Pjotr Prins

According to our database, Pjotr Prins authored at least 22 papers between 2010 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2025

Pangenome-Informed Language Models for Synthetic Genome Sequence Generation.

Pengzhi Huang, François Charton, Jan-Niklas M. Schmelzle, Shelby S. Darnell, Pjotr Prins, Erik Garrison, G. Edward Suh

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2025

2024

Cluster-efficient pangenome graph construction with nf-core/pangenome.

Simon Heumos, Michael L. Heuer, Friederike Hanssen, Lukas Heumos, Andrea Guarracino, Peter Heringer, Philipp Ehmele, Pjotr Prins, Erik Garrison, Sven Nahnsen

Bioinform., 2024

Pangenome graph layout by Path-Guided Stochastic Gradient Descent.

Simon Heumos, Andrea Guarracino, Jan-Niklas Schmelzle, Jiajie Li, Zhiru Zhang, Jörg Hagmann, Sven Nahnsen, Pjotr Prins, Erik Garrison

Bioinform., 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

Proceedings of the International Conference for High Performance Computing, 2024

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

ODGI: understanding pangenome graphs.

Andrea Guarracino, Simon Heumos, Sven Nahnsen, Pjotr Prins, Erik Garrison

Bioinform., 2022

2020

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, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven T. Bolleman, Evan E. Bolton, Raoul Jean Pierre Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin Bretonnel Cohen, Eric W. Deutsch, Jesualdo Tomás Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García Castro, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick S. Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yuki Naito, Takeru Nakazato, Jeremy NguyenXuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosinach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron R. Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark D. Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi

F1000Research, 2020

2018

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, Ariel Rokem, Tracy K. Teal, Roman Valls Guimera, Jacob VanderPlas

PeerJ Comput. Sci., 2018

2017

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), 2017

2016

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

2015

Sambamba: fast processing of NGS alignment formats.

Artem Tarasov, Albert J. Vilella, Edwin Cuppen, Isaac J. Nijman, Pjotr Prins

Bioinform., 2015

2014

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, Eri Kibukawa, David R. Powell, Pjotr Prins, Jacqueline Quinn, Olivier Sallou, Francesco Strozzi, Torsten Seemann, Clare Sloggett, Stian Soiland-Reyes, William Spooner, Sascha Steinbiss, Andreas Tille, Anthony J. Travis, Roman Guimera, Toshiaki Katayama, Brad A. Chapman

BMC Bioinform., 2014

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, Rutger A. Vos, Trevor J. Wennblom, Ben J. Woodcroft, Toshiaki Katayama, Pjotr Prins

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

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

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, 2012

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, Raoul Jean Pierre Bonnal, Richard M. Bruskiewich, Jan Christian Bryne, José María Fernández, Akira Funahashi, Paul M. K. Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard C. G. Holland, Yoshinobu Kano, Edward A. Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R. Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehväslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M. Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew R. Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwínski, Mark J. Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M. Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A. Vos, Mark D. Wilkinson, William S. York, Christian M. Zmasek, Kiyoshi Asai, Toshihisa Takagi

J. Biomed. Semant., 2010

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