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Using Semantic Web Technologies to Enable Cancer Genomics Discovery at Petabyte Scale.
Cejovic J, Radenkovic J, Mladenovic V, Stanojevic A, Miletic M, Radanovic S, Bajcic D, Djordjevic D, Jelic F, Nesic M, Lau J, Grady P, Groves-Kirkby N, Kural D, Davis-Dusenbery B. Cejovic J, et al. Among authors: kural d. Cancer Inform. 2018 Sep 28;17:1176935118774787. doi: 10.1177/1176935118774787. eCollection 2018. Cancer Inform. 2018. PMID: 30283230 Free PMC article. Review.
The Cancer Genomics Cloud: Collaborative, Reproducible, and Democratized-A New Paradigm in Large-Scale Computational Research.
Lau JW, Lehnert E, Sethi A, Malhotra R, Kaushik G, Onder Z, Groves-Kirkby N, Mihajlovic A, DiGiovanna J, Srdic M, Bajcic D, Radenkovic J, Mladenovic V, Krstanovic D, Arsenijevic V, Klisic D, Mitrovic M, Bogicevic I, Kural D, Davis-Dusenbery B; Seven Bridges CGC Team. Lau JW, et al. Among authors: kural d. Cancer Res. 2017 Nov 1;77(21):e3-e6. doi: 10.1158/0008-5472.CAN-17-0387. Cancer Res. 2017. PMID: 29092927 Free PMC article.
Comparing complex variants in family trios.
Toptas BÇ, Rakocevic G, Kómár P, Kural D. Toptas BÇ, et al. Among authors: kural d. Bioinformatics. 2018 Dec 15;34(24):4241-4247. doi: 10.1093/bioinformatics/bty443. Bioinformatics. 2018. PMID: 29868720 Free PMC article.
Fast and accurate genomic analyses using genome graphs.
Rakocevic G, Semenyuk V, Lee WP, Spencer J, Browning J, Johnson IJ, Arsenijevic V, Nadj J, Ghose K, Suciu MC, Ji SG, Demir G, Li L, Toptaş BÇ, Dolgoborodov A, Pollex B, Spulber I, Glotova I, Kómár P, Stachyra AL, Li Y, Popovic M, Källberg M, Jain A, Kural D. Rakocevic G, et al. Among authors: kural d. Nat Genet. 2019 Feb;51(2):354-362. doi: 10.1038/s41588-018-0316-4. Epub 2019 Jan 14. Nat Genet. 2019. PMID: 30643257
Integrative annotation of variants from 1092 humans: application to cancer genomics.
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F; 1000 Genomes Project Consortium; Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Khurana E, et al. Science. 2013 Oct 4;342(6154):1235587. doi: 10.1126/science.1235587. Science. 2013. PMID: 24092746 Free PMC article.
The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group. Danecek P, et al. Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7. Bioinformatics. 2011. PMID: 21653522 Free PMC article.
The 1000 Genomes Project: data management and community access.
Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P; 1000 Genomes Project Consortium. Clarke L, et al. Nat Methods. 2012 Apr 27;9(5):459-62. doi: 10.1038/nmeth.1974. Nat Methods. 2012. PMID: 22543379 Free PMC article.
25 results