustici, Gabriella and Gkoutos, Georgios V.},
TITLE = {Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {13},
PAGES = {1783-1789},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts250},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kim-Hu-Yim-Bae-Kim-Chung/12,
AUTHOR = {Kim, Ji-Hong and Hu, Hae-Jin and Yim, Seon-Hee and Bae, Joon Seol and Kim, Seon-Young and Chung, Yeun-Jun},
TITLE = {CNVRuler: A copy number variation-based case-control association analysis tool},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {13},
PAGES = {1790-1792},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts239},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Harris-Ponts-Le_Roch-Lonardi/12,
AUTHOR = {Harris, Elena Y. and Ponts, Nadia and Le Roch, Karine G. and Lonardi, Stefano},
TITLE = {BRAT-BW: Efficient and accurate mapping of bisulfite-treated reads},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {13},
PAGES = {1795-1796},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts264},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Khiripet-Khantuwan-Jungck/12,
AUTHOR = {Khiripet, Noppadon and Khantuwan, Wongarnet and Jungck, John R.},
TITLE = {Ka-me: A Voronoi image analyzer},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {13},
PAGES = {1802-1804},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts253},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jiao-Sherman-Huang-Stephens-Baseler-Lane-Lempicki/12,
AUTHOR = {Jiao, Xiaoli and Sherman, Brad T. and Huang, Da Wei and Stephens, Robert and Baseler, Michael W. and Lane, H. Clifford and Lempicki, Richard A.},
TITLE = {DAVID-WS: A stateful web service to facilitate gene/protein list analysis},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {13},
PAGES = {1805-1806},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts251},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bertozzi-Sanders-Sistrom-Gardner/12,
AUTHOR = {Bertozzi, Terry and Sanders, Kate L. and Sistrom, Mark J. and Gardner, Michael G.},
TITLE = {Anonymous nuclear loci in non-model organisms: Making the most of high-throughput genome surveys},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {14},
PAGES = {1807-1810},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts284},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Buenavista-Roche-McGuffin/12,
AUTHOR = {Buenavista, Maria T. and Roche, Daniel B. and McGuffin, Liam J.},
TITLE = {Improvement of 3D protein models using multiple templates guided by single-template model quality assessment},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {14},
PAGES = {1851-1857},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts292},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hoksza-Svozil/12,
AUTHOR = {Hoksza, David and Svozil, Daniel},
TITLE = {Efficient RNA pairwise structure comparison by SETTER method},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {14},
PAGES = {1858-1864},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts301},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Das-Mohammed-Yu/12,
AUTHOR = {Das, Jishnu and Mohammed, Jaaved and Yu, Haiyuan},
TITLE = {Genome-scale analysis of interaction dynamics reveals organization of biological networks},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {14},
PAGES = {1873-1878},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts283},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Beisser-Brunkhorst-Dandekar-Klau-Dittrich-Muller/12,
AUTHOR = {Beisser, Daniela and Brunkhorst, Stefan and Dandekar, Thomas and Klau, Gunnar W. and Dittrich, Marcus T. and M{\"u}ller, Tobias},
TITLE = {Robustness and accuracy of functional modules in integrated network analysis},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {14},
PAGES = {1887-1894},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts265},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hyatt-Pan/12,
AUTHOR = {Hyatt, Doug and Pan, Chongle},
TITLE = {Exhaustive database searching for amino acid mutations in proteomes},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {14},
PAGES = {1895-1901},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts274},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chibon-Schoof-Visser-Finkers/12,
AUTHOR = {Chibon, Pierre-Yves and Schoof, Heiko and Visser, Richard G.F. and Finkers, Richard},
TITLE = {Marker2sequence, mine your QTL regions for candidate genes},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {14},
PAGES = {1921-1922},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts298},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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TITLE = {BreakFusion: Targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {14},
PAGES = {1923-1924},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts272},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Claeys-Storms-Sun-Michoel-Marchal/12,
AUTHOR = {Claeys, Marleen and Storms, Valerie and Sun, Hong and Michoel, Tom and Marchal, Kathleen},
TITLE = {MotifSuite: Workflow for probabilistic motif detection and assessment},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {14},
PAGES = {1931-1932},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts293},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hu-Ge-Newman-Liu/12,
AUTHOR = {Hu, Jun and Ge, Huanying and Newman, Matt and Liu, Kejun},
TITLE = {OSA: A fast and accurate alignment tool for RNA-Seq},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {14},
PAGES = {1933-1934},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts294},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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AUTHOR = {Conway, Thomas and Wazny, Jeremy and Bromage, Andrew and Zobel, Justin and Beresford-Smith, Bryan},
TITLE = {Gossamer --- A resource-efficient de novo assembler},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {14},
PAGES = {1937-1938},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts297},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
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AUTHOR = {Dawson, John A. and Ye, Shuyun and Kendziorski, Christina},
TITLE = {R/EBcoexpress: An empirical Bayesian framework for discovering differential co-expression},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {14},
PAGES = {1939-1940},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts268},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{James-Rao-Chen-Goodell-Shaw/12,
AUTHOR = {James, Regis A. and Rao, Mitchell M. and Chen, Edward S. and Goodell, Margaret A. and Shaw, Chad A.},
