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DOE JGI Metagenome Workflow.
Clum A, Huntemann M, Bushnell B, Foster B, Foster B, Roux S, Hajek PP, Varghese N, Mukherjee S, Reddy TBK, Daum C, Yoshinaga Y, O'Malley R, Seshadri R, Kyrpides NC, Eloe-Fadrosh EA, Chen IA, Copeland A, Ivanova NN. Clum A, et al. mSystems. 2021 May 18;6(3):e00804-20. doi: 10.1128/mSystems.00804-20. mSystems. 2021. PMID: 34006627 Free PMC article.
Phased diploid genome assembly with single-molecule real-time sequencing.
Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O'Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer GR, Delledonne M, Luo C, Ecker JR, Cantu D, Rank DR, Schatz MC. Chin CS, et al. Nat Methods. 2016 Dec;13(12):1050-1054. doi: 10.1038/nmeth.4035. Epub 2016 Oct 17. Nat Methods. 2016. PMID: 27749838 Free PMC article.
Genome Sequencing.
Yoshinaga Y, Daum C, He G, O'Malley R. Yoshinaga Y, et al. Methods Mol Biol. 2018;1775:37-52. doi: 10.1007/978-1-4939-7804-5_4. Methods Mol Biol. 2018. PMID: 29876807
Draft Genome Sequences of New Isolates and the Known Species of the Family Microbacteriaceae Associated with Plants.
Vasilenko OV, Starodumova IP, Dorofeeva LV, Tarlachkov SV, Prisyazhnaya NV, Chizhov VN, Subbotin SA, Huntemann M, Clum A, Duffy K, Pillay M, Palaniappan K, Varghese N, Chen IA, Stamatis D, Reddy TBK, O'Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Whitman WB, Evtushenko LI. Vasilenko OV, et al. Microbiol Resour Announc. 2018 Sep 20;7(11):e01051-18. doi: 10.1128/MRA.01051-18. eCollection 2018 Sep. Microbiol Resour Announc. 2018. PMID: 30533634 Free PMC article.
Complete Genome Sequence of Serratia quinivorans Strain 124R, a Facultative Anaerobe Isolated on Organosolv Lignin as a Sole Carbon Source.
Chaput G, Ford J, DeDiego L, Narayanan A, Tam WY, Whalen M, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Chen IM, Stamatis D, Reddy TBK, O'Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Glavina Del Rio T, DeAngelis K. Chaput G, et al. Microbiol Resour Announc. 2019 May 2;8(18):e00409-19. doi: 10.1128/MRA.00409-19. Microbiol Resour Announc. 2019. PMID: 31048387 Free PMC article.
Draft Genome Sequence of Yokenella regensburgei Strain WCD67, Isolated from the Boxelder Bug.
Meyers DJ, Leigh BA, Huntemann M, Clum A, Ritter S, Palaniappan K, Chen IM, Stamatis D, Reddy TBK, O'Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Whitman WB. Meyers DJ, et al. Microbiol Resour Announc. 2020 Apr 9;9(15):e00104-20. doi: 10.1128/MRA.00104-20. Microbiol Resour Announc. 2020. PMID: 32273354 Free PMC article.
Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan.
Thomas SC, Payne D, Tamadonfar KO, Seymour CO, Jiao JY, Murugapiran SK, Lai D, Lau R, Bowen BP, Silva LP, Louie KB, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Chen IM, Stamatis D, Reddy TBK, O'Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Eloe-Fadrosh E, Hamilton TL, Dijkstra P, Dodsworth JA, Northen TR, Li WJ, Hedlund BP. Thomas SC, et al. Front Microbiol. 2021 May 3;12:632731. doi: 10.3389/fmicb.2021.632731. eCollection 2021. Front Microbiol. 2021. PMID: 34017316 Free PMC article.
Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading Consortium.
Chaput G, Ford J, DeDiego L, Narayanan A, Tam WY, Whalen M, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Chen IM, Stamatis D, Reddy TBK, O'Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Glavina Del Rio T, DeAngelis KM. Chaput G, et al. Microbiol Spectr. 2022 Jun 29;10(3):e0234621. doi: 10.1128/spectrum.02346-21. Epub 2022 May 17. Microbiol Spectr. 2022. PMID: 35579457 Free PMC article.
253 results