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Items: 36


AnnoTree: visualization and exploration of a functionally annotated microbial tree of life.

Mendler K, Chen H, Parks DH, Lobb B, Hug LA, Doxey AC.

Nucleic Acids Res. 2019 May 21;47(9):4442-4448. doi: 10.1093/nar/gkz246.


Distribution of reactive oxygen species defense mechanisms across domain bacteria.

Johnson LA, Hug LA.

Free Radic Biol Med. 2019 Aug 20;140:93-102. doi: 10.1016/j.freeradbiomed.2019.03.032. Epub 2019 Mar 29. Review.


Subsampled Assemblies and Hybrid Nucleotide Composition/Differential Coverage Binning for Genome-Resolved Metagenomics.

Hug LA.

Methods Mol Biol. 2018;1849:215-225. doi: 10.1007/978-1-4939-8728-3_14.


Sizing Up the Uncultured Microbial Majority.

Hug LA.

mSystems. 2018 Sep 25;3(5). pii: e00185-18. doi: 10.1128/mSystems.00185-18. eCollection 2018 Sep-Oct.


Widespread Antibiotic, Biocide, and Metal Resistance in Microbial Communities Inhabiting a Municipal Waste Environment and Anthropogenically Impacted River.

Collins-Fairclough AM, Co R, Ellis MC, Hug LA.

mSphere. 2018 Sep 26;3(5). pii: e00346-18. doi: 10.1128/mSphere.00346-18.


It Takes a Village: Microbial Communities Thrive through Interactions and Metabolic Handoffs.

Hug LA, Co R.

mSystems. 2018 Mar 13;3(2). pii: e00152-17. doi: 10.1128/mSystems.00152-17. eCollection 2018 Mar-Apr.


Corrigendum Correction to "Novel hydrogenosomes in the microaerophilic jakobid Stygiella incarcerata".

Leger MM, Eme L, Hug LA, Roger AJ.

Mol Biol Evol. 2017 Apr 1;34(4):1027. doi: 10.1093/molbev/msx059. No abstract available.


Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system.

Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, Thomas BC, Singh A, Wilkins MJ, Karaoz U, Brodie EL, Williams KH, Hubbard SS, Banfield JF.

Nat Commun. 2016 Oct 24;7:13219. doi: 10.1038/ncomms13219.


A new view of the tree of life.

Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdorf AW, Amano Y, Ise K, Suzuki Y, Dudek N, Relman DA, Finstad KM, Amundson R, Thomas BC, Banfield JF.

Nat Microbiol. 2016 Apr 11;1:16048. doi: 10.1038/nmicrobiol.2016.48.


Novel Hydrogenosomes in the Microaerophilic Jakobid Stygiella incarcerata.

Leger MM, Eme L, Hug LA, Roger AJ.

Mol Biol Evol. 2016 Sep;33(9):2318-36. doi: 10.1093/molbev/msw103. Epub 2016 Jun 8. Erratum in: Mol Biol Evol. 2017 Apr 1;34(4):1027.


Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations.

Probst AJ, Castelle CJ, Singh A, Brown CT, Anantharaman K, Sharon I, Hug LA, Burstein D, Emerson JB, Thomas BC, Banfield JF.

Environ Microbiol. 2017 Feb;19(2):459-474. doi: 10.1111/1462-2920.13362. Epub 2016 Jul 7.


Unusual biology across a group comprising more than 15% of domain Bacteria.

Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, Wilkins MJ, Wrighton KC, Williams KH, Banfield JF.

Nature. 2015 Jul 9;523(7559):208-11. doi: 10.1038/nature14486. Epub 2015 Jun 15.


Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages.

Hug LA, Thomas BC, Sharon I, Brown CT, Sharma R, Hettich RL, Wilkins MJ, Williams KH, Singh A, Banfield JF.

Environ Microbiol. 2016 Jan;18(1):159-73. doi: 10.1111/1462-2920.12930. Epub 2015 Jul 22.


Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem.

Andrade K, Logemann J, Heidelberg KB, Emerson JB, Comolli LR, Hug LA, Probst AJ, Keillar A, Thomas BC, Miller CS, Allen EE, Moreau JW, Brocks JJ, Banfield JF.

ISME J. 2015 Dec;9(12):2697-711. doi: 10.1038/ismej.2015.66. Epub 2015 Apr 28.


Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling.

Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, Frischkorn KR, Tringe SG, Singh A, Markillie LM, Taylor RC, Williams KH, Banfield JF.

Curr Biol. 2015 Mar 16;25(6):690-701. doi: 10.1016/j.cub.2015.01.014. Epub 2015 Feb 19.


Accurate, multi-kb reads resolve complex populations and detect rare microorganisms.

Sharon I, Kertesz M, Hug LA, Pushkarev D, Blauwkamp TA, Castelle CJ, Amirebrahimi M, Thomas BC, Burstein D, Tringe SG, Williams KH, Banfield JF.

Genome Res. 2015 Apr;25(4):534-43. doi: 10.1101/gr.183012.114. Epub 2015 Feb 9.


Aquifer environment selects for microbial species cohorts in sediment and groundwater.

Hug LA, Thomas BC, Brown CT, Frischkorn KR, Williams KH, Tringe SG, Banfield JF.

ISME J. 2015 Aug;9(8):1846-56. doi: 10.1038/ismej.2015.2. Epub 2015 Feb 3.


