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Items: 49

1.

One-time nitrogen fertilization shifts switchgrass soil microbiomes within a context of larger spatial and temporal variation.

Chen H, Yang ZK, Yip D, Morris RH, Lebreux SJ, Cregger MA, Klingeman DM, Hui D, Hettich RL, Wilhelm SW, Wang G, Löffler FE, Schadt CW.

PLoS One. 2019 Jun 18;14(6):e0211310. doi: 10.1371/journal.pone.0211310. eCollection 2019.

2.

Complete Genome Sequences of Two Megasphaera elsdenii Strains, NCIMB 702410 and ATCC 25940.

Hatmaker EA, Klingeman DM, O'Dell KB, Riley LA, Papanek B, Guss AM.

Microbiol Resour Announc. 2019 Jan 17;8(3). pii: e01430-18. doi: 10.1128/MRA.01430-18. eCollection 2019 Jan.

3.

Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times.

Liang X, Whitham JM, Holwerda EK, Shao X, Tian L, Wu YW, Lombard V, Henrissat B, Klingeman DM, Yang ZK, Podar M, Richard TL, Elkins JG, Brown SD, Lynd LR.

Biotechnol Biofuels. 2018 Sep 6;11:243. doi: 10.1186/s13068-018-1238-1. eCollection 2018.

4.

Transcriptomic and proteomic changes from medium supplementation and strain evolution in high-yielding Clostridium thermocellum strains.

Papanek B, O'Dell KB, Manga P, Giannone RJ, Klingeman DM, Hettich RL, Brown SD, Guss AM.

J Ind Microbiol Biotechnol. 2018 Nov;45(11):1007-1015. doi: 10.1007/s10295-018-2073-x. Epub 2018 Sep 5.

PMID:
30187243
5.

Rex in Caldicellulosiruptor bescii: Novel regulon members and its effect on the production of ethanol and overflow metabolites.

Sander K, Chung D, Hyatt D, Westpheling J, Klingeman DM, Rodriguez M Jr, Engle NL, Tschaplinski TJ, Davison BH, Brown SD.

Microbiologyopen. 2019 Feb;8(2):e00639. doi: 10.1002/mbo3.639. Epub 2018 May 23.

6.

Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics.

Whitham JM, Moon JW, Rodriguez M Jr, Engle NL, Klingeman DM, Rydzak T, Abel MM, Tschaplinski TJ, Guss AM, Brown SD.

Biotechnol Biofuels. 2018 Apr 5;11:98. doi: 10.1186/s13068-018-1095-y. eCollection 2018.

7.

A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies.

Utturkar SM, Klingeman DM, Hurt RA Jr, Brown SD.

Front Microbiol. 2017 Jul 18;8:1272. doi: 10.3389/fmicb.2017.01272. eCollection 2017.

8.

Corrigendum: Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum.

Verbeke TJ, Giannone RJ, Klingeman DM, Engle NL, Rydzak T, Guss AM, Tschaplinski TJ, Brown SD, Hettich RL, Elkins JG.

Sci Rep. 2017 Jul 27;7:46875. doi: 10.1038/srep46875.

9.

The LacI family protein GlyR3 co-regulates the celC operon and manB in Clostridium thermocellum.

Choi J, Klingeman DM, Brown SD, Cox CD.

Biotechnol Biofuels. 2017 Jun 24;10:163. doi: 10.1186/s13068-017-0849-2. eCollection 2017.

10.

Generation and Characterization of Acid Tolerant Fibrobacter succinogenes S85.

Wu CW, Spike T, Klingeman DM, Rodriguez M, Bremer VR, Brown SD.

Sci Rep. 2017 May 23;7(1):2277. doi: 10.1038/s41598-017-02628-w.

11.

Deletion of Type I glutamine synthetase deregulates nitrogen metabolism and increases ethanol production in Clostridium thermocellum.

Rydzak T, Garcia D, Stevenson DM, Sladek M, Klingeman DM, Holwerda EK, Amador-Noguez D, Brown SD, Guss AM.

Metab Eng. 2017 May;41:182-191. doi: 10.1016/j.ymben.2017.04.002. Epub 2017 Apr 8.

PMID:
28400329
12.

Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells.

Dumitrache A, Klingeman DM, Natzke J, Rodriguez M Jr, Giannone RJ, Hettich RL, Davison BH, Brown SD.

Sci Rep. 2017 Feb 27;7:43583. doi: 10.1038/srep43583.

13.

Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum.

Verbeke TJ, Giannone RJ, Klingeman DM, Engle NL, Rydzak T, Guss AM, Tschaplinski TJ, Brown SD, Hettich RL, Elkins JG.

Sci Rep. 2017 Feb 23;7:43355. doi: 10.1038/srep43355. Erratum in: Sci Rep. 2017 Jul 27;7:46875.

14.

Improved growth rate in Clostridium thermocellum hydrogenase mutant via perturbed sulfur metabolism.

Biswas R, Wilson CM, Giannone RJ, Klingeman DM, Rydzak T, Shah MB, Hettich RL, Brown SD, Guss AM.

Biotechnol Biofuels. 2017 Jan 3;10:6. doi: 10.1186/s13068-016-0684-x. eCollection 2017.

15.

LacI Transcriptional Regulatory Networks in Clostridium thermocellum DSM1313.

Wilson CM, Klingeman DM, Schlachter C, Syed MH, Wu CW, Guss AM, Brown SD.

Appl Environ Microbiol. 2017 Feb 15;83(5). pii: e02751-16. doi: 10.1128/AEM.02751-16. Print 2017 Mar 1.

16.

Application of Long Sequence Reads To Improve Genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.

Utturkar SM, Bayer EA, Borovok I, Lamed R, Hurt RA, Land ML, Klingeman DM, Elias D, Zhou J, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TB, Ngan CY, Daum C, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Brown SD.

Genome Announc. 2016 Sep 29;4(5). pii: e01043-16. doi: 10.1128/genomeA.01043-16.

17.

Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis.

Utturkar SM, Cude WN, Robeson MS Jr, Yang ZK, Klingeman DM, Land ML, Allman SL, Lu TY, Brown SD, Schadt CW, Podar M, Doktycz MJ, Pelletier DA.

Appl Environ Microbiol. 2016 Aug 30;82(18):5698-708. doi: 10.1128/AEM.01285-16. Print 2016 Sep 15.

18.

Strain and bioprocess improvement of a thermophilic anaerobe for the production of ethanol from wood.

Herring CD, Kenealy WR, Joe Shaw A, Covalla SF, Olson DG, Zhang J, Ryan Sillers W, Tsakraklides V, Bardsley JS, Rogers SR, