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Pjotr and (virtual) group

Table of Contents

Pjotr and group represent talented bioinformaticians/statisticians working on sequencing and genome-wide association studies in diverse species. Together they work on generic methods and software for scientific research. The group is mostly virtual because each individual is a member of a different institute/group. Some of our work I track on a rotating BLOG.


Pjotr Prins, PhD

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Pjotr is a bioinformatician at large & assistant (and coding) professor at the Department of Genetics, Genomics and Informatics at the University of Tennessee Health Science Center. Pjotr is also director of Genenetwork.org; a member and visiting research fellow of Oxford University Nuffield Department of Medicine honorary visiting research fellow in statistical genetics and formerly 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 (partial) virtual group and is a founder, editor and coder for the BioHackrXiv.org and a former editor for the Journal of Open Source Software (JOSS).

Pjotr's favorite computer languages include GNU Guile, Racket Lisp, Ruby and D.

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Christian Fischer, PhD student

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Christian is part of Pjotr's group at UTHSC in Memphis, TN, and writes software and is working on a PhD on the variation graph (VG) and logic programming (together with Groningen University).

Christian is a true lambda coder with a love for Haskell, Purescript, APL, Rust and Lisps.

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Joep de Ligt, PhD

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Joep is a lead researcher at the Bioinformatics & Genomics at Institute of Environmental Science and Research Ltd (ESR), New Zealand.

Until recently Joep was a biologist and bioinformatician coordinator UMCU Bioinformatics Expertise Core (UBEC) at UMC Utrecht and formerly at the Hubrecht Institute. Joep and Pjotr created the course Advanced Bioinformatics: data mining and integration for Life Sciences which was awarded the best Master’s course of the academic year 2018-2019. Joep has a broad experience in next generation sequencing, Oxford nanopore, and an active interest in Python, C and Javascript programming and using RDF for data integration.

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Danny Arends, PhD

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Danny is a postdoctoral researcher at the Humboldt University in Berlin (HU-Berlin) works on mouse, camel, goat and plant genomics and genetics. Danny did his PhD at Groningen Bioinformatics Centre (GBIC). Danny writes software in R, C, D, Javascript, Python etc. Danny's blog can be found here.

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George Githinji, PhD

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George is a bioinformatician at KEMRI|Wellcome Trust in Kenya, working on population sequence data of malaria and respiratory syncytial virus (RSV). George's favorite programming language is Ruby, but he also writes software in R and Python. George his BLOG can be found here.

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Francesco Strozzi, PhD student

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Francesco is a bioinformatician and group leader at Enterome, to improve patient health by translating the molecular understanding of the role of the human gut microbiome to deliver innovative medicines. Francesco formerly was group leader of the bioinformatics core facility of Parco Tecnologico Padano in Italy, where he was working on high throughput data analysis in microbial, plants, livestock and human genomics. Francesco's favorite programming languages are Ruby and Scala.

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Marco van Zwetselaar, PhD student

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Marco is a bioinformatician at Kilimanjaro Clinical Research Institute (KCRI) in Tanzania, working on sequence data of malaria and bacteria. Marco's favorite programming language is Haskell, but he writes software in all languages including Lisp. Marco's blog can be found here.

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Njagi Mwaniki, Master student

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Njagi is doing a masters at Pwani University in Kenya. Njagi is following the iDeal programme with KEMRI/Wellcome Trust and working on viral genomes using the variation graph. Njagi writes software in Lisp and Rust.

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Udit Gulati, Bachelor student

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Udit is wrapping up his computer science bachelors at Indian Institute of Information Technology, Una. Udit is interested in Graph theory and high performance computing and writes code in C, D, R, Ruby, Python and Javascript. Udit is part of the Ruby Science Foundation and is lead contributor to NumRuby and Ruby-Sparse projects. Udit's blog can be found here.

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Bonface Munyoki, software developer

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Bonface is a software developer with a keen interest in biology and anything computing related. His blog can be found here.

