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HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi.
Nuccio EE, Blazewicz SJ, Lafler M, Campbell AN, Kakouridis A, Kimbrel JA, Wollard J, Vyshenska D, Riley R, Tomatsu A, Hestrin R, Malmstrom RR, Firestone M, Pett-Ridge J. Nuccio EE, et al. Among authors: malmstrom rr. Microbiome. 2022 Nov 25;10(1):199. doi: 10.1186/s40168-022-01391-z. Microbiome. 2022. PMID: 36434737 Free PMC article.
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.
Niche differentiation is spatially and temporally regulated in the rhizosphere.
Nuccio EE, Starr E, Karaoz U, Brodie EL, Zhou J, Tringe SG, Malmstrom RR, Woyke T, Banfield JF, Firestone MK, Pett-Ridge J. Nuccio EE, et al. Among authors: malmstrom rr. ISME J. 2020 Apr;14(4):999-1014. doi: 10.1038/s41396-019-0582-x. Epub 2020 Jan 17. ISME J. 2020. PMID: 31953507 Free PMC article.
A pipeline for targeted metagenomics of environmental bacteria.
Grieb A, Bowers RM, Oggerin M, Goudeau D, Lee J, Malmstrom RR, Woyke T, Fuchs BM. Grieb A, et al. Among authors: malmstrom rr. Microbiome. 2020 Feb 15;8(1):21. doi: 10.1186/s40168-020-0790-7. Microbiome. 2020. PMID: 32061258 Free PMC article.
A standardized quantitative analysis strategy for stable isotope probing metagenomics.
Vyshenska D, Sampara P, Singh K, Tomatsu A, Kauffman WB, Nuccio EE, Blazewicz SJ, Pett-Ridge J, Louie KB, Varghese N, Kellom M, Clum A, Riley R, Roux S, Eloe-Fadrosh EA, Ziels RM, Malmstrom RR. Vyshenska D, et al. Among authors: malmstrom rr. mSystems. 2023 Aug 31;8(4):e0128022. doi: 10.1128/msystems.01280-22. Epub 2023 Jun 28. mSystems. 2023. PMID: 37377419 Free PMC article.
Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis.
Jarett JK, Nayfach S, Podar M, Inskeep W, Ivanova NN, Munson-McGee J, Schulz F, Young M, Jay ZJ, Beam JP, Kyrpides NC, Malmstrom RR, Stepanauskas R, Woyke T. Jarett JK, et al. Among authors: malmstrom rr. Microbiome. 2018 Sep 17;6(1):161. doi: 10.1186/s40168-018-0539-8. Microbiome. 2018. PMID: 30223889 Free PMC article.
Probing the active fraction of soil microbiomes using BONCAT-FACS.
Couradeau E, Sasse J, Goudeau D, Nath N, Hazen TC, Bowen BP, Chakraborty R, Malmstrom RR, Northen TR. Couradeau E, et al. Among authors: malmstrom rr. Nat Commun. 2019 Jun 24;10(1):2770. doi: 10.1038/s41467-019-10542-0. Nat Commun. 2019. PMID: 31235780 Free PMC article.
Thousands of small, novel genes predicted in global phage genomes.
Fremin BJ, Bhatt AS, Kyrpides NC; Global Phage Small Open Reading Frame (GP-SmORF) Consortium. Fremin BJ, et al. Cell Rep. 2022 Jun 21;39(12):110984. doi: 10.1016/j.celrep.2022.110984. Cell Rep. 2022. PMID: 35732113 Free PMC article.
65 results