TITLE = {The Hematopoietic Expression Viewer: Expanding mobile apps as a scientific tool},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {14},
PAGES = {1941-1942},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts279},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Fujimori-Hirai-Masuoka-Oshikubo-Yamashita-Washio-Saito-Nagasaki-Miyano-Miyamoto-Sato/12,
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TITLE = {IRView: A database and viewer for protein interacting regions},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {14},
PAGES = {1949-1950},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts289},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gyenesei-Moody-Semple-Haley-Wei/12,
AUTHOR = {Gyenesei, Attila and Moody, Jonathan and Semple, Colin A.M. and Haley, Chris S. and Wei, Wen-Hua},
TITLE = {High-throughput analysis of epistasis in genome-wide association studies with BiForce},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {15},
PAGES = {1957-1964},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts304},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Fu-Tang-Feng-Liu-Zhang/12,
AUTHOR = {Fu, Kai and Tang, Qianzi and Feng, Jianxing and Liu, X. Shirley and Zhang, Yong},
TITLE = {DiNuP: A systematic approach to identify regions of differential nucleosome positioning},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {15},
PAGES = {1965-1971},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts329},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gu-Xuan-Riggins-Chen-Wang-Clarke/12,
AUTHOR = {Gu, Jinghua and Xuan, Jianhua and Riggins, Rebecca B. and Chen, Li and Wang, Yue and Clarke, Robert},
TITLE = {Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {15},
PAGES = {1990-1997},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts296},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Ge-Sealfon/12,
AUTHOR = {Ge, Yongchao and Sealfon, Stuart C.},
TITLE = {flowPeaks: A fast unsupervised clustering for flow cytometry data via $K$-means and density peak finding},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {15},
PAGES = {2052-2058},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts300},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jeggari-Marks-Larsson/12,
AUTHOR = {Jeggari, Ashwini and Marks, Debora S. and Larsson, Erik},
TITLE = {miRcode: A map of putative microRNA target sites in the long non-coding transcriptome},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {15},
PAGES = {2062-2063},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts344},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Debastiani-Pillar/12,
AUTHOR = {Debastiani, Vanderlei J. and Pillar, Val{\'e}rio D.},
TITLE = {SYNCSA --- R tool for analysis of metacommunities based on functional traits and phylogeny of the community components},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {15},
PAGES = {2067-2068},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts325},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Braberg-Webb-Tjioe-Pieper-Sali-Madhusudhan/12,
AUTHOR = {Braberg, Hannes and Webb, Benjamin M. and Tjioe, Elina and Pieper, Ursula and Sali, Andrej and Madhusudhan, M.S.},
TITLE = {SALIGN: A web server for alignment of multiple protein sequences and structures},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {15},
PAGES = {2072-2073},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts302},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Domenico-Walsh-Martin-Tosatto/12,
AUTHOR = {Domenico, Tom{\'a}s Di and Walsh, Ian and Martin, Alberto J.M. and Tosatto, Silvio C.E.},
TITLE = {MobiDB: A comprehensive database of intrinsic protein disorder annotations},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {15},
PAGES = {2080-2081},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts327},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hao-Astle-De_Iorio-Ebbels/12,
AUTHOR = {Hao, Jie and Astle, William and De Iorio, Maria and Ebbels, Timothy},
TITLE = {BATMAN --- An R package for the automated quantification of metabolites from nuclear magnetic resonance spectra using a Bayesian model},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {15},
PAGES = {2088-2090},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts308},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gray-Kukurba-Kumar/12,
AUTHOR = {Gray, Vanessa E. and Kukurba, Kimberly R. and Kumar, Sudhir},
TITLE = {Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {16},
PAGES = {2093-2096},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts336},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chen-Bittinger-Charlson-Hoffmann-Lewis-Wu-Collman-Bushman-Li/12,
AUTHOR = {Chen, Jun and Bittinger, Kyle and Charlson, Emily S. and Hoffmann, Christian and Lewis, James and Wu, Gary D. and Collman, Ronald G. and Bushman, Frederic D. and Li, Hongzhe},
TITLE = {Associating microbiome composition with environmental covariates using generalized UniFrac distances},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {16},
PAGES = {2106-2113},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts342},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Abate-Acquaviva-Paciello-Foti-Ficarra-Ferrarini-Delledonne-Iacobucci-Soverini-Martinelli-Macii/12,
AUTHOR = {Abate, Francesco and Acquaviva, Andrea and Paciello, Giulia and Foti, Carmelo and Ficarra, Elisa and Ferrarini, Alberto and Delledonne, Massimo and Iacobucci, Ilaria and Soverini, Simona and Martinelli, Giovanni and Macii, Enrico},
TITLE = {Bellerophontes: An RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {16},
PAGES = {2114-2121},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts334},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Dong-Shin-Joo-Nam-Cho/12,
AUTHOR = {Dong, Chao-Yi and Shin, Dongkwan and Joo, Sunghoon and Nam, YoonKey and Cho, Kwang-Hyun},
TITLE = {Identification of feedback loops in neural networks based on multi-step Granger causality},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {16},
PAGES = {2146-2153},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts354},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gerner-Sarafraz-Bergman-Nenadic/12,
AUTHOR = {Gerner, Martin and Sarafraz, Farzaneh and Bergman, Casey M. and Nenadic, Goran},
TITLE = {BioContext: An integrated text mining system for large-scale extraction and contextualization of biomolecular events},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {16},
