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Items: 1 to 50 of 181

1.

Engineering Corynebacterium glutamicum to produce the biogasoline isopentenol from plant biomass hydrolysates.

Sasaki Y, Eng T, Herbert RA, Trinh J, Chen Y, Rodriguez A, Gladden J, Simmons BA, Petzold CJ, Mukhopadhyay A.

Biotechnol Biofuels. 2019 Feb 27;12:41. doi: 10.1186/s13068-019-1381-3. eCollection 2019.

2.

A new approach to Cas9-based genome editing in Aspergillus niger that is precise, efficient and selectable.

Leynaud-Kieffer LMC, Curran SC, Kim I, Magnuson JK, Gladden JM, Baker SE, Simmons BA.

PLoS One. 2019 Jan 17;14(1):e0210243. doi: 10.1371/journal.pone.0210243. eCollection 2019.

3.

Regulation of Yeast-to-Hyphae Transition in Yarrowia lipolytica.

Pomraning KR, Bredeweg EL, Kerkhoven EJ, Barry K, Haridas S, Hundley H, LaButti K, Lipzen A, Yan M, Magnuson JK, Simmons BA, Grigoriev IV, Nielsen J, Baker SE.

mSphere. 2018 Dec 5;3(6). pii: e00541-18. doi: 10.1128/mSphere.00541-18.

4.

Short-chain ketone production by engineered polyketide synthases in Streptomyces albus.

Yuzawa S, Mirsiaghi M, Jocic R, Fujii T, Masson F, Benites VT, Baidoo EEK, Sundstrom E, Tanjore D, Pray TR, George A, Davis RW, Gladden JM, Simmons BA, Katz L, Keasling JD.

Nat Commun. 2018 Nov 1;9(1):4569. doi: 10.1038/s41467-018-07040-0.

5.

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.

6.

Correction to: Cloning and Expression of Heterologous Cellulases and Enzymes in Aspergillus niger.

Reilly MC, Amaike Campen S, Simmons BA, Baker SE, Gladden JM, Magnuson JK.

Methods Mol Biol. 2018;1796:E1. doi: 10.1007/978-1-4939-7877-9_22.

PMID:
30374680
7.

Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri.

Vesth TC, Nybo JL, Theobald S, Frisvad JC, Larsen TO, Nielsen KF, Hoof JB, Brandl J, Salamov A, Riley R, Gladden JM, Phatale P, Nielsen MT, Lyhne EK, Kogle ME, Strasser K, McDonnell E, Barry K, Clum A, Chen C, LaButti K, Haridas S, Nolan M, Sandor L, Kuo A, Lipzen A, Hainaut M, Drula E, Tsang A, Magnuson JK, Henrissat B, Wiebenga A, Simmons BA, Mäkelä MR, de Vries RP, Grigoriev IV, Mortensen UH, Baker SE, Andersen MR.

Nat Genet. 2018 Dec;50(12):1688-1695. doi: 10.1038/s41588-018-0246-1. Epub 2018 Oct 22.

PMID:
30349117
8.

Structural Design of Ionic Liquids for Optimizing Aromatic Dissolution.

Jiang HJ, Imberti S, Simmons BA, Atkin R, Warr GG.

ChemSusChem. 2019 Jan 10;12(1):270-274. doi: 10.1002/cssc.201802016. Epub 2018 Nov 9.

PMID:
30300962
9.

Rapid characterization of the activities of lignin-modifying enzymes based on nanostructure-initiator mass spectrometry (NIMS).

Deng K, Zeng J, Cheng G, Gao J, Sale KL, Simmons BA, Singh AK, Adams PD, Northen TR.

Biotechnol Biofuels. 2018 Sep 27;11:266. doi: 10.1186/s13068-018-1261-2. eCollection 2018.

10.

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.

11.

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.

12.

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.

13.

Engineering glycoside hydrolase stability by the introduction of zinc binding.

Ellinghaus TL, Pereira JH, McAndrew RP, Welner DH, DeGiovanni AM, Guenther JM, Tran HM, Feldman T, Simmons BA, Sale KL, Adams PD.

