Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 135

1.

Influence of Light on Particulate Organic Matter Utilization by Attached and Free-Living Marine Bacteria.

Gómez-Consarnau L, Needham DM, Weber PK, Fuhrman JA, Mayali X.

Front Microbiol. 2019 Jun 4;10:1204. doi: 10.3389/fmicb.2019.01204. eCollection 2019.

2.

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.

3.

Multi-year dynamics of fine-scale marine cyanobacterial populations are more strongly explained by phage interactions than abiotic, bottom-up factors.

Ahlgren NA, Perelman JN, Yeh YC, Fuhrman JA.

Environ Microbiol. 2019 May 20. doi: 10.1111/1462-2920.14687. [Epub ahead of print]

PMID:
31106939
4.

Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes.

Sieradzki ET, Ignacio-Espinoza JC, Needham DM, Fichot EB, Fuhrman JA.

Nat Commun. 2019 Mar 12;10(1):1169. doi: 10.1038/s41467-019-09106-z.

5.

Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences.

Wang Z, Wang Y, Fuhrman JA, Sun F, Zhu S.

Brief Bioinform. 2019 Mar 11. pii: bbz025. doi: 10.1093/bib/bbz025. [Epub ahead of print]

PMID:
30860572
6.

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
7.

Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities.

Sieradzki ET, Fuhrman JA, Rivero-Calle S, Gómez-Consarnau L.

PeerJ. 2018 Oct 23;6:e5798. doi: 10.7717/peerj.5798. eCollection 2018.

8.

Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes.

Ahlgren NA, Fuchsman CA, Rocap G, Fuhrman JA.

ISME J. 2019 Mar;13(3):618-631. doi: 10.1038/s41396-018-0289-4. Epub 2018 Oct 12.

PMID:
30315316
9.

Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative.

Brown MV, van de Kamp J, Ostrowski M, Seymour JR, Ingleton T, Messer LF, Jeffries T, Siboni N, Laverock B, Bibiloni-Isaksson J, Nelson TM, Coman F, Davies CH, Frampton D, Rayner M, Goossen K, Robert S, Holmes B, Abell GCJ, Craw P, Kahlke T, Sow SLS, McAllister K, Windsor J, Skuza M, Crossing R, Patten N, Malthouse P, van Ruth PD, Paulsen I, Fuhrman JA, Richardson A, Koval J, Bissett A, Fitzgerald A, Moltmann T, Bodrossy L.

Sci Data. 2018 Jul 17;5:180130. doi: 10.1038/sdata.2018.130.

10.

Dynamics and interactions of highly resolved marine plankton via automated high-frequency sampling.

Needham DM, Fichot EB, Wang E, Berdjeb L, Cram JA, Fichot CG, Fuhrman JA.

ISME J. 2018 Oct;12(10):2417-2432. doi: 10.1038/s41396-018-0169-y. Epub 2018 Jun 13.

PMID:
29899514
11.

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 Nov;76(4):866-884. doi: 10.1007/s00248-018-1179-z. Epub 2018 Apr 19.

PMID:
29675703
12.

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 Aug;20(8):2809-2823. doi: 10.1111/1462-2920.14133. Epub 2018 May 11.

PMID:
29659156
13.

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.

14.

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 Aug;12(8):1907-1917. doi: 10.1038/s41396-018-0097-x. Epub 2018 Mar 29.

PMID:
29599520
15.

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
16.

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.

17.

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.

18.

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
19.

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.

20.

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.

21.

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.

22.

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
23.

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.

24.

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.

25.

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.

26.

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.

27.

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
28.

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. Erratum in: Nat Microbiol. 2017 Nov;2(11):1571.

PMID:
27572161
29.

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
30.

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge.

Lu YY, Chen T, Fuhrman JA, Sun F.

Bioinformatics. 2017 Mar 15;33(6):791-798. doi: 10.1093/bioinformatics/btw290.

PMID:
27256312
31.

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision.

Weiss S, Van Treuren W, Lozupone C, Faust K, Friedman J, Deng Y, Xia LC, Xu ZZ, Ursell L, Alm EJ, Birmingham A, Cram JA, Fuhrman JA, Raes J, Sun F, Zhou J, Knight R.

ISME J. 2016 Jul;10(7):1669-81. doi: 10.1038/ismej.2015.235. Epub 2016 Feb 23.

32.

Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria.