PAGES = {2154-2161},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts332},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chang-Ke-Lin-Chiang/12,
AUTHOR = {Chang, Darby Tien-Hao and Ke, Chao-Hsuan and Lin, Jung-Hsin and Chiang, Jung-Hsien},
TITLE = {AutoBind: Automatic extraction of protein-ligand-binding affinity data from biological literature},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {16},
PAGES = {2162-2168},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts367},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hoehndorf-Dumontier-Gkoutos/12,
AUTHOR = {Hoehndorf, Robert and Dumontier, Michel and Gkoutos, Georgios V.},
TITLE = {Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {16},
PAGES = {2169-2175},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts350},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bachman-Venner-Lua-Erdin-Lichtarge/12,
AUTHOR = {Bachman, Benjamin J. and Venner, Eric and Lua, Rhonald C. and Erdin, Serkan and Lichtarge, Olivier},
TITLE = {ETAscape: Analyzing protein networks to predict enzymatic function and substrates in Cytoscape},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {16},
PAGES = {2186-2188},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts331},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hung-Samudrala/12,
AUTHOR = {Hung, Ling-Hong and Samudrala, Ram},
TITLE = {Accelerated protein structure comparison using TM-score-GPU},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {16},
PAGES = {2191-2192},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts345},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Dahl-Chavent-Sansom/12,
AUTHOR = {Dahl, Anna Caroline E. and Chavent, Matthieu and Sansom, Mark S.P.},
TITLE = {Bendix: Intuitive helix geometry analysis and abstraction},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {16},
PAGES = {2193-2194},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts357},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Copeland-Krishnan-Beck-Settles-Foster-Cho-Day-Hickey-Schutte-Zhou-Williams-Forney-Abdo/12,
AUTHOR = {Copeland, Wade K. and Krishnan, Vandhana and Beck, Daniel and Settles, Matt and Foster, James A. and Cho, Kyu-Chul and Day, Mitch and Hickey, Roxana and Sch{\"u}tte, Ursel M.E. and Zhou, Xia and Williams, Christopher J. and Forney, Larry J. and Abdo, Zaid},
TITLE = {mcaGUI: Microbial community analysis R-Graphical User Interface (GUI)},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {16},
PAGES = {2198-2199},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts338},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{He-Gong/12,
AUTHOR = {He, Zengyou and Gong, Haipeng},
TITLE = {Comments on ``MMFPh: A Maximal Motif Finder for Phosphoproteomics Datasets''},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {16},
PAGES = {2211-2212},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts346},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hyatt-LoCascio-Hauser-Uberbacher/12,
AUTHOR = {Hyatt, Doug and LoCascio, Philip F. and Hauser, Loren J. and Uberbacher, Edward C.},
TITLE = {Gene and translation initiation site prediction in metagenomic sequences},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {17},
PAGES = {2223-2230},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts429},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Doose-Metzler/12,
AUTHOR = {Doose, Gero and Metzler, Dirk},
TITLE = {Bayesian sampling of evolutionarily conserved RNA secondary structures with pseudoknots},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {17},
PAGES = {2242-2248},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts369},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chuang-Boyington-Joyce-Zhu-Nabel-Kwong-Georgiev/12,
AUTHOR = {Chuang, Gwo-Yu and Boyington, Jeffrey C. and Joyce, M. Gordon and Zhu, Jiang and Nabel, Gary J. and Kwong, Peter D. and Georgiev, Ivelin},
TITLE = {Computational prediction of $N$-linked glycosylation incorporating structural properties and patterns},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {17},
PAGES = {2249-2255},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts426},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Habegger-Balasubramanian-Chen-Khurana-Sboner-Harmanci-Rozowsky-Clarke-Snyder-Gerstein/12,
AUTHOR = {Habegger, Lukas and Balasubramanian, Suganthi and Chen, David Z. and Khurana, Ekta and Sboner, Andrea and Harmanci, Arif and Rozowsky, Joel and Clarke, Declan and Snyder, Michael and Gerstein, Mark},
TITLE = {VAT: A computational framework to functionally annotate variants in personal genomes within a cloud-computing environment},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {17},
PAGES = {2267-2269},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts368},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gibb-Strimmer/12,
AUTHOR = {Gibb, Sebastian and Strimmer, Korbinian},
TITLE = {MALDIquant: A versatile R package for the analysis of mass spectrometry data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {17},
PAGES = {2270-2271},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts447},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Alachiotis-Stamatakis-Pavlidis/12,
AUTHOR = {Alachiotis, N. and Stamatakis, A. and Pavlidis, P.},
TITLE = {OmegaPlus: A scalable tool for rapid detection of selective sweeps in whole-genome datasets},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {17},
PAGES = {2274-2275},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts419},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Klein-Leupold-Biegler-Biedendieck-Munch-Jahn/12,
AUTHOR = {Klein, Johannes and Leupold, Stefan and Biegler, Ilona and Biedendieck, Rebekka and M{\"u}nch, Richard and Jahn, Dieter},
TITLE = {TLM-Tracker: Software for cell segmentation, tracking and lineage analysis in time-lapse microscopy movies},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {17},
PAGES = {2276-2277},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts424},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Grapov-Newman/12,
AUTHOR = {Grapov, Dmitry and Newman, John W.},
TITLE = {imDEV: A graphical user interface to R multivariate analysis tools in Microsoft Excel},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {17},
PAGES = {2288-2290},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts439},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gonen/12,
AUTHOR = {G{\"o}nen, M.},
TITLE = {Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {2304-2310},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts360},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Eduati-De_Las_Rivas-Di_Camillo-Toffolo-Saez-Rodriguez/12,
