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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. Batut B, et al. Among authors: hoogstrate y. Cell Syst. 2018 Jun 27;6(6):752-758.e1. doi: 10.1016/j.cels.2018.05.012. Cell Syst. 2018. PMID: 29953864 Free PMC article.
FuMa: reporting overlap in RNA-seq detected fusion genes.
Hoogstrate Y, Böttcher R, Hiltemann S, van der Spek PJ, Jenster G, Stubbs AP. Hoogstrate Y, et al. Bioinformatics. 2016 Apr 15;32(8):1226-8. doi: 10.1093/bioinformatics/btv721. Epub 2015 Dec 10. Bioinformatics. 2016. PMID: 26656567
AVAILABILITY AND IMPLEMENTATION: The code is available at: https://github.com/ErasmusMC-Bioinformatics/fuma and available for Galaxy in the tool sheds and directly accessible at https://bioinf-galaxian.erasmusmc.nl/galaxy/ CONTACT: y.hoogstrate@erasmusmc.nl or a.stu …
AVAILABILITY AND IMPLEMENTATION: The code is available at: https://github.com/ErasmusMC-Bioinformatics/fuma and available for Galaxy in the …
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. Hoogstrate Y, et al. F1000Res. 2016 Dec 12;5:ELIXIR-2841. doi: 10.12688/f1000research.10221.1. eCollection 2016. F1000Res. 2016. PMID: 28232859 Free PMC article.
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. Grüning BA, et al. Among authors: hoogstrate y. Nucleic Acids Res. 2017 Jul 3;45(W1):W560-W566. doi: 10.1093/nar/gkx409. Nucleic Acids Res. 2017. PMID: 28582575 Free PMC article.
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. Zhang C, et al. Among authors: hoogstrate y. F1000Res. 2017 Aug 16;6:ELIXIR-1488. doi: 10.12688/f1000research.12168.1. eCollection 2017. F1000Res. 2017. PMID: 29123641 Free PMC article.
Identification of Patients with Recurrent Glioblastoma Who May Benefit from Combined Bevacizumab and CCNU Therapy: A Report from the BELOB Trial.
Erdem-Eraslan L, van den Bent MJ, Hoogstrate Y, Naz-Khan H, Stubbs A, van der Spek P, Böttcher R, Gao Y, de Wit M, Taal W, Oosterkamp HM, Walenkamp A, Beerepoot LV, Hanse MC, Buter J, Honkoop AH, van der Holt B, Vernhout RM, Sillevis Smitt PA, Kros JM, French PJ. Erdem-Eraslan L, et al. Among authors: hoogstrate y. Cancer Res. 2016 Feb 1;76(3):525-34. doi: 10.1158/0008-5472.CAN-15-0776. Epub 2016 Jan 13. Cancer Res. 2016. PMID: 26762204 Clinical Trial.
30 results