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mrsFAST: a cache-oblivious algorithm for short-read mapping.
Hach F, Hormozdiari F, Alkan C, Hormozdiari F, Birol I, Eichler EE, Sahinalp SC. Hach F, et al. Among authors: hormozdiari f. Nat Methods. 2010 Aug;7(8):576-7. doi: 10.1038/nmeth0810-576. Nat Methods. 2010. PMID: 20676076 Free PMC article. No abstract available.
Sensitive and fast mapping of di-base encoded reads.
Hormozdiari F, Hach F, Sahinalp SC, Eichler EE, Alkan C. Hormozdiari F, et al. Bioinformatics. 2011 Jul 15;27(14):1915-21. doi: 10.1093/bioinformatics/btr303. Epub 2011 May 17. Bioinformatics. 2011. PMID: 21586516 Free PMC article.
Accelerating read mapping with FastHASH.
Xin H, Lee D, Hormozdiari F, Yedkar S, Mutlu O, Alkan C. Xin H, et al. Among authors: hormozdiari f. BMC Genomics. 2013;14 Suppl 1(Suppl 1):S13. doi: 10.1186/1471-2164-14-S1-S13. Epub 2013 Jan 21. BMC Genomics. 2013. PMID: 23369189 Free PMC article.
Fast and accurate mapping of Complete Genomics reads.
Lee D, Hormozdiari F, Xin H, Hach F, Mutlu O, Alkan C. Lee D, et al. Among authors: hormozdiari f. Methods. 2015 Jun;79-80:3-10. doi: 10.1016/j.ymeth.2014.10.012. Epub 2014 Oct 22. Methods. 2015. PMID: 25461772 Free PMC article.
Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs.
Freedman AH, Schweizer RM, Ortega-Del Vecchyo D, Han E, Davis BW, Gronau I, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Ramirez O, Hormozdiari F, Alkan C, Vilà C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Marques-Bonet T, Ostrander EA, Wayne RK, Novembre J. Freedman AH, et al. Among authors: hormozdiari f. PLoS Genet. 2016 Mar 4;12(3):e1005851. doi: 10.1371/journal.pgen.1005851. eCollection 2016 Mar. PLoS Genet. 2016. PMID: 26943675 Free PMC article.
Genome sequencing highlights the dynamic early history of dogs.
Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Beale H, Ramirez O, Hormozdiari F, Alkan C, Vilà C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Wilton A, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Ostrander EA, Marques-Bonet T, Wayne RK, Novembre J. Freedman AH, et al. Among authors: hormozdiari f. PLoS Genet. 2014 Jan;10(1):e1004016. doi: 10.1371/journal.pgen.1004016. Epub 2014 Jan 16. PLoS Genet. 2014. PMID: 24453982 Free PMC article.
The impact of rare variation on gene expression across tissues.
Li X, Kim Y, Tsang EK, Davis JR, Damani FN, Chiang C, Hess GT, Zappala Z, Strober BJ, Scott AJ, Li A, Ganna A, Bassik MC, Merker JD; GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site—NDRI; Biospecimen Collection Source Site—RPCI; Biospecimen Core Resource—VARI; Brain Bank Repository—University of Miami Brain Endowment Bank; Leidos Biomedical—Project Management; ELSI Study; Genome Browser Data Integration &Visualization—EBI; Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz; Hall IM, Battle A, Montgomery SB. Li X, et al. Nature. 2017 Oct 11;550(7675):239-243. doi: 10.1038/nature24267. Nature. 2017. PMID: 29022581 Free PMC article.
Landscape of X chromosome inactivation across human tissues.
Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Cummings BB, Castel SE, Karczewski KJ, Aguet F, Byrnes A; GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site—NDRI; Biospecimen Collection Source Site—RPCI; Biospecimen Core Resource—VARI; Brain Bank Repository—University of Miami Brain Endowment Bank; Leidos Biomedical—Project Management; ELSI Study; Genome Browser Data Integration &Visualization—EBI; Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz; Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG. Tukiainen T, et al. Nature. 2017 Oct 11;550(7675):244-248. doi: 10.1038/nature24265. Nature. 2017. PMID: 29022598 Free PMC article.
157 results