AUTHOR = {Eduati, Federica and De Las Rivas, Javier and Di Camillo, Barbara and Toffolo, Gianna and Saez-Rodriguez, Julio},
TITLE = {Integrating literature-constrained and data-driven inference of signalling networks},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {2311-2317},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts363},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Heinonen-Shen-Zamboni-Rousu/12,
AUTHOR = {Heinonen, Markus and Shen, Huibin and Zamboni, Nicola and Rousu, Juho},
TITLE = {Metabolite identification and molecular fingerprint prediction through machine learning},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {2333-2341},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts437},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Georgii-Salojarvi-Brosche-Kangasjarvi-Kaski/12,
AUTHOR = {Georgii, Elisabeth and Saloj{\"a}rvi, Jarkko and Brosch{\'e}, Mikael and Kangasj{\"a}rvi, Jaakko and Kaski, Samuel},
TITLE = {Targeted retrieval of gene expression measurements using regulatory models},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {2349-2356},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts361},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jones-Rajaraman-Tannier-Chauve/12,
AUTHOR = {Jones, Bradley R. and Rajaraman, Ashok and Tannier, Eric and Chauve, Cedric},
TITLE = {ANGES: Reconstructing ANcestral GEnomeS maps},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {18},
PAGES = {2388-2390},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts457},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Faust-Hall/12,
AUTHOR = {Faust, Gregory G. and Hall, Ira M.},
TITLE = {YAHA: Fast and flexible long-read alignment with optimal breakpoint detection},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {19},
PAGES = {2417-2424},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts456},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Freeman-Wimley/12,
AUTHOR = {Freeman, Thomas C., Jr and Wimley, William C.},
TITLE = {TMBB-DB: A transmembrane $\beta$-barrel proteome database},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {19},
PAGES = {2425-2430},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts478},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Fuglebakk-Echave-Reuter/12,
AUTHOR = {Fuglebakk, Edvin and Echave, Juli{\'a}n and Reuter, Nathalie},
TITLE = {Measuring and comparing structural fluctuation patterns in large protein datasets},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {19},
PAGES = {2431-2440},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts445},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bacardit-Widera-Marquez-Chamorro-Divina-Aguilar-Ruiz-Krasnogor/12,
AUTHOR = {Bacardit, Jaume and Widera, Pawe{\l} and M{\'a}rquez-Chamorro, Alfonso and Divina, Federico and Aguilar-Ruiz, Jes{\'u}s S. and Krasnogor, Natalio},
TITLE = {Contact map prediction using a large-scale ensemble of rule sets and the fusion of multiple predicted structural features},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {19},
PAGES = {2441-2448},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts472},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Di_Lena-Nagata-Baldi/12,
AUTHOR = {Di Lena, Pietro and Nagata, Ken and Baldi, Pierre},
TITLE = {Deep architectures for protein contact map prediction},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {19},
PAGES = {2449-2457},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts475},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Acuna-Milreu-Cottret-Marchetti-Spaccamela-Stougie-Sagot/12,
AUTHOR = {Acu{\~n}a, Vicente and Milreu, Paulo Vieira and Cottret, Ludovic and Marchetti-Spaccamela, Alberto and Stougie, Leen and Sagot, Marie-France},
TITLE = {Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {19},
PAGES = {2474-2483},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts423},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gusenleitner-Howe-Bentink-Quackenbush-Culhane/12,
AUTHOR = {Gusenleitner, Daniel and Howe, Eleanor A. and Bentink, Stefan and Quackenbush, John and Culhane, Aed{\'{i}}n C.},
TITLE = {iBBiG: Iterative binary bi-clustering of gene sets},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {19},
PAGES = {2484-2492},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts438},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bauer-Kohler-Schulz-Robinson/12,
AUTHOR = {Bauer, Sebastian and K{\"o}hler, Sebastian and Schulz, Marcel H. and Robinson, Peter N.},
TITLE = {Bayesian ontology querying for accurate and noise-tolerant semantic searches},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {19},
PAGES = {2502-2508},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts471},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hilker-Sickinger-Pedersen-Stoye/12,
AUTHOR = {Hilker, Rolf and Sickinger, Corinna and Pedersen, Christian N.S. and Stoye, Jens},
TITLE = {UniMoG --- A unifying framework for genomic distance calculation and sorting based on DCJ},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {19},
PAGES = {2509-2511},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts440},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kamphans-Krawitz/12,
AUTHOR = {Kamphans, Tom and Krawitz, Peter M.},
TITLE = {GeneTalk: An expert exchange platform for assessing rare sequence variants in personal genomes},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {19},
PAGES = {2515-2516},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts462},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Boeva-Lermine-Barette-Guillouf-Barillot/12,
AUTHOR = {Boeva, Valentina and Lermine, Alban and Barette, Camille and Guillouf, Christel and Barillot, Emmanuel},
TITLE = {Nebula --- A web-server for advanced ChIP-seq data analysis},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {19},
PAGES = {2517-2519},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts463},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Delhomme-Padioleau-Furlong-Steinmetz/12,
AUTHOR = {Delhomme, Nicolas and Padioleau, Isma{\"e}l and Furlong, Eileen E. and Steinmetz, Lars M.},
TITLE = {easyRNASeq: A bioconductor package for processing RNA-Seq data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {19},
PAGES = {2532-2533},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts477},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Goldstein-Crenshaw-Carey-Grant-Maguire-Fromer-ODushlaine-Moran-Chambert-Stevens-Consortium-Consortium-Sklar-Hultman-Purcell-McCarroll-Sullivan-Daly-Neale/12,
