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The Sequence Alignment/Map format and SAMtools.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. Li H, et al. Among authors: wysoker a. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. Bioinformatics. 2009. PMID: 19505943 Free PMC article.
Comparative analysis of RNA sequencing methods for degraded or low-input samples.
Adiconis X, Borges-Rivera D, Satija R, DeLuca DS, Busby MA, Berlin AM, Sivachenko A, Thompson DA, Wysoker A, Fennell T, Gnirke A, Pochet N, Regev A, Levin JZ. Adiconis X, et al. Among authors: wysoker a. Nat Methods. 2013 Jul;10(7):623-9. doi: 10.1038/nmeth.2483. Epub 2013 May 19. Nat Methods. 2013. PMID: 23685885 Free PMC article.
Integrated detection and population-genetic analysis of SNPs and copy number variation.
McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, Shapero MH, de Bakker PI, Maller JB, Kirby A, Elliott AL, Parkin M, Hubbell E, Webster T, Mei R, Veitch J, Collins PJ, Handsaker R, Lincoln S, Nizzari M, Blume J, Jones KW, Rava R, Daly MJ, Gabriel SB, Altshuler D. McCarroll SA, et al. Among authors: wysoker a. Nat Genet. 2008 Oct;40(10):1166-74. doi: 10.1038/ng.238. Epub 2008 Sep 7. Nat Genet. 2008. PMID: 18776908
Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain.
Saunders A, Macosko EZ, Wysoker A, Goldman M, Krienen FM, de Rivera H, Bien E, Baum M, Bortolin L, Wang S, Goeva A, Nemesh J, Kamitaki N, Brumbaugh S, Kulp D, McCarroll SA. Saunders A, et al. Among authors: wysoker a. Cell. 2018 Aug 9;174(4):1015-1030.e16. doi: 10.1016/j.cell.2018.07.028. Cell. 2018. PMID: 30096299 Free PMC article.
Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes.
Hammond TR, Dufort C, Dissing-Olesen L, Giera S, Young A, Wysoker A, Walker AJ, Gergits F, Segel M, Nemesh J, Marsh SE, Saunders A, Macosko E, Ginhoux F, Chen J, Franklin RJM, Piao X, McCarroll SA, Stevens B. Hammond TR, et al. Among authors: wysoker a. Immunity. 2019 Jan 15;50(1):253-271.e6. doi: 10.1016/j.immuni.2018.11.004. Epub 2018 Nov 21. Immunity. 2019. PMID: 30471926 Free PMC article.
Innovations present in the primate interneuron repertoire.
Krienen FM, Goldman M, Zhang Q, C H Del Rosario R, Florio M, Machold R, Saunders A, Levandowski K, Zaniewski H, Schuman B, Wu C, Lutservitz A, Mullally CD, Reed N, Bien E, Bortolin L, Fernandez-Otero M, Lin JD, Wysoker A, Nemesh J, Kulp D, Burns M, Tkachev V, Smith R, Walsh CA, Dimidschstein J, Rudy B, S Kean L, Berretta S, Fishell G, Feng G, McCarroll SA. Krienen FM, et al. Among authors: wysoker a. Nature. 2020 Oct;586(7828):262-269. doi: 10.1038/s41586-020-2781-z. Epub 2020 Sep 30. Nature. 2020. PMID: 32999462 Free PMC article.
Author Correction: Innovations present in the primate interneuron repertoire.
Krienen FM, Goldman M, Zhang Q, Del Rosario RCH, Florio M, Machold R, Saunders A, Levandowski K, Zaniewski H, Schuman B, Wu C, Lutservitz A, Mullally CD, Reed N, Bien E, Bortolin L, Fernandez-Otero M, Lin JD, Wysoker A, Nemesh J, Kulp D, Burns M, Tkachev V, Smith R, Walsh CA, Dimidschstein J, Rudy B, Kean LS, Berretta S, Fishell G, Feng G, McCarroll SA. Krienen FM, et al. Among authors: wysoker a. Nature. 2020 Dec;588(7837):E17. doi: 10.1038/s41586-020-2874-8. Nature. 2020. PMID: 33230336
Insights into variation in meiosis from 31,228 human sperm genomes.
Bell AD, Mello CJ, Nemesh J, Brumbaugh SA, Wysoker A, McCarroll SA. Bell AD, et al. Among authors: wysoker a. Nature. 2020 Jul;583(7815):259-264. doi: 10.1038/s41586-020-2347-0. Epub 2020 Jun 3. Nature. 2020. PMID: 32494014 Free PMC article.