Works matching AU Prins, Pjotr

Results: 29

Sambamba: fast processing of NGS alignment formats.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. 2032, doi. 10.1093/bioinformatics/btv098

By:

Tarasov, Artem;
Vilella, Albert J.;
Cuppen, Edwin;
Nijman, Isaac J.;
Prins, Pjotr

Publication type:

Article

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

Published in:

Bioinformatics, 2012, v. 28, n. 7, p. 1035, doi. 10.1093/bioinformatics/bts080

By:

Bonnal, Raoul J.P.;
Aerts, Jan;
Githinji, George;
Goto, Naohisa;
MacLean, Dan;
Miller, Chase A.;
Mishima, Hiroyuki;
Pagani, Massimiliano;
Ramirez-Gonzalez, Ricardo;
Smant, Geert;
Strozzi, Francesco;
Syme, Rob;
Vos, Rutger;
Wennblom, Trevor J.;
Woodcroft, Ben J.;
Katayama, Toshiaki;
Prins, Pjotr

Publication type:

Article

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

Published in:

Bioinformatics, 2012, v. 28, n. 7, p. 1042, doi. 10.1093/bioinformatics/bts049

By:

Arends, Danny;
van der Velde, K. Joeri;
Prins, Pjotr;
Broman, Karl W.;
Möller, Steffen;
Jansen, Ritsert C.;
Swertz, Morris A.

Publication type:

Article

R/qtl: high-throughput multiple QTL mapping.

Published in:

Bioinformatics, 2010, v. 26, n. 23, p. 2990, doi. 10.1093/bioinformatics/btq565

By:

Arends, Danny;
Prins, Pjotr;
Jansen, Ritsert C.;
Broman, Karl W.

Publication type:

Article

BioRuby: bioinformatics software for the Ruby programming language.

Published in:

Bioinformatics, 2010, v. 26, n. 20, p. 2617, doi. 10.1093/bioinformatics/btq475

By:

Goto, Naohisa;
Prins, Pjotr;
Nakao, Mitsuteru;
Bonnal, Raoul;
Aerts, Jan;
Katayama, Toshiaki

Publication type:

Article

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

Published in:

Theoretical & Applied Genetics, 2011, v. 123, n. 3, p. 493, doi. 10.1007/s00122-011-1602-z

By:

Bakker, Erin;
Borm, Theo;
Prins, Pjotr;
Vossen, Edwin;
Uenk, Gerda;
Arens, Marjon;
Boer, Jan;
Eck, Herman;
Muskens, Mariëlle;
Vossen, Jack;
Linden, Gerard;
Ham, Roeland;
Klein-Lankhorst, Rene;
Visser, Richard;
Smant, Geert;
Bakker, Jaap;
Goverse, Aska

Publication type:

Article

Fast probabilistic file fingerprinting for big data.

Published in:

BMC Genomics, 2013, v. 14, n. Suppl 2, p. 1, doi. 10.1186/1471-2164-14-S2-S8

By:

Tretyakov, Konstantin;
Laur, Sven;
Smant, Geert;
Vilo, Jaak;
Prins, Pjotr

Publication type:

Article

Pangenome graphs in infectious disease: a comprehensive genetic variation analysis of Neisseria meningitidis leveraging Oxford Nanopore long reads.

Published in:

Frontiers in Genetics, 2023, p. 1, doi. 10.3389/fgene.2023.1225248

By:

Zuyu Yang;
Guarracino, Andrea;
Biggs, Patrick J.;
Black, Michael A.;
Ismail, Nuzla;
Wold, Jana Renee;
Merriman, Tony R.;
Prins, Pjotr;
Garrison, Erik;
de Ligt, Joep

Publication type:

Article

The root‐knot nematode effector MiMSP32 targets host 12‐oxophytodienoate reductase 2 to regulate plant susceptibility.

Published in:

New Phytologist, 2023, v. 237, n. 6, p. 2360, doi. 10.1111/nph.18653

By:

Verhoeven, Ava;
Finkers‐Tomczak, Anna;
Prins, Pjotr;
Valkenburg‐van Raaij, Debbie R.;
van Schaik, Casper C.;
Overmars, Hein;
van Steenbrugge, Joris J. M.;
Tacken, Wannes;
Varossieau, Koen;
Slootweg, Erik J.;
Kappers, Iris F.;
Quentin, Michaël;
Goverse, Aska;
Sterken, Mark G.;
Smant, Geert

Publication type:

Article

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

Published in:

PLoS Genetics, 2015, v. 11, n. 10, p. 1, doi. 10.1371/journal.pgen.1005619

By:

Hassan, Musa A.;
Jensen, Kirk D.;
Butty, Vincent;
Hu, Kenneth;
Boedec, Erwan;
Prins, Pjotr;
Saeij, Jeroen P. J.

