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Items: 35

1.

A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators.

Needham DM, Yoshizawa S, Hosaka T, Poirier C, Choi CJ, Hehenberger E, Irwin NAT, Wilken S, Yung CM, Bachy C, Kurihara R, Nakajima Y, Kojima K, Kimura-Someya T, Leonard G, Malmstrom RR, Mende DR, Olson DK, Sudo Y, Sudek S, Richards TA, DeLong EF, Keeling PJ, Santoro AE, Shirouzu M, Iwasaki W, Worden AZ.

Proc Natl Acad Sci U S A. 2019 Oct 8;116(41):20574-20583. doi: 10.1073/pnas.1907517116. Epub 2019 Sep 23.

2.

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.

Nat Commun. 2019 Jun 24;10(1):2770. doi: 10.1038/s41467-019-10542-0.

3.

Advancing Genome-Resolved Metagenomics beyond the Shotgun.

Malmstrom RR, Eloe-Fadrosh EA.

mSystems. 2019 May 14;4(3). pii: e00118-19. doi: 10.1128/mSystems.00118-19.

4.

Optimizing de novo genome assembly from PCR-amplified metagenomes.

Roux S, Trubl G, Goudeau D, Nath N, Couradeau E, Ahlgren NA, Zhan Y, Marsan D, Chen F, Fuhrman JA, Northen TR, Sullivan MB, Rich VI, Malmstrom RR, Eloe-Fadrosh EA.

PeerJ. 2019 May 9;7:e6902. doi: 10.7717/peerj.6902. eCollection 2019.

5.

Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism.

Price MN, Ray J, Iavarone AT, Carlson HK, Ryan EM, Malmstrom RR, Arkin AP, Deutschbauer AM.

mSystems. 2019 Feb 5;4(1). pii: e00297-18. doi: 10.1128/mSystems.00297-18. eCollection 2019 Jan-Feb.

6.

Freshwater carbon and nutrient cycles revealed through reconstructed population genomes.

Linz AM, He S, Stevens SLR, Anantharaman K, Rohwer RR, Malmstrom RR, Bertilsson S, McMahon KD.

PeerJ. 2018 Dec 10;6:e6075. doi: 10.7717/peerj.6075. eCollection 2018.

7.

Minimum Information about an Uncultivated Virus Genome (MIUViG).

Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA.

Nat Biotechnol. 2019 Jan;37(1):29-37. doi: 10.1038/nbt.4306. Epub 2018 Dec 17.

PMID:
30556814
8.

Hidden diversity of soil giant viruses.

Schulz F, Alteio L, Goudeau D, Ryan EM, Yu FB, Malmstrom RR, Blanchard J, Woyke T.

Nat Commun. 2018 Nov 19;9(1):4881. doi: 10.1038/s41467-018-07335-2.

9.

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.

Microbiome. 2018 Sep 17;6(1):161. doi: 10.1186/s40168-018-0539-8.

10.

Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria.

Ganesh S, Bertagnolli AD, Bristow LA, Padilla CC, Blackwood N, Aldunate M, Bourbonnais A, Altabet MA, Malmstrom RR, Woyke T, Ulloa O, Konstantinidis KT, Thamdrup B, Stewart FJ.

ISME J. 2018 Nov;12(11):2706-2722. doi: 10.1038/s41396-018-0223-9. Epub 2018 Jul 10.

11.

Corrigendum: 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.

Nat Biotechnol. 2018 Jul 6;36(7):660. doi: 10.1038/nbt0718-660a. No abstract available.

PMID:
29979671
12.

Corrigendum: 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.

Nat Biotechnol. 2018 Feb 6;36(2):196. doi: 10.1038/nbt0218-196a. No abstract available.

13.

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface.

Probst AJ, Ladd B, Jarett JK, Geller-McGrath DE, Sieber CMK, Emerson JB, Anantharaman K, Thomas BC, Malmstrom RR, Stieglmeier M, Klingl A, Woyke T, Ryan MC, Banfield JF.

