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Items: 13

1.

Molecular characterization of colorectal adenomas reveals POFUT1 as a candidate driver of tumor progression.

Komor MA, de Wit M, van den Berg J, Martens de Kemp SR, Delis-van Diemen PM, Bolijn AS, Tijssen M, Schelfhorst T, Piersma SR, Chiasserini D, Sanders J, Rausch C, Hoogstrate Y, Stubbs AP, de Jong M, Jenster G, Carvalho B, Meijer GA, Jimenez CR, Fijneman RJ; NGS-ProToCol consortium.

Int J Cancer. 2019 Aug 14. doi: 10.1002/ijc.32627. [Epub ahead of print]

PMID:
31411736
2.

Widespread and Functional RNA Circularization in Localized Prostate Cancer.

Chen S, Huang V, Xu X, Livingstone J, Soares F, Jeon J, Zeng Y, Hua JT, Petricca J, Guo H, Wang M, Yousif F, Zhang Y, Donmez N, Ahmed M, Volik S, Lapuk A, Chua MLK, Heisler LE, Foucal A, Fox NS, Fraser M, Bhandari V, Shiah YJ, Guan J, Li J, Orain M, Picard V, Hovington H, Bergeron A, Lacombe L, Fradet Y, Têtu B, Liu S, Feng F, Wu X, Shao YW, Komor MA, Sahinalp C, Collins C, Hoogstrate Y, de Jong M, Fijneman RJA, Fei T, Jenster G, van der Kwast T, Bristow RG, Boutros PC, He HH.

Cell. 2019 Feb 7;176(4):831-843.e22. doi: 10.1016/j.cell.2019.01.025.

PMID:
30735634
3.

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:.

J Pathol. 2018 Nov;246(3):266-276. doi: 10.1002/path.5129. Epub 2018 Aug 31.

4.

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.

5.

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.

6.

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.

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.

A comprehensive repertoire of tRNA-derived fragments in prostate cancer.

Olvedy M, Scaravilli M, Hoogstrate Y, Visakorpi T, Jenster G, Martens-Uzunova ES.

Oncotarget. 2016 Apr 26;7(17):24766-77. doi: 10.18632/oncotarget.8293.

9.

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.

Cancer Res. 2016 Feb 1;76(3):525-34. doi: 10.1158/0008-5472.CAN-15-0776. Epub 2016 Jan 13.

10.

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
11.

C/D-box snoRNA-derived RNA production is associated with malignant transformation and metastatic progression in prostate cancer.

Martens-Uzunova ES, Hoogstrate Y, Kalsbeek A, Pigmans B, Vredenbregt-van den Berg M, Dits N, Nielsen SJ, Baker A, Visakorpi T, Bangma C, Jenster G.

Oncotarget. 2015 Jul 10;6(19):17430-44.

12.

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.

13.

FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.

Hoogstrate Y, Jenster G, Martens-Uzunova ES.

Bioinformatics. 2015 Mar 1;31(5):665-73. doi: 10.1093/bioinformatics/btu696. Epub 2014 Oct 22.

PMID:
25338717

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