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Items: 1 to 50 of 76

1.

Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere.

Doud DFR, Bowers RM, Schulz F, De Raad M, Deng K, Tarver A, Glasgow E, Vander Meulen K, Fox B, Deutsch S, Yoshikuni Y, Northen T, Hedlund BP, Singer SW, Ivanova N, Woyke T.

ISME J. 2019 Nov 21. doi: 10.1038/s41396-019-0557-y. [Epub ahead of print]

PMID:
31754206
2.

Isolation and Characterization of Bacterial Cellulase Producers for Biomass Deconstruction: A Microbiology Laboratory Course.

Barajas JF, Wehrs M, To M, Cruickshanks L, Urban R, McKee A, Gladden J, Goh EB, Brown ME, Pierotti D, Carothers JM, Mukhopadhyay A, Keasling JD, Fortman JL, Singer SW, Bailey CB.

J Microbiol Biol Educ. 2019 Jul 26;20(2). pii: 20.2.34. doi: 10.1128/jmbe.v20i2.1723. eCollection 2019.

3.

Guanidine Riboswitch-Regulated Efflux Transporters Protect Bacteria against Ionic Liquid Toxicity.

Higgins DA, Gladden JM, Kimbrel JA, Simmons BA, Singer SW, Thelen MP.

J Bacteriol. 2019 Jun 10;201(13). pii: e00069-19. doi: 10.1128/JB.00069-19. Print 2019 Jul 1.

4.

Methyl ketone production by Pseudomonas putida is enhanced by plant-derived amino acids.

Dong J, Chen Y, Benites VT, Baidoo EEK, Petzold CJ, Beller HR, Eudes A, Scheller HV, Adams PD, Mukhopadhyay A, Simmons BA, Singer SW.

Biotechnol Bioeng. 2019 Aug;116(8):1909-1922. doi: 10.1002/bit.26995. Epub 2019 Apr 29.

PMID:
30982958
5.

Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes.

Kothari A, Wu YW, Chandonia JM, Charrier M, Rajeev L, Rocha AM, Joyner DC, Hazen TC, Singer SW, Mukhopadhyay A.

MBio. 2019 Feb 26;10(1). pii: e02899-18. doi: 10.1128/mBio.02899-18.

6.

Author Correction: Jungle Express is a versatile repressor system for tight transcriptional control.

Ruegg TL, Pereira JH, Chen JC, DeGiovanni A, Novichkov P, Mutalik VK, Tomaleri GP, Singer SW, Hillson NJ, Simmons BA, Adams PD, Thelen MP.

Nat Commun. 2018 Oct 30;9(1):4596. doi: 10.1038/s41467-018-07111-2.

7.

Jungle Express is a versatile repressor system for tight transcriptional control.

Ruegg TL, Pereira JH, Chen JC, DeGiovanni A, Novichkov P, Mutalik VK, Tomaleri GP, Singer SW, Hillson NJ, Simmons BA, Adams PD, Thelen MP.

Nat Commun. 2018 Sep 6;9(1):3617. doi: 10.1038/s41467-018-05857-3. Erratum in: Nat Commun. 2018 Oct 30;9(1):4596.

8.

Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast.

Higgins DA, Young MKM, Tremaine M, Sardi M, Fletcher JM, Agnew M, Liu L, Dickinson Q, Peris D, Wrobel RL, Hittinger CT, Gasch AP, Singer SW, Simmons BA, Landick R, Thelen MP, Sato TK.

Genetics. 2018 Sep;210(1):219-234. doi: 10.1534/genetics.118.301161. Epub 2018 Jul 25.

9.

Microbial Community Structure and Functional Potential Along a Hypersaline Gradient.

Kimbrel JA, Ballor N, Wu YW, David MM, Hazen TC, Simmons BA, Singer SW, Jansson JK.

Front Microbiol. 2018 Jul 10;9:1492. doi: 10.3389/fmicb.2018.01492. eCollection 2018.

10.

Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists.

Martino E, Morin E, Grelet GA, Kuo A, Kohler A, Daghino S, Barry KW, Cichocki N, Clum A, Dockter RB, Hainaut M, Kuo RC, LaButti K, Lindahl BD, Lindquist EA, Lipzen A, Khouja HR, Magnuson J, Murat C, Ohm RA, Singer SW, Spatafora JW, Wang M, Veneault-Fourrey C, Henrissat B, Grigoriev IV, Martin FM, Perotto S.

New Phytol. 2018 Feb;217(3):1213-1229. doi: 10.1111/nph.14974. Epub 2018 Jan 7.

11.

Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger.

Amaike Campen S, Lynn J, Sibert SJ, Srikrishnan S, Phatale P, Feldman T, Guenther JM, Hiras J, Tran YTA, Singer SW, Adams PD, Sale KL, Simmons BA, Baker SE, Magnuson JK, Gladden JM.

