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Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock.

Lavy A, McGrath DG, Matheus Carnevali PB, Wan J, Dong W, Tokunaga TK, Thomas BC, Williams KH, Hubbard SS, Banfield JF.

Ecol Evol. 2019 Jun 13;9(12):6869-6900. doi: 10.1002/ece3.5254. eCollection 2019 Jun.


Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms.

Diamond S, Andeer PF, Li Z, Crits-Christoph A, Burstein D, Anantharaman K, Lane KR, Thomas BC, Pan C, Northen TR, Banfield JF.

Nat Microbiol. 2019 Aug;4(8):1356-1367. doi: 10.1038/s41564-019-0449-y. Epub 2019 May 20.


A Systematic Review of Studies of the STOPP/START 2015 and American Geriatric Society Beers 2015 Criteria in Patients ≥ 65 Years.

Thomas RE, Thomas BC.

Curr Aging Sci. 2019;12(2):121-154. doi: 10.2174/1874609812666190516093742.


Author Correction: Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria.

Matheus Carnevali PB, Schulz F, Castelle CJ, Kantor RS, Shih PM, Sharon I, Santini JM, Olm MR, Amano Y, Thomas BC, Anantharaman K, Burstein D, Becraft ED, Stepanauskas R, Woyke T, Banfield JF.

Nat Commun. 2019 Mar 26;10(1):1451. doi: 10.1038/s41467-019-09423-3.


Megaphages infect Prevotella and variants are widespread in gut microbiomes.

Devoto AE, Santini JM, Olm MR, Anantharaman K, Munk P, Tung J, Archie EA, Turnbaugh PJ, Seed KD, Blekhman R, Aarestrup FM, Thomas BC, Banfield JF.

Nat Microbiol. 2019 Apr;4(4):693-700. doi: 10.1038/s41564-018-0338-9. Epub 2019 Jan 28.


Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria.

Matheus Carnevali PB, Schulz F, Castelle CJ, Kantor RS, Shih PM, Sharon I, Santini JM, Olm MR, Amano Y, Thomas BC, Anantharaman K, Burstein D, Becraft ED, Stepanauskas R, Woyke T, Banfield JF.

Nat Commun. 2019 Jan 28;10(1):463. doi: 10.1038/s41467-018-08246-y. Erratum in: Nat Commun. 2019 Mar 26;10(1):1451.


A systematic review of injuries in gymnastics.

Thomas RE, Thomas BC.

Phys Sportsmed. 2019 Feb;47(1):96-121. doi: 10.1080/00913847.2018.1527646. Epub 2018 Oct 8.


Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome.

Goltsman DSA, Sun CL, Proctor DM, DiGiulio DB, Robaczewska A, Thomas BC, Shaw GM, Stevenson DK, Holmes SP, Banfield JF, Relman DA.

Genome Res. 2018 Oct;28(10):1467-1480. doi: 10.1101/gr.236000.118. Epub 2018 Sep 19.


Terrestrial effects of moderately nearby supernovae.

Melott AL, Thomas BC.

Lethaia. 2018 Jul;51(3):325-329. doi: 10.1111/let.12256. Epub 2018 Jan 15.


Development and Verification of an RNA Sequencing (RNA-Seq) Assay for the Detection of Gene Fusions in Tumors.

Winters JL, Davila JI, McDonald AM, Nair AA, Fadra N, Wehrs RN, Thomas BC, Balcom JR, Jin L, Wu X, Voss JS, Klee EW, Oliver GR, Graham RP, Neff JL, Rumilla KM, Aypar U, Kipp BR, Jenkins RB, Jen J, Halling KC.

J Mol Diagn. 2018 Jul;20(4):495-511. doi: 10.1016/j.jmoldx.2018.03.007. Epub 2018 Jun 19.


The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms.

Brooks B, Olm MR, Firek BA, Baker R, Geller-McGrath D, Reimer SR, Soenjoyo KR, Yip JS, Dahan D, Thomas BC, Morowitz MJ, Banfield JF.

Microbiome. 2018 Jun 20;6(1):112. doi: 10.1186/s40168-018-0493-5.


Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis.

Crits-Christoph A, Diamond S, Butterfield CN, Thomas BC, Banfield JF.

Nature. 2018 Jun;558(7710):440-444. doi: 10.1038/s41586-018-0207-y. Epub 2018 Jun 13.


Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy.

Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, Banfield JF.

Nat Microbiol. 2018 Jul;3(7):836-843. doi: 10.1038/s41564-018-0171-1. Epub 2018 May 28.


Spindle cell rhabdomyosarcoma of bone with FUS-TFCP2 fusion: confirmation of a very recently described rhabdomyosarcoma subtype.

Dashti NK, Wehrs RN, Thomas BC, Nair A, Davila J, Buckner JC, Martinez AP, Sukov WR, Halling KC, Howe BM, Folpe AL.

Histopathology. 2018 Sep;73(3):514-520. doi: 10.1111/his.13649. Epub 2018 Jun 29.


Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles.

Brown CT, Xiong W, Olm MR, Thomas BC, Baker R, Firek B, Morowitz MJ, Hettich RL, Banfield JF.

MBio. 2018 Apr 10;9(2). pii: e00441-18. doi: 10.1128/mBio.00441-18.


Response to Commercial Genetic Testing and the Future of the Genetic Counseling Profession.

Goodenberger ML, Thomas BC, Kruisselbrink T.

J Genet Couns. 2018 Jun;27(3):530-532. doi: 10.1007/s10897-018-0253-5. Epub 2018 Mar 23. No abstract available.


Genome-reconstruction for eukaryotes from complex natural microbial communities.

West PT, Probst AJ, Grigoriev IV, Thomas BC, Banfield JF.

Genome Res. 2018 Apr;28(4):569-580. doi: 10.1101/gr.228429.117. Epub 2018 Mar 1.


Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle.

Anantharaman K, Hausmann B, Jungbluth SP, Kantor RS, Lavy A, Warren LA, Rappé MS, Pester M, Loy A, Thomas BC, Banfield JF.

ISME J. 2018 Jun;12(7):1715-1728. doi: 10.1038/s41396-018-0078-0. Epub 2018 Feb 21.


Update on Family-Based Interventions to Prevent Children and Adolescents Using Tobacco.

Thomas RE, Baker P, Thomas BC.

Acad Pediatr. 2018 Jul;18(5):483-484. doi: 10.1016/j.acap.2018.02.004. Epub 2018 Feb 8. Review. No abstract available.


Increasing genetic counseling referral rates through bundled interventions after ovarian cancer diagnosis.

Swanson CL, Kumar A, Maharaj JM, Kemppainen JL, Thomas BC, Weinhold MR, Slaby KM, Mara KC, Wick MJ, Bakkum-Gamez JN.

Gynecol Oncol. 2018 Apr;149(1):121-126. doi: 10.1016/j.ygyno.2018.01.033. Epub 2018 Feb 3.


Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface.

Probst AJ, Ladd B, Jarett JK, Geller-McGrath DE, Sieber CMK, Emerson JB, Anantharaman K, Thomas BC, Malmstrom RR, Stieglmeier M, Klingl A, Woyke T, Ryan MC, Banfield JF.

Nat Microbiol. 2018 Mar;3(3):328-336. doi: 10.1038/s41564-017-0098-y. Epub 2018 Jan 29.


Systematic review of injuries in mixed martial arts.

Thomas RE, Thomas BC.

Phys Sportsmed. 2018 May;46(2):155-167. doi: 10.1080/00913847.2018.1430451. Epub 2018 Jan 25. Review.


Photobiological Effects at Earth's Surface Following a 50 pc Supernova.

Thomas BC.

Astrobiology. 2018 May;18(5):481-490. doi: 10.1089/ast.2017.1730. Epub 2017 Dec 28.


A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges.

Lavy A, Keren R, Yu K, Thomas BC, Alvarez-Cohen L, Banfield JF, Ilan M.

