Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S: Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 2007, 4: 651-657. 10.1038/nmeth1068.
Article
PubMed
CAS
Google Scholar
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008, 5: 621-628. 10.1038/nmeth.1226.
Article
PubMed
CAS
Google Scholar
Pepke S, Wold B, Mortazavi A: Computation for ChIP-seq and RNA-seq studies. Nat Methods. 2009, 6: S22-S32. 10.1038/nmeth.1371.
Article
PubMed
CAS
PubMed Central
Google Scholar
Statistics Using R with Biological Examples. [http://cran.r-project.org/doc/contrib/Seefeld_StatsRBio.pdf]
Introduction to Sequence Analysis using EMBOSS. [http://emboss.sourceforge.net/docs/emboss_tutorial/emboss_tutorial.html]
Gentleman R, Carey V, Bates D, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini A, Sawitzki G, Smith C, Smyth G, Tierney L, Yang J, Zhang J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5: R80-10.1186/gb-2004-5-10-r80.
Article
PubMed
PubMed Central
Google Scholar
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JGR, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E: The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002, 12: 1611-1618. 10.1101/gr.361602.
Article
PubMed
CAS
PubMed Central
Google Scholar
Rice P, Longden I, Bleasby A: EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 2000, 16: 276-277. 10.1016/S0168-9525(00)02024-2.
Article
PubMed
CAS
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410.
Article
PubMed
CAS
Google Scholar
Ioannidis JPA, Allison DB, Ball CA, Coulibaly I, Cui X, Culhane AC, Falchi M, Furlanello C, Game L, Jurman G, Mangion J, Mehta T, Nitzberg M, Page GP, Petretto E, van Noort V: Repeatability of published microarray gene expression analyses. Nat Genet. 2009, 41: 149-155. 10.1038/ng.295.
Article
PubMed
CAS
Google Scholar
Mesirov JP: Computer science. Accessible reproducible research. Science. 2010, 327: 415-416. 10.1126/science.1179653.
Article
PubMed
CAS
Google Scholar
Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP: GenePattern 2.0. Nat Genet. 2006, 38: 500-501. 10.1038/ng0506-500.
Article
PubMed
CAS
Google Scholar
Neron B, Menager H, Maufrais C, Joly N, Maupetit J, Letort S, Carrere S, Tuffery P, Letondal C: Mobyle: a new full web bioinformatics framework. Bioinformatics. 2009, 25: 3005-3011. 10.1093/bioinformatics/btp493.
Article
PubMed
CAS
PubMed Central
Google Scholar
Schwab M, Karrenbach M, Claerbout J: Making scientific computations reproducible. Computing Sci Eng. 2000, 2: 61-67. 10.1109/5992.881708.
Article
Google Scholar
Reproducible Research: A Bioinformatics Case Study. [http://ideas.repec.org/a/bpj/sagmbi/v4y2005i1n2.html]
Galaxy: an Open Platform for Accessible, Reproducible, and Transparent Biomedical Research. [http://galaxyproject.org]
Public Galaxy Service. [http://usegalaxy.org]
Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A: A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007, 17: 960-964. 10.1101/gr.5578007.
Article
PubMed
CAS
PubMed Central
Google Scholar
Taylor J, Schenck I, Blankenberg D, Nekrutenko A: Using galaxy to perform large-scale interactive data analyses. Curr Protoc Bioinformatics. 2007, Chapter 10: Unit 10.5.
Google Scholar
Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J: Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010, Chapter 19: Unit 19.10.1-21
Google Scholar
Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung W, Taylor J, Nekrutenko A: Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Res. 2009, 19: 2144-2153. 10.1101/gr.094508.109.
Article
PubMed
PubMed Central
Google Scholar
Galaxy | Published Page | Windshield Splatter. [http://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter]
Kikuchi R, Yagi S, Kusuhara H, Imai S, Sugiyama Y, Shiota K: Genome-wide analysis of epigenetic signatures for kidney-specific transporters. Kidney Int. 2010
Google Scholar
Gaulton KJ, Nammo T, Pasquali L, Simon JM, Giresi PG, Fogarty MP, Panhuis TM, Mieczkowski P, Secchi A, Bosco D, Berney T, Montanya E, Mohlke KL, Lieb JD, Ferrer J: A map of open chromatin in human pancreatic islets. Nat Genet. 2010, 42: 255-259. 10.1038/ng.530.
Article
PubMed
CAS
PubMed Central
Google Scholar
Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA: ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature. 2009, 457: 854-858. 10.1038/nature07730.
Article
PubMed
CAS
PubMed Central
Google Scholar
Peleg S, Sananbenesi F, Zovoilis A, Burkhardt S, Bahari-Javan S, Agis-Balboa RC, Cota P, Wittnam JL, Gogol-Doering A, Opitz L, Salinas-Riester G, Dettenhofer M, Kang H, Farinelli L, Chen W, Fischer A: Altered histone acetylation is associated with age-dependent memory impairment in mice. Science. 2010, 328: 753-756. 10.1126/science.1186088.
Article
PubMed
CAS
Google Scholar
Galaxy | Published History | SM_1186088. [http://main.g2.bx.psu.edu/u/fischerlab/h/sm1186088]
Nielsen J, Loranger H: Prioritizing Web Usability. 2006, New Riders Press, 1
Google Scholar
Gamma E, Helm R, Johnson R, Vlissides J: Design Patterns: Elements of Reusable Object-oriented Software. 1995, Addison-Wesley Longman Publishing Co., Inc
Google Scholar
GenomeSpace. [http://genomespace.org/]
Chapman B, Chang J: Biopython: Python tools for computational biology. ACM SIGBIO Newslett. 2000, 20: 15-19. 10.1145/360262.360268.
Article
Google Scholar
Leisch F: Sweave: dynamic generation of statistical reports using literate data analysis. Compstat 2002 - Proceedings in Computational Statistics: Berlin, Germany. Edited by: Härdle W, Rönz B. 2002, Springer, 575-580.
Google Scholar
Oinn T, Addis M, Ferris J, Marvin D, Greenwood M, Carver T, Pocock MR, Wipat A, Li P: Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics. 2004, 20: 3045-3054. 10.1093/bioinformatics/bth361.
Article
PubMed
CAS
Google Scholar
Goble CA, Bhagat J, Aleksejevs S, Cruickshank D, Michaelides D, Newman D, Borkum M, Bechhofer S, Roos M, Li P, De Roure D: myExperiment: a repository and social network for the sharing of bioinformatics workflows. Nucleic Acids Res. 2010, 38: W677-682. 10.1093/nar/gkq429.
Article
PubMed
CAS
PubMed Central
Google Scholar
Vision TJ: Open Data and the Social Contract of Scientific Publishing. BioScience. 2010, 60: 330-331. 10.1525/bio.2010.60.5.2.
Article
Google Scholar
Zdobnov EM, Apweiler R: InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics. 2001, 17: 847-848. 10.1093/bioinformatics/17.9.847.
Article
PubMed
CAS
Google Scholar