PLoS One. 2017 Dec 27;12(12):e0189604. doi: 10.1371/journal.pone.0189604. eCollection 2017.

12.

Xylose induces cellulase production in Thermoascus aurantiacus.

Schuerg T, Prahl JP, Gabriel R, Harth S, Tachea F, Chen CS, Miller M, Masson F, He Q, Brown S, Mirshiaghi M, Liang L, Tom LM, Tanjore D, Sun N, Pray TR, Singer SW.

Biotechnol Biofuels. 2017 Nov 15;10:271. doi: 10.1186/s13068-017-0965-z. eCollection 2017.

13.

Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution.

Mohamed ET, Wang S, Lennen RM, Herrgård MJ, Simmons BA, Singer SW, Feist AM.

Microb Cell Fact. 2017 Nov 16;16(1):204. doi: 10.1186/s12934-017-0819-1.

14.

A bacterial pioneer produces cellulase complexes that persist through community succession.

Kolinko S, Wu YW, Tachea F, Denzel E, Hiras J, Gabriel R, Bäcker N, Chan LJG, Eichorst SA, Frey D, Chen Q, Azadi P, Adams PD, Pray TR, Tanjore D, Petzold CJ, Gladden JM, Simmons BA, Singer SW.

Nat Microbiol. 2018 Jan;3(1):99-107. doi: 10.1038/s41564-017-0052-z. Epub 2017 Nov 6.

15.

Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts.

Yaegashi J, Kirby J, Ito M, Sun J, Dutta T, Mirsiaghi M, Sundstrom ER, Rodriguez A, Baidoo E, Tanjore D, Pray T, Sale K, Singh S, Keasling JD, Simmons BA, Singer SW, Magnuson JK, Arkin AP, Skerker JM, Gladden JM.

Biotechnol Biofuels. 2017 Oct 23;10:241. doi: 10.1186/s13068-017-0927-5. eCollection 2017.

16.

1-Ethyl-3-methylimidazolium tolerance and intracellular lipid accumulation of 38 oleaginous yeast species.

Sitepu IR, Garay LA, Enriquez L, Fry R, Butler JH, Lopez JM, Kanti A, Faulina SA, Nugroho AJ, Simmons BA, Singer SW, Simmons CW, Boundy-Mills K.

Appl Microbiol Biotechnol. 2017 Dec;101(23-24):8621-8631. doi: 10.1007/s00253-017-8506-z. Epub 2017 Oct 19.

PMID:
29051987
17.

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC.

Nat Methods. 2017 Nov;14(11):1063-1071. doi: 10.1038/nmeth.4458. Epub 2017 Oct 2.

18.

Ecological Insights into the Dynamics of Plant Biomass-Degrading Microbial Consortia.

Jiménez DJ, Dini-Andreote F, DeAngelis KM, Singer SW, Salles JF, van Elsas JD.

Trends Microbiol. 2017 Oct;25(10):788-796. doi: 10.1016/j.tim.2017.05.012. Epub 2017 Jun 22. Review.

PMID:
28648267
19.

Alteration of white-rot basidiomycetes cellulase and xylanase activities in the submerged co-cultivation and optimization of enzyme production by Irpex lacteus and Schizophyllum commune.

Metreveli E, Kachlishvili E, Singer SW, Elisashvili V.

Bioresour Technol. 2017 Oct;241:652-660. doi: 10.1016/j.biortech.2017.05.148. Epub 2017 May 26.

PMID:
28609753
20.

Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis.

Wu YW, Higgins B, Yu C, Reddy AP, Ceballos S, Joh LD, Simmons BA, Singer SW, VanderGheynst JS.

mSystems. 2016 Dec 13;1(6). pii: e00120-16. eCollection 2016 Nov-Dec.

21.

Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts.

Yu C, Simmons BA, Singer SW, Thelen MP, VanderGheynst JS.

Appl Microbiol Biotechnol. 2016 Dec;100(24):10237-10249. Epub 2016 Nov 12. Review.

22.

Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization.

Kothari A, Charrier M, Wu YW, Malfatti S, Zhou CE, Singer SW, Dugan L, Mukhopadhyay A.

FEMS Microbiol Lett. 2016 Oct;363(20). pii: fnw224. Epub 2016 Sep 22.

23.

Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis.

Hiras J, Wu YW, Deng K, Nicora CD, Aldrich JT, Frey D, Kolinko S, Robinson EW, Jacobs JM, Adams PD, Northen TR, Simmons BA, Singer SW.

MBio. 2016 Aug 23;7(4). pii: e01106-16. doi: 10.1128/mBio.01106-16.

24.

