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Items: 41

1.

Genome-Resolved Metagenomics Extends the Environmental Distribution of the Verrucomicrobia Phylum to the Deep Terrestrial Subsurface.

Nixon SL, Daly RA, Borton MA, Solden LM, Welch SA, Cole DR, Mouser PJ, Wilkins MJ, Wrighton KC.

mSphere. 2019 Dec 18;4(6). pii: e00613-19. doi: 10.1128/mSphere.00613-19.

2.

Uncovering the Diversity and Activity of Methylotrophic Methanogens in Freshwater Wetland Soils.

Narrowe AB, Borton MA, Hoyt DW, Smith GJ, Daly RA, Angle JC, Eder EK, Wong AR, Wolfe RA, Pappas A, Bohrer G, Miller CS, Wrighton KC.

mSystems. 2019 Dec 3;4(6). pii: e00320-19. doi: 10.1128/mSystems.00320-19.

3.

Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes.

Roux S, Krupovic M, Daly RA, Borges AL, Nayfach S, Schulz F, Sharrar A, Matheus Carnevali PB, Cheng JF, Ivanova NN, Bondy-Denomy J, Wrighton KC, Woyke T, Visel A, Kyrpides NC, Eloe-Fadrosh EA.

Nat Microbiol. 2019 Nov;4(11):1895-1906. doi: 10.1038/s41564-019-0510-x. Epub 2019 Jul 22.

4.

Deep-Subsurface Pressure Stimulates Metabolic Plasticity in Shale-Colonizing Halanaerobium spp.

Booker AE, Hoyt DW, Meulia T, Eder E, Nicora CD, Purvine SO, Daly RA, Moore JD, Wunch K, Pfiffner SM, Lipton MS, Mouser PJ, Wrighton KC, Wilkins MJ.

Appl Environ Microbiol. 2019 May 30;85(12). pii: e00018-19. doi: 10.1128/AEM.00018-19. Print 2019 Jun 15.

5.

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.

6.

Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing.

Daly RA, Roux S, Borton MA, Morgan DM, Johnston MD, Booker AE, Hoyt DW, Meulia T, Wolfe RA, Hanson AJ, Mouser PJ, Moore JD, Wunch K, Sullivan MB, Wrighton KC, Wilkins MJ.

Nat Microbiol. 2019 Feb;4(2):352-361. doi: 10.1038/s41564-018-0312-6. Epub 2018 Dec 3.

7.

Members of Marinobacter and Arcobacter Influence System Biogeochemistry During Early Production of Hydraulically Fractured Natural Gas Wells in the Appalachian Basin.

Evans MV, Panescu J, Hanson AJ, Welch SA, Sheets JM, Nastasi N, Daly RA, Cole DR, Darrah TH, Wilkins MJ, Wrighton KC, Mouser PJ.

Front Microbiol. 2018 Nov 15;9:2646. doi: 10.3389/fmicb.2018.02646. eCollection 2018.

8.

Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland.

Smith GJ, Angle JC, Solden LM, Borton MA, Morin TH, Daly RA, Johnston MD, Stefanik KC, Wolfe R, Gil B, Wrighton KC.

mBio. 2018 Nov 6;9(6). pii: e00815-18. doi: 10.1128/mBio.00815-18.

9.

Comparative genomics and physiology of the genus Methanohalophilus, a prevalent methanogen in hydraulically fractured shale.

Borton MA, Daly RA, O'Banion B, Hoyt DW, Marcus DN, Welch S, Hastings SS, Meulia T, Wolfe RA, Booker AE, Sharma S, Cole DR, Wunch K, Moore JD, Darrah TH, Wilkins MJ, Wrighton KC.

Environ Microbiol. 2018 Dec;20(12):4596-4611. doi: 10.1111/1462-2920.14467.

PMID:
30394652
10.

Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem.

Solden LM, Naas AE, Roux S, Daly RA, Collins WB, Nicora CD, Purvine SO, Hoyt DW, Schückel J, Jørgensen B, Willats W, Spalinger DE, Firkins JL, Lipton MS, Sullivan MB, Pope PB, Wrighton KC.

Nat Microbiol. 2018 Nov;3(11):1274-1284. doi: 10.1038/s41564-018-0225-4. Epub 2018 Oct 24.

11.

Characterizing the Deep Terrestrial Subsurface Microbiome.

Daly RA, Wrighton KC, Wilkins MJ.

Methods Mol Biol. 2018;1849:1-15. doi: 10.1007/978-1-4939-8728-3_1.

PMID:
30298244
12.

Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales.

