1 Pjotr Prins

NOTICE: this is the outdated HOME page of Pjotr Prins.

Pjotr is a bioinformatician at large and director of Genenetwork.org; a member and visiting research fellow of Rob William's group at The University of Tennessee Health Science Center. Pjotr is an Oxford University Nuffield Department of Medicine honorary visiting research fellow in statistical genetics and a visiting research fellow of the Personal genomics and bioinformatics Department of the University Medical Centre Utrecht and the Groningen Bioinformatics Centre of University of Groningen. Pjotr runs a virtual group and is an editor for the Journal of Open Source Software (JOSS).

Formerly Pjotr received his PhD and was employed by the Laboratory of Nematology, Wageningen University.

Always on a road of discovery. Recent write-ups include:

• Pjotr's progress BLOG on GeneNetwork related
• Small tools manifesto
• D is a dragon, or why D matters for Bioinformatics
• A Netgear router as a super computer
• Home automation with Coffeescript on a router
• Fast and smart VCF parser
• Fast BLAST XML parser

1.1 Articles

A full list of publications and citations can be found on Google Scholar and Pubmed.

• Tissue-specific mutation accumulation in human adult stem cells during life by Francis Blokzijl, Joep de Ligt, ..., Pjotr Prins, ..., Michael R. Stratton, Hans Clevers, Edwin Cuppen and Ruben van Boxtel et al., Nature 538 (7624), 260-264, 2016
• Correlation Trait Loci (CTL) mapping: phenotype network inference subject to genotype by Danny Arends, Yang Li, Gudrun A. Brockmann, Ritsert C. Jansen, Robert W. Williams and Pjotr Prins, Journal of Open Source Software, Vol 1, Number 6, Oct. 2016; doi:10.21105/joss.00087
• GeneNetwork: framework for web-based genetics by Zachary Sloan, Danny Arends, Karl W. Broman, Arthur Centeno, Nicholas Furlotte, Harm Nijveen, Lei Yan, Xiang Zhou, Robert W. Williams and Pjotr Prins, Journal of Open Source Software, Vol 1, Number 2, 2016; doi:10.21105/joss.00025
• Toward effective software solutions for big biology, by Pjotr Prins, Joep de Ligt, Artem Tarasov, Ritsert C Jansen, Edwin Cuppen and Philip E Bourne, Nature Biotechnology, 2015; 33, 686-687 (higly accessed)
• Transcriptional and Linkage Analyses Identify Loci that Mediate the Differential Macrophage Response to Inflammatory Stimuli and Infection, by Mussah Hassan, Kirk D. Jensen, Vincent Butty, Kenneth Hu, Erwan Boedec, Pjotr Prins and Jeroen P. J. Saeij, PLoS Genetics, October 28, 2015, doi:10.1371/journal.pgen.1005619
• Sambamba: fast processing of NGS alignment formats, by Artem Tarasov, Albert J. Vilella, Edwin Cuppen, Isaac J. Nijman and Pjotr Prins, Bioinformatics, 2015; Bioinformatics 31 (12): 2032-2034
• Small tools MANIFESTO for Bioinformatics, Prins, Katayama et al.. Zenodo, Aug. 18th 2014
• Community-driven development for computational biology at Sprints, Hackathons and Codefests, Moeller, Afgan et al., BMC Bioinformatics. 2014; 15(Suppl 14): S7.
• BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains, Katayama, Wilkinson et al., J Biomed Semantics. February 2014 5:5 (highly accessed)
• The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies, Katayama, Wilkinson et al., J Biomed Semantics. February 2013 4(1):6 (highly accessed)
• Fast Probabilistic File Fingerprinting for Big Data, by K Tretyakov, S Laur, G Smant, J Vilo, and P Prins, ISCB-Asia/SCCG 2012 supplement, BMC Genomics. Februari 2013 14(Suppl 2):S8
• Biogem: an effective tool based approach for scaling up open source software development in bioinformatics, by R. Bonnal, P Prins et al., Bioinformatics, February 2012
