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Items: 1 to 50 of 70

1.

Potential for primary productivity in a globally-distributed bacterial phototroph.

Graham ED, Heidelberg JF, Tully BJ.

ISME J. 2018 Jun;12(7):1861-1866. doi: 10.1038/s41396-018-0091-3. Epub 2018 Mar 9.

2.

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans.

Tully BJ, Graham ED, Heidelberg JF.

Sci Data. 2018 Jan 16;5:170203. doi: 10.1038/sdata.2017.203.

3.

290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology.

Tully BJ, Sachdeva R, Graham ED, Heidelberg JF.

PeerJ. 2017 Jul 10;5:e3558. doi: 10.7717/peerj.3558. eCollection 2017.

4.

BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation.

Graham ED, Heidelberg JF, Tully BJ.

PeerJ. 2017 Mar 8;5:e3035. doi: 10.7717/peerj.3035. eCollection 2017.

5.

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments.

Tully BJ, Heidelberg JF.

Appl Environ Microbiol. 2016 Jun 30;82(14):4232-43. doi: 10.1128/AEM.01023-16. Print 2016 Jul 15.

6.

Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat.

Melendrez MC, Becraft ED, Wood JM, Olsen MT, Bryant DA, Heidelberg JF, Rusch DB, Cohan FM, Ward DM.

Front Microbiol. 2016 Jan 14;6:1540. doi: 10.3389/fmicb.2015.01540. eCollection 2015.

7.

Similar Microbial Communities Found on Two Distant Seafloor Basalts.

Singer E, Chong LS, Heidelberg JF, Edwards KJ.

Front Microbiol. 2015 Dec 16;6:1409. doi: 10.3389/fmicb.2015.01409. eCollection 2015.

8.

Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle.

Walworth N, Pfreundt U, Nelson WC, Mincer T, Heidelberg JF, Fu F, Waterbury JB, Glavina del Rio T, Goodwin L, Kyrpides NC, Land ML, Woyke T, Hutchins DA, Hess WR, Webb EA.

Proc Natl Acad Sci U S A. 2015 Apr 7;112(14):4251-6. doi: 10.1073/pnas.1422332112. Epub 2015 Mar 23.

9.

Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using metagenomic data.

Tully BJ, Sachdeva R, Heidelberg KB, Heidelberg JF.

Microbiome. 2014 Sep 5;2:34. doi: 10.1186/2049-2618-2-34. eCollection 2014.

10.

Meeting report: Ocean 'omics science, technology and cyberinfrastructure: current challenges and future requirements (August 20-23, 2013).

Gilbert JA, Dick GJ, Jenkins B, Heidelberg J, Allen E, Mackey KR, DeLong EF.

Stand Genomic Sci. 2014 Mar 15;9(3):1252-8. doi: 10.4056/sigs.5749944. eCollection 2014 Jun 15.

11.

Microbial communities associated with ferromanganese nodules and the surrounding sediments.

Tully BJ, Heidelberg JF.

Front Microbiol. 2013 Jun 25;4:161. doi: 10.3389/fmicb.2013.00161. eCollection 2013.

12.

Metagenomic insights into the dominant Fe(II) oxidizing Zetaproteobacteria from an iron mat at Lō´ihi, Hawai´l.

Singer E, Heidelberg JF, Dhillon A, Edwards KJ.

Front Microbiol. 2013 Mar 19;4:52. doi: 10.3389/fmicb.2013.00052. eCollection 2013.

13.

Novel miniature transposable elements in thermophilic Synechococcus strains and their impact on an environmental population.

Nelson WC, Bhaya D, Heidelberg JF.

J Bacteriol. 2012 Jul;194(14):3636-42. doi: 10.1128/JB.00333-12. Epub 2012 May 4.

14.

Prospects for the study of evolution in the deep biosphere.

Biddle JF, Sylvan JB, Brazelton WJ, Tully BJ, Edwards KJ, Moyer CL, Heidelberg JF, Nelson WC.

Front Microbiol. 2012 Jan 24;2:285. doi: 10.3389/fmicb.2011.00285. eCollection 2011.

15.

Metagenomic analysis of a complex marine planktonic thaumarchaeal community from the Gulf of Maine.

Tully BJ, Nelson WC, Heidelberg JF.

Environ Microbiol. 2012 Jan;14(1):254-67. doi: 10.1111/j.1462-2920.2011.02628.x. Epub 2011 Nov 3.