Nat Microbiol. 2018 Mar;3(3):328-336. doi: 10.1038/s41564-017-0098-y. Epub 2018 Jan 29.

14.

Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations.

Garcia SL, Stevens SLR, Crary B, Martinez-Garcia M, Stepanauskas R, Woyke T, Tringe SG, Andersson SGE, Bertilsson S, Malmstrom RR, McMahon KD.

ISME J. 2018 Mar;12(3):742-755. doi: 10.1038/s41396-017-0001-0. Epub 2017 Dec 8.

15.

Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics.

Roux S, Chan LK, Egan R, Malmstrom RR, McMahon KD, Sullivan MB.

Nat Commun. 2017 Oct 11;8(1):858. doi: 10.1038/s41467-017-01086-2.

16.

Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes.

He S, Stevens SLR, Chan LK, Bertilsson S, Glavina Del Rio T, Tringe SG, Malmstrom RR, McMahon KD.

mSphere. 2017 Sep 27;2(5). pii: e00277-17. doi: 10.1128/mSphere.00277-17. eCollection 2017 Sep-Oct.

17.

Genome-wide identification of bacterial plant colonization genes.

Cole BJ, Feltcher ME, Waters RJ, Wetmore KM, Mucyn TS, Ryan EM, Wang G, Ul-Hasan S, McDonald M, Yoshikuni Y, Malmstrom RR, Deutschbauer AM, Dangl JL, Visel A.

PLoS Biol. 2017 Sep 22;15(9):e2002860. doi: 10.1371/journal.pbio.2002860. eCollection 2017 Sep.

18.

Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI.

Hamilton JJ, Garcia SL, Brown BS, Oyserman BO, Moya-Flores F, Bertilsson S, Malmstrom RR, Forest KT, McMahon KD.

mSystems. 2017 Aug 29;2(4). pii: e00091-17. doi: 10.1128/mSystems.00091-17. eCollection 2017 Jul-Aug.

19.

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.

Nat Biotechnol. 2017 Aug 8;35(8):725-731. doi: 10.1038/nbt.3893. Erratum in: Nat Biotechnol. 2018 Feb 6;36(2):196. Nat Biotechnol. 2018 Jul 6;36(7):660.

20.

SAR11 bacteria linked to ocean anoxia and nitrogen loss.

Tsementzi D, Wu J, Deutsch S, Nath S, Rodriguez-R LM, Burns AS, Ranjan P, Sarode N, Malmstrom RR, Padilla CC, Stone BK, Bristow LA, Larsen M, Glass JB, Thamdrup B, Woyke T, Konstantinidis KT, Stewart FJ.

Nature. 2016 Aug 11;536(7615):179-83. Epub 2016 Aug 3.

21.

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal-bacterial consortia.

Hatzenpichler R, Connon SA, Goudeau D, Malmstrom RR, Woyke T, Orphan VJ.

Proc Natl Acad Sci U S A. 2016 Jul 12;113(28):E4069-78. doi: 10.1073/pnas.1603757113. Epub 2016 Jun 28.

22.

Large-scale maps of variable infection efficiencies in aquatic Bacteroidetes phage-host model systems.

Holmfeldt K, Solonenko N, Howard-Varona C, Moreno M, Malmstrom RR, Blow MJ, Sullivan MB.

Environ Microbiol. 2016 Nov;18(11):3949-3961. doi: 10.1111/1462-2920.13392. Epub 2016 Jun 27.

23.

The Epigenomic Landscape of Prokaryotes.

Blow MJ, Clark TA, Daum CG, Deutschbauer AM, Fomenkov A, Fries R, Froula J, Kang DD, Malmstrom RR, Morgan RD, Posfai J, Singh K, Visel A, Wetmore K, Zhao Z, Rubin EM, Korlach J, Pennacchio LA, Roberts RJ.