Gómez-Consarnau L, González JM, Riedel T, Jaenicke S, Wagner-Döbler I, Sañudo-Wilhelmy SA, Fuhrman JA.

ISME J. 2016 May;10(5):1102-12. doi: 10.1038/ismej.2015.196. Epub 2015 Nov 17.

33.

Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains.

Xia LC, Ai D, Cram JA, Liang X, Fuhrman JA, Sun F.

BMC Bioinformatics. 2015 Sep 21;16:301. doi: 10.1186/s12859-015-0732-8.

34.

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples.

Parada AE, Needham DM, Fuhrman JA.

Environ Microbiol. 2016 May;18(5):1403-14. doi: 10.1111/1462-2920.13023. Epub 2015 Oct 14.

PMID:
26271760
35.

The ocean sampling day consortium.

Kopf A, Bicak M, Kottmann R, Schnetzer J, Kostadinov I, Lehmann K, Fernandez-Guerra A, Jeanthon C, Rahav E, Ullrich M, Wichels A, Gerdts G, Polymenakou P, Kotoulas G, Siam R, Abdallah RZ, Sonnenschein EC, Cariou T, O'Gara F, Jackson S, Orlic S, Steinke M, Busch J, Duarte B, Caçador I, Canning-Clode J, Bobrova O, Marteinsson V, Reynisson E, Loureiro CM, Luna GM, Quero GM, Löscher CR, Kremp A, DeLorenzo ME, Øvreås L, Tolman J, LaRoche J, Penna A, Frischer M, Davis T, Katherine B, Meyer CP, Ramos S, Magalhães C, Jude-Lemeilleur F, Aguirre-Macedo ML, Wang S, Poulton N, Jones S, Collin R, Fuhrman JA, Conan P, Alonso C, Stambler N, Goodwin K, Yakimov MM, Baltar F, Bodrossy L, Van De Kamp J, Frampton DM, Ostrowski M, Van Ruth P, Malthouse P, Claus S, Deneudt K, Mortelmans J, Pitois S, Wallom D, Salter I, Costa R, Schroeder DC, Kandil MM, Amaral V, Biancalana F, Santana R, Pedrotti ML, Yoshida T, Ogata H, Ingleton T, Munnik K, Rodriguez-Ezpeleta N, Berteaux-Lecellier V, Wecker P, Cancio I, Vaulot D, Bienhold C, Ghazal H, Chaouni B, Essayeh S, Ettamimi S, Zaid el H, Boukhatem N, Bouali A, Chahboune R, Barrijal S, Timinouni M, El Otmani F, Bennani M, Mea M, Todorova N, Karamfilov V, Ten Hoopen P, Cochrane G, L'Haridon S, Bizsel KC, Vezzi A, Lauro FM, Martin P, Jensen RM, Hinks J, Gebbels S, Rosselli R, De Pascale F, Schiavon R, Dos Santos A, Villar E, Pesant S, Cataletto B, Malfatti F, Edirisinghe R, Silveira JA, Barbier M, Turk V, Tinta T, Fuller WJ, Salihoglu I, Serakinci N, Ergoren MC, Bresnan E, Iriberri J, Nyhus PA, Bente E, Karlsen HE, Golyshin PN, Gasol JM, Moncheva S, Dzhembekova N, Johnson Z, Sinigalliano CD, Gidley ML, Zingone A, Danovaro R, Tsiamis G, Clark MS, Costa AC, El Bour M, Martins AM, Collins RE, Ducluzeau AL, Martinez J, Costello MJ, Amaral-Zettler LA, Gilbert JA, Davies N, Field D, Glöckner FO.

Gigascience. 2015 Jun 19;4:27. doi: 10.1186/s13742-015-0066-5. eCollection 2015.

36.

Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes.

Cram JA, Xia LC, Needham DM, Sachdeva R, Sun F, Fuhrman JA.

ISME J. 2015 Dec;9(12):2573-86. doi: 10.1038/ismej.2015.76. Epub 2015 May 19.

37.

Marine microbial community dynamics and their ecological interpretation.

Fuhrman JA, Cram JA, Needham DM.

Nat Rev Microbiol. 2015 Mar;13(3):133-46. doi: 10.1038/nrmicro3417. Epub 2015 Feb 9. Review.

PMID:
25659323
38.

A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes.

