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Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs.
Eloe-Fadrosh EA, Paez-Espino D, Jarett J, Dunfield PF, Hedlund BP, Dekas AE, Grasby SE, Brady AL, Dong H, Briggs BR, Li WJ, Goudeau D, Malmstrom R, Pati A, Pett-Ridge J, Rubin EM, Woyke T, Kyrpides NC, Ivanova NN. Eloe-Fadrosh EA, et al. Nat Commun. 2016 Jan 27;7:10476. doi: 10.1038/ncomms10476. Nat Commun. 2016. PMID: 26814032 Free PMC article.
A functional microbiome catalog crowdsourced from North American rivers.
Borton MA, McGivern BB, Willi KR, Woodcroft BJ, Mosier AC, Singleton DM, Bambakidis T, Pelly A, Liu F, Edirisinghe JN, Faria JP, Leleiwi I, Daly RA, Goldman AE, Wilkins MJ, Hall EK, Pennacchio C, Roux S, Eloe-Fadrosh EA, Good SP, Sullivan MB, Henry CS, Wood-Charlson EM, Ross MRV, Miller CS, Crump BC, Stegen JC, Wrighton KC. Borton MA, et al. Among authors: eloe fadrosh ea. bioRxiv [Preprint]. 2023 Jul 26:2023.07.22.550117. doi: 10.1101/2023.07.22.550117. bioRxiv. 2023. PMID: 37502915 Free PMC article. Preprint.
Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale.
Hu B, Canon S, Eloe-Fadrosh EA, Anubhav, Babinski M, Corilo Y, Davenport K, Duncan WD, Fagnan K, Flynn M, Foster B, Hays D, Huntemann M, Jackson EKP, Kelliher J, Li PE, Lo CC, Mans D, McCue LA, Mouncey N, Mungall CJ, Piehowski PD, Purvine SO, Smith M, Varghese NJ, Winston D, Xu Y, Chain PSG. Hu B, et al. Front Bioinform. 2022 Jan 17;1:826370. doi: 10.3389/fbinf.2021.826370. eCollection 2021. Front Bioinform. 2022. PMID: 36303775 Free PMC article. Review.
Uncovering Earth's virome.
Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, Rubin E, Ivanova NN, Kyrpides NC. Paez-Espino D, et al. Nature. 2016 Aug 25;536(7617):425-30. doi: 10.1038/nature19094. Epub 2016 Aug 17. Nature. 2016. PMID: 27533034
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.
Mukherjee S, Seshadri R, Varghese NJ, Eloe-Fadrosh EA, Meier-Kolthoff JP, Göker M, Coates RC, Hadjithomas M, Pavlopoulos GA, Paez-Espino D, Yoshikuni Y, Visel A, Whitman WB, Garrity GM, Eisen JA, Hugenholtz P, Pati A, Ivanova NN, Woyke T, Klenk HP, Kyrpides NC. Mukherjee S, et al. Nat Biotechnol. 2017 Jul;35(7):676-683. doi: 10.1038/nbt.3886. Epub 2017 Jun 12. Nat Biotechnol. 2017. PMID: 28604660
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. Nat Biotechnol. 2017 Aug 8;35(8):725-731. doi: 10.1038/nbt.3893. Nat Biotechnol. 2017. PMID: 28787424 Free PMC article.
Towards a balanced view of the bacterial tree of life.
Schulz F, Eloe-Fadrosh EA, Bowers RM, Jarett J, Nielsen T, Ivanova NN, Kyrpides NC, Woyke T. Schulz F, et al. Microbiome. 2017 Oct 17;5(1):140. doi: 10.1186/s40168-017-0360-9. Microbiome. 2017. PMID: 29041958 Free PMC article.
102 results