• xQTL workbench: a scalable web environment for multi-level QTL analysis by D. Arends et al., Bioinformatics, January 2012
• Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds by Peter C McKeown, Sylvia Laouielle-Duprat, Pjotr Prins, Philip Wolff, Marc W Schmid, Mark T.A. Donoghue, Antoine Fort, Dorota Duszynska, Aurelie Comte, Nga THI Lao, Trevor J Wennblom, Geert Smant, Claudia Kohler, Ueli Grossniklaus and Charles Spillane, BMC Plant Biology, August 12, 2011 doi:10.1186/1471-2229-11-113 (highly accessed).
• Bioinformatics tools and database resources for systems genetics analysis in mice - a short review and an evaluation of future needs by Caroline Durrant, Morris A. Swertz, Rudi Alberts, Danny Arends, Steffen Möller, Richard Mott, Pjotr Prins, K. Joeri van der Velde, Ritsert C. Jansen and Klaus Schughart, Briefings in Bioinformatics, July 8, 2011 doi:10.1093/bib/bbr026
• A genome-wide genetic map of NB-LRR disease resistance loci in potato by Bakker, E.H.; Borm, T.J.A.; Prins, J.C.P et al., Theoretical and Applied Genetics 2011. - ISSN 0040-5752 - p. 13. doi: 10.1007/s00122-011-1602-z
• Big data, but are we ready? by Oswaldo Trelles, Pjotr Prins, Marc Snir and Ritsert C. Jansen, Nature Reviews Genetics, 12, 224, March 2011 doi:10.1038/nrg2857-c1
• R/qtl: high throughput Multiple QTL mapping by Danny Arends, Pjotr Prins, Ritsert C. Jansen and Karl W. Broman, Bioinformatics, October 21, 2010, doi: 10.1093/bioinformatics/btq565
• BioRuby: Bioinformatics software for the Ruby programming language by Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts and Toshiaki Katayama, Bioinformatics, August 29, 2010, doi:10.1093/bioinformatics/btq475
• The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows by Toshiaki Katayama et al., Journal of Biomedical Semantics 2010, 1:8 doi:10.1186/2041-1480-1-8
• A Secreted SPRY Domain-Containing Protein (SPRYSEC) from the Plant-Parasitic Nematode Globodera rostochiensis Interacts with a CC-NB-LRR Protein from a Susceptible Tomato, by Sajid Rehman, Wiebe Postma, Tom Tytgat, Pjotr Prins, Ling Qin, Hein Overmars, Jack Vossen, Laurentiu-N. Spiridon, Andrei-J. Petrescu, Aska Goverse, Jaap Bakker, and Geert Smant, Molecular Plant-Microbe Interactions, March 2009, Volume 22, Number 3, Pages 330-340, DOI: 10.1094/MPMI-22-3-0330
• Nix fixes dependency hell on all Linux distributions, by Pjotr Prins, Jeeva Suresh, and Eelco Dolstra, linux.com, December 22, 2008
• Mapping Determinants of Gene Expression Plasticity by Genetical Genomics in C. elegans, by Yang Li, Olga Alda Alvarez, Evert W Gutteling, Marcel Tijsterman, Jingyuan Fu, Joost A. G. Riksen, Esther Hazendonk, Pjotr Prins, Ronald H. A. Plasterk, Ritsert C. Jansen, Rainer Breitling, Jan E Kammenga, PLoS Genetics, 2006, doi:10.1371/journal.pgen.0020222.eor
• Ruby: Productive Programming Language, by Pjotr Prins, Linux Journal 2002
• GenEST, a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP, by Ling Qin, Pjotr Prins, John T. Jones, Herman Popeijus, Geert Smant, Jaap Bakker and Johannes Helder, Nucleic Acids Research, 2001, Vol. 29, No. 7 1616-1622
• NUTRIND verkent toekomstig nutrientengebruik in de nederlandse landbouw by Pjotr Prins and Ruud Pothoven, Meststoffen : Dutch/English annual on fertilizers and fertilization, 1993, 71 - 74

1.2 PhD Thesis

• High-throughput open source computational methods for genetics and genomics by Prins, J.C.P. Wageningen University. Promotor(en): Jaap Bakker; R.C. Jansen, co-promotor(en): Geert Smant. - Wageningen : Wageningen University, - 136 p. 2015.

