Pangenome graphs in infectious disease: a comprehensive genetic variation analysis of Neisseria meningitidis leveraging Oxford Nanopore long reads

Authors: Zuyu Yang, Andrea Guarracino, Patrick J. Biggs, Michael A. Black, Nuzla Ismail, Jana Renee Wold, Tony R. Merriman, Pjotr Prins, Erik Garrison, Joep de Ligt

Source: Frontiers in Genetics, Vol 14 (2023)

Subject Terms: pangenome graphs, infectious diseases, genomic surveillance, comparative genomics, genetic variation, long-read sequencing, Genetics, QH426-470

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fgene.2023.1225248/full; https://doaj.org/toc/1664-8021

Access URL: https://doaj.org/article/ceef009a36e442af8b7829bafeada4dd

Epigenetic analysis in a murine genetic model of Gulf War illness

Authors: Khyobeni Mozhui, James P. O’Callaghan, David G. Ashbrook, Pjotr Prins, Wenyuan Zhao, Lu Lu, Byron C. Jones

Source: Frontiers in Toxicology, Vol 5 (2023)

Subject Terms: MBD-seq, DNA methylation, diisopropyl fluorophosphate, corticosterone, systems genetics, Toxicology. Poisons, RA1190-1270

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/ftox.2023.1162749/full; https://doaj.org/toc/2673-3080

Access URL: https://doaj.org/article/46d99daf5f1b41e38b60dbc925700c88

A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar.

Authors: Erik Garrison, Zev N Kronenberg, Eric T Dawson, Brent S Pedersen, Pjotr Prins

Source: PLoS Computational Biology, Vol 18, Iss 5, p e1009123 (2022)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/3ae05fe830ed411c84fe85dcbdd6247b

GeneCup: mining PubMed and GWAS catalog for gene–keyword relationships

Authors: Mustafa H Gunturkun, Efraim Flashner, Tengfei Wang, Megan K Mulligan, Robert W Williams, Pjotr Prins, Hao Chen

Source: G3: Genes, Genomes, Genetics, Vol 12, Iss 5 (2022)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/2160-1836

Access URL: https://doaj.org/article/6fe29b6e258c4f9ea16748656883ae20

Speeding up eQTL scans in the BXD population using GPUs

Authors: Chelsea Trotter, Hyeonju Kim, Gregory Farage, Pjotr Prins, Robert W Williams, Karl W Broman, Śaunak Sen

Source: G3: Genes, Genomes, Genetics, Vol 11, Iss 12 (2021)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/2160-1836

Access URL: https://doaj.org/article/4f186e152b0946b2babd8185cc0b7ec1

Genetic Modulation of Initial Sensitivity to Δ9-Tetrahydrocannabinol (THC) Among the BXD Family of Mice

Authors: Cory Parks, Chris M. Rogers, Pjotr Prins, Robert W. Williams, Hao Chen, Byron C. Jones, Bob M. Moore, Megan K. Mulligan

Source: Frontiers in Genetics, Vol 12 (2021)

Subject Terms: C57BL/6, DBA/2, THC, BXD family, cannabis, addiction, Genetics, QH426-470

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fgene.2021.659012/full; https://doaj.org/toc/1664-8021

Access URL: https://doaj.org/article/3970d577ea324bb787ca5089eb90dca0

Ten simple rules to run a successful BioHackathon.

Authors: Leyla Garcia, Erick Antezana, Alexander Garcia, Evan Bolton, Rafael Jimenez, Pjotr Prins, Juan M Banda, Toshiaki Katayama

Source: PLoS Computational Biology, Vol 16, Iss 5, p e1007808 (2020)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/f230c7760a2f4c43a5fd37855826711a

Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis

Authors: Steffen Möller, Stuart W. Prescott, Lars Wirzenius, Petter Reinholdtsen, Brad Chapman, Pjotr Prins, Stian Soiland-Reyes, Fabian Klötzl, Andrea Bagnacani, Matúš Kalaš, Andreas Tille, Michael R. Crusoe

Source: Data Science and Engineering, Vol 2, Iss 3, Pp 232-244 (2017)

Subject Terms: Continuous integration testing, Common workflow language, Container, Software distribution, Automated installation, Information technology, T58.5-58.64, Electronic computers. Computer science, QA75.5-76.95

File Description: electronic resource

Relation: http://link.springer.com/article/10.1007/s41019-017-0050-4; https://doaj.org/toc/2364-1185; https://doaj.org/toc/2364-1541

