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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. 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.
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. BMC Bioinformatics. 2012 Oct 3;13:254. doi: 10.1186/1471-2105-13-254. BMC Bioinformatics. 2012. PMID: 23031277 Free PMC article.
The Matchmaker Exchange: a platform for rare disease gene discovery.
Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall CJ, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL. Philippakis AA, et al. Hum Mutat. 2015 Oct;36(10):915-21. doi: 10.1002/humu.22858. Hum Mutat. 2015. PMID: 26295439 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. Hum Mutat. 2012 May;33(5):867-73. doi: 10.1002/humu.22070. Epub 2012 Apr 4. Hum Mutat. 2012. PMID: 22416047
The BioMart community portal: an innovative alternative to large, centralized data repositories.
Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH, Baldock R, Barbiera G, Bardou P, Beck T, Blake A, Bonierbale M, Brookes AJ, Bucci G, Buetti I, Burge S, Cabau C, Carlson JW, Chelala C, Chrysostomou C, Cittaro D, Collin O, Cordova R, Cutts RJ, Dassi E, Di Genova A, Djari A, Esposito A, Estrella H, Eyras E, Fernandez-Banet J, Forbes S, Free RC, Fujisawa T, Gadaleta E, Garcia-Manteiga JM, Goodstein D, Gray K, Guerra-Assunção JA, Haggarty B, Han DJ, Han BW, Harris T, Harshbarger J, Hastings RK, Hayes RD, Hoede C, Hu S, Hu ZL, Hutchins L, Kan Z, Kawaji H, Keliet A, Kerhornou A, Kim S, Kinsella R, Klopp C, Kong L, Lawson D, Lazarevic D, Lee JH, Letellier T, Li CY, Lio P, Liu CJ, Luo J, Maass A, Mariette J, Maurel T, Merella S, Mohamed AM, Moreews F, Nabihoudine I, Ndegwa N, Noirot C, Perez-Llamas C, Primig M, Quattrone A, Quesneville H, Rambaldi D, Reecy J, Riba M, Rosanoff S, Saddiq AA, Salas E, Sallou O, Shepherd R, Simon R, Sperling L, Spooner W, Staines DM, Steinbach D, Stone K, Stupka E, Teague JW, Dayem Ullah AZ, Wang J, Ware D, Wong-Erasmus M, Youens-Clark K, Zadissa A, Zhang SJ, Kasprzyk A. Smedley D, et al. Nucleic Acids Res. 2015 Jul 1;43(W1):W589-98. doi: 10.1093/nar/gkv350. Epub 2015 Apr 20. Nucleic Acids Res. 2015. PMID: 25897122 Free PMC article.
HGVbaseG2P: a central genetic association database.
Thorisson GA, Lancaster O, Free RC, Hastings RK, Sarmah P, Dash D, Brahmachari SK, Brookes AJ. Thorisson GA, et al. Nucleic Acids Res. 2009 Jan;37(Database issue):D797-802. doi: 10.1093/nar/gkn748. Epub 2008 Oct 23. Nucleic Acids Res. 2009. PMID: 18948288 Free PMC article.
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