PMID:
22050608
16.

Mariprofundus ferrooxydans PV-1 the first genome of a marine Fe(II) oxidizing Zetaproteobacterium.

Singer E, Emerson D, Webb EA, Barco RA, Kuenen JG, Nelson WC, Chan CS, Comolli LR, Ferriera S, Johnson J, Heidelberg JF, Edwards KJ.

PLoS One. 2011;6(9):e25386. doi: 10.1371/journal.pone.0025386. Epub 2011 Sep 23.

17.

Activity of abundant and rare bacteria in a coastal ocean.

Campbell BJ, Yu L, Heidelberg JF, Kirchman DL.

Proc Natl Acad Sci U S A. 2011 Aug 2;108(31):12776-81. doi: 10.1073/pnas.1101405108. Epub 2011 Jul 18.

18.

Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential.

Klatt CG, Wood JM, Rusch DB, Bateson MM, Hamamura N, Heidelberg JF, Grossman AR, Bhaya D, Cohan FM, Kühl M, Bryant DA, Ward DM.

ISME J. 2011 Aug;5(8):1262-78. doi: 10.1038/ismej.2011.73. Epub 2011 Jun 23.

19.

Analysis of insertion sequences in thermophilic cyanobacteria: exploring the mechanisms of establishing, maintaining, and withstanding high insertion sequence abundance.

Nelson WC, Wollerman L, Bhaya D, Heidelberg JF.

Appl Environ Microbiol. 2011 Aug;77(15):5458-66. doi: 10.1128/AEM.05090-11. Epub 2011 Jun 10.

20.

Genomic potential of Marinobacter aquaeolei, a biogeochemical "opportunitroph".

Singer E, Webb EA, Nelson WC, Heidelberg JF, Ivanova N, Pati A, Edwards KJ.

Appl Environ Microbiol. 2011 Apr;77(8):2763-71. doi: 10.1128/AEM.01866-10. Epub 2011 Feb 18.

21.

Complete and draft genome sequences of six members of the Aquificales.

Reysenbach AL, Hamamura N, Podar M, Griffiths E, Ferreira S, Hochstein R, Heidelberg J, Johnson J, Mead D, Pohorille A, Sarmiento M, Schweighofer K, Seshadri R, Voytek MA.

J Bacteriol. 2009 Mar;191(6):1992-3. doi: 10.1128/JB.01645-08. Epub 2009 Jan 9.

22.

Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes.

Heidelberg JF, Nelson WC, Schoenfeld T, Bhaya D.

PLoS One. 2009;4(1):e4169. doi: 10.1371/journal.pone.0004169. Epub 2009 Jan 9.

23.

Widespread distribution of a unique marine protistan lineage.

Cuvelier ML, Ortiz A, Kim E, Moehlig H, Richardson DE, Heidelberg JF, Archibald JM, Worden AZ.

Environ Microbiol. 2008 Jun;10(6):1621-34. doi: 10.1111/j.1462-2920.2008.01580.x. Epub 2008 Mar 12.

24.

Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses.

Bhaya D, Grossman AR, Steunou AS, Khuri N, Cohan FM, Hamamura N, Melendrez MC, Bateson MM, Ward DM, Heidelberg JF.

ISME J. 2007 Dec;1(8):703-13. Epub 2007 Oct 25.

PMID:
18059494
25.

The ISME journal: multidisciplinary journal of microbial ecology.

Kowalchuk GA, Heidelberg JF, Bailey MJ.

ISME J. 2007 May;1(1):1-3. No abstract available.

PMID:
18043606
26.

Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic Acidobacterium.

Bryant DA, Costas AM, Maresca JA, Chew AG, Klatt CG, Bateson MM, Tallon LJ, Hostetler J, Nelson WC, Heidelberg JF, Ward DM.

Science. 2007 Jul 27;317(5837):523-6.

27.

Genomics, environmental genomics and the issue of microbial species.

Ward DM, Cohan FM, Bhaya D, Heidelberg JF, Kühl M, Grossman A.

Heredity (Edinb). 2008 Feb;100(2):207-19. Epub 2007 Jun 6. Review.

28.

Vertical distribution of picoeukaryotic diversity in the Sargasso Sea.

Not F, Gausling R, Azam F, Heidelberg JF, Worden AZ.