Acta Crystallogr D Struct Biol. 2018 Jul 1;74(Pt 7):702-710. doi: 10.1107/S2059798318006678. Epub 2018 Jun 27.

14.

Cloning and Expression of Heterologous Cellulases and Enzymes in Aspergillus niger.

Reilly MC, Amaike Campen S, Simmons BA, Baker SE, Gladden JM, Magnuson JK.

Methods Mol Biol. 2018;1796:123-133. doi: 10.1007/978-1-4939-7877-9_10. Erratum in: Methods Mol Biol. 2018;1796:E1.

PMID:
29856051
15.

Structure-based Engineering of a Plant-Fungal Hybrid Peroxidase for Enhanced Temperature and pH Tolerance.

Kohler AC, Simmons BA, Sale KL.

Cell Chem Biol. 2018 Aug 16;25(8):974-983.e3. doi: 10.1016/j.chembiol.2018.04.014. Epub 2018 May 24.

PMID:
29805035
16.

Annotation of the Corymbia terpene synthase gene family shows broad conservation but dynamic evolution of physical clusters relative to Eucalyptus.

Butler JB, Freeman JS, Potts BM, Vaillancourt RE, Grattapaglia D, Silva-Junior OB, Simmons BA, Healey AL, Schmutz J, Barry KW, Lee DJ, Henry RJ, King GJ, Baten A, Shepherd M.

Heredity (Edinb). 2018 Jul;121(1):87-104. doi: 10.1038/s41437-018-0058-1. Epub 2018 Mar 10.

PMID:
29523839
17.

Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides.

Coradetti ST, Pinel D, Geiselman GM, Ito M, Mondo SJ, Reilly MC, Cheng YF, Bauer S, Grigoriev IV, Gladden JM, Simmons BA, Brem RB, Arkin AP, Skerker JM.

Elife. 2018 Mar 9;7. pii: e32110. doi: 10.7554/eLife.32110.

18.

Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species.

Kjærbølling I, Vesth TC, Frisvad JC, Nybo JL, Theobald S, Kuo A, Bowyer P, Matsuda Y, Mondo S, Lyhne EK, Kogle ME, Clum A, Lipzen A, Salamov A, Ngan CY, Daum C, Chiniquy J, Barry K, LaButti K, Haridas S, Simmons BA, Magnuson JK, Mortensen UH, Larsen TO, Grigoriev IV, Baker SE, Andersen MR.

Proc Natl Acad Sci U S A. 2018 Jan 23;115(4):E753-E761. doi: 10.1073/pnas.1715954115. Epub 2018 Jan 9.

19.

Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger.

Reilly MC, Kim J, Lynn J, Simmons BA, Gladden JM, Magnuson JK, Baker SE.

Appl Microbiol Biotechnol. 2018 Feb;102(4):1797-1807. doi: 10.1007/s00253-017-8717-3. Epub 2018 Jan 6.

20.

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.

21.

Solubilization and Upgrading of High Polyethylene Terephthalate Loadings in a Low-Costing Bifunctional Ionic Liquid.

Sun J, Liu D, Young RP, Cruz AG, Isern NG, Schuerg T, Cort JR, Simmons BA, Singh S.

ChemSusChem. 2018 Feb 22;11(4):781-792. doi: 10.1002/cssc.201701798. Epub 2018 Jan 26.

PMID:
29178551
22.

Cascade Production of Lactic Acid from Universal Types of Sugars Catalyzed by Lanthanum Triflate.

Liu D, Kim KH, Sun J, Simmons BA, Singh S.

ChemSusChem. 2018 Feb 9;11(3):598-604. doi: 10.1002/cssc.201701902. Epub 2018 Jan 17.

PMID:
29178399
23.

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.

24.

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.

25.

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.

26.

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
27.

Low cost ionic liquid-water mixtures for effective extraction of carbohydrate and lipid from algae.

To TQ, Procter K, Simmons BA, Subashchandrabose S, Atkin R.