AUTHOR = {Goldstein, Jacqueline I. and Crenshaw, Andrew and Carey, Jason and Grant, George B. and Maguire, Jared and Fromer, Menachem and O'Dushlaine, Colm and Moran, Jennifer L. and Chambert, Kimberly and Stevens, Christine and Consortium, Swedish Schizophrenia and Consortium, ARRA Autism Sequencing and Sklar, Pamela and Hultman, Christina M. and Purcell, Shaun and McCarroll, Steven A. and Sullivan, Patrick F. and Daly, Mark J. and Neale, Benjamin M.},
TITLE = {zCall: A rare variant caller for array-based genotyping},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {19},
PAGES = {2543-2545},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts479},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Girbig-Selbig-Grimbs/12,
AUTHOR = {Girbig, Dorothee and Selbig, Joachim and Grimbs, Sergio},
TITLE = {A MATLAB toolbox for structural kinetic modeling},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {19},
PAGES = {2546-2547},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts473},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jiang-Wang-Brudno/12,
AUTHOR = {Jiang, Yue and Wang, Yadong and Brudno, Michael},
TITLE = {PRISM: Pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {20},
PAGES = {2576-2583},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts484},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Brenke-Hall-Chuang-Comeau-Bohnuud-Beglov-Schueler-Furman-Vajda-Kozakov/12,
AUTHOR = {Brenke, Ryan and Hall, David R. and Chuang, Gwo-Yu and Comeau, Stephen R. and Bohnuud, Tanggis and Beglov, Dmitri and Schueler-Furman, Ora and Vajda, Sandor and Kozakov, Dima},
TITLE = {Application of asymmetric statistical potentials to antibody-protein docking},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {20},
PAGES = {2608-2614},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts493},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Buchel-Wrzodek-Mittag-Drager-Eichner-Rodriguez-Le_Novere-Zell/12,
AUTHOR = {B{\"u}chel, Finja and Wrzodek, Clemens and Mittag, Florian and Dr{\"a}ger, Andreas and Eichner, Johannes and Rodriguez, Nicolas and Le Nov{`e}re, Nicolas and Zell, Andreas},
TITLE = {Qualitative translation of relations from BioPAX to SBML qual},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {20},
PAGES = {2648-2653},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts508},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bui-Sloot/12,
AUTHOR = {Bui, Quoc-Chinh and Sloot, Peter M.A.},
TITLE = {A robust approach to extract biomedical events from literature},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {20},
PAGES = {2654-2661},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts487},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gross-Hartung-Prufer-Kelso-Rahm/12,
AUTHOR = {Gro{\ss}, Anika and Hartung, Michael and Pr{\"u}fer, Kay and Kelso, Janet and Rahm, Erhard},
TITLE = {Impact of ontology evolution on functional analyses},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {20},
PAGES = {2671-2677},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts498},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Garcia-Alcalde-Okonechnikov-Carbonell-Cruz-Gotz-Tarazona-Dopazo-Meyer-Conesa/12,
AUTHOR = {Garc{\'{i}}a-Alcalde, Fernando and Okonechnikov, Konstantin and Carbonell, Jos{\'e} and Cruz, Luis M. and G{\"o}tz, Stefan and Tarazona, Sonia and Dopazo, Joaqu{\'{i}}n and Meyer, Thomas F. and Conesa, Ana},
TITLE = {Qualimap: Evaluating next-generation sequencing alignment data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {20},
PAGES = {2678-2679},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts503},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hower-Starfield-Roberts-Pachter/12,
AUTHOR = {Hower, Valerie and Starfield, Richard and Roberts, Adam and Pachter, Lior},
TITLE = {Quantifying uniformity of mapped reads},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {20},
PAGES = {2680-2682},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts451},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gaspar-Oliveira-Frommlet-Santos-Moura/12,
AUTHOR = {Gaspar, Paulo and Oliveira, Jos{\'e} Lu{\'{i}}s and Frommlet, J{\"o}rg and Santos, Manuel A.S. and Moura, Gabriela},
TITLE = {EuGene: Maximizing synthetic gene design for heterologous expression},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {20},
PAGES = {2683-2684},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts465},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gupta-Markmann-Pedersen-Stougaard-Andersen/12,
AUTHOR = {Gupta, Vikas and Markmann, Katharina and Pedersen, Christian N.S. and Stougaard, Jens and Andersen, Stig U.},
TITLE = {shortran : A pipeline for small RNA-seq data analysis},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {20},
PAGES = {2698-2700},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts496},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Aichaoui-Jules-Le_Chat-Aymerich-Fromion-Goelzer/12,
AUTHOR = {A{\"{i}}chaoui, Leslie and Jules, Matthieu and Le Chat, Ludovic and Aymerich, St{\'e}phane and Fromion, Vincent and Goelzer, Anne},
TITLE = {BasyLiCA: A tool for automatic processing of a Bacterial Live Cell Array},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {20},
PAGES = {2705-2706},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts422},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Dai-Dai/12,
AUTHOR = {Dai, Zhiming and Dai, Xianhua},
TITLE = {Antisense transcription is coupled to nucleosome occupancy in sense promoters},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {21},
PAGES = {2719-2723},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts534},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chong-Ruan-Wu/12,
AUTHOR = {Chong, Zechen and Ruan, Jue and Wu, Chung-I.},
TITLE = {Rainbow: An integrated tool for efficient clustering and assembling RAD-seq reads},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {21},
PAGES = {2732-2737},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts482},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Feng-Meyer-Wang-Liu-Liu-Zhang/12,
AUTHOR = {Feng, Jianxing and Meyer, Clifford A. and Wang, Qian and Liu, Jun S. and Liu, X. Shirley and Zhang, Yong},
TITLE = {GFOLD: A generalized fold change for ranking differentially expressed genes from RNA-seq data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {21},
PAGES = {2782-2788},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts515},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Churbanov-Ryan-Hasan-Bailey-Chen-Milligan-Houde/12,
AUTHOR = {Churbanov, Alexander and Ryan, Rachael and Hasan, Nabeeh and Bailey, Donovan and Chen, Haofeng and Milligan, Brook and Houde, Peter},
TITLE = {HighSSR: High-throughput SSR characterization and locus development from next-gen sequencing data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {21},
PAGES = {2797-2803},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts524},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hill-Lu-Molina-Heiser-Spellman-Speed-Gray-Mills-Mukherjee/12,
AUTHOR = {Hill, Steven M. and Lu, Yiling and Molina, Jennifer and Heiser, Laura M. and Spellman, Paul T. and Speed, Terence P. and Gray, Joe W. and Mills, Gordon B. and Mukherjee, Sach},
TITLE = {Bayesian Inference of Signaling Network Topology in a Cancer Cell Line},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {21},
PAGES = {2804-2810},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts514},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Feiglin-Hacohen-Sarusi-Fisher-Unger-Ofran/12,
AUTHOR = {Feiglin, Ariel and Hacohen, Adar and Sarusi, Avital and Fisher, Jasmin and Unger, Ron and Ofran, Yanay},
TITLE = {Static network structure can be used to model the phenotypic effects of perturbations in regulatory networks},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {21},
PAGES = {2811-2818},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts517},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Barber-Babbitt/12,
AUTHOR = {Barber II, Alan E. and Babbitt, Patricia C.},
TITLE = {Pythoscape: A framework for generation of large protein similarity networks},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {21},
PAGES = {2845-2846},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts532},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Cheng-Wang-Bryant/12,
AUTHOR = {Cheng, Tiejun and Wang, Yanli and Bryant, Stephen H.},
TITLE = {FSelector: A Ruby gem for feature selection},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {21},
PAGES = {2851-2852},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts528},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Jiang-Chan-Liao-Zheng-Leung-Chiu-Lo-Sun/12,
AUTHOR = {Jiang, Peiyong and Chan, K.C. Allen and Liao, Gary J.W. and Zheng, Yama W.L. and Leung, Tak Y. and Chiu, Rossa W.K. and Lo, Yuk Ming Dennis and Sun, Hao},
TITLE = {FetalQuant: Deducing fractional fetal DNA concentration from massively parallel sequencing of DNA in maternal plasma},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {22},
PAGES = {2883-2890},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts549},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bonder-Abeln-Zaura-Brandt/12,
AUTHOR = {Bonder, Marc J. and Abeln, Sanne and Zaura, Egija and Brandt, Bernd W.},
TITLE = {Comparing clustering and pre-processing in taxonomy analysis},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {22},
PAGES = {2891-2897},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts552},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Allred-Renshaw-Weaver-Tesh-Wang/12,
AUTHOR = {Allred, Adam F. and Renshaw, Hilary and Weaver, Scott and Tesh, Robert B. and Wang, David},
TITLE = {VIPR HMM: A hidden Markov model for detecting recombination with microbial detection microarrays},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {22},
PAGES = {2922-2929},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts560},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Huang-He/12,
AUTHOR = {Huang, Ting and He, Zengyou},
TITLE = {A linear programming model for protein inference problem in shotgun proteomics},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {22},
PAGES = {2956-2962},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts540},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{French-Lane-Xu-Siu-Kwok-Chen-Krebs-Pavlidis/12,
AUTHOR = {French, Leon and Lane, Suzanne and Xu, Lydia and Siu, Celia and Kwok, Cathy and Chen, Yiqi and Krebs, Claudia and Pavlidis, Paul},
TITLE = {Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {22},
PAGES = {2963-2970},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts542},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kalwarczyk-Tabaka-Holyst/12,
AUTHOR = {Kalwarczyk, Tomasz and Tabaka, Marcin and Holyst, Robert},
TITLE = {Biologistics --- Diffusion coefficients for complete proteome of Escherichia coli},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {22},
PAGES = {2971-2978},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts537},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chen-Wang-Stram-Sobel-Lange/12,
AUTHOR = {Chen, Gary K. and Wang, Kai and Stram, Alex H. and Sobel, Eric M. and Lange, Kenneth},
TITLE = {Mendel-GPU: Haplotyping and genotype imputation on graphics processing units},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {22},
PAGES = {2979-2980},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts536},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Cazier-Holmes-Broxholme/12,
AUTHOR = {Cazier, Jean-Baptiste and Holmes, Chris C. and Broxholme, John},
TITLE = {GREVE: Genomic Recurrent Event ViEwer to assist the identification of patterns across individual cancer samples},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {22},
PAGES = {2981-2982},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts547},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Coll-Mallard-Preston-Bentley-Parkhill-McNerney-Martin-Clark/12,
AUTHOR = {Coll, Francesc and Mallard, Kim and Preston, Mark D. and Bentley, Stephen and Parkhill, Julian and McNerney, Ruth and Martin, Nigel and Clark, Taane G.},
TITLE = {SpolPred: Rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {22},
PAGES = {2991-2993},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts544},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kalev-Mechelke-Kopec-Holder-Carstens-Habeck/12,
AUTHOR = {Kalev, Ivan and Mechelke, Martin and Kopec, Klaus O. and Holder, Thomas and Carstens, Simeon and Habeck, Michael},
TITLE = {CSB: A Python framework for structural bioinformatics},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {22},
PAGES = {2996-2997},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts538},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Eargle-Luthey-Schulten/12,
AUTHOR = {Eargle, John and Luthey-Schulten, Zaida},
TITLE = {NetworkView: 3D display and analysis of protein RNA interaction networks},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {22},
PAGES = {3000-3001},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts546},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Athanasiadis-Cournia-Spyrou/12,