Enrichment of microbial communities tolerant to the ionic liquids tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate.

Pace S, Ceballos SJ, Harrold D, Stannard W, Simmons BA, Singer SW, Thelen MP, VanderGheynst JS.

Appl Microbiol Biotechnol. 2016 Jun;100(12):5639-52. doi: 10.1007/s00253-016-7525-5. Epub 2016 Apr 22.

25.

Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage.

Mosier AC, Miller CS, Frischkorn KR, Ohm RA, Li Z, LaButti K, Lapidus A, Lipzen A, Chen C, Johnson J, Lindquist EA, Pan C, Hettich RL, Grigoriev IV, Singer SW, Banfield JF.

Front Microbiol. 2016 Mar 3;7:238. doi: 10.3389/fmicb.2016.00238. eCollection 2016.

26.

Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions.

Yu C, Reddy AP, Simmons CW, Simmons BA, Singer SW, VanderGheynst JS.

Biotechnol Biofuels. 2015 Dec 2;8:206. doi: 10.1186/s13068-015-0392-y. eCollection 2015.

27.

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets.

Wu YW, Simmons BA, Singer SW.

Bioinformatics. 2016 Feb 15;32(4):605-7. doi: 10.1093/bioinformatics/btv638. Epub 2015 Oct 29.

PMID:
26515820
28.

Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage.

Hiras J, Wu YW, Eichorst SA, Simmons BA, Singer SW.

ISME J. 2016 Apr;10(4):833-45. doi: 10.1038/ismej.2015.158. Epub 2015 Sep 1.

29.

Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw.

Simmons CW, Reddy AP, D'haeseleer P, Khudyakov J, Billis K, Pati A, Simmons BA, Singer SW, Thelen MP, VanderGheynst JS.

Biotechnol Biofuels. 2014 Dec 31;7(1):495. doi: 10.1186/s13068-014-0180-0. eCollection 2014.

30.

Changes in protein expression across laboratory and field experiments in Geobacter bemidjiensis.

Merkley ED, Wrighton KC, Castelle CJ, Anderson BJ, Wilkins MJ, Shah V, Arbour T, Brown JN, Singer SW, Smith RD, Lipton MS.

J Proteome Res. 2015 Mar 6;14(3):1361-75. doi: 10.1021/pr500983v. Epub 2015 Feb 3.

PMID:
25496566
31.

Yeast tolerance to the ionic liquid 1-ethyl-3-methylimidazolium acetate.

Sitepu IR, Shi S, Simmons BA, Singer SW, Boundy-Mills K, Simmons CW.

FEMS Yeast Res. 2014 Dec;14(8):1286-94. doi: 10.1111/1567-1364.12224. Epub 2014 Nov 12.

32.

Revisiting N₂ fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach.

Woebken D, Burow LC, Behnam F, Mayali X, Schintlmeister A, Fleming ED, Prufert-Bebout L, Singer SW, Cortés AL, Hoehler TM, Pett-Ridge J, Spormann AM, Wagner M, Weber PK, Bebout BM.

ISME J. 2015 Feb;9(2):485-96. doi: 10.1038/ismej.2014.144. Epub 2014 Oct 10.

33.

Substrate-Specific Development of Thermophilic Bacterial Consortia by Using Chemically Pretreated Switchgrass.

Eichorst SA, Joshua C, Sathitsuksanoh N, Singh S, Simmons BA, Singer SW.

Appl Environ Microbiol. 2014 Dec;80(23):7423-32. doi: 10.1128/AEM.02795-14. Epub 2014 Sep 26.

34.

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm.

Wu YW, Tang YH, Tringe SG, Simmons BA, Singer SW.

Microbiome. 2014 Aug 1;2:26. doi: 10.1186/2049-2618-2-26. eCollection 2014.

35.

Effect of inoculum source on the enrichment of microbial communities on two lignocellulosic bioenergy crops under thermophilic and high-solids conditions.

Simmons CW, Reddy AP, Simmons BA, Singer SW, VanderGheynst JS.

J Appl Microbiol. 2014 Oct;117(4):1025-34. doi: 10.1111/jam.12609. Epub 2014 Aug 18.

36.

Identification of Desulfobacterales as primary hydrogenotrophs in a complex microbial mat community.

Burow LC, Woebken D, Marshall IP, Singer SW, Pett-Ridge J, Prufert-Bebout L, Spormann AM, Bebout BM, Weber PK, Hoehler TM.

Geobiology. 2014 May;12(3):221-30. doi: 10.1111/gbi.12080.

PMID:
24730641
37.

An auto-inducible mechanism for ionic liquid resistance in microbial biofuel production.

Ruegg TL, Kim EM, Simmons BA, Keasling JD, Singer SW, Lee TS, Thelen MP.

