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Items: 1 to 20 of 26

1.

AraQTL - workbench and archive for systems genetics in Arabidopsis thaliana.

Nijveen H, Ligterink W, Keurentjes JJ, Loudet O, Long J, Sterken MG, Prins P, Hilhorst HW, de Ridder D, Kammenga JE, Snoek BL.

Plant J. 2016 Dec 20. doi: 10.1111/tpj.13457. [Epub ahead of print]

PMID:
27995664
2.

GeneNetwork: A Toolbox for Systems Genetics.

Mulligan MK, Mozhui K, Prins P, Williams RW.

Methods Mol Biol. 2017;1488:75-120.

PMID:
27933521
3.

Tissue-specific mutation accumulation in human adult stem cells during life.

Blokzijl F, de Ligt J, Jager M, Sasselli V, Roerink S, Sasaki N, Huch M, Boymans S, Kuijk E, Prins P, Nijman IJ, Martincorena I, Mokry M, Wiegerinck CL, Middendorp S, Sato T, Schwank G, Nieuwenhuis EE, Verstegen MM, van der Laan LJ, de Jonge J, IJzermans JN, Vries RG, van de Wetering M, Stratton MR, Clevers H, Cuppen E, van Boxtel R.

Nature. 2016 Oct 13;538(7624):260-264. doi: 10.1038/nature19768.

PMID:
27698416
4.

Transcriptional and Linkage Analyses Identify Loci that Mediate the Differential Macrophage Response to Inflammatory Stimuli and Infection.

Hassan MA, Jensen KD, Butty V, Hu K, Boedec E, Prins P, Saeij JP.

PLoS Genet. 2015 Oct 28;11(10):e1005619. doi: 10.1371/journal.pgen.1005619.

5.

Toward effective software solutions for big biology.

Prins P, de Ligt J, Tarasov A, Jansen RC, Cuppen E, Bourne PE.

Nat Biotechnol. 2015 Jul;33(7):686-7. doi: 10.1038/nbt.3240. No abstract available.

PMID:
26154002
6.

Sambamba: fast processing of NGS alignment formats.

Tarasov A, Vilella AJ, Cuppen E, Nijman IJ, Prins P.

Bioinformatics. 2015 Jun 15;31(12):2032-4. doi: 10.1093/bioinformatics/btv098.

7.

Community-driven development for computational biology at Sprints, Hackathons and Codefests.

Möller S, Afgan E, Banck M, Bonnal RJ, Booth T, Chilton J, Cock PJ, Gumbel M, Harris N, Holland R, Kalaš M, Kaján L, Kibukawa E, Powel DR, Prins P, Quinn J, Sallou O, Strozzi F, Seemann T, Sloggett C, Soiland-Reyes S, Spooner W, Steinbiss S, Tille A, Travis AJ, Guimera R, Katayama T, Chapman BA.

BMC Bioinformatics. 2014;15 Suppl 14:S7. doi: 10.1186/1471-2105-15-S14-S7.

8.

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kalaš M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T.

J Biomed Semantics. 2014 Feb 5;5(1):5. doi: 10.1186/2041-1480-5-5.

9.

Fast probabilistic file fingerprinting for big data.

Tretyakov K, Laur S, Smant G, Vilo J, Prins P.

BMC Genomics. 2013;14 Suppl 2:S8. doi: 10.1186/1471-2164-14-S2-S8.