Access URL: https://doaj.org/article/dc6f615420f949e497aea96eb2551a47

BioHackathon 2015: Semantics of data for life sciences and reproducible research [version 1; peer review: 2 approved]

Authors: 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 Bolton, Raoul J. P. Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin B. Cohen, Eric W. Deutsch, Jesualdo T. Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick 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 Nguyen-Xuan, 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 Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi

Source: F1000Research, Vol 9 (2020)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/9-136/v1; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/6d102248ecd24affbea7a5223da6573a

Evaluating the performance of tools used to call minority variants from whole genome short-read data [version 2; referees: 2 approved]

Authors: Khadija Said Mohammed, Nelson Kibinge, Pjotr Prins, Charles N. Agoti, Matthew Cotten, D.J. Nokes, Samuel Brand, George Githinji

Source: Wellcome Open Research, Vol 3 (2018)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://wellcomeopenresearch.org/articles/3-21/v2; https://doaj.org/toc/2398-502X

Access URL: https://doaj.org/article/732f0cff20de4c108cb9d08e266e1439

Genetic Contribution to Initial and Progressive Alcohol Intake Among Recombinant Inbred Strains of Mice

Authors: Megan K. Mulligan, Wenyuan Zhao, Morgan Dickerson, Danny Arends, Pjotr Prins, Sonia A. Cavigelli, Elena Terenina, Pierre Mormede, Lu Lu, Byron C. Jones

Source: Frontiers in Genetics, Vol 9 (2018)

Subject Terms: BXD, DID, QTL, alcoholism, alcohol intake, genetic variation, Genetics, QH426-470

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fgene.2018.00370/full; https://doaj.org/toc/1664-8021

Access URL: https://doaj.org/article/2f4e634a844047dcb709a89af3f9ec40

Journal of Open Source Software (JOSS): design and first-year review

Authors: 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 T. Vanderplas

Source: PeerJ Computer Science, Vol 4, p e147 (2018)

Subject Terms: Research software, Code review, Computational research, Software citation, Open-source software, Scholarly publishing, Electronic computers. Computer science, QA75.5-76.95

File Description: electronic resource

Relation: https://peerj.com/articles/cs-147.pdf; https://peerj.com/articles/cs-147/; https://doaj.org/toc/2376-5992

Access URL: https://doaj.org/article/cdf7d23ef0484a458a23571931451784

A Secreted SPRY Domain-Containing Protein (SPRYSEC) from the Plant-Parasitic Nematode Globodera rostochiensis Interacts with a CC-NB-LRR Protein from a Susceptible Tomato

Authors: Sajid Rehman, Wiebe Postma, Tom Tytgat, Pjotr Prins, Ling Qin, Hein Overmars, Jack Vossen, Laurentiu-N. Spiridon, Andrei-J. Petrescu, Aska Goverse, Jaap Bakker, Geert Smant

Source: Molecular Plant-Microbe Interactions, Vol 22, Iss 3, Pp 330-340 (2009)

Subject Terms: Microbiology, QR1-502, Botany, QK1-989

File Description: electronic resource

Relation: https://doaj.org/toc/0894-0282; https://doaj.org/toc/1943-7706

Access URL: https://doaj.org/article/4bb94a0fe18642da8a6f5190cb4f19b1

Transcriptional and Linkage Analyses Identify Loci that Mediate the Differential Macrophage Response to Inflammatory Stimuli and Infection.

Authors: Musa A Hassan, Kirk D Jensen, Vincent Butty, Kenneth Hu, Erwan Boedec, Pjotr Prins, Jeroen P J Saeij

Source: PLoS Genetics, Vol 11, Iss 10, p e1005619 (2015)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC4625001?pdf=render; https://doaj.org/toc/1553-7390; https://doaj.org/toc/1553-7404

Access URL: https://doaj.org/article/a63cf0a927f24fbc9ce421efb35b8f1d

Mapping determinants of gene expression plasticity by genetical genomics in C. elegans.

Authors: Yang Li, Olga Alda Alvarez, Evert W Gutteling, Marcel Tijsterman, Jingyuan Fu, Joost A G Riksen, Esther Hazendonk, Pjotr Prins, Ronald H A Plasterk, Ritsert C Jansen, Rainer Breitling, Jan E Kammenga

Source: PLoS Genetics, Vol 2, Iss 12, p e222 (2006)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC1756913?pdf=render; https://doaj.org/toc/1553-7390; https://doaj.org/toc/1553-7404

Access URL: https://doaj.org/article/bc0b7a045d514e2aabc177e1d077f6eb

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