Publications

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

2023

• Kerimov, N., Tambets, R., Hayhurst, J. D., Rahu, I., Kolberg, P., Raudvere, U., Kuzmin, I., Chowdhary, A., Vija, A., Teras, H. J., Kanai, M., Ulirsch, J., Ryten, M., Hardy, J., Guelfi, S., Trabzuni, D., Kim-Hellmuth, S., Rayner, W., Finucane, H., Peterson, H., Mosaku, A., Parkinson, H., Alasoo, K. eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs, PLoS Genetics 19(9): e1010932. Available from https://doi.org/10.1371/journal.pgen.1010932
• Kolberg, L., Raudvere, U., Kuzmin, I., Adler, P., Vilo, J. and Peterson, H., 2023. g: Profiler—interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update). Nucleic Acids Research, p.gkad347. Available from http://doi.org/10.1093/nar/gkad347
• Koeppel, J., Weller, J., Peets, E.M., Pallaseni, A., Kuzmin, I., Raudvere, U., Peterson, H., Liberante, F.G. and Parts, L., 2023. Prediction of prime editing insertion efficiencies using sequence features and DNA repair determinants. Nature Biotechnology, pp.1-11. Available from http://doi.org/10.1038/s41587-023-01678-y. 

2022

• Uusküla A, Kalda R, Solvak M, Jürisson M, Käärik M, Fischer K, Keis A, Raudvere U, Vilo J, Peterson H, Käärik E., Metspalu M., Jürgenson T., Milani L., Kolberg L., Tiit E.-M., Vassil K. The 1st year of the COVID-19 epidemic in Estonia: a population-based nationwide sequential/consecutive cross-sectional study. Public Health. 2022 Apr 1;205:150-6. Available from https://doi.org/10.1016/j.puhe.2022.02.004

2021

• Kerimov N, Hayhurst JD, Peikova K, Manning JR, Walter P, Kolberg L, Samoviča M, Sakthivel MP, Kuzmin I, Trevanion SJ, Burdett T. A compendium of uniformly processed human gene expression and splicing quantitative trait loci. Nature genetics. 2021 Sep;53(9):1290-9. Available from: https://doi.org/10.1038/s41588-021-00924-w

2020

• Fishman D, Kuzmin I, Adler P, Vilo J, Peterson H. PAWER: Protein Array Web ExploreR. BMC Bioinformatics [Internet]. 2020 Sep; 21, 411. Available from: http://dx.doi.org/10.1186/s12859-020-03722-z
• Kolberg L, Raudvere U, Kuzmin I, Vilo J, Peterson H. gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler. F1000Res [Internet]. 2020 Jul 15;9:709. Available from: http://dx.doi.org/10.12688/f1000research.24956.1
• Gurwitz KT, Singh Gaur P, Bellis LJ, Larcombe L, Alloza E, Balint BL, Botzki A, Dimec J, Dominguez del Angel V, Fernandes PL, Korpelainen E, Krause R, Kuzak M, Le Pera L, Leskošek B, Lindvall JM, Marek D, Martinez PA, Muyldermans T, Nygård S, Palagi PM, Peterson H, Psomopoulos F, Spiwok V, van Gelder CWG, Via A, Vidak M, Wibberg D, Morgan SL, Rustici G. A framework to assess the quality and impact of bioinformatics training across ELIXIR. Ouellette F, editor. PLoS Comput Biol [Internet]. 2020 Jul 23;16(7):e1007976. Available from: http://dx.doi.org/10.1371/journal.pcbi.1007976

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

• Kõressaar T, Lepamets M, Kaplinski L, Raime K, Andreson R, Remm M. Primer3_masker: integrating masking of template sequence with primer design software. Hancock J, editor. Bioinformatics [Internet]. 2018 Jan 19;34(11):1937–8. Available from: http://dx.doi.org/10.1093/bioinformatics/bty036
• Kolberg L, Kuzmin I, Adler P, Vilo J, Peterson H. funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data. BMC Genomics [Internet]. 2018 Nov 14;19(1). Available from: http://dx.doi.org/10.1186/s12864-018-5176-x

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

• Reimand J, Arak T, Adler P, Kolberg L, Reisberg S, Peterson H, Vilo J. g:Profiler—a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Res [Internet]. 2016 Apr 20;44(W1):W83–9. Available from: http://dx.doi.org/10.1093/nar/gkw199

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

Earlier

• Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG. Primer3—new capabilities and interfaces. Nucleic Acids Research [Internet]. 2012 Jun 21;40(15):e115–e115. Available from: http://dx.doi.org/10.1093/nar/gks596
• Reimand J, Arak T, Vilo J. g:Profiler—a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Research [Internet]. 2011 Jun 6;39(suppl_2):W307–15. Available from: http://dx.doi.org/10.1093/nar/gkr378
• Adler P, Kolde R, Kull M, Tkachenko A, Peterson H, Reimand J, Vilo J. Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods. Genome Biol [Internet]. 2009;10(12):R139. Available from: http://dx.doi.org/10.1186/gb-2009-10-12-r139
• Reimand J, Tooming L, Peterson H, Adler P, Vilo J. GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. Nucleic Acids Research [Internet]. 2008 May 19;36(Web Server):W452–9. Available from: http://dx.doi.org/10.1093/nar/gkn230
• Adler P, Reimand J, Janes J, Kolde R, Peterson H, Vilo J. KEGGanim: pathway animations for high-throughput data. Bioinformatics [Internet]. 2007 Dec 1;24(4):588–90. Available from: http://dx.doi.org/10.1093/bioinformatics/btm581
• Reimand J, Kull M, Peterson H, Hansen J, Vilo J. g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Research [Internet]. 2007 Jul;35(suppl_2):W193–200. Available from: http://dx.doi.org/10.1093/nar/gkm226
• Koressaar T, Remm M. Enhancements and modifications of primer design program Primer3. Bioinformatics [Internet]. 2007 Mar 22;23(10):1289–91. Available from: http://dx.doi.org/10.1093/bioinformatics/btm091
• Andreson R, Puurand T, Remm M. SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes. Nucleic Acids Research [Internet]. 2006 Jul 1;34(Web Server):W651–5. Available from: http://dx.doi.org/10.1093/nar/gkl125