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Items: 1 to 50 of 97

1.

Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea.

Borrel G, Adam PS, McKay LJ, Chen LX, Sierra-García IN, Sieber CMK, Letourneur Q, Ghozlane A, Andersen GL, Li WJ, Hallam SJ, Muyzer G, de Oliveira VM, Inskeep WP, Banfield JF, Gribaldo S.

Nat Microbiol. 2019 Mar 4. doi: 10.1038/s41564-019-0363-3. [Epub ahead of print]

PMID:
30833729
2.

Toward unrestricted use of public genomic data.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.

Science. 2019 Jan 25;363(6425):350-352. doi: 10.1126/science.aaw1280. No abstract available.

3.

Author Correction: A compendium of geochemical information from the Saanich Inlet water column.

Torres-Beltrán M, Hawley AK, Capelle D, Zaikova E, Walsh DA, Mueller A, Scofield M, Payne C, Pakhomova L, Kheirandish S, Finke J, Bhatia M, Shevchuk O, Gies EA, Fairley D, Michiels C, Suttle CA, Whitney F, Crowe SA, Tortell PD, Hallam SJ.

Sci Data. 2019 Jan 15;6(1):1. doi: 10.1038/s41597-018-0005-2.

4.

Seasonal and ecohydrological regulation of active microbial populations involved in DOC, CO2, and CH4 fluxes in temperate rainforest soil.

Levy-Booth DJ, Giesbrecht IJW, Kellogg CTE, Heger TJ, D'Amore DV, Keeling PJ, Hallam SJ, Mohn WW.

ISME J. 2018 Dec 11. doi: 10.1038/s41396-018-0334-3. [Epub ahead of print]

PMID:
30538276
5.

Recovering cellular biomass from fluids using chemical flocculation.

Kenward PA, Simister RL, Morgan-Lang C, Finke N, Sturm A, Hallam SJ, Crowe SA.

Environ Microbiol Rep. 2018 Dec;10(6):686-694. doi: 10.1111/1758-2229.12690. Epub 2018 Oct 16.

PMID:
30230256
6.

Review of Mammarenavirus Biology and Replication.

Hallam SJ, Koma T, Maruyama J, Paessler S.

Front Microbiol. 2018 Aug 3;9:1751. doi: 10.3389/fmicb.2018.01751. eCollection 2018.

7.

Microbial and geochemical controls on waste rock weathering and drainage quality.

Blackmore S, Vriens B, Sorensen M, Power IM, Smith L, Hallam SJ, Mayer KU, Beckie RD.

Sci Total Environ. 2018 Nov 1;640-641:1004-1014. doi: 10.1016/j.scitotenv.2018.05.374. Epub 2018 Jun 5.

PMID:
30021267
8.

Metagenomics reveals functional synergy and novel polysaccharide utilization loci in the Castor canadensis fecal microbiome.

Armstrong Z, Mewis K, Liu F, Morgan-Lang C, Scofield M, Durno E, Chen HM, Mehr K, Withers SG, Hallam SJ.

ISME J. 2018 Nov;12(11):2757-2769. doi: 10.1038/s41396-018-0215-9. Epub 2018 Jul 16.

9.

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
10.

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.

11.

Metagenomes Reveal Global Distribution of Bacterial Steroid Catabolism in Natural, Engineered, and Host Environments.

Holert J, Cardenas E, Bergstrand LH, Zaikova E, Hahn AS, Hallam SJ, Mohn WW.

MBio. 2018 Jan 30;9(1). pii: e02345-17. doi: 10.1128/mBio.02345-17.

12.

Structural and mechanistic analysis of a β-glycoside phosphorylase identified by screening a metagenomic library.

Macdonald SS, Patel A, Larmour VLC, Morgan-Lang C, Hallam SJ, Mark BL, Withers SG.

J Biol Chem. 2018 Mar 2;293(9):3451-3467. doi: 10.1074/jbc.RA117.000948. Epub 2018 Jan 9.

13.

An Improved Whole-Cell Biosensor for the Discovery of Lignin-Transforming Enzymes in Functional Metagenomic Screens.

Ho JCH, Pawar SV, Hallam SJ, Yadav VG.

ACS Synth Biol. 2018 Feb 16;7(2):392-398. doi: 10.1021/acssynbio.7b00412. Epub 2017 Dec 4.

