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A single-cell genomics pipeline for environmental microbial eukaryotes.
Ciobanu D, Clum A, Ahrendt S, Andreopoulos WB, Salamov A, Chan S, Quandt CA, Foster B, Meier-Kolthoff JP, Tang YT, Schwientek P, Benny GL, Smith ME, Bauer D, Deshpande S, Barry K, Copeland A, Singer SW, Woyke T, Grigoriev IV, James TY, Cheng JF. Ciobanu D, et al. Among authors: singer sw. iScience. 2021 Mar 10;24(4):102290. doi: 10.1016/j.isci.2021.102290. eCollection 2021 Apr 23. iScience. 2021. PMID: 33870123 Free PMC article.
Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage.
Mosier AC, Miller CS, Frischkorn KR, Ohm RA, Li Z, LaButti K, Lapidus A, Lipzen A, Chen C, Johnson J, Lindquist EA, Pan C, Hettich RL, Grigoriev IV, Singer SW, Banfield JF. Mosier AC, et al. Among authors: singer sw. Front Microbiol. 2016 Mar 3;7:238. doi: 10.3389/fmicb.2016.00238. eCollection 2016. Front Microbiol. 2016. PMID: 26973616 Free PMC article.
Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists.
Martino E, Morin E, Grelet GA, Kuo A, Kohler A, Daghino S, Barry KW, Cichocki N, Clum A, Dockter RB, Hainaut M, Kuo RC, LaButti K, Lindahl BD, Lindquist EA, Lipzen A, Khouja HR, Magnuson J, Murat C, Ohm RA, Singer SW, Spatafora JW, Wang M, Veneault-Fourrey C, Henrissat B, Grigoriev IV, Martin FM, Perotto S. Martino E, et al. Among authors: singer sw. New Phytol. 2018 Feb;217(3):1213-1229. doi: 10.1111/nph.14974. Epub 2018 Jan 7. New Phytol. 2018. PMID: 29315638 Free article.
Lignin deconstruction by anaerobic fungi.
Lankiewicz TS, Choudhary H, Gao Y, Amer B, Lillington SP, Leggieri PA, Brown JL, Swift CL, Lipzen A, Na H, Amirebrahimi M, Theodorou MK, Baidoo EEK, Barry K, Grigoriev IV, Timokhin VI, Gladden J, Singh S, Mortimer JC, Ralph J, Simmons BA, Singer SW, O'Malley MA. Lankiewicz TS, et al. Among authors: singer sw. Nat Microbiol. 2023 Apr;8(4):596-610. doi: 10.1038/s41564-023-01336-8. Epub 2023 Mar 9. Nat Microbiol. 2023. PMID: 36894634 Free PMC article.
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: singer sw. 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.
Expansion of the global RNA virome reveals diverse clades of bacteriophages.
Neri U, Wolf YI, Roux S, Camargo AP, Lee B, Kazlauskas D, Chen IM, Ivanova N, Zeigler Allen L, Paez-Espino D, Bryant DA, Bhaya D; RNA Virus Discovery Consortium; Krupovic M, Dolja VV, Kyrpides NC, Koonin EV, Gophna U. Neri U, et al. Cell. 2022 Oct 13;185(21):4023-4037.e18. doi: 10.1016/j.cell.2022.08.023. Epub 2022 Sep 28. Cell. 2022. PMID: 36174579 Free article.
105 results