Rapid GPU-Based Pangenome Graph Layout - Jiajie Li; Jan-Niklas Schmelzle; Yixiao Du; Simon Heumos; Andrea Guarracino; Giulia Guidi; Pjotr Prins; Erik Garrison; Zhiru Zhang (Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis, SC 2024, Atlanta, GA, USA, November 17-22, 2024, 2024)

Rapid GPU-Based Pangenome Graph Layout - Jiajie Li; Jan-Niklas Schmelzle; Yixiao Du; Simon Heumos; Andrea Guarracino; Giulia Guidi; Pjotr Prins; Erik Garrison; Zhiru Zhang (CoRR, 2024)

ODGI: understanding pangenome graphs - Andrea Guarracino; Simon Heumos; Sven Nahnsen; Pjotr Prins; Erik Garrison (Bioinform., 2022)

A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar - Erik Garrison; Zev N. Kronenberg; Eric T. Dawson; Brent S. Pedersen; Pjotr Prins (PLoS Comput. Biol., 2022)

Ten simple rules to run a successful BioHackathon - Leyla J. García; Erick Antezana; Alexander García Castro; Evan Bolton; Rafael C. Jiménez; Pjotr Prins; Juan M. Banda; Toshiaki Katayama (PLoS Comput. Biol., 2020)

BioHackathon 2015: Semantics of data for life sciences and reproducible research - Rutger A. Vos; Toshiaki Katayama; Hiroyuki Mishima; Shin Kawano; Shuichi Kawashima; Jin-Dong Kim; Yuki Moriya; Toshiaki Tokimatsu; Atsuko Yamaguchi; Yasunori Yamamoto; Hongyan Wu; Peter Amstutz; et al. (F1000Research, 2020)

Journal of Open Source Software (JOSS): design and first-year review - Arfon M. Smith; Kyle E. Niemeyer; Daniel S. Katz; Lorena A. Barba; George Githinji; Melissa Gymrek; Kathryn D. Huff; Christopher R. Madan; Abigail Cabunoc Mayes; Kevin M. Moerman; Pjotr Prins; Karthik Ram; et al. (PeerJ Comput. Sci., 2018)

Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis - Steffen Möller; Stuart W. Prescott; Lars Wirzenius; Petter Reinholdtsen; Brad Chapman; Pjotr Prins; Stian Soiland-Reyes; Fabian Klötzl; Andrea Bagnacani; Matús Kalas; Andreas Tille; Michael R. Crusoe (Data Sci. Eng., 2017)

Shō-coin: A Knowledge-Based Economy for Life Sciences - Alexander García Castro; Erick Antezana; Jael García; Olga L. Giraldo; Pjotr Prins; Rutger A. Vos (Proceedings of the 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4LS 2017), Rome, Italy, December 4-7, 2017, 2017)

Journal of Open Source Software (JOSS): design and first-year review - Arfon M. Smith; Kyle E. Niemeyer; Daniel S. Katz; Lorena A. Barba; George Githinji; Melissa Gymrek; Kathryn D. Huff; Christopher R. Madan; Abigail Cabunoc Mayes; Kevin Mattheus Moerman; Pjotr Prins; Karthik Ram; et al. (CoRR, 2017)

GeneNetwork: framework for web-based genetics - Zachary Sloan; Danny Arends; Karl W. Broman; Arthur Centeno; Nicholas A. Furlotte; Harm Nijveen; Lei Yan; Xiang Zhou; Robert W. Williams; Pjotr Prins (J. Open Source Softw., 2016)

Correlation Trait Loci (CTL) mapping: phenotype network inference subject to genotype - Danny Arends; Yang Li; Gudrun A. Brockmann; Ritsert C. Jansen; Robert W. Williams; Pjotr Prins (J. Open Source Softw., 2016)

Sambamba: fast processing of NGS alignment formats - Artem Tarasov; Albert J. Vilella; Edwin Cuppen; Isaac J. Nijman; Pjotr Prins (Bioinform., 2015)

Community-driven development for computational biology at Sprints, Hackathons and Codefests - Steffen Möller; Enis Afgan; Michael Banck; Raoul Jean Pierre Bonnal; Timothy Booth; John Chilton; Peter J. A. Cock; Markus Gumbel; Nomi L. Harris; Richard C. G. Holland; Matús Kalas; László Kaján; et al. (BMC Bioinform., 2014)

Bioinformatics tools and database resources for systems genetics analysis in mice - a short review and an evaluation of future needs - Caroline Durrant; Morris A. Swertz; Rudi Alberts; Danny Arends; Steffen Möller; Richard Mott; Pjotr Prins; K. Joeri van der Velde; Ritsert C. Jansen; Klaus Schughart (Briefings Bioinform., 2012)

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics - Raoul Jean Pierre Bonnal; Jan Aerts; George Githinji; Naohisa Goto; Daniel MacLean; Chase A. Miller; Hiroyuki Mishima; Massimiliano Pagani; Ricardo Ramirez-Gonzalez; Geert Smant; Francesco Strozzi; Rob Syme; et al. (Bioinform., 2012)

xQTL workbench: a scalable web environment for multi-level QTL analysis - Danny Arends; K. Joeri van der Velde; Pjotr Prins; Karl W. Broman; Steffen Möller; Ritsert C. Jansen; Morris A. Swertz (Bioinform., 2012)

High-throughput Molecular Docking Now in Reach for a Wider Biochemical Community - Dhananjay M. Balan; Tomas Malinauskas; Pjotr Prins; Steffen Möller (Proceedings of the 20th Euromicro International Conference on Parallel, Distributed and Network-Based Processing, PDP 2012, Munich, Germany, February 15-17, 2012, 2012)

BioRuby: bioinformatics software for the Ruby programming language - Naohisa Goto; Pjotr Prins; Mitsuteru Nakao; Raoul Jean Pierre Bonnal; Jan Aerts; Toshiaki Katayama (Bioinform., 2010)

R/qtl: high-throughput multiple QTL mapping - Danny Arends; Pjotr Prins; Ritsert C. Jansen; Karl W. Broman (Bioinform., 2010)

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows - Toshiaki Katayama; Kazuharu Arakawa; Mitsuteru Nakao; Keiichiro Ono; Kiyoko F. Aoki-Kinoshita; Yasunori Yamamoto; Atsuko Yamaguchi; Shuichi Kawashima; Hong-Woo Chun; Jan Aerts; Bruno Aranda; Lord H. Barboza; et al. (J. Biomed. Semant., 2010)