PMID:
29182267
14.

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation.

Pachiadaki MG, Sintes E, Bergauer K, Brown JM, Record NR, Swan BK, Mathyer ME, Hallam SJ, Lopez-Garcia P, Takaki Y, Nunoura T, Woyke T, Herndl GJ, Stepanauskas R.

Science. 2017 Nov 24;358(6366):1046-1051. doi: 10.1126/science.aan8260.

PMID:
29170234
15.

Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients.

Hawley AK, Nobu MK, Wright JJ, Durno WE, Morgan-Lang C, Sage B, Schwientek P, Swan BK, Rinke C, Torres-Beltrán M, Mewis K, Liu WT, Stepanauskas R, Woyke T, Hallam SJ.

Nat Commun. 2017 Nov 15;8(1):1507. doi: 10.1038/s41467-017-01376-9.

16.

A compendium of geochemical information from the Saanich Inlet water column.

Torres-Beltrán M, Hawley AK, Capelle D, Zaikova E, Walsh DA, Mueller A, Scofield M, Payne C, Pakhomova L, Kheirandish S, Finke J, Bhatia M, Shevchuk O, Gies EA, Fairley D, Michiels C, Suttle CA, Whitney F, Crowe SA, Tortell PD, Hallam SJ.

Sci Data. 2017 Oct 31;4:170159. doi: 10.1038/sdata.2017.159. Erratum in: Sci Data. 2019 Jan 15;6(1):1.

17.

Monitoring microbial responses to ocean deoxygenation in a model oxygen minimum zone.

Hallam SJ, Torres-Beltrán M, Hawley AK.

Sci Data. 2017 Oct 31;4:170158. doi: 10.1038/sdata.2017.158.

18.

A compendium of multi-omic sequence information from the Saanich Inlet water column.

Hawley AK, Torres-Beltrán M, Zaikova E, Walsh DA, Mueller A, Scofield M, Kheirandish S, Payne C, Pakhomova L, Bhatia M, Shevchuk O, Gies EA, Fairley D, Malfatti SA, Norbeck AD, Brewer HM, Pasa-Tolic L, Del Rio TG, Suttle CA, Tringe S, Hallam SJ.

Sci Data. 2017 Oct 31;4:170160. doi: 10.1038/sdata.2017.160.

19.

Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates.

Strassert JFH, Karnkowska A, Hehenberger E, Del Campo J, Kolisko M, Okamoto N, Burki F, Janouškovec J, Poirier C, Leonard G, Hallam SJ, Richards TA, Worden AZ, Santoro AE, Keeling PJ.

ISME J. 2018 Jan;12(1):304-308. doi: 10.1038/ismej.2017.167. Epub 2017 Oct 10.

20.

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.

PMID:
28787424
21.

Nutrient Acquisition and the Metabolic Potential of Photoferrotrophic Chlorobi.

Thompson KJ, Simister RL, Hahn AS, Hallam SJ, Crowe SA.

Front Microbiol. 2017 Jul 6;8:1212. doi: 10.3389/fmicb.2017.01212. eCollection 2017.

22.

Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae.

Collingro A, Köstlbacher S, Mussmann M, Stepanauskas R, Hallam SJ, Horn M.

ISME J. 2017 Oct;11(10):2334-2344. doi: 10.1038/ismej.2017.95. Epub 2017 Jun 23.

23.

A geographically-diverse collection of 418 human gut microbiome pathway genome databases.

Hahn AS, Altman T, Konwar KM, Hanson NW, Kim D, Relman DA, Dill DL, Hallam SJ.

Sci Data. 2017 Apr 11;4:170035. doi: 10.1038/sdata.2017.35.

24.

Draft Genome Sequence of the Pelagic Photoferrotroph Chlorobium phaeoferrooxidans.

Crowe SA, Hahn AS, Morgan-Lang C, Thompson KJ, Simister RL, Llirós M, Hirst M, Hallam SJ.

Genome Announc. 2017 Mar 30;5(13). pii: e01584-16. doi: 10.1128/genomeA.01584-16.

25.