Environ Microbiol. 2007 May;9(5):1233-52.

PMID:
17472637
29.

Genomic analysis of the Mozambique strain of Vibrio cholerae O1 reveals the origin of El Tor strains carrying classical CTX prophage.

Faruque SM, Tam VC, Chowdhury N, Diraphat P, Dziejman M, Heidelberg JF, Clemens JD, Mekalanos JJ, Nair GB.

Proc Natl Acad Sci U S A. 2007 Mar 20;104(12):5151-6. Epub 2007 Mar 12.

30.

The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific.

Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcón LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC.

PLoS Biol. 2007 Mar;5(3):e77.

31.

Genome sequence of Aeromonas hydrophila ATCC 7966T: jack of all trades.

Seshadri R, Joseph SW, Chopra AK, Sha J, Shaw J, Graf J, Haft D, Wu M, Ren Q, Rosovitz MJ, Madupu R, Tallon L, Kim M, Jin S, Vuong H, Stine OC, Ali A, Horneman AJ, Heidelberg JF.

J Bacteriol. 2006 Dec;188(23):8272-82. Epub 2006 Sep 15.

32.

Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment.

Palenik B, Ren Q, Dupont CL, Myers GS, Heidelberg JF, Badger JH, Madupu R, Nelson WC, Brinkac LM, Dodson RJ, Durkin AS, Daugherty SC, Sullivan SA, Khouri H, Mohamoud Y, Halpin R, Paulsen IT.

Proc Natl Acad Sci U S A. 2006 Sep 5;103(36):13555-9. Epub 2006 Aug 25.

33.

Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system.

Pukatzki S, Ma AT, Sturtevant D, Krastins B, Sarracino D, Nelson WC, Heidelberg JF, Mekalanos JJ.

Proc Natl Acad Sci U S A. 2006 Jan 31;103(5):1528-33. Epub 2006 Jan 23.

34.

Bacteria to the rescue.

Seshadri R, Heidelberg J.

Nat Biotechnol. 2005 Oct;23(10):1236-7. No abstract available.

PMID:
16211064
35.

Genomic characterization of non-O1, non-O139 Vibrio cholerae reveals genes for a type III secretion system.

Dziejman M, Serruto D, Tam VC, Sturtevant D, Diraphat P, Faruque SM, Rahman MH, Heidelberg JF, Decker J, Li L, Montgomery KT, Grills G, Kucherlapati R, Mekalanos JJ.

Proc Natl Acad Sci U S A. 2005 Mar 1;102(9):3465-70. Epub 2005 Feb 22.

36.

Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes.

Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, Deboy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Nelson KE, Kang KH, Impraim M, Tran K, Robinson JM, Forberger HA, Fraser CM, Zinder SH, Heidelberg JF.

Science. 2005 Jan 7;307(5706):105-8.

37.

Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment.

Moran MA, Buchan A, González JM, Heidelberg JF, Whitman WB, Kiene RP, Henriksen JR, King GM, Belas R, Fuqua C, Brinkac L, Lewis M, Johri S, Weaver B, Pai G, Eisen JA, Rahe E, Sheldon WM, Ye W, Miller TR, Carlton J, Rasko DA, Paulsen IT, Ren Q, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Rosovitz MJ, Haft DH, Selengut J, Ward N.

Nature. 2004 Dec 16;432(7019):910-3.

PMID:
15602564
38.

Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath).

Ward N, Larsen Ø, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH, Lewis M, Nelson KE, Methé B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren Q, Read T, DeBoy RT, Seshadri R, Salzberg SL, Jensen HB, Birkeland NK, Nelson WC, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Utterback T, Feldblyum TV, Fraser CM, Lillehaug JR, Eisen JA.

PLoS Biol. 2004 Oct;2(10):e303. Epub 2004 Sep 21.

39.

The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.

Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B, Brinkac LM, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Fouts D, Haft DH, Selengut J, Peterson JD, Davidsen TM, Zafar N, Zhou L, Radune D, Dimitrov G, Hance M, Tran K, Khouri H, Gill J, Utterback TR, Feldblyum TV, Wall JD, Voordouw G, Fraser CM.

Nat Biotechnol. 2004 May;22(5):554-9. Epub 2004 Apr 11.

PMID:
15077118
40.

Environmental genome shotgun sequencing of the Sargasso Sea.

Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO.