1.3 Book Contributions

• GeneNetwork - A toolbox for systems genetics, by Mulligan MK, Mozhui K, Prins P, Williams RW (2016). Chapter in Systems Genetics, Methods in Molecular Biology; Schughart K, Williams RW eds.; Humana (in press) 2016

• Genetical Genomics for Evolutionary Studies by Pjotr Prins Geert Smant and Ritsert C. Jansen, chapter 19 in Evolutionary Genomics: statistical and computational methods, ed. Anisimova M. within Meth. Mol. Biol. Series of Humana-Springer 2012 (Update planned in 2017!)
• Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies, by Pjotr Prins, Naohisa Goto, Andrew Yates, Laurent Gautier, Scooter Willis, Christopher Fields and Toshiaki Katayama, chapter 21 in Evolutionary Genomics: statistical and computational methods, ed. Anisimova M. within Meth. Mol. Biol. Series of Humana-Springer 2012
• Scalable Computing for Evolutionary Genomics by Pjotr Prins, Dominique Belhachemi, Steffen Möller and Geert Smant, chapter 22 in Evolutionary Genomics: statistical and computational methods, ed. Anisimova M. within Meth. Mol. Biol. Series of Humana-Springer 2012
• Linking cDNA-AFLP-Based Gene Expression Patterns and ESTs Ling Qin, Pjotr Prins, and Johannes Helder, Chapter Differential Display Methods and Protocols of series Methods Mol Biol 317, 123-138, Edited by Peng Liang, ([2nd edition] October 2005) ISBN: 1-59259-968-0

1.4 Talks

• GeneNetwork: the future, on invitation of Rob W. Williams (UTHSC, Memphis TN, 9 November 2016)
• Scaling up biomedical analysis beyond R, on invitation of Saunak Sen (UTHSC, Memphis TN, 7 November 2016)
• GNU Guix and D, Dconf, (Berlin, 4 May 2016)
• Foreign packages in GNU Guix, FOSDEM, (Brussels, 30 January 2016)
• The state of bioinformatics, Wellcome Trust/KEMRI, on invitation by Etienne Villiers and James Nokes (Kenya, 14 January 2016)
• Software Challenges in the Age of (Human) Big Data, on invitation of Saunak Sen (UTHSC, Memphis TN, 12 November 2015)
• The future of genetics and genomics with GeneNetwork.org, on invitation by Nick Furlotte (23andMe, Mountain View CA, 9 November 2015)
• On Sharing pipelines (11:00 hrs at @ErasmusMC, 27 October 2015)
• Writing FOSS software for big biology, on invitation by Toshiaki Katayama (BioHackathon, 13 September 2015, Nagasaki, Japan)
• Biogems: Challenges in distributed software development in bioinformatics by Pjotr Prins, George Githinji, Ben Woodcroft, Raoul Bonnal, Toshiaki Katayama, Naohisa Goto et al (BOSC 12 July 2015, Dublin)
• Developing an Arvados BWA-GATK pipeline, by Pjotr Prins, Joep de Ligt, Isaac Nijman, Ward Vandewege, Bryan~Cosca and Peter Amstutz, Bioinformatics Open Source Conference (BOSC 11 July 2015, Dublin)
• Addressing GWAS challenges for the 21st Century, on invitation by Rob W. Williams (Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, 21 May 2015)
• Big Data but are we ready?, on invitation by Roel Vermeulen, as part of the Short Course: Molecular Epidemiology of Chronic Disease and the Exposome (IRAS, Utrecht University, 27 March 2015)
• The state of open source Bioinformatics software, Dutch Techcentre for Life Sciences (DTLS) NGS PI meeting, 15 October 2014
• Small tools for bioinformatics: sambamba, pfff, once-only, bio-vcf by Pjotr Prins, Artem Tarasov, Konstantin Tretyakov, Bioinformatics Open Source Conference (BOSC 12 July 2014, Boston, USA)
• BioRuby and distributed development, at Bioinformatics Open Source Conference (BOSC 11 July 2014 Boston, USA)
• Status, ideas, roadmap from bioinformatics open source community, Pjotr Prins & Ies Nijman, DTLS NGS (Utrecht 15 April 2014)
• Impact of next generation sequencing in cancer, Wellcome Trust/KEMRI, on invitation by Etienne Villiers (Kenya, 10 February 2014)
• NGS data processing tools: Sambamba, Pfff, and more , BioAssist/nbic (Utrecht, 14 November 2013)
• Computational Challenges in Human Cancer Research , eScience Centre, on invitation by Scott Lusher (Amsterdam, 19 September 2013)
• Design principles and programming in Ruby for Bioinformatics using bio-table as an example, BioHackathon (Toyama, 16 September 2012)
• Software resources for Bioinformatics, including biogems.info, EU-codefest (Lody, 19 July 2012)
• Programming Open Source Software in Bioinformatics, on invitation by Harm Nijveen, as part of the advanced bioinformatics course (Wageningen, February 29, 2012)
• QTL Mapping in the Evolutionary Context, ETH Zurich, invited by Maria Anisimova (Zurich, November 23, 2011)
• The Challenge of Big Data Genetical Genomics, NCSA, invited by Victor Jongeneel and Chris Fields (Urbana, IL, May 20, 2011)
• R/qtl for Big Data, MIT Department of Biology, invited by Jeroen PJ Saeij (Boston, MA, May 11, 2011)
• R/qtl2 for RNA-seq, (Biometris, WUR, Wageningen, February 7th, 2011)
• R/qtl Multiple QTL Model mapping, Theme 4 Genome Plasticity symposium of the Graduate School Experimental Plant Sciences, (Wageningen, Dec. 10, 2010)
• BioLib, Meeting of WG3 meeting of COST ACTION BM0901 (SYSGENET) (Groningen, 7 September 2010)
• MQM: Multiple QTL Model mapping with R/qtl, Pjotr Prins, Danny Arends, Ritsert Jansen and Karl Broman, 1st SYSGENET meeting (Braunschweig, April 8, 2010)
• R/xqtl: High throughput modeling, mapping and exploration of Big Data , Danny Arends, Pjotr Prins, Ritsert Jansen and Karl Broman, 1st SYSGENET meeting (Braunschweig, April 8, 2010)
• High throughput complex trait analysis with xQTL, Invited lecture at Centre for Bioinformatics, University of Kerala, with Dr Achuthsankar S Nair (Trivandrum, March 4th, 2010)
• High throughput complex trait analysis with xQTL, Invited lecture at Department of Crystallography and Biophysics, University of Madras, with Dr. P. Karthe (Chennai, Feb. 18th, 2010)
• Open Source Software (OSS) development in Biology, Invited lecture at the Institute of Bioinformatics and Applied Biotechnology (IBAB), with Prof. Yathindra (Bangalore, Feb. 16th, 2010)
• Open Source Software (OSS) development in Biology, Invited lecture at the Indian Institute of Science (IISc), with Dr. Nagasuma Chandra (Bangalore, Feb. 15th, 2010)
• Qnorm: A library of parallel methods for gene-expression Q-normalization, BOSC 2009 (Stockholm, Sweden, June 27-28 2009)
• BioLib Development Report, BOSC 2009 (Stockholm, Sweden, June 27-28 2009)
• Introducing BioLib - C and C++ libraries for BioPerl, BioJAVA, BioPython, BioRuby, BOSC 2008 lightning talk (in absentia) BOSC 2008 (Toronto Canada, July 19th, 2008)
• Microarray experiments - dealing with noise, symposium organised by Prof. Oswaldo Trelles, Computer Architecture Department University of Malaga (Malaga, May 15, 2008)
• Bio* Projects - some observations BioHackathon 2008, Towards integrated web service in life science with Open Bio* libraries organised by Database Center for Life Science DBCLS (Tokyo, 15 February 2008)
• Linux: Wheels within wheels - on virtualisation, Using Linux - MAC/OSX mini-symposium at WUR (June 2007)
• Searching the genome for pathogen protein-protein interactions, exploring evidence of positive selection, BIOEXPLOIT meeting (March 2007)
• 7th annual Bioinformatics Open Source Conference (BOSC 2006 in conjunction with ISMB, Fortaleza Brasil): Ruby in Bioinformatics (cancelled because of airline problems)
• Groningen Bioinfomatics Center Seminar: MAQi using Cancer Classification, GBiC (12 June 2006)
• NLUUG Conference Languages and Tools: Introducing Ruby on Rails for systemadministration, NLUUG autumn conference (November 2005)
• Genetical genomics approaches for C. elegans - with Olga Alvarez - specifically Assessing quality of microarrays in relation to genetical genomics experiments, 4th Annual Meeting of the Complex Trait Consortium (July 2005)
• Introducing Cfruby / Cfengine for management of large scale (and heterogenous) computing environments WURLUG (December 2004)
• GlLug talk on ROCK Linux: Power to the user (London September 2001, see http://gllug.linux.co.uk/meetSept2001.html)
• OxLug talk on the Deployment of ROCK Linux and CFengine in large environments (Oxford Februari 2001, see http://www.oxlug.org/events.html)
• Co-chaired SANE 2000 conference BoF session on ROCK Linux, see http://www.nluug.nl/events/sane2000/daily/24/bof.html (May 2000)
• NLUUG Conference Multi-platform Open Source Projects (see http://www.nluug.nl/events/vj99/algemeen/index.html) (June 1999)