Borton MA, Hoyt DW, Roux S, Daly RA, Welch SA, Nicora CD, Purvine S, Eder EK, Hanson AJ, Sheets JM, Morgan DM, Wolfe RA, Sharma S, Carr TR, Cole DR, Mouser PJ, Lipton MS, Wilkins MJ, Wrighton KC.

Proc Natl Acad Sci U S A. 2018 Jul 10;115(28):E6585-E6594. doi: 10.1073/pnas.1800155115. Epub 2018 Jun 25.

13.

Draft Genome Sequences of Two Chemosynthetic Arcobacter Strains Isolated from Hydraulically Fractured Wells in Marcellus and Utica Shales.

Panescu J, Daly RA, Wrighton KC, Mouser PJ.

Genome Announc. 2018 May 17;6(20). pii: e00159-18. doi: 10.1128/genomeA.00159-18.

14.

Draft Genome Sequences of Marinobacter Strains Recovered from Utica Shale-Produced Fluids.

Tummings S, Panescu J, Daly RA, Wrighton KC, Mouser PJ.

Genome Announc. 2018 Apr 5;6(14). pii: e00155-18. doi: 10.1128/genomeA.00155-18.

15.

Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions.

Angle JC, Morin TH, Solden LM, Narrowe AB, Smith GJ, Borton MA, Rey-Sanchez C, Daly RA, Mirfenderesgi G, Hoyt DW, Riley WJ, Miller CS, Bohrer G, Wrighton KC.

Nat Commun. 2017 Nov 16;8(1):1567. doi: 10.1038/s41467-017-01753-4.

16.

Draft Genome Sequences of Multiple Frackibacter Strains Isolated from Hydraulically Fractured Shale Environments.

Booker AE, Johnston MD, Daly RA, Wrighton KC, Wilkins MJ.

Genome Announc. 2017 Aug 10;5(32). pii: e00608-17. doi: 10.1128/genomeA.00608-17.

17.

Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales.

Booker AE, Borton MA, Daly RA, Welch SA, Nicora CD, Hoyt DW, Wilson T, Purvine SO, Wolfe RA, Sharma S, Mouser PJ, Cole DR, Lipton MS, Wrighton KC, Wilkins MJ.

mSphere. 2017 Jul 5;2(4). pii: e00257-17. doi: 10.1128/mSphereDirect.00257-17. eCollection 2017 Jul-Aug.

18.

Chemical and pathogen-induced inflammation disrupt the murine intestinal microbiome.

Borton MA, Sabag-Daigle A, Wu J, Solden LM, O'Banion BS, Daly RA, Wolfe RA, Gonzalez JF, Wysocki VH, Ahmer BMM, Wrighton KC.

Microbiome. 2017 Apr 27;5(1):47. doi: 10.1186/s40168-017-0264-8.

19.

High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils.

Narrowe AB, Angle JC, Daly RA, Stefanik KC, Wrighton KC, Miller CS.

Environ Microbiol. 2017 Jun;19(6):2192-2209. doi: 10.1111/1462-2920.13703. Epub 2017 Mar 28.

PMID:
28217877
20.

New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11.

Solden LM, Hoyt DW, Collins WB, Plank JE, Daly RA, Hildebrand E, Beavers TJ, Wolfe R, Nicora CD, Purvine SO, Carstensen M, Lipton MS, Spalinger DE, Firkins JL, Wolfe BA, Wrighton KC.

ISME J. 2017 Mar;11(3):691-703. doi: 10.1038/ismej.2016.150. Epub 2016 Dec 13.

21.

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales.

Daly RA, Borton MA, Wilkins MJ, Hoyt DW, Kountz DJ, Wolfe RA, Welch SA, Marcus DN, Trexler RV, MacRae JD, Krzycki JA, Cole DR, Mouser PJ, Wrighton KC.

Nat Microbiol. 2016 Sep 5;1:16146. doi: 10.1038/nmicrobiol.2016.146.

PMID:
27595198
22.

Trends and future challenges in sampling the deep terrestrial biosphere.

Wilkins MJ, Daly RA, Mouser PJ, Trexler R, Sharma S, Cole DR, Wrighton KC, Biddle JF, Denis EH, Fredrickson JK, Kieft TL, Onstott TC, Peterson L, Pfiffner SM, Phelps TJ, Schrenk MO.

Front Microbiol. 2014 Sep 12;5:481. doi: 10.3389/fmicb.2014.00481. eCollection 2014.

23.

Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains.

Doll HM, Armitage DW, Daly RA, Emerson JB, Goltsman DS, Yelton AP, Kerekes J, Firestone MK, Potts MD.