Faraday Discuss. 2017 Dec 14;206:93-112. doi: 10.1039/c7fd00158d.

PMID:
28936499
28.

Rhorix: An interface between quantum chemical topology and the 3D graphics program blender.

Mills MJL, Sale KL, Simmons BA, Popelier PLA.

J Comput Chem. 2017 Nov 5;38(29):2538-2552. doi: 10.1002/jcc.25054. Epub 2017 Aug 31.

29.

Reply to Kiser: Dioxygen binding in NOV1 crystal structures.

McAndrew RP, Sathitsuksanoh N, Mbughuni MM, Heins RA, Pereira JH, George A, Sale KL, Fox BG, Simmons BA, Adams PD.

Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):E6029-E6030. doi: 10.1073/pnas.1708124114. Epub 2017 Jul 5. No abstract available.

30.

Efficient dehydration and recovery of ionic liquid after lignocellulosic processing using pervaporation.

Sun J, Shi J, Murthy Konda NVSN, Campos D, Liu D, Nemser S, Shamshina J, Dutta T, Berton P, Gurau G, Rogers RD, Simmons BA, Singh S.

Biotechnol Biofuels. 2017 Jun 15;10:154. doi: 10.1186/s13068-017-0842-9. eCollection 2017.

31.

Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks.

d'Espaux L, Ghosh A, Runguphan W, Wehrs M, Xu F, Konzock O, Dev I, Nhan M, Gin J, Reider Apel A, Petzold CJ, Singh S, Simmons BA, Mukhopadhyay A, García Martín H, Keasling JD.

Metab Eng. 2017 Jul;42:115-125. doi: 10.1016/j.ymben.2017.06.004. Epub 2017 Jun 10.

PMID:
28606738
32.

Parametric study for the optimization of ionic liquid pretreatment of corn stover.

Papa G, Feldman T, Sale KL, Adani F, Singh S, Simmons BA.

Bioresour Technol. 2017 Oct;241:627-637. doi: 10.1016/j.biortech.2017.05.167. Epub 2017 May 30.

PMID:
28605727
33.

SbCOMT (Bmr12) is involved in the biosynthesis of tricin-lignin in sorghum.

Eudes A, Dutta T, Deng K, Jacquet N, Sinha A, Benites VT, Baidoo EEK, Richel A, Sattler SE, Northen TR, Singh S, Simmons BA, Loqué D.

PLoS One. 2017 Jun 8;12(6):e0178160. doi: 10.1371/journal.pone.0178160. eCollection 2017.

34.

Structure and activity of thermophilic methanogenic microbial communities exposed to quaternary ammonium sanitizer.

Fernandez-Bayo JD, Toniato J, Simmons BA, Simmons CW.

J Environ Sci (China). 2017 Jun;56:164-168. doi: 10.1016/j.jes.2016.10.005. Epub 2016 Oct 27.

PMID:
28571852
35.

High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.

Woo HL, DeAngelis KM, Teshima H, Davenport K, Daligault H, Erkkila T, Goodwin L, Gu W, Lo CC, Munk C, Scholz M, Xu Y, Chain P, Bruce D, Detter C, Tapia R, Han C, Simmons BA, Hazen TC.

Genome Announc. 2017 May 4;5(18). pii: e00300-17. doi: 10.1128/genomeA.00300-17.

36.

Impact of lignin polymer backbone esters on ionic liquid pretreatment of poplar.

Kim KH, Dutta T, Ralph J, Mansfield SD, Simmons BA, Singh S.

Biotechnol Biofuels. 2017 Apr 20;10:101. doi: 10.1186/s13068-017-0784-2. eCollection 2017.

37.

Structure of aryl O-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism.

Kohler AC, Mills MJL, Adams PD, Simmons BA, Sale KL.

Proc Natl Acad Sci U S A. 2017 Apr 18;114(16):E3205-E3214. doi: 10.1073/pnas.1619263114. Epub 2017 Apr 3.

38.