Metatranscriptome of an anaerobic benzene-degrading, nitrate-reducing enrichment culture reveals involvement of carboxylation in benzene ring activation.

Luo F, Gitiafroz R, Devine CE, Gong Y, Hug LA, Raskin L, Edwards EA.

Appl Environ Microbiol. 2014 Jul;80(14):4095-107. doi: 10.1128/AEM.00717-14. Epub 2014 May 2.


New insights into Dehalococcoides mccartyi metabolism from a reconstructed metabolic network-based systems-level analysis of D. mccartyi transcriptomes.

Islam MA, Waller AS, Hug LA, Provart NJ, Edwards EA, Mahadevan R.

PLoS One. 2014 Apr 14;9(4):e94808. doi: 10.1371/journal.pone.0094808. eCollection 2014.


Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer.

Wrighton KC, Castelle CJ, Wilkins MJ, Hug LA, Sharon I, Thomas BC, Handley KM, Mullin SW, Nicora CD, Singh A, Lipton MS, Long PE, Williams KH, Banfield JF.

ISME J. 2014 Jul;8(7):1452-63. doi: 10.1038/ismej.2013.249. Epub 2014 Mar 13.


Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling.

Hug LA, Castelle CJ, Wrighton KC, Thomas BC, Sharon I, Frischkorn KR, Williams KH, Tringe SG, Banfield JF.

Microbiome. 2013 Aug 5;1(1):22. doi: 10.1186/2049-2618-1-22.


Diversity of reductive dehalogenase genes from environmental samples and enrichment cultures identified with degenerate primer PCR screens.

Hug LA, Edwards EA.

Front Microbiol. 2013 Nov 19;4:341. doi: 10.3389/fmicb.2013.00341. eCollection 2013. Erratum in: Front Microbiol. 2015;6:30.


Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla.

Kantor RS, Wrighton KC, Handley KM, Sharon I, Hug LA, Castelle CJ, Thomas BC, Banfield JF.

mBio. 2013 Oct 22;4(5):e00708-13. doi: 10.1128/mBio.00708-13.


The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria.

Di Rienzi SC, Sharon I, Wrighton KC, Koren O, Hug LA, Thomas BC, Goodrich JK, Bell JT, Spector TD, Banfield JF, Ley RE.

Elife. 2013 Oct 1;2:e01102. doi: 10.7554/eLife.01102.


Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment.

Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen JA, Banfield JF.

Nat Commun. 2013;4:2120. doi: 10.1038/ncomms3120.


Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases.

Hug LA, Maphosa F, Leys D, Löffler FE, Smidt H, Edwards EA, Adrian L.

Philos Trans R Soc Lond B Biol Sci. 2013 Mar 11;368(1616):20120322. doi: 10.1098/rstb.2012.0322. Print 2013 Apr 19. Review.


Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community.

Hug LA, Beiko RG, Rowe AR, Richardson RE, Edwards EA.

BMC Genomics. 2012 Jul 23;13:327. doi: 10.1186/1471-2164-13-327.


Discovery of a trans-dichloroethene-respiring Dehalogenimonas species in the 1,1,2,2-tetrachloroethane-dechlorinating WBC-2 consortium.

Manchester MJ, Hug LA, Zarek M, Zila A, Edwards EA.

Appl Environ Microbiol. 2012 Aug;78(15):5280-7. doi: 10.1128/AEM.00384-12. Epub 2012 May 25.


Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae.

Wagner DD, Hug LA, Hatt JK, Spitzmiller MR, Padilla-Crespo E, Ritalahti KM, Edwards EA, Konstantinidis KT, Löffler FE.

BMC Genomics. 2012 May 22;13:200. doi: 10.1186/1471-2164-13-200.


Transcriptional analysis of a Dehalococcoides-containing microbial consortium reveals prophage activation.

Waller AS, Hug LA, Mo K, Radford DR, Maxwell KL, Edwards EA.

Appl Environ Microbiol. 2012 Feb;78(4):1178-86. doi: 10.1128/AEM.06416-11. Epub 2011 Dec 16.


Design and verification of a pangenome microarray oligonucleotide probe set for Dehalococcoides spp.

Hug LA, Salehi M, Nuin P, Tillier ER, Edwards EA.

Appl Environ Microbiol. 2011 Aug;77(15):5361-9. doi: 10.1128/AEM.00063-11. Epub 2011 Jun 10.


Site-specific mobilization of vinyl chloride respiration islands by a mechanism common in Dehalococcoides.

McMurdie PJ, Hug LA, Edwards EA, Holmes S, Spormann AM.

BMC Genomics. 2011 Jun 2;12:287. doi: 10.1186/1471-2164-12-287.


Phylogenetic distributions and histories of proteins involved in anaerobic pyruvate metabolism in eukaryotes.

Hug LA, Stechmann A, Roger AJ.

Mol Biol Evol. 2010 Feb;27(2):311-24. doi: 10.1093/molbev/msp237. Epub 2009 Oct 5.


The impact of fossils and taxon sampling on ancient molecular dating analyses.

Hug LA, Roger AJ.

Mol Biol Evol. 2007 Aug;24(8):1889-97. Epub 2007 Jun 7.


The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation.

Roger AJ, Hug LA.

Philos Trans R Soc Lond B Biol Sci. 2006 Jun 29;361(1470):1039-54. Review.

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