AUTHOR = {Athanasiadis, Emmanouil and Cournia, Zoe and Spyrou, George},
TITLE = {ChemBioServer: A web-based pipeline for filtering, clustering and visualization of chemical compounds used in drug discovery},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {22},
PAGES = {3002-3003},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts551},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Cordero-Lucks-Das/12,
AUTHOR = {Cordero, Pablo and Lucks, Julius B. and Das, Rhiju},
TITLE = {An RNA Mapping DataBase for curating RNA structure mapping experiments},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {22},
PAGES = {3006-3008},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts554},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Fier-Won-Prokopenko-AlChawa-Ludwig-Fimmers-Silverman-Pagano-Mangold-Lange/12,
AUTHOR = {Fier, Heide and Won, Sungho and Prokopenko, Dmitry and AlChawa, Taofik and Ludwig, Kerstin U. and Fimmers, Rolf and Silverman, Edwin K. and Pagano, Marcello and Mangold, Elisabeth and Lange, Christoph},
TITLE = {``Location, Location, Location'': A spatial approach for rare variant analysis and an application to a study on non-syndromic cleft lip with or without cleft palate},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {23},
PAGES = {3027-3033},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts568},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gascoigne-Cheetham-Cattenoz-Clark-Amaral-Taft-Wilhelm-Dinger-Mattick/12,
AUTHOR = {Gascoigne, Dennis K. and Cheetham, Seth W. and Cattenoz, Pierre B. and Clark, Michael B. and Amaral, Paulo P. and Taft, Ryan J. and Wilhelm, Dagmar and Dinger, Marcel E. and Mattick, John S.},
TITLE = {Pinstripe: A suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {23},
PAGES = {3042-3050},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts582},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hach-Numanagic-Alkan-Sahinalp/12,
AUTHOR = {Hach, Faraz and Numanagi{\'c}, Ibrahim and Alkan, Can and Sahinalp, S. Cenk},
TITLE = {SCALCE: Boosting sequence compression algorithms using locally consistent encoding},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {23},
PAGES = {3051-3057},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts593},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Eickholt-Cheng/12,
AUTHOR = {Eickholt, Jesse and Cheng, Jianlin},
TITLE = {Predicting protein residue-residue contacts using deep networks and boosting},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {23},
PAGES = {3066-3072},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts598},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Bornigen-Tranchevent-Bonachela-Capdevila-Devriendt-De_Moor-De_Causmaecker-Moreau/12,
AUTHOR = {B{\"o}rnigen, Daniela and Tranchevent, L{\'e}on-Charles and Bonachela-Capdevila, Francisco and Devriendt, Koenraad and De Moor, Bart and De Causmaecker, Patrick and Moreau, Yves},
TITLE = {An unbiased evaluation of gene prioritization tools},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {23},
PAGES = {3081-3088},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts581},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Flassig-Sundmacher/12,
AUTHOR = {Flassig, R.J. and Sundmacher, K.},
TITLE = {Optimal design of stimulus experiments for robust discrimination of biochemical reaction networks},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {23},
PAGES = {3089-3096},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts585},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Costanza-Carapezza-Angione-Lio-Nicosia/12,
AUTHOR = {Costanza, Jole and Carapezza, Giovanni and Angione, Claudio and Li{\'o}, Pietro and Nicosia, Giuseppe},
TITLE = {Robust design of microbial strains},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {23},
PAGES = {3097-3104},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts590},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Johnson-Guo-Gosink-Wang-Hauben/12,
AUTHOR = {Johnson, Kjell and Guo, Cen and Gosink, Mark and Wang, Vicky and Hauben, Manfred},
TITLE = {Multinomial modeling and an evaluation of common data-mining algorithms for identifying signals of disproportionate reporting in pharmacovigilance databases},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {23},
PAGES = {3123-3130},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts576},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hu-Deng-Selvaraj-Qin-Ren-Liu/12,
AUTHOR = {Hu, Ming and Deng, Ke and Selvaraj, Siddarth and Qin, Zhaohui and Ren, Bing and Liu, Jun S.},
TITLE = {HiCNorm: Removing biases in Hi-C data via Poisson regression},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {23},
PAGES = {3131-3133},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts570},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gray-Stewart-Tenesa/12,
AUTHOR = {Gray, A. and Stewart, I. and Tenesa, A.},
TITLE = {Advanced Complex Trait Analysis},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {23},
PAGES = {3134-3136},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts571},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Frech-Choo-Chen/12,
AUTHOR = {Frech, Christian and Choo, Caleb and Chen, Nansheng},
TITLE = {FeatureStack: Perl module for comparative visualization of gene features},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {23},
PAGES = {3137-3138},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts572},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Katoh-Frith/12,
AUTHOR = {Katoh, Kazutaka and Frith, Martin C.},
TITLE = {Adding unaligned sequences into an existing alignment using MAFFT and LAST},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {23},
PAGES = {3144-3146},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts578},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chen-Servant-Toedling-Sarazin-Marchais-Duvernois-Berthet-Cognat-Colot-Voinnet-Heard-Ciaudo-Barillot/12,
AUTHOR = {Chen, Chong-Jian and Servant, Nicolas and Toedling, Joern and Sarazin, Alexis and Marchais, Antonin and Duvernois-Berthet, Evelyne and Cognat, Val{\'e}rie and Colot, Vincent and Voinnet, Olivier and Heard, Edith and Ciaudo, Constance and Barillot, Emmanuel},
TITLE = {ncPRO-seq: A tool for annotation and profiling of ncRNAs in sRNA-seq data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {23},
PAGES = {3147-3149},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts587},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Fu-Niu-Zhu-Wu-Li/12,
