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Journal of Open Source Software (JOSS): design and first-year review.
Smith AM, Niemeyer KE, Katz DS, Barba LA, Githinji G, Gymrek M, Huff KD, Madan CR, Mayes AC, Moerman KM, Prins P, Ram K, Rokem A, Teal TK, Guimera RV, Vanderplas JT. Smith AM, et al. Among authors: katz ds. PeerJ Prepr. 2018;4:e147. doi: 10.7717/peerj-cs.147. Epub 2018 Feb 12. PeerJ Prepr. 2018. PMID: 32704456 Free PMC article.
A multi-disciplinary perspective on emergent and future innovations in peer review.
Tennant JP, Dugan JM, Graziotin D, Jacques DC, Waldner F, Mietchen D, Elkhatib Y, B Collister L, Pikas CK, Crick T, Masuzzo P, Caravaggi A, Berg DR, Niemeyer KE, Ross-Hellauer T, Mannheimer S, Rigling L, Katz DS, Greshake Tzovaras B, Pacheco-Mendoza J, Fatima N, Poblet M, Isaakidis M, Irawan DE, Renaut S, Madan CR, Matthias L, Nørgaard Kjær J, O'Donnell DP, Neylon C, Kearns S, Selvaraju M, Colomb J. Tennant JP, et al. Among authors: katz ds. F1000Res. 2017 Jul 20;6:1151. doi: 10.12688/f1000research.12037.3. eCollection 2017. F1000Res. 2017. PMID: 29188015 Free PMC article. Review.
The principles of tomorrow's university.
Katz DS, Allen G, Barba LA, Berg DR, Bik H, Boettiger C, Borgman CL, Brown CT, Buck S, Burd R, de Waard A, Eve MP, Granger BE, Greenberg J, Howe A, Howe B, Khanna M, Killeen TL, Mayernik M, McKiernan E, Mentzel C, Merchant N, Niemeyer KE, Noren L, Nusser SM, Reed DA, Seidel E, Smith M, Spies JR, Turk M, Van Horn JD, Walsh J. Katz DS, et al. F1000Res. 2018 Dec 11;7:1926. doi: 10.12688/f1000research.17425.1. eCollection 2018. F1000Res. 2018. PMID: 30687499 Free PMC article.
FAIR-USE4OS: Guidelines for creating impactful open-source software.
Sonabend R, Gruson H, Wolansky L, Kiragga A, Katz DS. Sonabend R, et al. Among authors: katz ds. PLoS Comput Biol. 2024 May 9;20(5):e1012045. doi: 10.1371/journal.pcbi.1012045. eCollection 2024 May. PLoS Comput Biol. 2024. PMID: 38722873 Free PMC article.
Four simple recommendations to encourage best practices in research software.
Jiménez RC, Kuzak M, Alhamdoosh M, Barker M, Batut B, Borg M, Capella-Gutierrez S, Chue Hong N, Cook M, Corpas M, Flannery M, Garcia L, Gelpí JL, Gladman S, Goble C, González Ferreiro M, Gonzalez-Beltran A, Griffin PC, Grüning B, Hagberg J, Holub P, Hooft R, Ison J, Katz DS, Leskošek B, López Gómez F, Oliveira LJ, Mellor D, Mosbergen R, Mulder N, Perez-Riverol Y, Pergl R, Pichler H, Pope B, Sanz F, Schneider MV, Stodden V, Suchecki R, Svobodová Vařeková R, Talvik HA, Todorov I, Treloar A, Tyagi S, van Gompel M, Vaughan D, Via A, Wang X, Watson-Haigh NS, Crouch S. Jiménez RC, et al. Among authors: katz ds. F1000Res. 2017 Jun 13;6:ELIXIR-876. doi: 10.12688/f1000research.11407.1. eCollection 2017. F1000Res. 2017. PMID: 28751965 Free PMC article.
Managing genomic variant calling workflows with Swift/T.
Ahmed AE, Heldenbrand J, Asmann Y, Fadlelmola FM, Katz DS, Kendig K, Kendzior MC, Li T, Ren Y, Rodriguez E, Weber MR, Wozniak JM, Zermeno J, Mainzer LS. Ahmed AE, et al. Among authors: katz ds. PLoS One. 2019 Jul 9;14(7):e0211608. doi: 10.1371/journal.pone.0211608. eCollection 2019. PLoS One. 2019. PMID: 31287816 Free PMC article.
331 results