BMC Microbiol. 2013 Nov 15;13:259. doi: 10.1186/1471-2180-13-259.

24.

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses.

Blazewicz SJ, Barnard RL, Daly RA, Firestone MK.

ISME J. 2013 Nov;7(11):2061-8. doi: 10.1038/ismej.2013.102. Epub 2013 Jul 4.

25.

Piracy in the high trees: ectomycorrhizal fungi from an aerial 'canopy soil' microhabitat.

Orlovich DA, Draffin SJ, Daly RA, Stephenson SL.

Mycologia. 2013 Jan-Feb;105(1):52-60. doi: 10.3852/11-307. Epub 2012 Jul 9.

PMID:
22778170
26.

Posterior dislocation of sternoclavicular joint encroaching on ipsilateral vessels in 2 pediatric patients.

Sykes JA, Ezetendu C, Sivitz A, Lee J Jr, Desai H, Norton K, Daly RA, Kalyanaraman M.

Pediatr Emerg Care. 2011 Apr;27(4):327-30. doi: 10.1097/PEC.0b013e318217b58f.

PMID:
21467887
27.

Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients.

Cox MJ, Allgaier M, Taylor B, Baek MS, Huang YJ, Daly RA, Karaoz U, Andersen GL, Brown R, Fujimura KE, Wu B, Tran D, Koff J, Kleinhenz ME, Nielson D, Brodie EL, Lynch SV.

PLoS One. 2010 Jun 23;5(6):e11044. doi: 10.1371/journal.pone.0011044.

28.

Bacterial community structure corresponds to performance during cathodic nitrate reduction.

Wrighton KC, Virdis B, Clauwaert P, Read ST, Daly RA, Boon N, Piceno Y, Andersen GL, Coates JD, Rabaey K.

ISME J. 2010 Nov;4(11):1443-55. doi: 10.1038/ismej.2010.66. Epub 2010 Jun 3.

PMID:
20520654
29.

Influences of organic carbon supply rate on uranium bioreduction in initially oxidizing, contaminated sediment.

Tokunaga TK, Wan J, Kim Y, Daly RA, Brodie EL, Hazen TC, Herman D, Firestone MK.

Environ Sci Technol. 2008 Dec 1;42(23):8901-7.

PMID:
19192816
30.

Genetic analysis of the Salmonella transcription factor HilA.

Daly RA, Lostroh CP.

Can J Microbiol. 2008 Oct;54(10):854-60. doi: 10.1139/w08-075.

PMID:
18923554
31.

The treatment of typhoid carriers with penicillin and sulphathiazole.

BIGGER JW, DALY RA.

Lancet. 1949 Feb 19;1(6547):296-9. No abstract available.

PMID:
18112608
32.

Densities of Rocks Calculated from Their Chemical Analyses.

Daly RA.

Proc Natl Acad Sci U S A. 1935 Dec;21(12):657-63. No abstract available.

33.

THE DEPTHS OF THE EARTH.

Daly RA.

Science. 1933 Jan 27;77(1987):95-102. No abstract available.

PMID:
17797838
34.

GARDINER ON CORAL REEFS.

Daly RA.

Science. 1931 Dec 4;74(1927):566-7. No abstract available.

PMID:
17807633
35.

JAY BACKUS WOODWORTH.

Daly RA, Palache C, Mather KF.

Science. 1925 Nov 20;62(1612):450-1. No abstract available.

PMID:
17835617
36.

A General Sinking of Sea-Level in Recent Time.

Daly RA.

Proc Natl Acad Sci U S A. 1920 May;6(5):246-50. No abstract available.

37.

Low-Temperature Formation of Alkaline Feldspars in Limestones.

Daly RA.

Proc Natl Acad Sci U S A. 1917 Nov;3(11):659-65. No abstract available.

38.

A New Test of the Subsidence Theory of Coral Reefs.

Daly RA.

Proc Natl Acad Sci U S A. 1916 Dec;2(12):664-70. No abstract available.

39.

MACHINE-MADE LINE DRAWINS FOR THE ILLUSTRATION OF SCIENTIFIC PAPERS.

Daly RA.

Science. 1905 Jul 21;22(551):91-3. No abstract available.

PMID:
17817687
40.

NOTES ON OCEANOGRAPHY.

Daly RA.

Science. 1901 Jun 14;13(337):951-4. No abstract available.

PMID:
17733661
41.

SCIENTIFIC EXPEDITION TO ICELAND, GREENLAND AND LABRADOR.

Daly RA.

Science. 1901 Feb 1;13(318):192. No abstract available.

PMID:
17816318

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