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Reuse of public genome-wide gene expression data.
Rung J, Brazma A. Rung J, et al. Nat Rev Genet. 2013 Feb;14(2):89-99. doi: 10.1038/nrg3394. Epub 2012 Dec 27. Nat Rev Genet. 2013. PMID: 23269463 Review.
Adaptive Mistranslation Accelerates the Evolution of Fluconazole Resistance and Induces Major Genomic and Gene Expression Alterations in Candida albicans.
Weil T, Santamaría R, Lee W, Rung J, Tocci N, Abbey D, Bezerra AR, Carreto L, Moura GR, Bayés M, Gut IG, Csikasz-Nagy A, Cavalieri D, Berman J, Santos MAS. Weil T, et al. mSphere. 2017 Aug 9;2(4):e00167-17. doi: 10.1128/mSphere.00167-17. eCollection 2017 Jul-Aug. mSphere. 2017. PMID: 28808688 Free PMC article.
Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression.
Torrente A, Lukk M, Xue V, Parkinson H, Rung J, Brazma A. Torrente A, et al. PLoS One. 2016 Jun 20;11(6):e0157484. doi: 10.1371/journal.pone.0157484. eCollection 2016. PLoS One. 2016. PMID: 27322383 Free PMC article.
Building and analysing genome-wide gene disruption networks.
Rung J, Schlitt T, Brazma A, Freivalds K, Vilo J. Rung J, et al. Bioinformatics. 2002;18 Suppl 2:S202-10. doi: 10.1093/bioinformatics/18.suppl_2.s202. Bioinformatics. 2002. PMID: 12386004
A genome-wide association study identifies novel risk loci for type 2 diabetes.
Sladek R, Rocheleau G, Rung J, Dina C, Shen L, Serre D, Boutin P, Vincent D, Belisle A, Hadjadj S, Balkau B, Heude B, Charpentier G, Hudson TJ, Montpetit A, Pshezhetsky AV, Prentki M, Posner BI, Balding DJ, Meyre D, Polychronakos C, Froguel P. Sladek R, et al. Nature. 2007 Feb 22;445(7130):881-5. doi: 10.1038/nature05616. Epub 2007 Feb 11. Nature. 2007. PMID: 17293876
The impact of low-frequency and rare variants on lipid levels.
Surakka I, Horikoshi M, Mägi R, Sarin AP, Mahajan A, Lagou V, Marullo L, Ferreira T, Miraglio B, Timonen S, Kettunen J, Pirinen M, Karjalainen J, Thorleifsson G, Hägg S, Hottenga JJ, Isaacs A, Ladenvall C, Beekman M, Esko T, Ried JS, Nelson CP, Willenborg C, Gustafsson S, Westra HJ, Blades M, de Craen AJ, de Geus EJ, Deelen J, Grallert H, Hamsten A, Havulinna AS, Hengstenberg C, Houwing-Duistermaat JJ, Hyppönen E, Karssen LC, Lehtimäki T, Lyssenko V, Magnusson PK, Mihailov E, Müller-Nurasyid M, Mpindi JP, Pedersen NL, Penninx BW, Perola M, Pers TH, Peters A, Rung J, Smit JH, Steinthorsdottir V, Tobin MD, Tsernikova N, van Leeuwen EM, Viikari JS, Willems SM, Willemsen G, Schunkert H, Erdmann J, Samani NJ, Kaprio J, Lind L, Gieger C, Metspalu A, Slagboom PE, Groop L, van Duijn CM, Eriksson JG, Jula A, Salomaa V, Boomsma DI, Power C, Raitakari OT, Ingelsson E, Järvelin MR, Thorsteinsdottir U, Franke L, Ikonen E, Kallioniemi O, Pietiäinen V, Lindgren CM, Stefansson K, Palotie A, McCarthy MI, Morris AP, Prokopenko I, Ripatti S; ENGAGE Consortium. Surakka I, et al. Nat Genet. 2015 Jun;47(6):589-97. doi: 10.1038/ng.3300. Epub 2015 May 11. Nat Genet. 2015. PMID: 25961943 Free PMC article.
Variation in genomic landscape of clear cell renal cell carcinoma across Europe.
Scelo G, Riazalhosseini Y, Greger L, Letourneau L, Gonzàlez-Porta M, Wozniak MB, Bourgey M, Harnden P, Egevad L, Jackson SM, Karimzadeh M, Arseneault M, Lepage P, How-Kit A, Daunay A, Renault V, Blanché H, Tubacher E, Sehmoun J, Viksna J, Celms E, Opmanis M, Zarins A, Vasudev NS, Seywright M, Abedi-Ardekani B, Carreira C, Selby PJ, Cartledge JJ, Byrnes G, Zavadil J, Su J, Holcatova I, Brisuda A, Zaridze D, Moukeria A, Foretova L, Navratilova M, Mates D, Jinga V, Artemov A, Nedoluzhko A, Mazur A, Rastorguev S, Boulygina E, Heath S, Gut M, Bihoreau MT, Lechner D, Foglio M, Gut IG, Skryabin K, Prokhortchouk E, Cambon-Thomsen A, Rung J, Bourque G, Brennan P, Tost J, Banks RE, Brazma A, Lathrop GM. Scelo G, et al. Nat Commun. 2014 Oct 29;5:5135. doi: 10.1038/ncomms6135. Nat Commun. 2014. PMID: 25351205
TCF7L2 is a master regulator of insulin production and processing.
Zhou Y, Park SY, Su J, Bailey K, Ottosson-Laakso E, Shcherbina L, Oskolkov N, Zhang E, Thevenin T, Fadista J, Bennet H, Vikman P, Wierup N, Fex M, Rung J, Wollheim C, Nobrega M, Renström E, Groop L, Hansson O. Zhou Y, et al. Hum Mol Genet. 2014 Dec 15;23(24):6419-31. doi: 10.1093/hmg/ddu359. Epub 2014 Jul 11. Hum Mol Genet. 2014. PMID: 25015099 Free PMC article.
Tools for mapping high-throughput sequencing data.
Fonseca NA, Rung J, Brazma A, Marioni JC. Fonseca NA, et al. Bioinformatics. 2012 Dec 15;28(24):3169-77. doi: 10.1093/bioinformatics/bts605. Epub 2012 Oct 11. Bioinformatics. 2012. PMID: 23060614
ArrayExpress update--trends in database growth and links to data analysis tools.
Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, Tikhonov A, Welter D, Williams E, Brazma A, Parkinson H, Sarkans U. Rustici G, et al. Nucleic Acids Res. 2013 Jan;41(Database issue):D987-90. doi: 10.1093/nar/gks1174. Epub 2012 Nov 27. Nucleic Acids Res. 2013. PMID: 23193272 Free PMC article.
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