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

Paez-Espino D, Chen IA, Palaniappan K, Ratner A, Chu K, Szeto E, Pillay M, Huang J, Markowitz VM, Nielsen T, Huntemann M, K Reddy TB, Pavlopoulos GA, Sullivan MB, Campbell BJ, Chen F, McMahon K, Hallam SJ, Denef V, Cavicchioli R, Caffrey SM, Streit WR, Webster J, Handley KM, Salekdeh GH, Tsesmetzis N, Setubal JC, Pope PB, Liu WT, Rivers AR, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2017 Jan 4;45(D1):D457-D465. doi: 10.1093/nar/gkw1030. Epub 2016 Oct 30.

26.

Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone.

Louca S, Hawley AK, Katsev S, Torres-Beltran M, Bhatia MP, Kheirandish S, Michiels CC, Capelle D, Lavik G, Doebeli M, Crowe SA, Hallam SJ.

Proc Natl Acad Sci U S A. 2016 Oct 4;113(40):E5925-E5933. Epub 2016 Sep 21.

27.

Ammonium and nitrite oxidation at nanomolar oxygen concentrations in oxygen minimum zone waters.

Bristow LA, Dalsgaard T, Tiano L, Mills DB, Bertagnolli AD, Wright JJ, Hallam SJ, Ulloa O, Canfield DE, Revsbech NP, Thamdrup B.

Proc Natl Acad Sci U S A. 2016 Sep 20;113(38):10601-6. doi: 10.1073/pnas.1600359113. Epub 2016 Sep 6.

28.

LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes.

Hanson NW, Konwar KM, Hallam SJ.

Bioinformatics. 2016 Dec 1;32(23):3535-3542. Epub 2016 Aug 11.

29.

Editorial overview: Remapping the body of the world: Exploring interactions at the interface of microbial ecology, biological engineering and information science.

Hallam SJ, Vásquez M.

Curr Opin Microbiol. 2016 Jun;31:v-vii. doi: 10.1016/j.mib.2016.05.001. Epub 2016 May 16. No abstract available.

PMID:
27199093
30.

The information science of microbial ecology.

Hahn AS, Konwar KM, Louca S, Hanson NW, Hallam SJ.

Curr Opin Microbiol. 2016 Jun;31:209-216. doi: 10.1016/j.mib.2016.04.014. Epub 2016 May 13. Review.

31.

High-resolution phylogenetic microbial community profiling.

Singer E, Bushnell B, Coleman-Derr D, Bowman B, Bowers RM, Levy A, Gies EA, Cheng JF, Copeland A, Klenk HP, Hallam SJ, Hugenholtz P, Tringe SG, Woyke T.

ISME J. 2016 Aug;10(8):2020-32. doi: 10.1038/ismej.2015.249. Epub 2016 Feb 9.

32.

Synthesis and evaluation of a series of 6-chloro-4-methylumbelliferyl glycosides as fluorogenic reagents for screening metagenomic libraries for glycosidase activity.

Chen HM, Armstrong Z, Hallam SJ, Withers SG.

Carbohydr Res. 2016 Feb 8;421:33-39. doi: 10.1016/j.carres.2015.12.010. Epub 2016 Jan 5.

PMID:
26774876
33.

Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities.

Lawson CE, Strachan CR, Williams DD, Koziel S, Hallam SJ, Budwill K.

Appl Environ Microbiol. 2015 Nov;81(22):7924-37. doi: 10.1128/AEM.01737-15. Epub 2015 Sep 4.

34.

Biocatalysts for biomass deconstruction from environmental genomics.

Armstrong Z, Mewis K, Strachan C, Hallam SJ.

Curr Opin Chem Biol. 2015 Dec;29:18-25. doi: 10.1016/j.cbpa.2015.06.032. Epub 2015 Jul 29. Review.

PMID:
26231123
35.

Viral dark matter and virus-host interactions resolved from publicly available microbial genomes.

Roux S, Hallam SJ, Woyke T, Sullivan MB.

Elife. 2015 Jul 22;4. doi: 10.7554/eLife.08490.

36.

Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics.

Nobu MK, Dodsworth JA, Murugapiran SK, Rinke C, Gies EA, Webster G, Schwientek P, Kille P, Parkes RJ, Sass H, Jørgensen BB, Weightman AJ, Liu WT, Hallam SJ, Tsiamis G, Woyke T, Hedlund BP.

ISME J. 2016 Feb;10(2):273-86. doi: 10.1038/ismej.2015.97. Epub 2015 Jun 19.

37.

MetaPathways v2.5: quantitative functional, taxonomic and usability improvements.

