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Pjotr Prins

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Pjotr is a bioinformatician at large & associate (coding) professor and runs a research lab at the Department of Genetics, Genomics and Informatics at the University of Tennessee Health Science Center. Pjotr is also director of Genenetwork.org; an Oxford University Nuffield Department of Medicine honorary visiting research fellow in statistical genetics, and a former visiting research fellow of the Personal genomics and bioinformatics department of the University Medical Center Utrecht and the Groningen Bioinformatics Center. As of 2021 Pjotr has been appointed adjunct associate professor at Pwani University, Kenya, and is a member of the ERIBA Laboratory of Genome Structure and Ageing at UMC Groningen, the Netherlands. Pjotr is a founder, editor and coder for the BioHackrXiv.org and a former editor for the Journal of Open Source Software (JOSS).

Pjotr received his PhD at the Laboratory of Nematology, Wageningen University, the Netherlands.

1. Highlighted Publications

  1. A draft human pangenome reference by Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ, Buonaiuto S, Chang XH, Cheng H, Chu J, Colonna V, Eizenga JM, Feng X, Fischer C, Fulton RS, Garg S, Groza C, Guarracino A, Harvey WT, Heumos S, Howe K, Jain M, Lu TY, Markello C, Martin FJ, Mitchell MW, Munson KM, Mwaniki MN, Novak AM, Olsen HE, Pesout T, Porubsky D, Prins P, Sibbesen JA, Siren J, Tomlinson C, Villani F, Vollger MR, Antonacci-Fulton LL, Baid G, Baker CA, Belyaeva A, Billis K, Carroll A, Chang PC, Cody S, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld AL, Formenti G, Frankish A, Gao Y, Garrison NA, Giron CG, Green RE, Haggerty L, Hoekzema K, Hourlier T, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Magalhaes H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson ND, Popejoy AB, Puiu D, Rautiainen M, Regier AA, Rhie A, Sacco S, Sanders AD, Schneider VA, Schultz BI, Shafin K, Smith MW, Sofia HJ, Abou Tayoun AN, Thibaud-Nissen F, Tricomi FF, Wagner J, Walenz B, Wood JMD, Zimin AV, Bourque G, Chaisson MJP, Flicek P, Phillippy AM, Zook JM, Eichler EE, Haussler D, Wang T, Jarvis ED, Miga KH, Garrison E, Marschall T, Hall IM, Li H and Paten B, Nature (2023) Vol 617 p. 312-324, 10.1038/s41586-023-05896-x
  2. Private Genomes and Public SNPs: Homomorphic Encryption of Genotypes and Phenotypes for Shared Quantitative Genetics by Mott R, Fischer C, Prins P and Davies RW, Genetics (2020) Vol 215 p. 359-372, DOI: 10.1534/genetics.120.303153 (open access)
  3. Systems Genetics for Evolutionary Studies by Prins P, Smant G, Arends D, Mulligan MK, Williams RW and Jansen RC, Methods Mol Biol (2019) Vol 1910 p. 635-652 (second edition), DOI: 10.1007/978-1-4939-9074-021 (open access)
  4. R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations by Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Śen S, Yandell BS and Churchill GA, Genetics (2019) Vol 211 p. 495-502, DOI: 10.1534/genetics.118.301595 (open access)
  5. An Integrated Systems Genetics and Omics Toolkit to Probe Gene Function by 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, Velazquez-Villegas LA, Gariani K, Kutalik Z, Schoonjans K, Radcliffe RA, Prins P, Morgenthaler S, Williams RW and Auwerx J, Cell Syst (2018) Vol 6 p. 90-102.e4, DOI: 10.1016/j.cels.2017.10.016 (open access, highly accessed: in the 99th percentile)
  6. Tissue-specific mutation accumulation in human adult stem cells during life by Blokzijl F, 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, Laan LJ, Jonge J, IJzermans JN, Vries RG, Wetering M, Stratton MR, Clevers H, Cuppen E and Boxtel R, Nature (2016) Vol 538 p. 260-264, DOI: 10.1038/nature19768 (highly accessed: in the 99th percentile)
  7. Sambamba: fast processing of NGS alignment formats by Tarasov A, Vilella AJ, Cuppen E, Nijman IJ and Prins P, Bioinformatics (2015) Vol 31 p. 2032-2034, DOI: 10.1093/bioinformatics/btv098 (highly cited)
  8. Toward effective software solutions for big biology by Prins P, Ligt J, Tarasov A, Jansen RC, Cuppen E and Bourne PE, Nat Biotechnol (2015) Vol 33 p. 686-687, DOI: 10.1038/nbt.3240 (open access, highly accessed: in the 99th percentile)
  9. Big data, but are we ready? by Trelles O, Prins P, Snir M and Jansen RC, Nat Rev Genet (2011) Vol 12 p. 224, DOI: 10.1038/nrg2857-c1 (open access)

