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Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato.
Alonge M, Wang X, Benoit M, Soyk S, Pereira L, Zhang L, Suresh H, Ramakrishnan S, Maumus F, Ciren D, Levy Y, Harel TH, Shalev-Schlosser G, Amsellem Z, Razifard H, Caicedo AL, Tieman DM, Klee H, Kirsche M, Aganezov S, Ranallo-Benavidez TR, Lemmon ZH, Kim J, Robitaille G, Kramer M, Goodwin S, McCombie WR, Hutton S, Van Eck J, Gillis J, Eshed Y, Sedlazeck FJ, van der Knaap E, Schatz MC, Lippman ZB. Alonge M, et al. Among authors: ramakrishnan s. Cell. 2020 Jul 9;182(1):145-161.e23. doi: 10.1016/j.cell.2020.05.021. Epub 2020 Jun 17. Cell. 2020. PMID: 32553272 Free PMC article.
The bracteatus pineapple genome and domestication of clonally propagated crops.
Chen LY, VanBuren R, Paris M, Zhou H, Zhang X, Wai CM, Yan H, Chen S, Alonge M, Ramakrishnan S, Liao Z, Liu J, Lin J, Yue J, Fatima M, Lin Z, Zhang J, Huang L, Wang H, Hwa TY, Kao SM, Choi JY, Sharma A, Song J, Wang L, Yim WC, Cushman JC, Paull RE, Matsumoto T, Qin Y, Wu Q, Wang J, Yu Q, Wu J, Zhang S, Boches P, Tung CW, Wang ML, Coppens d'Eeckenbrugge G, Sanewski GM, Purugganan MD, Schatz MC, Bennetzen JL, Lexer C, Ming R. Chen LY, et al. Among authors: ramakrishnan s. Nat Genet. 2019 Oct;51(10):1549-1558. doi: 10.1038/s41588-019-0506-8. Epub 2019 Sep 30. Nat Genet. 2019. PMID: 31570895
RaGOO: fast and accurate reference-guided scaffolding of draft genomes.
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC. Alonge M, et al. Among authors: ramakrishnan s. Genome Biol. 2019 Oct 28;20(1):224. doi: 10.1186/s13059-019-1829-6. Genome Biol. 2019. PMID: 31661016 Free PMC article.
Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area.
Thielen PM, Wohl S, Mehoke T, Ramakrishnan S, Kirsche M, Falade-Nwulia O, Trovão NS, Ernlund A, Howser C, Sadowski N, Morris CP, Hopkins M, Schwartz M, Fan Y, Gniazdowski V, Lessler J, Sauer L, Schatz MC, Evans JD, Ray SC, Timp W, Mostafa HH. Thielen PM, et al. Among authors: ramakrishnan s. JCI Insight. 2021 Mar 22;6(6):e144350. doi: 10.1172/jci.insight.144350. JCI Insight. 2021. PMID: 33749660 Free PMC article.
A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor.
Vornhagen J, Bassis CM, Ramakrishnan S, Hein R, Mason S, Bergman Y, Sunshine N, Fan Y, Holmes CL, Timp W, Schatz MC, Young VB, Simner PJ, Bachman MA. Vornhagen J, et al. Among authors: ramakrishnan s. PLoS Pathog. 2021 Apr 30;17(4):e1009537. doi: 10.1371/journal.ppat.1009537. eCollection 2021 Apr. PLoS Pathog. 2021. PMID: 33930099 Free PMC article.
Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes.
Hunt M, Letcher B, Malone KM, Nguyen G, Hall MB, Colquhoun RM, Lima L, Schatz MC, Ramakrishnan S; CRyPTIC consortium; Iqbal Z. Hunt M, et al. Among authors: ramakrishnan s. Genome Biol. 2022 Jul 5;23(1):147. doi: 10.1186/s13059-022-02714-x. Genome Biol. 2022. PMID: 35791022 Free PMC article.
Multicentre genetic diversity study of carbapenem-resistant Enterobacterales: predominance of untypeable pUVA-like blaKPC bearing plasmids.
Simner PJ, Bergman Y, Fan Y, Jacobs EB, Ramakrishnan S, Lu J, Lewis S, Hanlon A, Tamma PD, Schatz MC, Timp W, Carroll KC. Simner PJ, et al. Among authors: ramakrishnan s. JAC Antimicrob Resist. 2023 May 26;5(3):dlad061. doi: 10.1093/jacamr/dlad061. eCollection 2023 Jun. JAC Antimicrob Resist. 2023. PMID: 37251303 Free PMC article.
Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region.
Thielen PM, Wohl S, Mehoke T, Ramakrishnan S, Kirsche M, Falade-Nwulia O, Trovão NS, Ernlund A, Howser C, Sadowski N, Morris P, Hopkins M, Schwartz M, Fan Y, Gniazdowski V, Lessler J, Sauer L, Schatz MC, Evans JD, Ray SC, Timp W, Mostafa HH. Thielen PM, et al. Among authors: ramakrishnan s. medRxiv [Preprint]. 2020 Aug 23:2020.08.13.20174136. doi: 10.1101/2020.08.13.20174136. medRxiv. 2020. PMID: 32817965 Free PMC article. Updated. Preprint.
1,475 results