Science. 2004 Apr 2;304(5667):66-74. Epub 2004 Mar 4.

41.

Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes.

Seshadri R, Myers GS, Tettelin H, Eisen JA, Heidelberg JF, Dodson RJ, Davidsen TM, DeBoy RT, Fouts DE, Haft DH, Selengut J, Ren Q, Brinkac LM, Madupu R, Kolonay J, Durkin SA, Daugherty SC, Shetty J, Shvartsbeyn A, Gebregeorgis E, Geer K, Tsegaye G, Malek J, Ayodeji B, Shatsman S, McLeod MP, Smajs D, Howell JK, Pal S, Amin A, Vashisth P, McNeill TZ, Xiang Q, Sodergren E, Baca E, Weinstock GM, Norris SJ, Fraser CM, Paulsen IT.

Proc Natl Acad Sci U S A. 2004 Apr 13;101(15):5646-51. Epub 2004 Apr 2.

42.

Genome of Geobacter sulfurreducens: metal reduction in subsurface environments.

Methé BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, Heidelberg JF, Wu D, Wu M, Ward N, Beanan MJ, Dodson RJ, Madupu R, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Gwinn M, Kolonay JF, Sullivan SA, Haft DH, Selengut J, Davidsen TM, Zafar N, White O, Tran B, Romero C, Forberger HA, Weidman J, Khouri H, Feldblyum TV, Utterback TR, Van Aken SE, Lovley DR, Fraser CM.

Science. 2003 Dec 12;302(5652):1967-9.

43.
44.

Proteorhodopsin genes are distributed among divergent marine bacterial taxa.

de la Torre JR, Christianson LM, Béjà O, Suzuki MT, Karl DM, Heidelberg J, DeLong EF.

Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12830-5. Epub 2003 Oct 17.

45.

Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage.

Miller ES, Heidelberg JF, Eisen JA, Nelson WC, Durkin AS, Ciecko A, Feldblyum TV, White O, Paulsen IT, Nierman WC, Lee J, Szczypinski B, Fraser CM.

J Bacteriol. 2003 Sep;185(17):5220-33.

46.

Gene expression analysis of energy metabolism mutants of Desulfovibrio vulgaris Hildenborough indicates an important role for alcohol dehydrogenase.

Haveman SA, Brunelle V, Voordouw JK, Voordouw G, Heidelberg JF, Rabus R.

J Bacteriol. 2003 Aug;185(15):4345-53.

47.

Complete genome sequence of the Q-fever pathogen Coxiella burnetii.

Seshadri R, Paulsen IT, Eisen JA, Read TD, Nelson KE, Nelson WC, Ward NL, Tettelin H, Davidsen TM, Beanan MJ, Deboy RT, Daugherty SC, Brinkac LM, Madupu R, Dodson RJ, Khouri HM, Lee KH, Carty HA, Scanlan D, Heinzen RA, Thompson HA, Samuel JE, Fraser CM, Heidelberg JF.

Proc Natl Acad Sci U S A. 2003 Apr 29;100(9):5455-60. Epub 2003 Apr 18.

48.

Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae.

Read TD, Myers GS, Brunham RC, Nelson WC, Paulsen IT, Heidelberg J, Holtzapple E, Khouri H, Federova NB, Carty HA, Umayam LA, Haft DH, Peterson J, Beanan MJ, White O, Salzberg SL, Hsia RC, McClarty G, Rank RG, Bavoil PM, Fraser CM.

Nucleic Acids Res. 2003 Apr 15;31(8):2134-47.

49.

Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis.

Paulsen IT, Banerjei L, Myers GS, Nelson KE, Seshadri R, Read TD, Fouts DE, Eisen JA, Gill SR, Heidelberg JF, Tettelin H, Dodson RJ, Umayam L, Brinkac L, Beanan M, Daugherty S, DeBoy RT, Durkin S, Kolonay J, Madupu R, Nelson W, Vamathevan J, Tran B, Upton J, Hansen T, Shetty J, Khouri H, Utterback T, Radune D, Ketchum KA, Dougherty BA, Fraser CM.

Science. 2003 Mar 28;299(5615):2071-4.

50.

Bacteria of the gamma-subclass Proteobacteria associated with zooplankton in Chesapeake Bay.

Heidelberg JF, Heidelberg KB, Colwell RR.

Appl Environ Microbiol. 2002 Nov;68(11):5498-507.

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