A full list of 60-odd publications and citations can be found below and on Scholar Archive, Google Scholar, Orcid and Pubmed.

2. Awards

October 2020: the Utrecht University Graduate School of Life Sciences awarded Advanced Bioinformatics: data mining and integration for Life Sciences the best Master’s course of the academic year 2018-2019. The Utrecht Bioinformatics Center is very proud of the teaching team who realised this course: Joep de Ligt, Pjotr Prins and Mark Wilkinson.

3. Source code

Pjotr is heavily involved in the following projects

Note: because Github is non-neutral we moved work to our own shiny git server. Most repositories are still mirrored on github.

4. PhD thesis

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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



5. Full list of publications

A full list of 60+ publications and citations can be found on Scholar Archive, Google Scholar, Orcid and Pubmed.

  1. Pangenome-informed language models for privacy-preserving synthetic genome sequence generation by Huang P, Charton F, Schmelzle JM, Darnell SS, Prins P, Garrison E and Suh GE, bioRxiv (2024), 10.1101/2024.09.18.612131
  2. Rapid GPU-based pangenome graph layout by Li J, Schmelzle J, Du Y, Heumos S, Guarracino A, Guidi G, Prins P, Garrison E and Zhang Z (2024)
  3. Pangenome reconstruction in rats enhances genotype-phenotype mapping and novel variant discovery by Villani F, Guarracino A, Ward RR, Green T, Emms M, Pravenec M, Prins P, Garrison E, Williams RW, Chen H and Colonna V, bioRxiv (2024), 10.1101/2024.01.10.575041
  4. Pangenome graph layout by Path-Guided Stochastic Gradient Descent by Heumos S, Guarracino A, Schmelzle JM, Li J, Zhang Z, Hagmann J, Nahnsen S, Prins P and Garrison E, Bioinformatics (2024) Vol 40, 10.1093/bioinformatics/btae363
  5. Building pangenome graphs by Garrison E, Guarracino A, Heumos S, Villani F, Bao Z, Tattini L, Hagmann J, Vorbrugg S, Marco-Sola S, Kubica C, Ashbrook DG, Thorell K, Rusholme-Pilcher RL, Liti G, Rudbeck E, Nahnsen S, Yang Z, Moses MN, Nobrega FL, Wu Y, Chen H, Ligt J, Sudmant PH, Soranzo N, Colonna V, Williams RW and Prins P, bioRxiv (2023), 10.1101/2023.04.05.535718
  6. A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats by Jong TV, Pan Y, Rastas P, Munro D, Tutaj M, Akil H, Benner C, Chen D, Chitre AS, Chow W, Colonna V, Dalgard CL, Demos WM, Doris PA, Garrison E, Geurts AM, Gunturkun HM, Guryev V, Hourlier T, Howe K, Huang J, Kalbfleisch T, Kim P, Li L, Mahaffey S, Martin FJ, Mohammadi P, Ozel AB, Polesskaya O, Pravenec M, Prins P, Sebat J, Smith JR, Solberg Woods LC, Tabakoff B, Tracey A, Uliano-Silva M, Villani F, Wang H, Sharp BM, Telese F, Jiang Z, Saba L, Wang X, Murphy TD, Palmer AA, Kwitek AE, Dwinell MMR, Williams RW, Li JZ and Chen H, bioRxiv (2023), 10.1101/2023.04.13.536694
  7. Epigenetic analysis in a murine genetic model of gulf war illness by Mozhui K, O’Callaghan JP, Ashbrook DG, Prins P, Zhao W, Lu L and Jones BC, Frontiers in Toxicology (2023) Vol 5, 10.3389/ftox.2023.1162749