Environ Microbiol. 2018 Feb;20(2):800-814. doi: 10.1111/1462-2920.14013. Epub 2017 Dec 15.


Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome.

Brooks B, Olm MR, Firek BA, Baker R, Thomas BC, Morowitz MJ, Banfield JF.

Nat Commun. 2017 Nov 27;8(1):1814. doi: 10.1038/s41467-017-02018-w.


Complete 4.55-Megabase-Pair Genome of "Candidatus Fluviicola riflensis," Curated from Short-Read Metagenomic Sequences.

Banfield JF, Anantharaman K, Williams KH, Thomas BC.

Genome Announc. 2017 Nov 22;5(47). pii: e01299-17. doi: 10.1128/genomeA.01299-17.


Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome.

Dudek NK, Sun CL, Burstein D, Kantor RS, Aliaga Goltsman DS, Bik EM, Thomas BC, Banfield JF, Relman DA.

Curr Biol. 2017 Dec 18;27(24):3752-3762.e6. doi: 10.1016/j.cub.2017.10.040. Epub 2017 Nov 16.


Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment.

Ino K, Hernsdorf AW, Konno U, Kouduka M, Yanagawa K, Kato S, Sunamura M, Hirota A, Togo YS, Ito K, Fukuda A, Iwatsuki T, Mizuno T, Komatsu DD, Tsunogai U, Ishimura T, Amano Y, Thomas BC, Banfield JF, Suzuki Y.

ISME J. 2018 Jan;12(1):31-47. doi: 10.1038/ismej.2017.140. Epub 2017 Sep 8.


Injuries in taekwando: systematic review.

Thomas RE, Thomas BC, Vaska MM.

Phys Sportsmed. 2017 Nov;45(4):372-390. doi: 10.1080/00913847.2017.1369193. Epub 2017 Sep 8. Review.


Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics.

Finstad KM, Probst AJ, Thomas BC, Andersen GL, Demergasso C, Echeverría A, Amundson RG, Banfield JF.

Front Microbiol. 2017 Jul 28;8:1435. doi: 10.3389/fmicb.2017.01435. eCollection 2017.


Clinical outcomes after implantation of a toric intraocular lens with a transitional conic toric surface.

Thomas BC, Khoramnia R, Auffarth GU, Holzer MP.

Br J Ophthalmol. 2018 Mar;102(3):313-316. doi: 10.1136/bjophthalmol-2017-310386. Epub 2017 Aug 3.


A Supernova at 50 pc: Effects on the Earth's Atmosphere and Biota.

Melott AL, Thomas BC, Kachelrieß M, Semikoz DV, Overholt AC.

Astrophys J. 2017 May 10;840(2). pii: 105. doi: 10.3847/1538-4357/aa6c57. Epub 2017 May 12.


Commentary: restarting NTD programme activities after the Ebola outbreak in Liberia.

Thomas BC, Kollie K, Koudou B, Mackenzie C.

Infect Dis Poverty. 2017 May 1;6(1):52. doi: 10.1186/s40249-017-0272-8.


Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea.

Paul BG, Burstein D, Castelle CJ, Handa S, Arambula D, Czornyj E, Thomas BC, Ghosh P, Miller JF, Banfield JF, Valentine DL.

Nat Microbiol. 2017 Apr 3;2:17045. doi: 10.1038/nmicrobiol.2017.45.


Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments.

Hernsdorf AW, Amano Y, Miyakawa K, Ise K, Suzuki Y, Anantharaman K, Probst A, Burstein D, Thomas BC, Banfield JF.

ISME J. 2017 Aug;11(8):1915-1929. doi: 10.1038/ismej.2017.39. Epub 2017 Mar 28.


The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis.

Olm MR, Butterfield CN, Copeland A, Boles TC, Thomas BC, Banfield JF.

MBio. 2017 Feb 21;8(1). pii: e01969-16. doi: 10.1128/mBio.01969-16.


Genome-resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings.