AUTHOR = {Fu, Limin and Niu, Beifang and Zhu, Zhengwei and Wu, Sitao and Li, Weizhong},
TITLE = {CD-HIT: Accelerated for clustering the next-generation sequencing data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {23},
PAGES = {3150-3152},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts565},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Fange-Mahmutovic-Elf/12,
AUTHOR = {Fange, David and Mahmutovic, Anel and Elf, Johan},
TITLE = {MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {23},
PAGES = {3155-3157},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts584},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kilicoglu-Shin-Fiszman-Rosemblat-Rindflesch/12,
AUTHOR = {Kilicoglu, Halil and Shin, Dongwook and Fiszman, Marcelo and Rosemblat, Graciela and Rindflesch, Thomas C.},
TITLE = {SemMedDB: A PubMed-scale repository of biomedical semantic predications},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {23},
PAGES = {3158-3160},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts591},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Fonseca-Rung-Brazma-Marioni/12,
AUTHOR = {Fonseca, Nuno A. and Rung, Johan and Brazma, Alvis and Marioni, John C.},
TITLE = {Tools for mapping high-throughput sequencing data},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {24},
PAGES = {3169-3177},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts605},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Chen-Chen-Juan-Huang/12,
AUTHOR = {Chen, Cho-Yi and Chen, Shui-Tein and Juan, Hsueh-Fen and Huang, Hsuan-Cheng},
TITLE = {Lengthening of 3$^{\prime}$ UTR increases with morphological complexity in animal evolution},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {24},
PAGES = {3178-3181},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts623},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Evans/12,
AUTHOR = {Evans, John Spencer},
TITLE = {Aragonite-associated biomineralization proteins are disordered and contain interactive motifs},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {24},
PAGES = {3182-3185},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts604},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kazlauskas-Venclovas/12,
AUTHOR = {Kazlauskas, Darius and Venclovas, {\v{C}}eslovas},
TITLE = {Two distinct SSB protein families in nucleo-cytoplasmic large DNA viruses},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {24},
PAGES = {3186-3190},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts626},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Hu-Gao/12,
AUTHOR = {Hu, Jinyu and Gao, David Zhiwei},
TITLE = {Distinction immune genes of hepatitis-induced heptatocellular carcinoma},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {24},
PAGES = {3191-3194},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts624},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Ashkenazi-Snir-Ofran/12,
AUTHOR = {Ashkenazi, Shaul and Snir, Rotem and Ofran, Yanay},
TITLE = {Assessing the relationship between conservation of function and conservation of sequence using photosynthetic proteins},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {24},
PAGES = {3203-3210},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts608},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Dutilh-Schmieder-Nulton-Felts-Salamon-Edwards-Mokili/12,
AUTHOR = {Dutilh, Bas E. and Schmieder, Robert and Nulton, Jim and Felts, Ben and Salamon, Peter and Edwards, Robert A. and Mokili, John L.},
TITLE = {Reference-independent comparative metagenomics using cross-assembly: crASS},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {24},
PAGES = {3225-3231},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts613},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Benelli-Pescucci-Marseglia-Severgnini-Torricelli-Magi/12,
AUTHOR = {Benelli, Matteo and Pescucci, Chiara and Marseglia, Giuseppina and Severgnini, Marco and Torricelli, Francesca and Magi, Alberto},
TITLE = {Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {24},
PAGES = {3232-3239},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts617},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Angermuller-Biegert-Soding/12,
AUTHOR = {Angerm{\"u}ller, Christof and Biegert, Andreas and S{\"o}ding, Johannes},
TITLE = {Discriminative modelling of context-specific amino acid substitution probabilities},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {24},
PAGES = {3240-3247},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts622},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Kirk-Griffin-Savage-Ghahramani-Wild/12,
AUTHOR = {Kirk, Paul and Griffin, Jim E. and Savage, Richard S. and Ghahramani, Zoubin and Wild, David L.},
TITLE = {Bayesian correlated clustering to integrate multiple datasets},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {24},
PAGES = {3290-3297},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts595},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Edwards-Olson-Disz-Pusch-Vonstein-Stevens-Overbeek/12,
AUTHOR = {Edwards, Robert A. and Olson, Robert and Disz, Terry and Pusch, Gordon D. and Vonstein, Veronika and Stevens, Rick and Overbeek, Ross},
TITLE = {Real Time Metagenomics: Using $k$-mers to annotate metagenomes},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {24},
PAGES = {3316-3317},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts599},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Aszodi/12,
AUTHOR = {Asz{\'o}di, Andr{\'a}s},
TITLE = {MULTOVL: Fast multiple overlaps of genomic regions},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {24},
PAGES = {3318-3319},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts607},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}
@article{Gogarten-Bhangale-Conomos-Laurie-McHugh-Painter-Zheng-Crosslin-Levine-Lumley-Nelson-Rice-Shen-Swarnkar-Weir-Laurie/12,
AUTHOR = {Gogarten, Stephanie M. and Bhangale, Tushar and Conomos, Matthew P. and Laurie, Cecelia A. and McHugh, Caitlin P. and Painter, Ian and Zheng, Xiuwen and Crosslin, David R. and Levine, David and Lumley, Thomas and Nelson, Sarah C. and Rice, Kenneth and Shen, Jess and Swarnkar, Rohit and Weir, Bruce S. and Laurie, Cathy C.},
TITLE = {GWASTools: An R/Bioconductor package for quality control and analysis of genome-wide association studies},
JOURNAL = {Bioinformatics},
VOLUME = {28},
NUMBER = {24},
PAGES = {3329-3331},
YEAR = {2012},
EDITOR = {Bateman, Alex and Valencia, Alfonso},
URL = {doi:10.1093/bioinformatics/bts610},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford-New York},
}