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Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.
Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC. Sczyrba A, et al. Among authors: rattei t. Nat Methods. 2017 Nov;14(11):1063-1071. doi: 10.1038/nmeth.4458. Epub 2017 Oct 2. Nat Methods. 2017. PMID: 28967888 Free PMC article.
The dynamic genome of Hydra.
Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T, Weinmaier T, Rattei T, Balasubramanian PG, Borman J, Busam D, Disbennett K, Pfannkoch C, Sumin N, Sutton GG, Viswanathan LD, Walenz B, Goodstein DM, Hellsten U, Kawashima T, Prochnik SE, Putnam NH, Shu S, Blumberg B, Dana CE, Gee L, Kibler DF, Law L, Lindgens D, Martinez DE, Peng J, Wigge PA, Bertulat B, Guder C, Nakamura Y, Ozbek S, Watanabe H, Khalturin K, Hemmrich G, Franke A, Augustin R, Fraune S, Hayakawa E, Hayakawa S, Hirose M, Hwang JS, Ikeo K, Nishimiya-Fujisawa C, Ogura A, Takahashi T, Steinmetz PR, Zhang X, Aufschnaiter R, Eder MK, Gorny AK, Salvenmoser W, Heimberg AM, Wheeler BM, Peterson KJ, Böttger A, Tischler P, Wolf A, Gojobori T, Remington KA, Strausberg RL, Venter JC, Technau U, Hobmayer B, Bosch TC, Holstein TW, Fujisawa T, Bode HR, David CN, Rokhsar DS, Steele RE. Chapman JA, et al. Among authors: rattei t. Nature. 2010 Mar 25;464(7288):592-6. doi: 10.1038/nature08830. Epub 2010 Mar 14. Nature. 2010. PMID: 20228792 Free PMC article.
Complete genome sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and Desulfosporosinus acidiphilus DSM22704T.
Pester M, Brambilla E, Alazard D, Rattei T, Weinmaier T, Han J, Lucas S, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Peters L, Ovchinnikova G, Teshima H, Detter JC, Han CS, Tapia R, Land ML, Hauser L, Kyrpides NC, Ivanova NN, Pagani I, Huntmann M, Wei CL, Davenport KW, Daligault H, Chain PS, Chen A, Mavromatis K, Markowitz V, Szeto E, Mikhailova N, Pati A, Wagner M, Woyke T, Ollivier B, Klenk HP, Spring S, Loy A. Pester M, et al. Among authors: rattei t. J Bacteriol. 2012 Nov;194(22):6300-1. doi: 10.1128/JB.01392-12. J Bacteriol. 2012. PMID: 23105050 Free PMC article.
Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies.
Güllert S, Fischer MA, Turaev D, Noebauer B, Ilmberger N, Wemheuer B, Alawi M, Rattei T, Daniel R, Schmitz RA, Grundhoff A, Streit WR. Güllert S, et al. Among authors: rattei t. Biotechnol Biofuels. 2016 Jun 7;9:121. doi: 10.1186/s13068-016-0534-x. eCollection 2016. Biotechnol Biofuels. 2016. PMID: 27279900 Free PMC article.
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium; Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Bowers RM, et al. Among authors: rattei t. Nat Biotechnol. 2017 Aug 8;35(8):725-731. doi: 10.1038/nbt.3893. Nat Biotechnol. 2017. PMID: 28787424 Free PMC article.
Reef invertebrate viromics: diversity, host specificity and functional capacity.
Laffy PW, Wood-Charlson EM, Turaev D, Jutz S, Pascelli C, Botté ES, Bell SC, Peirce TE, Weynberg KD, van Oppen MJH, Rattei T, Webster NS. Laffy PW, et al. Among authors: rattei t. Environ Microbiol. 2018 Jun;20(6):2125-2141. doi: 10.1111/1462-2920.14110. Epub 2018 Apr 30. Environ Microbiol. 2018. PMID: 29575552
179 results