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The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.
Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET, Lops J, Thorisson GA, Arends D, Byelas G, Muilu J, Brookes AJ, de Brock EO, Jansen RC, Parkinson H. Swertz MA, et al. Among authors: Muilu J. BMC Bioinformatics. 2010 Dec 21;11 Suppl 12(Suppl 12):S12. doi: 10.1186/1471-2105-11-S12-S12. BMC Bioinformatics. 2010. PMID: 21210979 Free PMC article.
Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies.
Viennas E, Komianou A, Mizzi C, Stojiljkovic M, Mitropoulou C, Muilu J, Vihinen M, Grypioti P, Papadaki S, Pavlidis C, Zukic B, Katsila T, van der Spek PJ, Pavlovic S, Tzimas G, Patrinos GP. Viennas E, et al. Among authors: Muilu J. Nucleic Acids Res. 2017 Jan 4;45(D1):D846-D853. doi: 10.1093/nar/gkw949. Epub 2016 Oct 18. Nucleic Acids Res. 2017. PMID: 27924022 Free PMC article.
VarioML framework for comprehensive variation data representation and exchange.
Byrne M, Fokkema IF, Lancaster O, Adamusiak T, Ahonen-Bishopp A, Atlan D, Béroud C, Cornell M, Dalgleish R, Devereau A, Patrinos GP, Swertz MA, Taschner PE, Thorisson GA, Vihinen M, Brookes AJ, Muilu J. Byrne M, et al. Among authors: Muilu J. BMC Bioinformatics. 2012 Oct 3;13:254. doi: 10.1186/1471-2105-13-254. BMC Bioinformatics. 2012. PMID: 23031277 Free PMC article.
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.
McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H. McMurry JA, et al. Among authors: Muilu J. PLoS Biol. 2017 Jun 29;15(6):e2001414. doi: 10.1371/journal.pbio.2001414. eCollection 2017 Jun. PLoS Biol. 2017. PMID: 28662064 Free PMC article.
Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information.
Adamusiak T, Parkinson H, Muilu J, Roos E, van der Velde KJ, Thorisson GA, Byrne M, Pang C, Gollapudi S, Ferretti V, Hillege H, Brookes AJ, Swertz MA. Adamusiak T, et al. Among authors: Muilu J. Hum Mutat. 2012 May;33(5):867-73. doi: 10.1002/humu.22070. Epub 2012 Apr 4. Hum Mutat. 2012. PMID: 22416047
The phenotype and genotype experiment object model (PaGE-OM): a robust data structure for information related to DNA variation.
Brookes AJ, Lehvaslaiho H, Muilu J, Shigemoto Y, Oroguchi T, Tomiki T, Mukaiyama A, Konagaya A, Kojima T, Inoue I, Kuroda M, Mizushima H, Thorisson GA, Dash D, Rajeevan H, Darlison MW, Woon M, Fredman D, Smith AV, Senger M, Naito K, Sugawara H. Brookes AJ, et al. Among authors: Muilu J. Hum Mutat. 2009 Jun;30(6):968-77. doi: 10.1002/humu.20973. Hum Mutat. 2009. PMID: 19479963
The Finnish disease heritage database (FinDis) update-a database for the genes mutated in the Finnish disease heritage brought to the next-generation sequencing era.
Polvi A, Linturi H, Varilo T, Anttonen AK, Byrne M, Fokkema IF, Almusa H, Metzidis A, Avela K, Aula P, Kestilä M, Muilu J. Polvi A, et al. Among authors: Muilu J. Hum Mutat. 2013 Nov;34(11):1458-66. doi: 10.1002/humu.22389. Epub 2013 Sep 13. Hum Mutat. 2013. PMID: 23904198
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