  8. A draft human pangenome reference by Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ, Buonaiuto S, Chang XH, Cheng H, Chu J, Colonna V, Eizenga JM, Feng X, Fischer C, Fulton RS, Garg S, Groza C, Guarracino A, Harvey WT, Heumos S, Howe K, Jain M, Lu TY, Markello C, Martin FJ, Mitchell MW, Munson KM, Mwaniki MN, Novak AM, Olsen HE, Pesout T, Porubsky D, Prins P, Sibbesen JA, Siren J, Tomlinson C, Villani F, Vollger MR, Antonacci-Fulton LL, Baid G, Baker CA, Belyaeva A, Billis K, Carroll A, Chang PC, Cody S, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld AL, Formenti G, Frankish A, Gao Y, Garrison NA, Giron CG, Green RE, Haggerty L, Hoekzema K, Hourlier T, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Magalhaes H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson ND, Popejoy AB, Puiu D, Rautiainen M, Regier AA, Rhie A, Sacco S, Sanders AD, Schneider VA, Schultz BI, Shafin K, Smith MW, Sofia HJ, Abou Tayoun AN, Thibaud-Nissen F, Tricomi FF, Wagner J, Walenz B, Wood JMD, Zimin AV, Bourque G, Chaisson MJP, Flicek P, Phillippy AM, Zook JM, Eichler EE, Haussler D, Wang T, Jarvis ED, Miga KH, Garrison E, Marschall T, Hall IM, Li H and Paten B, Nature (2023) Vol 617 p. 312-324, 10.1038/s41586-023-05896-x
  9. The root-knot nematode effector MiMSP32 targets host 12-oxophytodienoate reductase 2 to regulate plant susceptibility by Verhoeven A, Finkers-Tomczak A, Prins P, Valkenburg-van Raaij DR, Schaik CC, Overmars H, Steenbrugge JJM, Tacken W, Varossieau K, Slootweg EJ, Kappers IF, Quentin M, Goverse A, Sterken MG and Smant G, New Phytol (2023) Vol 237 p. 2360-2374, 10.1111/nph.18653
  10. Pangenome graphs in infectious disease: a comprehensive genetic variation analysis of Neisseria meningitidis leveraging Oxford Nanopore long reads by Yang Z, Guarracino A, Biggs PJ, Black MA, Ismail N, Wold JR, Merriman TR, Prins P, Garrison E and Ligt J, Front Genet (2023) Vol 14 p. 1225248, 10.3389/fgene.2023.1225248
  11. Metadata for BioHackrXiv markdown publications by Prins P, Ohta T, Castro LJ and Katayama T (2022), 10.37044/osf.io/ueqkj
  12. CiTO support for BioHackrXiv by Willighagen E, Ohta T, Castro LJ and Prins P (2023), 10.37044/osf.io/6rjvc
  13. A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar by Garrison E, Kronenberg ZN, Dawson ET, Pedersen BS and Prins P, PLoS Comput Biol (2022) Vol 18 p. e1009123, 10.1371/journal.pcbi.1009123
  14. ODGI: understanding pangenome graphs by Guarracino A, Heumos S, Nahnsen S, Prins P and Garrison E, Bioinformatics (2022), 10.1093/bioinformatics/btac308
  15. GeneCup: mining PubMed and GWAS catalog for gene-keyword relationships by Gunturkun MH, Flashner E, Wang T, Mulligan MK, Williams RW, Prins P and Chen H, G3 (Bethesda) (2022) Vol 12, 10.1093/g3journal/jkac059
  16. A systems genetics approach delineates the role of Bcl2 in leukemia pathogenesis by Wang X, Bajpai AK, Gu Q, Centeno A, Starlard-Davenport A, Prins P, Xu F and Lu L, Leuk Res (2022) Vol 114 p. 106804, 10.1016/j.leukres.2022.106804
  17. LMM-MQM time series mapping - an application in a murine advanced intercross line identifies novel growth QTLs by Arends D, Hesse D, Kärst S, Heise S, Lyu S, Korkuc P, Delpero M, Mulligan MK, Prins P and Brockmann GA, bioRxiv (2022), 10.1101/2022.01.23.477441
  18. Speeding up eQTL scans in the BXD population using GPUs by Trotter C, Kim H, Farage G, Prins P, Williams RW, Broman KW and Sen S, G3 (Bethesda) (2021) Vol 11, 10.1093/g3journal/jkab254
  19. A platform for experimental precision medicine: The extended BXD mouse family by Ashbrook DG, Arends D, Prins P, Mulligan MK, Roy S, Williams EG, Lutz CM, Valenzuela A, Bohl CJ, Ingels JF, McCarty MS, Centeno AG, Hager R, Auwerx J, Lu L and Williams RW, Cell Syst (2021) Vol 12 p. 235-247.e9, 10.1016/j.cels.2020.12.002