1.5 Education/courses organised

• Advanced Bioinformatics and Data Integration, CSND UMC Utrecht/Hubrecht, one week Ph.D. course, March 2017, in preparation, Utrecht
• Advanced Bioinformatics and Data Integration, CSND UMC Utrecht/Hubrecht, one week Ph.D. course, April 2016, Utrecht
• Workshop and discussion on Next Generation Sequencing research, Wellcome Trust/KEMRI, one week Ph.D. course, January 2016, Kilifi Kenya
• Basics of Next Generation Sequencing, Wellcome Trust/KEMRI, one week Ph.D. course, February 2015, Kilifi Kenya
• Sequencing and de novo assembly, Kilimanjaro Clinical Research Institute (KCRI), one week Ph.D. course, January 2015, Moshi, Tanzania
• Advanced Bioinformatics and Data Integration, CSND UMC Utrecht/Hubrecht, one week Ph.D. course, 31 March 2014 - 4 April 2014, Utrecht
• Advanced Bioinformatics and Data Integration, Wellcome Trust/KEMRI, one week Ph.D. course, 11 February 2014 - 14 February 2014, Kilifi Kenya

1.6 Posters

• BOSC 2015, Developing an Arvados BWA-GATK pipeline Pjotr Prins, Peter Amstutz, Joep de Ligt, Isaac J Nijman, Bryan Cosca, Ward Vandewege et al
• CTC, May 30th, 2013 Transcriptional and linkage analyses identify loci that mediate differential macrophage response to inflammatory stimuli and infection by Musa A. Hassan, Kirk D. Jensen, Vincent Butty, Pjotr Prins, Jeroen P. J. Saeij Complex Trait Consortium (CTC) 2013, Madison, WI, USA
• TTI/Groene Genetica Networking Event, 12 September 2011, Nieuwegein: Dissecting natural variations in quantitative resistances to parasites by genetical genomics, Pjotr Prins, Danny Arends, Joeri van der Velde, Geert Smant, Jaap Bakker, and Ritsert Jansen
• Systems Genetics: from man to microbe, from genotype to phenotype, 1-2 October 2009, Groningen: User friendly cluster computing for QTL analysis, Danny Arends, K. Joeri van der Velde, Pjotr Prins, Ritsert C. Jansen, Morris A. Swertz

1.7 Conference Proceedings and Meeting Reports

• High-throughput Molecular Docking Now in Reach for a Wider Biochemical Community by Balan D.M., Malinauskas T, Prins P., Moller S., Conference on Parallel, Distributed and Network-Based Processing (PDP), 2012, 20th Euromicro International (May 2012)
• SYSGENET: a meeting report from a new European network for systems genetics, by Schughart, K. et al., Mammalian Genome, 2010, vol 21
• Adaptive Hypermedia Conference 2004 Programming adaptivity of course material by use of an action module by Egbert Heuvelman, Pjotr Prins and Sander Steenbergen (August 2004)

1.8 Tutorials

• BioRuby tutorial
• MQM for R/qtl tutorial

1.9 Other

• SciRuby/OBF Org admin for the 2013-2016 Google Summer of Code
• BioRuby Mentor for the 2011 and 2012 Google Summer of Code
• BioPerl Mentor for the 2010 Google Summer of Code (for Nescent and the Open Bioinformatics Foundation) on (BioPerl) Alignment Subsystem Refactoring
• Google Summer of Code mentor 2009 for Biolib and Ruby::PhyloXML (as part of of the Nescent SoC program ).

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1.10 Projects

• WURLUG Wageningen University Linux User Group

and much more on Github

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1.11 Other

• Open cycle map and Open streetmap projects; Openstreetmap on the Garmin
• I run Linux OpenWrt on my Wifi routers

If you want to reach Pjotr send an E-mail to pjotr.public01 @ thebird.nl;