Publications

Publications

Publications from ELIXIR collaborations are printed in cursive. Tools and services are linked from the title of the corresponding paper.

2020

2019

  • Ison J, Ienasescu H, Chmura P, Rydza E, Ménager H, Kalaš M, Schwämmle V, Grüning B, Beard N, Lopez R, Duvaud S, Stockinger H, Persson B, Vařeková RS, Raček T, Vondrášek J, Peterson H, Salumets A, Jonassen I, Hooft R, Nyrönen T, Valencia A, Capella S, Gelpí J, Zambelli F, Savakis B, Leskošek B, Rapacki K, Blanchet C, Jimenez R, Oliveira A, Vriend G, Collin O, van Helden J, Løngreen P, Brunak S. The bio.tools registry of software tools and data resources for the life sciences. Genome Biol [Internet]. 2019 Aug 12;20(1). Available from: http://dx.doi.org/10.1186/s13059-019-1772-6
  • Raudvere U, Kolberg L, Kuzmin I, Arak T, Adler P, Peterson H, Vilo J. g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic Acids Research [Internet]. 2019 May 8;47(W1):W191–8. Available from: http://dx.doi.org/10.1093/nar/gkz369
  • Ison J, Ménager H, Brancotte B, Jaaniso E, Salumets A, Raček T, Lamprecht A-L, Palmblad M, Kalaš M, Chmura P, Hancock JM, Schwämmle V, Ienasescu H-I. Community curation of bioinformatics software and data resources. Briefings in Bioinformatics [Internet]. 2019 Oct 16; Available from: http://dx.doi.org/10.1093/bib/bbz075

2018

2017

  • Modhukur V, Iljasenko T, Metsalu T, Lokk K, Laisk-Podar T, Vilo J. MethSurv: a web tool to perform multivariable survival analysis using DNA methylation data. Epigenomics [Internet]. 2018 Mar;10(3):277–88. Available from: http://dx.doi.org/10.2217/epi-2017-0118
  • 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 JLl, 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 H-A, Todorov I, Treloar A, Tyagi S, van Gompel M, Vaughan D, Via A, Wang X, Watson-Haigh NS, Crouch S. Four simple recommendations to encourage best practices in research software. F1000Res [Internet]. 2017 Jun 13;6:876. Available from: http://dx.doi.org/10.12688/f1000research.11407.1
  • Hillion K-H, Kuzmin I, Khodak A, Rasche E, Crusoe M, Peterson H, Ison J, Ménager H. Using bio.tools to generate and annotate workbench tool descriptions. F1000Res [Internet]. 2017 Nov 30;6:2074. Available from: http://dx.doi.org/10.12688/f1000research.12974.1

2016

2015

  • Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li J-W, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SCE, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res [Internet]. 2015 Nov 3;44(D1):D38–47. Available from: http://dx.doi.org/10.1093/nar/gkv1116
  • Metsalu T, Vilo J. ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap. Nucleic Acids Res [Internet]. 2015 May 12;43(W1):W566–70. Available from: http://dx.doi.org/10.1093/nar/gkv468
  • Kaplinski L, Remm M. MultiPLX. In: PCR Primer Design [Internet]. Humana Press; 2007. p. 287–303. Available from: http://dx.doi.org/10.1007/978-1-59745-528-2_14

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