  20. Integration of evidence across human and model organism studies: A meeting report by Palmer RHC, Johnson EC, Won H, Polimanti R, Kapoor M, Chitre A, Bogue MA, Benca-Bachman CE, Parker CC, Verma A, Reynolds T, Ernst J, Bray M, Kwon SB, Lai D, Quach BC, Gaddis NC, Saba L, Chen H, Hawrylycz M, Zhang S, Zhou Y, Mahaffey S, Fischer C, Sanchez-Roige S, Bandrowski A, Lu Q, Shen L, Philip V, Gelernter J, Bierut LJ, Hancock DB, Edenberg HJ, Johnson EO, Nestler EJ, Barr PB, Prins P, Smith DJ, Akbarian S, Thorgeirsson T, Walton D, Baker E, Jacobson D, Palmer AA, Miles M, Chesler EJ, Emerson J, Agrawal A, Martone M and Williams RW, Genes Brain Behav (2021) p. e12738, 10.1111/gbb.12738
  21. Genetic Modulation of Initial Sensitivity to Delta9-Tetrahydrocannabinol (THC) Among the BXD Family of Mice by Parks C, Rogers CM, Prins P, Williams RW, Chen H, Jones BC, Moore BM2 and Mulligan MK, Front Genet (2021) Vol 12 p. 659012, 10.3389/fgene.2021.659012
  22. ODGI: Understanding pangenome graphs by Guarracino A, Heumos S, Nahnsen S, Prins P and Garrison E, bioRxiv (2021), 10.1101/2021.11.10.467921
  23. Highlights from the Era of Open Source Web-Based Tools by Anderson KR, Harris JA, Ng L, Prins P, Memar S, Ljungquist B, Furth D, Williams RW, Ascoli GA and Dumitriu D, J Neurosci (2021) Vol 41 p. 927-936, 10.1523/JNEUROSCI.1657-20.2020
  24. Conserved codon adaptation in highly expressed genes is associated with higher regularity in mRNA secondary structures by Sterken MG, Wilbers RHP, Prins P, Snoek BL, Giambasu GM, Slootweg E, Holterman MHM, Helder J, Kammenga JE, Schots A, Bakker J and Westerhof LB, bioRxiv (2020), 10.1101/2020.11.23.393322
  25. Speeding up eQTL scans in the BXD population using GPUs by Trotter C, Kim H, Farage G, Broman KW, Williams RW, Prins P and Sen Ś (2020), 10.1101/2020.06.22.153742
  26. Private Genomes and Public SNPs: Homomorphic Encryption of Genotypes and Phenotypes for Shared Quantitative Genetics by Mott R, Fischer C, Prins P and Davies RW, Genetics (2020) Vol 215 p. 359-372, DOI: 10.1534/genetics.120.303153 (open access)
  27. Ten simple rules to run a successful BioHackathon by Garcia L, Antezana E, Garcia A, Bolton E, Jimenez R, Prins P, Banda JM and Katayama T, PLoS Comput Biol (2020) Vol 16 p. e1007808, DOI: 10.1371/journal.pcbi.1007808
  28. Speeding up eQTL scans in the BXD population using GPUs by Trotter C, Kim H, Farage G, Broman KW, Williams RW, Prins P and Sen S (2020)
  29. BioHackathon 2015: Semantics of data for life sciences and reproducible research by Vos RA, Katayama T, Mishima H, Kawano S, Kawashima S, Kim JD, Moriya Y, Tokimatsu T, Yamaguchi A, Yamamoto Y, Wu H, Amstutz P, Antezana E, Aoki NP, Arakawa K, Bolleman JT, Bolton E, Bonnal RJP, Bono H, Burger K, Chiba H, Cohen KB, Deutsch EW, Fernandez-Breis JT, Fu G, Fujisawa T, Fukushima A, Garcia A, Goto N, Groza T, Hercus C, Hoehndorf R, Itaya K, Juty N, Kawashima T, Kim JH, Kinjo AR, Kotera M, Kozaki K, Kumagai S, Kushida T, Lutteke T, Matsubara M, Miyamoto J, Mohsen A, Mori H, Naito Y, Nakazato T, Nguyen-Xuan J, Nishida K, Nishida N, Nishide H, Ogishima S, Ohta T, Okuda S, Paten B, Perret JL, Prathipati P, Prins P, Queralt-Rosinach N, Shinmachi D, Suzuki S, Tabata T, Takatsuki T, Taylor K, Thompson M, Uchiyama I, Vieira B, Wei CH, Wilkinson M, Yamada I, Yamanaka R, Yoshitake K, Yoshizawa AC, Dumontier M, Kosaki K and Takagi T, F1000Res (2020) Vol 9 p. 136, DOI: 10.12688/f1000research.18236.1