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Ryan Routsong, software developer

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Ryan is a software developer and computational biologist originally from Dallas, TX. Ryan has a masters in computer science and works on machine learning and diagnostic PCR and 3GS kits for clinical and research means. See http://ryanroutsong.me. Ryan is fluent in D and Python.

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Former members

Former group members Artem Tarasov and Naoki Nishida can be found here.



Group publications

The following publications were written as group collaborations

  1. The expanded BXD family of mice: A cohort for experimental systems genetics and precision medicine by David G. Ashbrook, Danny Arends, Pjotr Prins, Megan K. Mulligan, Suheeta Roy, Evan G. Williams, Cathleen M. Lutz, Alicia Valenzuela, Casey J. Bohl, Jesse F. Ingels, Melinda S. McCarty, Arthur G. Centeno, Reinmar Hager, Johan Auwerx, Saunak Sen, Lu Lu and Robert W. Williams, bioRxiv (2019), DOI: 10.1101/672097
  2. The molecular genetic make-up of male breast cancer by C. B. Moelans, J. Ligt, P. Groep, P. Prins, N. J. M. Besselink, M. Hoogstraat, N. D. Ter Hoeve, M. M. Lacle, R. Kornegoor, C. C. Pol, W. W. J. Leng, E. Barbe, B. Vegt, J. Martens, P. Bult, V. T. H. B. M. Smit, M. J. Koudijs, I. J. Nijman, E. E. Voest, P. Selenica, B. Weigelt, J. S. Reis-Filho, E. Wall, E. Cuppen and P. J. Diest, Endocr Relat Cancer (2019) Vol 26 p. 779-794, DOI: 10.1530/ERC-19-0278
  3. 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) Vol 1910 p. 635-652, DOI: 10.1007/978-1-4939-9074-021
  4. 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) Vol 1910 p. 723-745, DOI: 10.1007/978-1-4939-9074-024
  5. Giving software its due through community-driven review and publication by Lorena A Barba, Juanjo Bazán, Jed Brown, Roman V Guimera, Melissa Gymrek, Alex Hanna, Lindsey J Heagy, Kathryn D Huff, Daniel S Katz, Christopher R Madan and al. (2019), DOI: 10.31219/osf.io/f4vx6
  6. 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) Vol 1910 p. 747-766, DOI: 10.1007/978-1-4939-9074-025
  7. An Integrated Systems Genetics and Omics Toolkit to Probe Gene Function by H. Li, X. Wang, D. Rukina, Q. Huang, T. Lin, V. Sorrentino, H. Zhang, M. Bou Sleiman, D. Arends, A. McDaid, P. Luan, N. Ziari, L. A. Velazquez-Villegas, K. Gariani, Z. Kutalik, K. Schoonjans, R. A. Radcliffe, P. Prins, S. Morgenthaler, R. W. Williams and J. Auwerx, Cell Syst (2018) Vol 6 p. 90-102.e4, DOI: 10.1016/j.cels.2017.10.016
  8. Evaluating the performance of tools used to call minority variants from whole genome short-read data by K. Said Mohammed, N. Kibinge, P. Prins, C. N. Agoti, M. Cotten, D. J. Nokes, S. Brand and G. Githinji, Wellcome Open Res (2018) Vol 3 p. 21, DOI: 10.12688/wellcomeopenres.13538.2
  9. Genetic Contribution to Initial and Progressive Alcohol Intake Among Recombinant Inbred Strains of Mice by M. K. Mulligan, W. Zhao, M. Dickerson, D. Arends, P. Prins, S. A. Cavigelli, E. Terenina, P. Mormede, L. Lu and B. C. Jones, Front Genet (2018) Vol 9 p. 370, DOI: 10.3389/fgene.2018.00370
