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Items: 9

1.

The RNA workbench 2.0: next generation RNA data analysis.

Fallmann J, Videm P, Bagnacani A, Batut B, Doyle MA, Klingstrom T, Eggenhofer F, Stadler PF, Backofen R, Grüning B.

Nucleic Acids Res. 2019 Jul 2;47(W1):W511-W515. doi: 10.1093/nar/gkz353.

2.

Community-Driven Data Analysis Training for Biology.

Batut B, Hiltemann S, Bagnacani A, Baker D, Bhardwaj V, Blank C, Bretaudeau A, Brillet-Guéguen L, Čech M, Chilton J, Clements D, Doppelt-Azeroual O, Erxleben A, Freeberg MA, Gladman S, Hoogstrate Y, Hotz HR, Houwaart T, Jagtap P, Larivière D, Le Corguillé G, Manke T, Mareuil F, Ramírez F, Ryan D, Sigloch FC, Soranzo N, Wolff J, Videm P, Wolfien M, Wubuli A, Yusuf D; Galaxy Training Network, Taylor J, Backofen R, Nekrutenko A, Grüning B.

Cell Syst. 2018 Jun 27;6(6):752-758.e1. doi: 10.1016/j.cels.2018.05.012.

3.

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.

Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Grüning BA, Guerler A, Hillman-Jackson J, Hiltemann S, Jalili V, Rasche H, Soranzo N, Goecks J, Taylor J, Nekrutenko A, Blankenberg D.

Nucleic Acids Res. 2018 Jul 2;46(W1):W537-W544. doi: 10.1093/nar/gky379.

4.

ASaiM: a Galaxy-based framework to analyze microbiota data.

Batut B, Gravouil K, Defois C, Hiltemann S, Brugère JF, Peyretaillade E, Peyret P.

Gigascience. 2018 Jun 1;7(6). doi: 10.1093/gigascience/giy057.

5.

Environmental Pollutant Benzo[a]Pyrene Impacts the Volatile Metabolome and Transcriptome of the Human Gut Microbiota.

Defois C, Ratel J, Denis S, Batut B, Beugnot R, Peyretaillade E, Engel E, Peyret P.

Front Microbiol. 2017 Aug 15;8:1562. doi: 10.3389/fmicb.2017.01562. eCollection 2017.

6.

Four simple recommendations to encourage best practices in research software.

Jiménez RC, Kuzak M, Alhamdoosh M, Barker M, Batut B, Borg M, Capella-Gutierrez S, Chue Hong N, Cook M, Corpas M, Flannery M, Garcia L, Gelpí JL, Gladman S, Goble C, González Ferreiro M, Gonzalez-Beltran A, Griffin PC, Grüning B, Hagberg J, Holub P, Hooft R, Ison J, Katz DS, Leskošek B, López Gómez F, Oliveira LJ, Mellor D, Mosbergen R, Mulder N, Perez-Riverol Y, Pergl R, Pichler H, Pope B, Sanz F, Schneider MV, Stodden V, Suchecki R, Svobodová Vařeková R, Talvik HA, Todorov I, Treloar A, Tyagi S, van Gompel M, Vaughan D, Via A, Wang X, Watson-Haigh NS, Crouch S.

F1000Res. 2017 Jun 13;6. pii: ELIXIR-876. doi: 10.12688/f1000research.11407.1. eCollection 2017.

7.

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.

Grüning BA, Fallmann J, Yusuf D, Will S, Erxleben A, Eggenhofer F, Houwaart T, Batut B, Videm P, Bagnacani A, Wolfien M, Lott SC, Hoogstrate Y, Hess WR, Wolkenhauer O, Hoffmann S, Akalin A, Ohler U, Stadler PF, Backofen R.

Nucleic Acids Res. 2017 Jul 3;45(W1):W560-W566. doi: 10.1093/nar/gkx409.

8.

Reductive genome evolution at both ends of the bacterial population size spectrum.

Batut B, Knibbe C, Marais G, Daubin V.

Nat Rev Microbiol. 2014 Dec;12(12):841-50. doi: 10.1038/nrmicro3331. Epub 2014 Sep 15. Review.

PMID:
25220308
9.

In silico experimental evolution: a tool to test evolutionary scenarios.

Batut B, Parsons DP, Fischer S, Beslon G, Knibbe C.

BMC Bioinformatics. 2013;14 Suppl 15:S11. doi: 10.1186/1471-2105-14-S15-S11. Epub 2013 Oct 15.

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