  30. Logic programming for the biomedical sciences by Mungall C, Chiba H, Kawashima S, Amin N, Uni D, Prins P, Yamamoto Y and Byrd WE, BioHackrXiv (2020), DOI: 10.37044/osf.io/km9ux
  31. The expanded BXD family of mice: A cohort for experimental systems genetics and precision medicine by Ashbrook DG, Arends D, Prins P, Mulligan MK, Roy S, Williams EG, Lutz CM, Valenzuela A, Bohl CJ, Ingels JF, McCarty MS, Centeno AG, Hager R, Auwerx J, Śen S, Lu L and Williams RW, bioRxiv (2019), DOI: 10.1101/672097
  32. The molecular genetic make-up of male breast cancer by Moelans CB, Ligt J, Groep P, Prins P, Besselink NJM, Hoogstraat M, Ter Hoeve ND, Lacle MM, Kornegoor R, Pol CC, Leng WWJ, Barbe E, Vegt B, Martens J, Bult P, Smit VTHBM, Koudijs MJ, Nijman IJ, Voest EE, Selenica P, Weigelt B, Reis-Filho JS, Wall E, Cuppen E and Diest PJ, Endocr Relat Cancer (2019) Vol 26 p. 779-794, DOI: 10.1530/ERC-19-0278
  33. Systems Genetics for Evolutionary Studies by Prins P, Smant G, Arends D, Mulligan MK, Williams RW and Jansen RC, Methods Mol Biol (2019) Vol 1910 p. 635-652 (second edition), DOI: 10.1007/978-1-4939-9074-021 (open access)
  34. R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations by Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Śen S, Yandell BS and Churchill GA, Genetics (2019) Vol 211 p. 495-502, DOI: 10.1534/genetics.118.301595 (open access)
  35. Scalable Workflows and Reproducible Data Analysis for Genomics by Strozzi F, Janssen R, Wurmus R, Crusoe MR, Githinji G, Di Tommaso P, Belhachemi D, Möller S, Smant G, Ligt J and Prins P, Methods Mol Biol (2019) Vol 1910 p. 723-745, DOI: 10.1007/978-1-4939-9074-024 (open access)
  36. Sharing Programming Resources Between Bio\* Projects by Bonnal RJP, Yates A, Goto N, Gautier L, Willis S, Fields C, Katayama T and Prins P, Methods Mol Biol (2019) Vol 1910 p. 747-766 (second edition), DOI: 10.1007/978-1-4939-9074-025 (open access)
  37. An Integrated Systems Genetics and Omics Toolkit to Probe Gene Function by 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, Velazquez-Villegas LA, Gariani K, Kutalik Z, Schoonjans K, Radcliffe RA, Prins P, Morgenthaler S, Williams RW and Auwerx J, Cell Syst (2018) Vol 6 p. 90-102.e4, DOI: 10.1016/j.cels.2017.10.016 (open access, highly accessed: in the 99th percentile)
  38. Evaluating the performance of tools used to call minority variants from whole genome short-read data by Said Mohammed K, Kibinge N, Prins P, Agoti CN, Cotten M, Nokes DJ, Brand S and Githinji G, Wellcome Open Res (2018) Vol 3 p. 21, DOI: 10.12688/wellcomeopenres.13538.2
  39. Genetic Contribution to Initial and Progressive Alcohol Intake Among Recombinant Inbred Strains of Mice by Mulligan MK, Zhao W, Dickerson M, Arends D, Prins P, Cavigelli SA, Terenina E, Mormede P, Lu L and Jones BC, Front Genet (2018) Vol 9 p. 370, DOI: 10.3389/fgene.2018.00370
  40. Journal of Open Source Software (JOSS): Design and first-year review by Smith A, Niemeyer K, Katz DS, Barba L, Githinji G, Gymrek M, Huff K, Madan C, Mayes A, Moerman K, Prins P, Ram K, Rokem A, Teal T, Guimera R and Vanderplas J, PeerJ Computer Science (2017) Vol 4, DOI: 10.7717/peerj-cs.147