Publication type:

Article

Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis.

Published in:

Data Science & Engineering, 2017, v. 2, n. 3, p. 232, doi. 10.1007/s41019-017-0050-4

By:

Möller, Steffen;
Prescott, Stuart;
Wirzenius, Lars;
Reinholdtsen, Petter;
Chapman, Brad;
Prins, Pjotr;
Soiland-Reyes, Stian;
Klötzl, Fabian;
Bagnacani, Andrea;
Kalaš, Matúš;
Tille, Andreas;
Crusoe, Michael

Publication type:

Article

Private Genomes and Public SNPs: Homomorphic Encryption of Genotypes and Phenotypes for Shared Quantitative Genetics.

Published in:

Genetics, 2020, v. 215, n. 2, p. 359, doi. 10.1534/genetics.120.303153

By:

Mott, Richard;
Fischer, Christian;
Prins, Pjotr;
Davies, Robert William

Publication type:

Article

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

Published in:

Genetics, 2019, v. 211, n. 2, p. 495, doi. 10.1534/genetics.118.301595

By:

Broman, Karl W.;
Gatti, Daniel M.;
Simecek, Petr;
Furlotte, Nicholas A.;
Prins, Pjotr;
Sen, Śaunak;
Yandell, Brian S.;
Churchill, Gary A.

Publication type:

Article

Ara QTL - workbench and archive for systems genetics in Arabidopsis thaliana.

Published in:

Plant Journal, 2017, v. 89, n. 6, p. 1225, doi. 10.1111/tpj.13457

By:

Nijveen, Harm;
Ligterink, Wilco;
Keurentjes, Joost J. B.;
Loudet, Olivier;
Long, Jiao;
Sterken, Mark G.;
Prins, Pjotr;
Hilhorst, Henk W.;
Ridder, Dick;
Kammenga, Jan E.;
Snoek, Basten L.

Publication type:

Article

Big data, but are we ready?

Published in:

2011

By:

Trelles, Oswaldo;
Prins, Pjotr;
Snir, Marc;
Jansen, Ritsert C.

Publication type:

Letter

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

Published in:

Briefings in Bioinformatics, 2012, v. 13, n. 2, p. 135, doi. 10.1093/bib/bbr026

By:

Durrant, Caroline;
Swertz, Morris A.;
Alberts, Rudi;
Arends, Danny;
Möller, Steffen;
Mott, Richard;
Prins, Pjotr;
van der Velde, K. Joeri;
Jansen, Ritsert C.;
Schughart, Klaus

Publication type:

Article

Genetic Modulation of Initial Sensitivity to Δ9-Tetrahydrocannabinol (THC) Among the BXD Family of Mice.

Published in:

Frontiers in Genetics, 2021, v. 12, p. 1, doi. 10.3389/fgene.2021.659012

By:

Parks, Cory;
Rogers, Chris M.;
Prins, Pjotr;
Williams, Robert W.;
Chen, Hao;
Jones, Byron C.;
Moore II, Bob M.;
Mulligan, Megan K.

Publication type:

Article

A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 5, p. 1, doi. 10.1371/journal.pcbi.1009123

By:

Garrison, Erik;
Kronenberg, Zev N.;
Dawson, Eric T.;
Pedersen, Brent S.;
Prins, Pjotr

Publication type:

Article

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

Published in:

Frontiers in Genetics, 2018, p. N.PAG, doi. 10.3389/fgene.2018.00370

By:

Mulligan, Megan K.;
Zhao, Wenyuan;
Dickerson, Morgan;
Arends, Danny;
Prins, Pjotr;
Cavigelli, Sonia A.;
Terenina, Elena;
Mormede, Pierre;
Lu, Lu;
Jones, Byron C.

Publication type:

Article

Highlights from the Era of Open Source Web-Based Tools.