PLoS Genet. 2016 Feb 12;12(2):e1005854. doi: 10.1371/journal.pgen.1005854. eCollection 2016 Feb. Erratum in: PLoS Genet. 2016 May;12(5):e1006064.

24.

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations.

Bendall ML, Stevens SL, Chan LK, Malfatti S, Schwientek P, Tremblay J, Schackwitz W, Martin J, Pati A, Bushnell B, Froula J, Kang D, Tringe SG, Bertilsson S, Moran MA, Shade A, Newton RJ, McMahon KD, Malmstrom RR.

ISME J. 2016 Jul;10(7):1589-601. doi: 10.1038/ismej.2015.241. Epub 2016 Jan 8.

25.

Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk.

O'Connor RM, Fung JM, Sharp KH, Benner JS, McClung C, Cushing S, Lamkin ER, Fomenkov AI, Henrissat B, Londer YY, Scholz MB, Posfai J, Malfatti S, Tringe SG, Woyke T, Malmstrom RR, Coleman-Derr D, Altamia MA, Dedrick S, Kaluziak ST, Haygood MG, Distel DL.

Proc Natl Acad Sci U S A. 2014 Nov 25;111(47):E5096-104. doi: 10.1073/pnas.1413110111. Epub 2014 Nov 10.

26.

Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus.

Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, Malmstrom RR, Stocker R, Follows MJ, Stepanauskas R, Chisholm SW.

Science. 2014 Apr 25;344(6182):416-20. doi: 10.1126/science.1248575.

27.

Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1.

Bendall ML, Luong K, Wetmore KM, Blow M, Korlach J, Deutschbauer A, Malmstrom RR.

J Bacteriol. 2013 Nov;195(21):4966-74. doi: 10.1128/JB.00935-13. Epub 2013 Aug 30.

28.

Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis.

Malmstrom RR, Rodrigue S, Huang KH, Kelly L, Kern SE, Thompson A, Roggensack S, Berube PM, Henn MR, Chisholm SW.

ISME J. 2013 Jan;7(1):184-98. doi: 10.1038/ismej.2012.89. Epub 2012 Aug 16.

29.

Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea.

McCarren J, Becker JW, Repeta DJ, Shi Y, Young CR, Malmstrom RR, Chisholm SW, DeLong EF.

Proc Natl Acad Sci U S A. 2010 Sep 21;107(38):16420-7. doi: 10.1073/pnas.1010732107. Epub 2010 Aug 31.

30.

Unlocking short read sequencing for metagenomics.

Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, Malmstrom RR, Alm EJ, Chisholm SW.

PLoS One. 2010 Jul 28;5(7):e11840. doi: 10.1371/journal.pone.0011840.

31.

Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans.

Malmstrom RR, Coe A, Kettler GC, Martiny AC, Frias-Lopez J, Zinser ER, Chisholm SW.

ISME J. 2010 Oct;4(10):1252-64. doi: 10.1038/ismej.2010.60. Epub 2010 May 13.

PMID:
20463762
32.

Whole genome amplification and de novo assembly of single bacterial cells.

Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW.

PLoS One. 2009 Sep 2;4(9):e6864. doi: 10.1371/journal.pone.0006864.

33.

Assimilation of polysaccharides and glucose by major bacterial groups in the Delaware Estuary.

Elifantz H, Malmstrom RR, Cottrell MT, Kirchman DL.

Appl Environ Microbiol. 2005 Dec;71(12):7799-805.

34.

Biomass production and assimilation of dissolved organic matter by SAR11 bacteria in the Northwest Atlantic Ocean.

Malmstrom RR, Cottrell MT, Elifantz H, Kirchman DL.

Appl Environ Microbiol. 2005 Jun;71(6):2979-86.

35.

Contribution of SAR11 bacteria to dissolved dimethylsulfoniopropionate and amino acid uptake in the North Atlantic ocean.

Malmstrom RR, Kiene RP, Cottrell MT, Kirchman DL.

Appl Environ Microbiol. 2004 Jul;70(7):4129-35.

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