  41. GeneNetwork: A Toolbox for Systems Genetics by Mulligan MK, Mozhui K, Prins P and Williams RW, Methods Mol Biol (2017) Vol 1488 p. 75-120, DOI: 10.1007/978-1-4939-6427-74
  42. AraQTL - workbench and archive for systems genetics in Arabidopsis thaliana by Nijveen H, Ligterink W, Keurentjes JJ, Loudet O, Long J, Sterken MG, Prins P, Hilhorst HW, Ridder D, Kammenga JE and Snoek BL, Plant J (2017) Vol 89 p. 1225-1235, DOI: 10.1111/tpj.13457
  43. Correlation trait loci (ctl) mapping: Phenotype network inference subject to genotype by Arends D, Li Y, Brockmann G, Jansen R, Williams R and Prins P, The Journal of Open Source Software (2016) Vol 1, DOI: 10.21105/joss.00087
  44. Tissue-specific mutation accumulation in human adult stem cells during life by Blokzijl F, 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, Laan LJ, Jonge J, IJzermans JN, Vries RG, Wetering M, Stratton MR, Clevers H, Cuppen E and Boxtel R, Nature (2016) Vol 538 p. 260-264, DOI: 10.1038/nature19768 (highly accessed: in the 99th percentile)
  45. GeneNetwork: Framework for web-based genetics by Sloan Z, Arends D, Broman K, Centeno A, Furlotte N, Nijveen H, Yan L, Zhou X, Williams R and Prins P, The Journal of Open Source Software (2016) Vol 1 p. 8-10, DOI: 10.21105/joss.00025
  46. Transcriptional and Linkage Analyses Identify Loci that Mediate the Differential Macrophage Response to Inflammatory Stimuli and Infection by Hassan MA, Jensen KD, Butty V, Hu K, Boedec E, Prins P and Saeij JP, PLoS Genet (2015) Vol 11 p. e1005619, DOI: 10.1371/journal.pgen.1005619
  47. Sambamba: fast processing of NGS alignment formats by Tarasov A, Vilella AJ, Cuppen E, Nijman IJ and Prins P, Bioinformatics (2015) Vol 31 p. 2032-2034, DOI: 10.1093/bioinformatics/btv098 (highly cited)
  48. Toward effective software solutions for big biology by Prins P, Ligt J, Tarasov A, Jansen RC, Cuppen E and Bourne PE, Nat Biotechnol (2015) Vol 33 p. 686-687, DOI: 10.1038/nbt.3240 (open access, highly accessed: in the 99th percentile)
  49. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains by 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, Kalas M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lutteke 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 and Takagi T, J Biomed Semantics (2014) Vol 5 p. 5, DOI: 10.1186/2041-1480-5-5
  50. Community-driven development for computational biology at Sprints, Hackathons and Codefests by Möller S, Afgan E, Banck M, Bonnal RJ, Booth T, Chilton J, Cock PJ, Gumbel M, Harris N, Holland R, Kalas M, Kajan 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 and Chapman BA, BMC Bioinformatics (2014) Vol 15 Suppl 14 p. S7, DOI: 10.1186/1471-2105-15-S14-S7
  51. Fast probabilistic file fingerprinting for big data by Tretyakov K, Laur S, Smant G, Vilo J and Prins P, BMC Genomics (2013) Vol 14 Suppl 2 p. S8, DOI: 10.1186/1471-2164-14-S2-S8
  52. The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies by 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 and Takagi T, J Biomed Semantics (2013) Vol 4 p. 6, DOI: 10.1186/2041-1480-4-6
  53. Genetical genomics for evolutionary studies by Prins P, Smant G and Jansen RC, Methods Mol Biol (2012) Vol 856 p. 469-485, DOI: 10.1007/978-1-61779-585-519
  54. Bioinformatics tools and database resources for systems genetics analysis in mice–a short review and an evaluation of future needs by Durrant C, Swertz MA, Alberts R, Arends D, Möller S, Mott R, Prins P, Velde KJ, Jansen RC and Schughart K, Brief Bioinform (2012) Vol 13 p. 135-142, DOI: 10.1093/bib/bbr026
