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Items: 1 to 20 of 156

1.

Vertical and Seasonal Patterns Control Bacterioplankton Communities at Two Horizontally Coherent Coastal Upwelling Sites off Galicia (NW Spain).

Hernando-Morales V, Varela MM, Needham DM, Cram J, Fuhrman JA, Teira E.

Microb Ecol. 2018 Apr 19. doi: 10.1007/s00248-018-1179-z. [Epub ahead of print]

PMID:
29675703
2.

Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community.

Gómez-Consarnau L, Sachdeva R, Gifford SM, Cutter LS, Fuhrman JA, Sañudo-Wilhelmy SA, Moran MA.

Environ Microbiol. 2018 Apr 16. doi: 10.1111/1462-2920.14133. [Epub ahead of print]

PMID:
29659156
3.

Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run.

Yeh YC, Needham DM, Sieradzki ET, Fuhrman JA.

mSystems. 2018 Apr 3;3(3). pii: e00023-18. doi: 10.1128/mSystems.00023-18. eCollection 2018 May-Jun.

4.

Short-term dynamics and interactions of marine protist communities during the spring-summer transition.

Berdjeb L, Parada A, Needham DM, Fuhrman JA.

ISME J. 2018 Mar 29. doi: 10.1038/s41396-018-0097-x. [Epub ahead of print]

PMID:
29599520
5.

A non-tailed twist in the viral tale.

Ignacio-Espinoza JC, Fuhrman JA.

Nature. 2018 Feb 1;554(7690):38-39. doi: 10.1038/d41586-018-00923-8. No abstract available.

PMID:
29388959
6.

A communal catalogue reveals Earth's multiscale microbial diversity.

Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R; Earth Microbiome Project Consortium.

Nature. 2017 Nov 23;551(7681):457-463. doi: 10.1038/nature24621. Epub 2017 Nov 1.

PMID:
29088705
7.

Towards enhanced and interpretable clustering/classification in integrative genomics.

Lu YY, Lv J, Fuhrman JA, Sun F.

Nucleic Acids Res. 2017 Nov 16;45(20):e169. doi: 10.1093/nar/gkx767.

8.

Author Correction: Re-examination of the relationship between marine virus and microbial cell abundances.

Wigington CH, Sonderegger D, Brussaard CPD, Buchan A, Finke JF, Fuhrman JA, Lennon JT, Middelboe M, Suttle CA, Stock C, Wilson WH, Wommack KE, Wilhelm SW, Weitz JS.

Nat Microbiol. 2017 Nov;2(11):1571. doi: 10.1038/s41564-017-0042-1.

PMID:
28974689
9.

Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor.

Parada AE, Fuhrman JA.

ISME J. 2017 Nov;11(11):2510-2525. doi: 10.1038/ismej.2017.104. Epub 2017 Jul 21.

PMID:
28731479
10.

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data.

Ren J, Ahlgren NA, Lu YY, Fuhrman JA, Sun F.

Microbiome. 2017 Jul 6;5(1):69. doi: 10.1186/s40168-017-0283-5.

11.

CAFE: aCcelerated Alignment-FrEe sequence analysis.

Lu YY, Tang K, Ren J, Fuhrman JA, Waterman MS, Sun F.

Nucleic Acids Res. 2017 Jul 3;45(W1):W554-W559. doi: 10.1093/nar/gkx351.

12.

Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems.

Ahlgren NA, Chen Y, Needham DM, Parada AE, Sachdeva R, Trinh V, Chen T, Fuhrman JA.

Environ Microbiol. 2017 Jun;19(6):2434-2452. doi: 10.1111/1462-2920.13768. Epub 2017 May 26.

PMID:
28418097
13.

Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters.

Needham DM, Sachdeva R, Fuhrman JA.

ISME J. 2017 Jul;11(7):1614-1629. doi: 10.1038/ismej.2017.29. Epub 2017 Apr 11.

PMID:
28398348
14.

Prediction of virus-host infectious association by supervised learning methods.

Zhang M, Yang L, Ren J, Ahlgren NA, Fuhrman JA, Sun F.

BMC Bioinformatics. 2017 Mar 14;18(Suppl 3):60. doi: 10.1186/s12859-017-1473-7.

15.

Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences.

Ahlgren NA, Ren J, Lu YY, Fuhrman JA, Sun F.

Nucleic Acids Res. 2017 Jan 9;45(1):39-53. doi: 10.1093/nar/gkw1002. Epub 2016 Nov 28.

16.

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys.

Walters W, Hyde ER, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, Gilbert JA, Jansson JK, Caporaso JG, Fuhrman JA, Apprill A, Knight R.

mSystems. 2015 Dec 22;1(1). pii: e00009-15. eCollection 2016 Jan-Feb.

17.

Nutrient-dense, Plant-rich Dietary Intervention Effective at Reducing Cardiovascular Disease Risk Factors for Worksites: A Pilot Study.

Sutliffe JT, Fuhrman JH, Carnot MJ, Beetham RM, Peddy MS.

Altern Ther Health Med. 2016 Sep;22(5):32-6.

PMID:
27622958
18.

Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom.

Needham DM, Fuhrman JA.

Nat Microbiol. 2016 Feb 29;1:16005. doi: 10.1038/nmicrobiol.2016.5.

PMID:
27572439
19.

Re-examination of the relationship between marine virus and microbial cell abundances.

Wigington CH, Sonderegger D, Brussaard CP, Buchan A, Finke JF, Fuhrman JA, Lennon JT, Middelboe M, Suttle CA, Stock C, Wilson WH, Wommack KE, Wilhelm SW, Weitz JS.

Nat Microbiol. 2016 Jan 25;1:15024. doi: 10.1038/nmicrobiol.2015.24.

PMID:
27572161
20.

Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes.

Bálint M, Bahram M, Eren AM, Faust K, Fuhrman JA, Lindahl B, O'Hara RB, Öpik M, Sogin ML, Unterseher M, Tedersoo L.

FEMS Microbiol Rev. 2016 Sep;40(5):686-700. doi: 10.1093/femsre/fuw017. Epub 2016 Jun 29. Review.

PMID:
27358393

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