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Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA-minus RNA sequencing data.
Hoogstrate Y, Komor MA, Böttcher R, van Riet J, van de Werken HJG, van Lieshout S, Hoffmann R, van den Broek E, Bolijn AS, Dits N, Sie D, van der Meer D, Pepers F, Bangma CH, van Leenders GJLH, Smid M, French PJ, Martens JWM, van Workum W, van der Spek PJ, Janssen B, Caldenhoven E, Rausch C, de Jong M, Stubbs AP, Meijer GA, Fijneman RJA, Jenster GW. Hoogstrate Y, et al. Gigascience. 2021 Dec 9;10(12):giab080. doi: 10.1093/gigascience/giab080. Gigascience. 2021. PMID: 34891161 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 …
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.
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.
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.
Consensus molecular subtype classification of colorectal adenomas.
Komor MA, Bosch LJ, Bounova G, Bolijn AS, Delis-van Diemen PM, Rausch C, Hoogstrate Y, Stubbs AP, de Jong M, Jenster G, van Grieken NC, Carvalho B, Wessels LF, Jimenez CR, Fijneman RJ, Meijer GA; NGS-ProToCol Consortium:. Komor MA, et al. Among authors: hoogstrate y. J Pathol. 2018 Nov;246(3):266-276. doi: 10.1002/path.5129. Epub 2018 Aug 31. J Pathol. 2018. PMID: 29968252 Free PMC article.
30 results