  55. Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics by 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 and Prins P, Bioinformatics (2012) Vol 28 p. 1035-1037, DOI: 10.1093/bioinformatics/bts080
  56. Sharing programming resources between Bio\* projects through remote procedure call and native call stack strategies by Prins P, Goto N, Yates A, Gautier L, Willis S, Fields C and Katayama T, Methods Mol Biol (2012) Vol 856 p. 513-527, DOI: 10.1007/978-1-61779-585-521
  57. xQTL workbench: a scalable web environment for multi-level QTL analysis by Arends D, Velde KJ, Prins P, Broman KW, Möller S, Jansen RC and Swertz MA, Bioinformatics (2012) Vol 28 p. 1042-1044, DOI: 10.1093/bioinformatics/bts049
  58. Scalable computing for evolutionary genomics by Prins P, Belhachemi D, Möller S and Smant G, Methods Mol Biol (2012) Vol 856 p. 529-545, DOI: 10.1007/978-1-61779-585-522
  59. Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds by 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, Kohler C, Grossniklaus U and Spillane C, BMC Plant Biol (2011) Vol 11 p. 113, DOI: 10.1186/1471-2229-11-113
  60. Big data, but are we ready? by Trelles O, Prins P, Snir M and Jansen RC, Nat Rev Genet (2011) Vol 12 p. 224, DOI: 10.1038/nrg2857-c1 (open access)
  61. A genome-wide genetic map of NB-LRR disease resistance loci in potato by Bakker E, Borm T, Prins P, Vossen E, Uenk G, Arens M, Boer J, Eck H, Muskens M, Vossen J, Linden G, Ham R, Klein-Lankhorst R, Visser R, Smant G, Bakker J and Goverse A, Theor Appl Genet (2011) Vol 123 p. 493-508, DOI: 10.1007/s00122-011-1602-z
  62. R/qtl: high-throughput multiple QTL mapping by Arends D, Prins P, Jansen RC and Broman KW, Bioinformatics (2010) Vol 26 p. 2990-2992, DOI: 10.1093/bioinformatics/btq565 (highly cited)
  63. The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium\* by Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernandez JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K and Takagi T, J Biomed Semantics (2010) Vol 1 p. 8, DOI: 10.1186/2041-1480-1-8
  64. BioRuby: bioinformatics software for the Ruby programming language by Goto N, Prins P, Nakao M, Bonnal R, Aerts J and Katayama T, Bioinformatics (2010) Vol 26 p. 2617-2619, DOI: 10.1093/bioinformatics/btq475
  65. 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 Rehman S, Postma W, Tytgat T, Prins P, Qin L, Overmars H, Vossen J, Spiridon LN, Petrescu AJ, Goverse A, Bakker J and Smant G, Mol Plant Microbe Interact (2009) Vol 22 p. 330-340, DOI: 10.1094/MPMI-22-3-0330
  66. Mapping determinants of gene expression plasticity by genetical genomics in C. elegans by Li Y, Alvarez OA, Gutteling EW, Tijsterman M, Fu J, Riksen JA, Hazendonk E, Prins P, Plasterk RH, Jansen RC, Breitling R and Kammenga JE, PLoS Genet (2006) Vol 2 p. e222, DOI: 10.1371/journal.pgen.0020222
  67. Linking cDNA-AFLP-based gene expression patterns and ESTs by Qin L, Prins P and Helder J, Methods Mol Biol (2006) Vol 317 p. 123-138, DOI: 10.1385/1-59259-968-0:123
  68. GenEST, a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP by Qin L, Prins P, Jones JT, Popeijus H, Smant G, Bakker J and Helder J, Nucleic Acids Res (2001) Vol 29 p. 1616-1622, DOI: 10.1093/nar/29.7.1616

