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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 (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

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

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

Joep de Ligt, PhD

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

Joep is a former biologist and bioinformatician coordinator UMCU Bioinformatics Expertise Core (UBEC) at UMC Utrecht and formerly at the Hubrecht Institute. Joep has a broad experience in next generation sequencing and an active interest in Python, C and Javascript programming and using RDF for data integration.

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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. Marco's blog can be found here.

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



Group publications

(WIP)

  1. Evaluating the performance of tools used to call minority variants from whole genome short-read data, by Khadija Said Mohamme, Nelson Kibinge, Pjotr Prins, Charles N. Agoti, Matthew Cotten, D.J. Nokes, Samuel Brand, George Githinji, Wellcome Open Res 2018, 3:21
  2. 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 (2015) (higly accessed)
  3. 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
  4. Small tools MANIFESTO for Bioinformatics, Pjotr Prins, Francesco Strozzi, Artem Tarasov, Joep de Ligt, George Githinji et al. http://dx.doi.org/10.5281/zenodo.11321, Aug. 18th 2014
  5. 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

Other publications of Pjotr can be found here.

Author: Pjotr Prins

Created: 2020-02-14 Fri 16:15

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