Published in:

Journal of Neuroscience, 2021, v. 41, n. 5, p. 927, doi. 10.1523/JNEUROSCI.1657-20.2020

By:

Anderson, Kristin R.;
Harris, Julie A.;
Ng, Lydia;
Prins, Pjotr;
Memar, Sara;
Ljungquist, Bengt;
Fürth, Daniel;
Williams, Robert W.;
Ascoli, Giorgio A.;
Dumitriu, Dani

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2014, v. 15, n. Suppl 14, p. 1, doi. 10.1186/1471-2105-15-S14-S7

By:

Möller, Steffen;
Afgan, Enis;
Banck, Michael;
Bonnal, Raoul J. P.;
Booth, Timothy;
Chilton, John;
Cock, Peter J. A.;
Gumbel, Markus;
Harris, Nomi;
Holland, Richard;
Kalaš, Matúš;
Kaján, László;
Eri Kibukawa;
Powel, David R.;
Prins, Pjotr;
Quinn, Jacqueline;
Sallou, Olivier;
Strozzi, Francesco;
Seemann, Torsten;
Sloggett, Clare

Publication type:

Article

Ten simple rules to run a successful BioHackathon.

Published in:

2020

By:

Garcia, Leyla;
Antezana, Erick;
Garcia, Alexander;
Bolton, Evan;
Jimenez, Rafael;
Prins, Pjotr;
Banda, Juan M.;
Katayama, Toshiaki

Publication type:

Editorial

Cluster-efficient pangenome graph construction with nf-core/pangenome.

Published in:

Bioinformatics, 2024, v. 40, n. 11, p. 1, doi. 10.1093/bioinformatics/btae609

By:

Heumos, Simon;
Heuer, Michael L;
Hanssen, Friederike;
Heumos, Lukas;
Guarracino, Andrea;
Heringer, Peter;
Ehmele, Philipp;
Prins, Pjotr;
Garrison, Erik;
Nahnsen, Sven

Publication type:

Article

Pangenome graph layout by Path-Guided Stochastic Gradient Descent.

Published in:

Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae363

By:

Heumos, Simon;
Guarracino, Andrea;
Schmelzle, Jan-Niklas M;
Li, Jiajie;
Zhang, Zhiru;
Hagmann, Jörg;
Nahnsen, Sven;
Prins, Pjotr;
Garrison, Erik

Publication type:

Article

ODGI: understanding pangenome graphs.

Published in:

Bioinformatics, 2022, v. 38, n. 13, p. 3319, doi. 10.1093/bioinformatics/btac308

By:

Guarracino, Andrea;
Heumos, Simon;
Nahnsen, Sven;
Prins, Pjotr;
Garrison, Erik

Publication type:

Article

GeneCup: mining PubMed and GWAS catalog for gene--keyword relationships.

Published in:

G3: Genes | Genomes | Genetics, 2022, v. 12, n. 5, p. 1, doi. 10.1093/g3journal/jkac059

By:

Gunturkun, Mustafa H.;
Flashner, Efraim;
Wang, Tengfei;
Mulligan, Megan K.;
Williams, Robert W.;
Prins, Pjotr;
Hao Chen

Publication type:

Article

Speeding up eQTL scans in the BXD population using GPUs.

Published in:

G3: Genes | Genomes | Genetics, 2021, v. 11, n. 12, p. 1, doi. 10.1093/g3journal/jkab254

By:

Trotter, Chelsea;
Hyeonju Kim;
Farage, Gregory;
Prins, Pjotr;
Williams, Robert W.;
Broman, Karl W.;
Saunak Sen

Publication type:

Article

Toward effective software solutions for big biology.

Published in:

Nature Biotechnology, 2015, v. 33, n. 7, p. 686, doi. 10.1038/nbt.3240

By:

Prins, Pjotr;
de Ligt, Joep;
Tarasov, Artem;
Jansen, Ritsert C;
Cuppen, Edwin;
Bourne, Philip E

Publication type:

Article

Mapping Determinants of Gene Expression Plasticity by Genetical Genomics in C. elegans.

Published in:

PLoS Genetics, 2006, v. 3, n. 6, p. 2155, doi. 10.1371/journal.pgen.0020222

By:

Yang Li;
Álvarez, Olga Alda;
Gutteling, Evert W.;
Tijsterman, Marcel;
Jingyuan Fu;
Riksen, Joost A. G.;
Hazendonk, Esther;
Prins, Pjotr;
Plasterk, Ronald H. A.;
Jansen, Ritsert C.;
Breitling, Rainer;
Kammenga, Jan E.

Publication type:

Article