Weitz JS, Stock CA, Wilhelm SW, Bourouiba L, Coleman ML, Buchan A, Follows MJ, Fuhrman JA, Jover LF, Lennon JT, Middelboe M, Sonderegger DL, Suttle CA, Taylor BP, Frede Thingstad T, Wilson WH, Eric Wommack K.

ISME J. 2015 Jun;9(6):1352-64. doi: 10.1038/ismej.2014.220. Epub 2015 Jan 30.

39.

Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years.

Cram JA, Chow CE, Sachdeva R, Needham DM, Parada AE, Steele JA, Fuhrman JA.

ISME J. 2015 Mar;9(3):563-80. doi: 10.1038/ismej.2014.153. Epub 2014 Sep 9.

40.

Beta diversity of marine bacteria depends on temporal scale.

Hatosy SM, Martiny JB, Sachdeva R, Steele J, Fuhrman JA, Martiny AC.

Ecology. 2013 Sep;94(9):1898-904.

41.

Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists.

Chow CE, Kim DY, Sachdeva R, Caron DA, Fuhrman JA.

ISME J. 2014 Apr;8(4):816-29. doi: 10.1038/ismej.2013.199. Epub 2013 Nov 7.

42.

Strong seasonality and interannual recurrence in marine myovirus communities.

Pagarete A, Chow CE, Johannessen T, Fuhrman JA, Thingstad TF, Sandaa RA.

Appl Environ Microbiol. 2013 Oct;79(20):6253-9. doi: 10.1128/AEM.01075-13. Epub 2013 Aug 2.

43.

Performance of viruses and bacteriophages for fecal source determination in a multi-laboratory, comparative study.

Harwood VJ, Boehm AB, Sassoubre LM, Vijayavel K, Stewart JR, Fong TT, Caprais MP, Converse RR, Diston D, Ebdon J, Fuhrman JA, Gourmelon M, Gentry-Shields J, Griffith JF, Kashian DR, Noble RT, Taylor H, Wicki M.

Water Res. 2013 Nov 15;47(18):6929-43. doi: 10.1016/j.watres.2013.04.064. Epub 2013 Jul 4.

PMID:
23886543
44.

Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight.

Chow CE, Sachdeva R, Cram JA, Steele JA, Needham DM, Patel A, Parada AE, Fuhrman JA.

ISME J. 2013 Dec;7(12):2259-73. doi: 10.1038/ismej.2013.122. Epub 2013 Jul 18.

45.

Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein.

Riedel T, Gómez-Consarnau L, Tomasch J, Martin M, Jarek M, González JM, Spring S, Rohlfs M, Brinkhoff T, Cypionka H, Göker M, Fiebig A, Klein J, Goesmann A, Fuhrman JA, Wagner-Döbler I.

PLoS One. 2013;8(3):e57487. doi: 10.1371/journal.pone.0057487. Epub 2013 Mar 4.

46.

Short-term observations of marine bacterial and viral communities: patterns, connections and resilience.

Needham DM, Chow CE, Cram JA, Sachdeva R, Parada A, Fuhrman JA.

ISME J. 2013 Jul;7(7):1274-85. doi: 10.1038/ismej.2013.19. Epub 2013 Feb 28.

47.

Efficient statistical significance approximation for local similarity analysis of high-throughput time series data.

Xia LC, Ai D, Cram J, Fuhrman JA, Sun F.

Bioinformatics. 2013 Jan 15;29(2):230-7. doi: 10.1093/bioinformatics/bts668. Epub 2012 Nov 23.

48.

Metagenomics and its connection to microbial community organization.

Fuhrman JA.

F1000 Biol Rep. 2012;4:15. doi: 10.3410/B4-15. Epub 2012 Aug 1.

49.

Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates.

Xia LC, Steele JA, Cram JA, Cardon ZG, Simmons SL, Vallino JJ, Fuhrman JA, Sun F.

BMC Syst Biol. 2011;5 Suppl 2:S15. doi: 10.1186/1752-0509-5-S2-S15. Epub 2011 Dec 14.

50.

Pharyngeal polysaccharide deacetylases affect development in the nematode C. elegans and deacetylate chitin in vitro.

Heustis RJ, Ng HK, Brand KJ, Rogers MC, Le LT, Specht CA, Fuhrman JA.

PLoS One. 2012;7(7):e40426. doi: 10.1371/journal.pone.0040426. Epub 2012 Jul 13.

Supplemental Content

Loading ...
Support Center