10.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

Katayama T, Wilkinson MD, Micklem G, Kawashima S, Yamaguchi A, Nakao M, Yamamoto Y, Okamoto S, Oouchida K, Chun HW, Aerts J, Afzal H, Antezana E, Arakawa K, Aranda B, Belleau F, Bolleman J, Bonnal RJ, Chapman B, Cock PJ, Eriksson T, Gordon PM, Goto N, Hayashi K, Horn H, Ishiwata R, Kaminuma E, Kasprzyk A, Kawaji H, Kido N, Kim YJ, Kinjo AR, Konishi F, Kwon KH, Labarga A, Lamprecht AL, Lin Y, Lindenbaum P, McCarthy L, Morita H, Murakami K, Nagao K, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Ono K, Oshita K, Park KJ, Prins P, Saito TL, Samwald M, Satagopam VP, Shigemoto Y, Smith R, Splendiani A, Sugawara H, Taylor J, Vos RA, Withers D, Yamasaki C, Zmasek CM, Kawamoto S, Okubo K, Asai K, Takagi T.

J Biomed Semantics. 2013 Feb 11;4(1):6. doi: 10.1186/2041-1480-4-6.

11.

Scalable computing for evolutionary genomics.

Prins P, Belhachemi D, Möller S, Smant G.

Methods Mol Biol. 2012;856:529-45. doi: 10.1007/978-1-61779-585-5_22.

PMID:
22399474
12.

Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies.

Prins P, Goto N, Yates A, Gautier L, Willis S, Fields C, Katayama T.

Methods Mol Biol. 2012;856:513-27. doi: 10.1007/978-1-61779-585-5_21.

PMID:
22399473
13.

Genetical genomics for evolutionary studies.

Prins P, Smant G, Jansen RC.

Methods Mol Biol. 2012;856:469-85. doi: 10.1007/978-1-61779-585-5_19.

PMID:
22399471
14.

Bioinformatics tools and database resources for systems genetics analysis in mice--a short review and an evaluation of future needs.

Durrant C, Swertz MA, Alberts R, Arends D, Möller S, Mott R, Prins P, van der Velde KJ, Jansen RC, Schughart K.

Brief Bioinform. 2012 Mar;13(2):135-42. doi: 10.1093/bib/bbr026. Review.

15.

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.

Bonnal RJ, Aerts J, Githinji G, Goto N, MacLean D, Miller CA, Mishima H, Pagani M, Ramirez-Gonzalez R, Smant G, Strozzi F, Syme R, Vos R, Wennblom TJ, Woodcroft BJ, Katayama T, Prins P.

Bioinformatics. 2012 Apr 1;28(7):1035-7. doi: 10.1093/bioinformatics/bts080.

16.

xQTL workbench: a scalable web environment for multi-level QTL analysis.

Arends D, van der Velde KJ, Prins P, Broman KW, Möller S, Jansen RC, Swertz MA.

Bioinformatics. 2012 Apr 1;28(7):1042-4. doi: 10.1093/bioinformatics/bts049.

17.

Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds.

McKeown PC, Laouielle-Duprat S, Prins P, Wolff P, Schmid MW, Donoghue MT, Fort A, Duszynska D, Comte A, Lao NT, Wennblom TJ, Smant G, Köhler C, Grossniklaus U, Spillane C.

BMC Plant Biol. 2011 Aug 12;11:113. doi: 10.1186/1471-2229-11-113.

18.

A genome-wide genetic map of NB-LRR disease resistance loci in potato.

Bakker E, Borm T, Prins P, van der Vossen E, Uenk G, Arens M, de Boer J, van Eck H, Muskens M, Vossen J, van der Linden G, van Ham R, Klein-Lankhorst R, Visser R, Smant G, Bakker J, Goverse A.

Theor Appl Genet. 2011 Aug;123(3):493-508. doi: 10.1007/s00122-011-1602-z.

19.

Big data, but are we ready?

Trelles O, Prins P, Snir M, Jansen RC.

Nat Rev Genet. 2011 Mar;12(3):224. doi: 10.1038/nrg2857-c1. No abstract available.

PMID:
21301471
20.

R/qtl: high-throughput multiple QTL mapping.

Arends D, Prins P, Jansen RC, Broman KW.

Bioinformatics. 2010 Dec 1;26(23):2990-2. doi: 10.1093/bioinformatics/btq565.

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