Nat Commun. 2014 Mar 26;5:3490. doi: 10.1038/ncomms4490.

PMID:
24667370
38.

Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community.

Gladden JM, Park JI, Bergmann J, Reyes-Ortiz V, D'haeseleer P, Quirino BF, Sale KL, Simmons BA, Singer SW.

Biotechnol Biofuels. 2014 Jan 29;7(1):15. doi: 10.1186/1754-6834-7-15.

39.

Bacillus coagulans tolerance to 1-ethyl-3-methylimidazolium-based ionic liquids in aqueous and solid-state thermophilic culture.

Simmons CW, Reddy AP, Vandergheynst JS, Simmons BA, Singer SW.

Biotechnol Prog. 2014 Mar-Apr;30(2):311-6. doi: 10.1002/btpr.1859. Epub 2014 Jan 11.

40.

High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal β-glucosidase production.

Cheng X, Hiras J, Deng K, Bowen B, Simmons BA, Adams PD, Singer SW, Northen TR.

Front Microbiol. 2013 Dec 6;4:365. doi: 10.3389/fmicb.2013.00365. eCollection 2013.

41.

Development of a broad-host synthetic biology toolbox for Ralstonia eutropha and its application to engineering hydrocarbon biofuel production.

Bi C, Su P, Müller J, Yeh YC, Chhabra SR, Beller HR, Singer SW, Hillson NJ.

Microb Cell Fact. 2013 Nov 13;12:107. doi: 10.1186/1475-2859-12-107.

42.

Discovery of microorganisms and enzymes involved in high-solids decomposition of rice straw using metagenomic analyses.

Reddy AP, Simmons CW, D'haeseleer P, Khudyakov J, Burd H, Hadi M, Simmons BA, Singer SW, Thelen MP, Vandergheynst JS.

PLoS One. 2013 Oct 25;8(10):e77985. doi: 10.1371/journal.pone.0077985. eCollection 2013.

43.

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.

44.

Draft Genome Sequence of an Oscillatorian Cyanobacterium, Strain ESFC-1.

Everroad RC, Woebken D, Singer SW, Burow LC, Kyrpides N, Woyke T, Goodwin L, Detweiler A, Prufert-Bebout L, Pett-Ridge J.

Genome Announc. 2013 Aug 1;1(4). pii: e00527-13. doi: 10.1128/genomeA.00527-13.

45.

Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass.

D'haeseleer P, Gladden JM, Allgaier M, Chain PS, Tringe SG, Malfatti SA, Aldrich JT, Nicora CD, Robinson EW, Paša-Tolić L, Hugenholtz P, Simmons BA, Singer SW.

PLoS One. 2013 Jul 19;8(7):e68465. doi: 10.1371/journal.pone.0068465. Print 2013.

46.

Community dynamics of cellulose-adapted thermophilic bacterial consortia.

Eichorst SA, Varanasi P, Stavila V, Zemla M, Auer M, Singh S, Simmons BA, Singer SW.

Environ Microbiol. 2013 Sep;15(9):2573-87. doi: 10.1111/1462-2920.12159. Epub 2013 Jun 13.

PMID:
23763762
47.

Engineering of Ralstonia eutropha H16 for autotrophic and heterotrophic production of methyl ketones.

Müller J, MacEachran D, Burd H, Sathitsuksanoh N, Bi C, Yeh YC, Lee TS, Hillson NJ, Chhabra SR, Singer SW, Beller HR.

Appl Environ Microbiol. 2013 Jul;79(14):4433-9. doi: 10.1128/AEM.00973-13. Epub 2013 May 17.

48.

Functionalizing bacterial cell surfaces with a phage protein.

Yeh YC, Müller J, Bi C, Hillson NJ, Beller HR, Chhabra SR, Singer SW.

Chem Commun (Camb). 2013 Jan 30;49(9):910-2. doi: 10.1039/c2cc37883c.

PMID:
23247551
49.

Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics.

Burow LC, Woebken D, Marshall IP, Lindquist EA, Bebout BM, Prufert-Bebout L, Hoehler TM, Tringe SG, Pett-Ridge J, Weber PK, Spormann AM, Singer SW.

ISME J. 2013 Apr;7(4):817-29. doi: 10.1038/ismej.2012.150. Epub 2012 Nov 29.

50.

Thermophilic enrichment of microbial communities in the presence of the ionic liquid 1-ethyl-3-methylimidazolium acetate.

Reddy AP, Simmons CW, Claypool J, Jabusch L, Burd H, Hadi MZ, Simmons BA, Singer SW, VanderGheynst JS.

J Appl Microbiol. 2012 Dec;113(6):1362-70. doi: 10.1111/jam.12002. Epub 2012 Oct 1.

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