Pjotr and (virtual) group

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 have closures and include GNU Guile, Racket Lisp, Ruby, Rust and D.

Erik Garrison is assistant (and coding) professor at the same Department of Genetics, Genomics and Informatics at the University of Tennessee Health Science Center. Erik has written a great range of free software tools and is working on the next generation of pangenome solutions for population genomics. With years of C++ under his belt, Erik is increasingly using Rust as a programming language.

Christian is part of Pjotr's group at UTHSC in Memphis, TN. Christian 's a scientific software engineer with many interests and is aiming for a PhD on pangenomes and logic programming (with Groningen University).

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

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.

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 created a webserver from scratch and his blog can be found here.

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.

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.

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.

Andrea is a bioinformatics PhD student in cellular and molecular biology at the University of Rome Tor Vergata. An information engineer fallen in love with the unknown side of the biology. Currently integrating multi-omics data from (NGS) technologies to guide the design of precision immunotherapies in human colorectal cancer. Andrea is an active contributor to COVID-19 PubSeq and writes software in C++, Python and Rust.

Njagi has completed a masters at Pwani University in Kenya and is now a bioinformatician working on SARS-CoV-2 and pangenomes. Njagi was part of the iDeal programme with KEMRI/Wellcome Trust and working on viral genomes using the variation graph under supervision of George and Pjotr. Njagi loves writing software in Lisp and Rust.

Udit has wrapped up his computer science bachelors at Indian Institute of Information Technology, Una, and is employed in the Indian IT scene. 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.

Bonface is pursuing a Masters in data science at Strathmore University, Kenya. Bonface is a software developer at heart with a keen interest in biology and anything computing related. His blog can be found here.

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.

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

The following publications were written as group collaborations

1. 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, 10.1534/genetics.120.303153 (open access)
2. 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), 10.1101/672097
3. 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, 10.1530/ERC-19-0278
4. 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), 10.1007/978-1-4939-9074-0_21 (open access)
5. 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, 10.1007/978-1-4939-9074-0_24 (open access)
6. Giving software its due through community-driven review and publication by Barba LA, Bazán J, Brown J, Guimera RV, Gymrek M, Hanna A, Heagy LJ, Huff KD, Katz DS, Madan CR, Prins P and al.  (2019), 10.31219/osf.io/f4vx6
7. 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), 10.1007/978-1-4939-9074-0_25 (open access)
8. 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, 10.12688/wellcomeopenres.13538.2
9. 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, 10.3389/fgene.2018.00370
10. 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, 10.7717/peerj-cs.147
11. 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, 10.21105/joss.00087
12. 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, 10.1038/nature19768 (highly accessed: in the 99th percentile)
13. 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, 10.21105/joss.00025
14. 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, 10.1093/bioinformatics/btv098 (highly cited)
15. 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, 10.1038/nbt.3240 (open access, highly accessed: in the 99th percentile)
16. Small tools MANIFESTO for Bioinformatics by Prins P, Strozzi F, Tarasov A, Ligt J, Githinji G and   (2014), 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 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, 10.1093/bib/bbr026
18. 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, 10.1093/bioinformatics/bts080
19. 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, 10.1007/978-1-61779-585-5_21
20. 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, 10.1093/bioinformatics/bts049
21. R/qtl: high-throughput multiple QTL mapping by Arends D, Prins P, Jansen RC and Broman KW, Bioinformatics (2010) Vol 26 p. 2990-2992, 10.1093/bioinformatics/btq565 (highly cited)

Other publications can be found here.