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Items: 16

1.

Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur.

Hiltemann SD, Boers SA, van der Spek PJ, Jansen R, Hays JP, Stubbs AP.

Gigascience. 2019 Feb 1;8(2). pii: giy166. doi: 10.1093/gigascience/giy166.

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.

Development and evaluation of a culture-free microbiota profiling platform (MYcrobiota) for clinical diagnostics.

Boers SA, Hiltemann SD, Stubbs AP, Jansen R, Hays JP.

Eur J Clin Microbiol Infect Dis. 2018 Jun;37(6):1081-1089. doi: 10.1007/s10096-018-3220-z. Epub 2018 Mar 16.

6.

Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data.

Zhang C, Bijlard J, Staiger C, Scollen S, van Enckevort D, Hoogstrate Y, Senf A, Hiltemann S, Repo S, Pipping W, Bierkens M, Payralbe S, Stringer B, Heringa J, Stubbs A, Bonino Da Silva Santos LO, Belien J, Weistra W, Azevedo R, van Bochove K, Meijer G, Boiten JW, Rambla J, Fijneman R, Spalding JD, Abeln S.

F1000Res. 2017 Aug 16;6. pii: ELIXIR-1488. doi: 10.12688/f1000research.12168.1. eCollection 2017.

7.

Integration of EGA secure data access into Galaxy.

Hoogstrate Y, Zhang C, Senf A, Bijlard J, Hiltemann S, van Enckevort D, Repo S, Heringa J, Jenster G, J A Fijneman R, Boiten JW, A Meijer G, Stubbs A, Rambla J, Spalding D, Abeln S.

F1000Res. 2016 Dec 12;5. pii: ELIXIR-2841. doi: 10.12688/f1000research.10221.1. eCollection 2016.

8.

FuMa: reporting overlap in RNA-seq detected fusion genes.

Hoogstrate Y, Böttcher R, Hiltemann S, van der Spek PJ, Jenster G, Stubbs AP.

Bioinformatics. 2016 Apr 15;32(8):1226-8. doi: 10.1093/bioinformatics/btv721. Epub 2015 Dec 10.

PMID:
26656567
9.

Discriminating somatic and germline mutations in tumor DNA samples without matching normals.

Hiltemann S, Jenster G, Trapman J, van der Spek P, Stubbs A.

Genome Res. 2015 Sep;25(9):1382-90. doi: 10.1101/gr.183053.114. Epub 2015 Jul 24.

10.

ImmunoGlobulin galaxy (IGGalaxy) for simple determination and quantitation of immunoglobulin heavy chain rearrangements from NGS.

Moorhouse MJ, van Zessen D, IJspeert H, Hiltemann S, Horsman S, van der Spek PJ, van der Burg M, Stubbs AP.

BMC Immunol. 2014 Dec 13;15:59. doi: 10.1186/s12865-014-0059-7.

11.

iReport: a generalised Galaxy solution for integrated experimental reporting.

Hiltemann S, Hoogstrate Y, der Spek Pv, Jenster G, Stubbs A.

Gigascience. 2014 Oct 13;3:19. doi: 10.1186/2047-217X-3-19. eCollection 2014.

12.

Next-generation sequencing reveals novel rare fusion events with functional implication in prostate cancer.

Teles Alves I, Hartjes T, McClellan E, Hiltemann S, Böttcher R, Dits N, Temanni MR, Janssen B, van Workum W, van der Spek P, Stubbs A, de Klein A, Eussen B, Trapman J, Jenster G.

Oncogene. 2015 Jan 29;34(5):568-77. doi: 10.1038/onc.2013.591. Epub 2014 Feb 3.

PMID:
24488012
13.

CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy.

Hiltemann S, Mei H, de Hollander M, Palli I, van der Spek P, Jenster G, Stubbs A.

Gigascience. 2014 Jan 24;3(1):1. doi: 10.1186/2047-217X-3-1.

14.

iFUSE: integrated fusion gene explorer.

Hiltemann S, McClellan EA, van Nijnatten J, Horsman S, Palli I, Teles Alves I, Hartjes T, Trapman J, van der Spek P, Jenster G, Stubbs A.

Bioinformatics. 2013 Jul 1;29(13):1700-1. doi: 10.1093/bioinformatics/btt252. Epub 2013 May 9.

PMID:
23661695
15.

Gene fusions by chromothripsis of chromosome 5q in the VCaP prostate cancer cell line.

Teles Alves I, Hiltemann S, Hartjes T, van der Spek P, Stubbs A, Trapman J, Jenster G.

Hum Genet. 2013 Jun;132(6):709-13. doi: 10.1007/s00439-013-1308-1. Epub 2013 Apr 25.

PMID:
23615946
16.

Huvariome: a web server resource of whole genome next-generation sequencing allelic frequencies to aid in pathological candidate gene selection.

Stubbs A, McClellan EA, Horsman S, Hiltemann SD, Palli I, Nouwens S, Koning AH, Hoogland F, Reumers J, Heijsman D, Swagemakers S, Kremer A, Meijerink J, Lambrechts D, van der Spek PJ.

J Clin Bioinforma. 2012 Nov 19;2(1):19. doi: 10.1186/2043-9113-2-19.

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