Rahman SF, Kantor RS, Huddy R, Thomas BC, van Zyl AW, Harrison STL, Banfield JF.

Microbiologyopen. 2017 Jun;6(3). doi: 10.1002/mbo3.446. Epub 2017 Feb 19.


Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation.

Kantor RS, Huddy RJ, Iyer R, Thomas BC, Brown CT, Anantharaman K, Tringe S, Hettich RL, Harrison ST, Banfield JF.

Environ Sci Technol. 2017 Mar 7;51(5):2944-2953. doi: 10.1021/acs.est.6b04477. Epub 2017 Feb 13.


Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates.

Olm MR, Brown CT, Brooks B, Firek B, Baker R, Burstein D, Soenjoyo K, Thomas BC, Morowitz M, Banfield JF.

Genome Res. 2017 Apr;27(4):601-612. doi: 10.1101/gr.213256.116. Epub 2017 Jan 10.


Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation.

Castelle CJ, Brown CT, Thomas BC, Williams KH, Banfield JF.

Sci Rep. 2017 Jan 9;7:40101. doi: 10.1038/srep40101.


New CRISPR-Cas systems from uncultivated microbes.

Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K, Thomas BC, Doudna JA, Banfield JF.

Nature. 2017 Feb 9;542(7640):237-241. doi: 10.1038/nature21059. Epub 2016 Dec 22.


Influence on intraocular lens power calculation of corneal radii measurement using an image-guided system.

Thomas BC, Mueller A, Auffarth GU, Holzer MP.

J Cataract Refract Surg. 2016 Nov;42(11):1588-1594. doi: 10.1016/j.jcrs.2016.08.028.


Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone.

Butterfield CN, Li Z, Andeer PF, Spaulding S, Thomas BC, Singh A, Hettich RL, Suttle KB, Probst AJ, Tringe SG, Northen T, Pan C, Banfield JF.

PeerJ. 2016 Nov 8;4:e2687. eCollection 2016.


Measurement of bacterial replication rates in microbial communities.

Brown CT, Olm MR, Thomas BC, Banfield JF.

Nat Biotechnol. 2016 Dec;34(12):1256-1263. doi: 10.1038/nbt.3704. Epub 2016 Nov 7.


Atmospheric constituents and surface-level UVB: Implications for a paleoaltimetry proxy and attempts to reconstruct UV exposure during volcanic episodes.

Thomas BC, Goracke BD, Dalton SM.

Earth Planet Sci Lett. 2016 Nov 1;453:141-151. doi: 10.1016/j.epsl.2016.08.014. Epub 2016 Aug 26.


RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria.

Wrighton KC, Castelle CJ, Varaljay VA, Satagopan S, Brown CT, Wilkins MJ, Thomas BC, Sharon I, Williams KH, Tabita FR, Banfield JF.

ISME J. 2016 Nov;10(11):2702-2714. doi: 10.1038/ismej.2016.53. Epub 2016 May 3.


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.


Evolution and oncological outcomes of a contemporary radical prostatectomy practice in a UK regional tertiary referral centre.

Gnanapragasam VJ, Thurtle D, Srinivasan A, Volanis D, George A, Lophatananon A, Stearn S, Warren AY, Lamb AD, Shaw G, Sharma N, Thomas BC, Tran MG, Neal DE, Shah NC.

BJU Int. 2016 Nov;118(5):779-784. doi: 10.1111/bju.13513. Epub 2016 May 24.


Whole blood mRNA in prostate cancer reveals a four-gene androgen regulated panel.

Thomas BC, Kay JD, Menon S, Vowler SL, Dawson SN, Bucklow LJ, Luxton HJ, Johnston T, Massie CE, Pugh M, Warren AY, Barker P, Burling K, Lynch AG, George A, Burge J, Corcoran M, Stearn S, Lamb AD, Sharma NL, Shaw GL, Neal DE, Whitaker HC.

Endocr Relat Cancer. 2016 Oct;23(10):797-812. doi: 10.1530/ERC-16-0287. Epub 2016 Aug 30.


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.


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