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Items: 1 to 20 of 30

1.

R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multi-parent Populations.

Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Sen Ś, Yandell BS, Churchill GA.

Genetics. 2018 Dec 27. pii: genetics.301595.2018. doi: 10.1534/genetics.118.301595. [Epub ahead of print]

2.

Evaluating the performance of tools used to call minority variants from whole genome short-read data.

Said Mohammed K, Kibinge N, Prins P, Agoti CN, Cotten M, Nokes DJ, Brand S, Githinji G.

Version 2. Wellcome Open Res. 2018 Sep 13 [revised 2018 Jan 1];3:21. doi: 10.12688/wellcomeopenres.13538.2. eCollection 2018.

3.

Genetic Contribution to Initial and Progressive Alcohol Intake Among Recombinant Inbred Strains of Mice.

Mulligan MK, Zhao W, Dickerson M, Arends D, Prins P, Cavigelli SA, Terenina E, Mormede P, Lu L, Jones BC.

Front Genet. 2018 Sep 25;9:370. doi: 10.3389/fgene.2018.00370. eCollection 2018.

4.

An Integrated Systems Genetics and Omics Toolkit to Probe Gene Function.

Li H, Wang X, Rukina D, Huang Q, Lin T, Sorrentino V, Zhang H, Bou Sleiman M, Arends D, McDaid A, Luan P, Ziari N, Velázquez-Villegas LA, Gariani K, Kutalik Z, Schoonjans K, Radcliffe RA, Prins P, Morgenthaler S, Williams RW, Auwerx J.

Cell Syst. 2018 Jan 24;6(1):90-102.e4. doi: 10.1016/j.cels.2017.10.016. Epub 2017 Nov 30.

5.

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. 2017 Mar;89(6):1225-1235. doi: 10.1111/tpj.13457. Epub 2017 Feb 13.

6.

GeneNetwork: A Toolbox for Systems Genetics.

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

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

PMID:
27933521
7.

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. Epub 2016 Oct 3.

8.

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. eCollection 2015 Oct.

9.

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
10.

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. Epub 2015 Feb 19.

11.

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. Epub 2014 Nov 27.

12.

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.

13.

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. Epub 2013 Feb 15.

14.

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.

15.

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
16.

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
17.

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
18.

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. Epub 2011 Jul 8. Review.

19.

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. Epub 2012 Feb 12.

20.

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. Epub 2012 Feb 3.

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