Literature DB >> 15461798

Bioconductor: open software development for computational biology and bioinformatics.

Robert C Gentleman1, Vincent J Carey, Douglas M Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J Rossini, Gunther Sawitzki, Colin Smith, Gordon Smyth, Luke Tierney, Jean Y H Yang, Jianhua Zhang.   

Abstract

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.

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Year:  2004        PMID： 15461798      PMCID： PMC545600          DOI： 10.1186/gb-2004-5-10-r80

Source DB:  PubMed          Journal:  Genome Biol        ISSN： 1474-7596            Impact factor:   13.583


  7 in total

1.  Creating a bioinformatics nation.

Authors:  Lincoln Stein
Journal:  Nature       Date:  2002-05-09       Impact factor: 49.962

2.  Expression array annotation using the BioMediator biological data integration system and the BioConductor analytic platform.

Authors:  H Mei; P Tarczy-Hornoch; P Mork; A J Rossini; R Shaker; L Donelson
Journal:  AMIA Annu Symp Proc       Date:  2003

3.  The Bioperl toolkit: Perl modules for the life sciences.

Authors:  Jason E Stajich; David Block; Kris Boulez; Steven E Brenner; Stephen A Chervitz; Chris Dagdigian; Georg Fuellen; James G R Gilbert; Ian Korf; Hilmar Lapp; Heikki Lehväslaiho; Chad Matsalla; Chris J Mungall; Brian I Osborne; Matthew R Pocock; Peter Schattner; Martin Senger; Lincoln D Stein; Elia Stupka; Mark D Wilkinson; Ewan Birney
Journal:  Genome Res       Date:  2002-10       Impact factor: 9.043

4.  An extensible application for assembling annotation for genomic data.

Authors:  Jianhua Zhang; Vincent Carey; Robert Gentleman
Journal:  Bioinformatics       Date:  2003-01       Impact factor: 6.937

5.  [''R"--project for statistical computing].

Authors:  Ram Benny Dessau; Christian Bressen Pipper
Journal:  Ugeskr Laeger       Date:  2008-01-28

6.  Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival.

Authors:  Sabina Chiaretti; Xiaochun Li; Robert Gentleman; Antonella Vitale; Marco Vignetti; Franco Mandelli; Jerome Ritz; Robin Foa
Journal:  Blood       Date:  2003-12-18       Impact factor: 22.113

7.  Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection.

Authors:  C Li; W H Wong
Journal:  Proc Natl Acad Sci U S A       Date:  2001-01-02       Impact factor: 11.205
  7 in total
  2000 in total

1.  Cutting edge: microRNA regulation of macrophage fusion into multinucleated giant cells.

Authors:  James R Sissons; Jacques J Peschon; Frank Schmitz; Rosa Suen; Mark Gilchrist; Alan Aderem
Journal:  J Immunol       Date:  2012-06-01       Impact factor: 5.422

2.  Maize HapMap2 identifies extant variation from a genome in flux.

Authors:  Jer-Ming Chia; Chi Song; Peter J Bradbury; Denise Costich; Natalia de Leon; John Doebley; Robert J Elshire; Brandon Gaut; Laura Geller; Jeffrey C Glaubitz; Michael Gore; Kate E Guill; Jim Holland; Matthew B Hufford; Jinsheng Lai; Meng Li; Xin Liu; Yanli Lu; Richard McCombie; Rebecca Nelson; Jesse Poland; Boddupalli M Prasanna; Tanja Pyhäjärvi; Tingzhao Rong; Rajandeep S Sekhon; Qi Sun; Maud I Tenaillon; Feng Tian; Jun Wang; Xun Xu; Zhiwu Zhang; Shawn M Kaeppler; Jeffrey Ross-Ibarra; Michael D McMullen; Edward S Buckler; Gengyun Zhang; Yunbi Xu; Doreen Ware
Journal:  Nat Genet       Date:  2012-06-03       Impact factor: 38.330

3.  Listeria monocytogenes {sigma}B has a small core regulon and a conserved role in virulence but makes differential contributions to stress tolerance across a diverse collection of strains.

Authors:  H F Oliver; R H Orsi; M Wiedmann; K J Boor
Journal:  Appl Environ Microbiol       Date:  2010-05-07       Impact factor: 4.792

4.  Characterization of the transcriptome of chorioamniotic membranes at the site of rupture in spontaneous labor at term.

Authors:  Chia-Ling Nhan-Chang; Roberto Romero; Adi L Tarca; Pooja Mittal; Juan Pedro Kusanovic; Offer Erez; Shali Mazaki-Tovi; Tinnakorn Chaiworapongsa; John Hotra; Nandor Gabor Than; Jung-Sun Kim; Sonia S Hassan; Chong Jai Kim
Journal:  Am J Obstet Gynecol       Date:  2010-05       Impact factor: 8.661

5.  Consistent annotation of gene expression arrays.

Authors:  Benoît Ballester; Nathan Johnson; Glenn Proctor; Paul Flicek
Journal:  BMC Genomics       Date:  2010-05-11       Impact factor: 3.969

6.  Identification of the transcriptional targets of FOXP2, a gene linked to speech and language, in developing human brain.

Authors:  Elizabeth Spiteri; Genevieve Konopka; Giovanni Coppola; Jamee Bomar; Michael Oldham; Jing Ou; Sonja C Vernes; Simon E Fisher; Bing Ren; Daniel H Geschwind
Journal:  Am J Hum Genet       Date:  2007-10-31       Impact factor: 11.025

7.  Distinct Gene Expression Profiles Define Anaplastic Grade in Retinoblastoma.

Authors:  Lauren E Hudson; Pia Mendoza; William H Hudson; Alison Ziesel; G Baker Hubbard; Jill Wells; Bhakti Dwivedi; Jeanne Kowalski; Sandra Seby; Viren Patel; Eldon Geisert; Charles Specht; Hans E Grossniklaus
Journal:  Am J Pathol       Date:  2018-07-21       Impact factor: 4.307

8.  Emergence of pathway-level composite biomarkers from converging gene set signals of heterogeneous transcriptomic responses.

Authors:  Samir Rachid Zaim; Qike Li; A Grant Schissler; Yves A Lussier
Journal:  Pac Symp Biocomput       Date:  2018

9.  Over-expression of cathepsin E and trefoil factor 1 in sessile serrated adenomas of the colorectum identified by gene expression analysis.

Authors:  Maria Caruso; James Moore; Gregory J Goodall; Michelle Thomas; Stuart Phillis; Anna Tyskin; Glenice Cheetham; Nancy Lerda; Hiroyuki Takahashi; Andrew Ruszkiewicz
Journal:  Virchows Arch       Date:  2009-01-27       Impact factor: 4.064

10.  Nodal points and complexity of Notch-Ras signal integration.

Authors:  Gregory D Hurlbut; Mark W Kankel; Spyros Artavanis-Tsakonas
Journal:  Proc Natl Acad Sci U S A       Date:  2009-01-26       Impact factor: 11.205
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