  10. Journal of Open Source Software (JOSS): Design and first-year review by Arfon Smith, Kyle Niemeyer, Daniel S. Katz, Lorena Barba, George Githinji, Melissa Gymrek, Kathryn Huff, Christopher Madan, Abigail Mayes, Kevin Moerman, Pjotr Prins, Karthik Ram, Ariel Rokem, Tracy Teal, Roman Guimera and Jacob Vanderplas, PeerJ Computer Science (2017) Vol 4, DOI: 10.7717/peerj-cs.147
  11. Correlation trait loci (ctl) mapping: Phenotype network inference subject to genotype by Danny Arends, Yang Li, Gudrun Brockmann, Ritsert Jansen, Robert Williams and Pjotr Prins, The Journal of Open Source Software (2016) Vol 1, DOI: 10.21105/joss.00087
  12. Tissue-specific mutation accumulation in human adult stem cells during life by F. Blokzijl, J. Ligt, M. Jager, V. Sasselli, S. Roerink, N. Sasaki, M. Huch, S. Boymans, E. Kuijk, P. Prins, I. J. Nijman, I. Martincorena, M. Mokry, C. L. Wiegerinck, S. Middendorp, T. Sato, G. Schwank, E. E. Nieuwenhuis, M. M. Verstegen, L. J. Laan, J. Jonge, J. N. IJzermans, R. G. Vries, M. Wetering, M. R. Stratton, H. Clevers, E. Cuppen and R. Boxtel, Nature (2016) Vol 538 p. 260-264, DOI: 10.1038/nature19768 (highly accessed: in the 99th percentile)
  13. GeneNetwork: Framework for web-based genetics by Zachary Sloan, Danny Arends, Karl Broman, Arthur Centeno, Nicholas Furlotte, Harm Nijveen, Lei Yan, Xiang Zhou, Robert Williams and Pjotr Prins, The Journal of Open Source Software (2016) p. 8-10, DOI: 10.21105/joss.00025
  14. Sambamba: fast processing of NGS alignment formats by A. Tarasov, A. J. Vilella, E. Cuppen, I. J. Nijman and P. Prins, Bioinformatics (2015) Vol 31 p. 2032-2034, DOI: 10.1093/bioinformatics/btv098 (highly cited)
  15. Toward effective software solutions for big biology by P. Prins, J. Ligt, A. Tarasov, R. C. Jansen, E. Cuppen and P. E. Bourne, Nat Biotechnol (2015) Vol 33 p. 686-687, DOI: 10.1038/nbt.3240 (highly accessed: in the 99th percentile)
  16. Small tools MANIFESTO for Bioinformatics by Pjotr Prins, Francesco Strozzi, Artem Tarasov, Joep Ligt, George Githinji and (2014), DOI: 10.5281/zenodo.11321
  17. Bioinformatics tools and database resources for systems genetics analysis in mice–a short review and an evaluation of future needs by C. Durrant, M. A. Swertz, R. Alberts, D. Arends, S. Moller, R. Mott, P. Prins, K. J. Velde, R. C. Jansen and K. Schughart, Brief Bioinform (2012) Vol 13 p. 135-142, DOI: 10.1093/bib/bbr026
  18. Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics by R. J. Bonnal, J. Aerts, G. Githinji, N. Goto, D. MacLean, C. A. Miller, H. Mishima, M. Pagani, R. Ramirez-Gonzalez, G. Smant, F. Strozzi, R. Syme, R. Vos, T. J. Wennblom, B. J. Woodcroft, T. Katayama and P. Prins, Bioinformatics (2012) Vol 28 p. 1035-1037, DOI: 10.1093/bioinformatics/bts080
  19. xQTL workbench: a scalable web environment for multi-level QTL analysis by D. Arends, K. J. Velde, P. Prins, K. W. Broman, S. Moller, R. C. Jansen and M. A. Swertz, Bioinformatics (2012) Vol 28 p. 1042-1044, DOI: 10.1093/bioinformatics/bts049
  20. R/qtl: high-throughput multiple QTL mapping by D. Arends, P. Prins, R. C. Jansen and K. W. Broman, Bioinformatics (2010) Vol 26 p. 2990-2992, DOI: 10.1093/bioinformatics/btq565 (highly cited)

Other publications can be found here.


Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-04-26 Sun 14:25
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