Konwar KM, Hanson NW, Bhatia MP, Kim D, Wu SJ, Hahn AS, Morgan-Lang C, Cheung HK, Hallam SJ.

Bioinformatics. 2015 Oct 15;31(20):3345-7. doi: 10.1093/bioinformatics/btv361. Epub 2015 Jun 15.

38.

In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3).

Youssef NH, Farag IF, Rinke C, Hallam SJ, Woyke T, Elshahed MS.

PLoS One. 2015 Jun 3;10(6):e0127499. doi: 10.1371/journal.pone.0127499. eCollection 2015.

39.

Previously unknown evolutionary groups dominate the ssDNA gokushoviruses in oxic and anoxic waters of a coastal marine environment.

Labonté JM, Hallam SJ, Suttle CA.

Front Microbiol. 2015 Apr 22;6:315. doi: 10.3389/fmicb.2015.00315. eCollection 2015.

40.

Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions.

Chow CE, Winget DM, White RA 3rd, Hallam SJ, Suttle CA.

Front Microbiol. 2015 Apr 10;6:265. doi: 10.3389/fmicb.2015.00265. eCollection 2015.

41.

Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils.

VanInsberghe D, Maas KR, Cardenas E, Strachan CR, Hallam SJ, Mohn WW.

ISME J. 2015 Nov;9(11):2435-41. doi: 10.1038/ismej.2015.54. Epub 2015 Apr 24.

42.

Rare taxa have potential to make metabolic contributions in enhanced biological phosphorus removal ecosystems.

Lawson CE, Strachan BJ, Hanson NW, Hahn AS, Hall ER, Rabinowitz B, Mavinic DS, Ramey WD, Hallam SJ.

Environ Microbiol. 2015 Dec;17(12):4979-93. doi: 10.1111/1462-2920.12875. Epub 2015 May 14.

PMID:
25857222
43.

Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton.

Labonté JM, Swan BK, Poulos B, Luo H, Koren S, Hallam SJ, Sullivan MB, Woyke T, Wommack KE, Stepanauskas R.

ISME J. 2015 Nov;9(11):2386-99. doi: 10.1038/ismej.2015.48. Epub 2015 Apr 7.

44.

Development of human B cells and antibodies following human hematopoietic stem cell transplantation to Rag2(-/-)γc(-/-) mice.

Tanner A, Hallam SJ, Nielsen SJ, Cuadra GI, Berges BK.

Transpl Immunol. 2015 Jun;32(3):144-50. doi: 10.1016/j.trim.2015.03.002. Epub 2015 Apr 2.

PMID:
25843523
45.

Microbes don't play solitaire: how cooperation trumps isolation in the microbial world.

Hallam SJ, McCutcheon JP.

Environ Microbiol Rep. 2015 Feb;7(1):26-8. doi: 10.1111/1758-2229.12248. No abstract available.

PMID:
25721597
46.

Illuminating microbial dark matter in meromictic Sakinaw Lake.

Gies EA, Konwar KM, Beatty JT, Hallam SJ.

Appl Environ Microbiol. 2014 Nov;80(21):6807-18. doi: 10.1128/AEM.01774-14. Epub 2014 Aug 29.

47.

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics.

Roux S, Hawley AK, Torres Beltran M, Scofield M, Schwientek P, Stepanauskas R, Woyke T, Hallam SJ, Sullivan MB.

Elife. 2014 Aug 29;3:e03125. doi: 10.7554/eLife.03125.

48.

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes.

Hawley AK, Brewer HM, Norbeck AD, Paša-Tolić L, Hallam SJ.

Proc Natl Acad Sci U S A. 2014 Aug 5;111(31):11395-400. doi: 10.1073/pnas.1322132111. Epub 2014 Jul 22.

49.

Metabolic pathways for the whole community.

Hanson NW, Konwar KM, Hawley AK, Altman T, Karp PD, Hallam SJ.

BMC Genomics. 2014 Jul 22;15:619. doi: 10.1186/1471-2164-15-619.

50.

Metagenomic scaffolds enable combinatorial lignin transformation.

Strachan CR, Singh R, VanInsberghe D, Ievdokymenko K, Budwill K, Mohn WW, Eltis LD, Hallam SJ.

Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):10143-8. doi: 10.1073/pnas.1401631111. Epub 2014 Jun 30.

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