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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.
Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PI, Duzkale H, Dworzyński P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, MacArthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJ, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, DeLuca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovrečić L, Palanda… See abstract for full author list ➔ Brownstein CA, et al. Among authors: kural d. Genome Biol. 2014 Mar 25;15(3):R53. doi: 10.1186/gb-2014-15-3-r53. Genome Biol. 2014. PMID: 24667040 Free PMC article.
Mapping copy number variation by population-scale genome sequencing.
Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO; 1000 Genomes Project. Mills RE, et al. Among authors: kural d. Nature. 2011 Feb 3;470(7332):59-65. doi: 10.1038/nature09708. Nature. 2011. PMID: 21293372 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
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.
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.
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.
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