Also: Google Scholar Orcid and Pubmed.

6. Book contributions

springer1.jpg

  1. Systems Genetics for Evolutionary Studies by P.Prins, G.Smant, D.Arends, M.K.Mulligan, R.W.Williams and R.C.Jansen, Methods Mol Biol (2019) Vol1910 p. 635-652 (second edition), DOI: 10.1007/978-1-4939-9074-021 (open access)
  2. Scalable Workflows and Reproducible Data Analysis for Genomics by F.Strozzi, R.Janssen, R.Wurmus, M.R.Crusoe, G.Githinji, P.Di Tommaso, D.Belhachemi, S.Moller, G.Smant, J.Ligt and P.Prins, Methods Mol Biol (2019) Vol1910 p. 723-745, DOI: 10.1007/978-1-4939-9074-024 (open access)
  3. Sharing Programming Resources Between Bio\* Projects by R.J.P.Bonnal, A.Yates, N.Goto, L.Gautier, S.Willis, C.Fields, T.Katayama and P.Prins, Methods Mol Biol (2019) Vol1910 p. 747-766 (second edition), DOI: 10.1007/978-1-4939-9074-025 (open access)
  4. GeneNetwork: A Toolbox for Systems Genetics by M.K.Mulligan, K.Mozhui, P.Prins and R.W.Williams, Methods Mol Biol (2017) Vol1488 p. 75-120, DOI: 10.1007/978-1-4939-6427-74
  5. Genetical genomics for evolutionary studies by P.Prins, G.Smant and R.C.Jansen, Methods Mol Biol (2012) Vol856 p. 469-485, DOI: 10.1007/978-1-61779-585-519
  6. Sharing programming resources between Bio\* projects through remote procedure call and native call stack strategies by P.Prins, N.Goto, A.Yates, L.Gautier, S.Willis, C.Fields and T.Katayama, Methods Mol Biol (2012) Vol856 p. 513-527, DOI: 10.1007/978-1-61779-585-521
  7. Scalable computing for evolutionary genomics by P.Prins, D.Belhachemi, S.Moller and G.Smant, Methods Mol Biol (2012) Vol856 p. 529-545, DOI: 10.1007/978-1-61779-585-522
  8. Linking cDNA-AFLP-based gene expression patterns and ESTs by L.Qin, P.Prins and J.Helder, Methods Mol Biol (2006) Vol317 p. 123-138, DOI: 10.1385/1-59259-968-0:123

7. Other

Always on a road of discovery Pjotr is a terminal jockey and lives life in plain text. Write-ups include:

Talks include

Still need to update this section. See the older home page.

Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2024-09-24 Tue 03:27.