Ternary ionic liquid-water pretreatment systems of an agave bagasse and municipal solid waste blend.

Perez-Pimienta JA, Sathitsuksanoh N, Thompson VS, Tran K, Ponce-Noyola T, Stavila V, Singh S, Simmons BA.

Biotechnol Biofuels. 2017 Mar 21;10:72. doi: 10.1186/s13068-017-0758-4. eCollection 2017.

39.

Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments.

Daly P, van Munster JM, Blythe MJ, Ibbett R, Kokolski M, Gaddipati S, Lindquist E, Singan VR, Barry KW, Lipzen A, Ngan CY, Petzold CJ, Chan LJG, Pullan ST, Delmas S, Waldron PR, Grigoriev IV, Tucker GA, Simmons BA, Archer DB.

Biotechnol Biofuels. 2017 Feb 7;10:35. doi: 10.1186/s13068-017-0700-9. eCollection 2017.

40.

Scale-up and process integration of sugar production by acidolysis of municipal solid waste/corn stover blends in ionic liquids.

Li C, Liang L, Sun N, Thompson VS, Xu F, Narani A, He Q, Tanjore D, Pray TR, Simmons BA, Singh S.

Biotechnol Biofuels. 2017 Jan 5;10:13. doi: 10.1186/s13068-016-0694-8. eCollection 2017.

41.

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.

42.

Evaluation of Relationships between Growth Rate, Tree Size, Lignocellulose Composition, and Enzymatic Saccharification in Interspecific Corymbia Hybrids and Parental Taxa.

Healey AL, Lee DJ, Lupoi JS, Papa G, Guenther JM, Corno L, Adani F, Singh S, Simmons BA, Henry RJ.

Front Plant Sci. 2016 Nov 18;7:1705. eCollection 2016.

43.

Structure and mechanism of NOV1, a resveratrol-cleaving dioxygenase.

McAndrew RP, Sathitsuksanoh N, Mbughuni MM, Heins RA, Pereira JH, George A, Sale KL, Fox BG, Simmons BA, Adams PD.

Proc Natl Acad Sci U S A. 2016 Dec 13;113(50):14324-14329. Epub 2016 Nov 30.

44.

Sequential enzymatic saccharification and fermentation of ionic liquid and organosolv pretreated agave bagasse for ethanol production.

Pérez-Pimienta JA, Vargas-Tah A, López-Ortega KM, Medina-López YN, Mendoza-Pérez JA, Avila S, Singh S, Simmons BA, Loaces I, Martinez A.

Bioresour Technol. 2017 Feb;225:191-198. doi: 10.1016/j.biortech.2016.11.064. Epub 2016 Nov 16.

PMID:
27889478
45.

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.

46.

Dynamic changes of substrate reactivity and enzyme adsorption on partially hydrolyzed cellulose.

Shi J, Wu D, Zhang L, Simmons BA, Singh S, Yang B, Wyman CE.

Biotechnol Bioeng. 2017 Mar;114(3):503-515. doi: 10.1002/bit.26180. Epub 2016 Nov 28.

47.

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.

48.

Expression of S-adenosylmethionine Hydrolase in Tissues Synthesizing Secondary Cell Walls Alters Specific Methylated Cell Wall Fractions and Improves Biomass Digestibility.

Eudes A, Zhao N, Sathitsuksanoh N, Baidoo EE, Lao J, Wang G, Yogiswara S, Lee TS, Singh S, Mortimer JC, Keasling JD, Simmons BA, Loqué D.

Front Bioeng Biotechnol. 2016 Jul 19;4:58. doi: 10.3389/fbioe.2016.00058. eCollection 2016.

49.

Activation of lignocellulosic biomass for higher sugar yields using aqueous ionic liquid at low severity process conditions.

Parthasarathi R, Sun J, Dutta T, Sun N, Pattathil S, Murthy Konda NV, Peralta AG, Simmons BA, Singh S.

Biotechnol Biofuels. 2016 Aug 2;9:160. doi: 10.1186/s13068-016-0561-7. eCollection 2016.

50.

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.

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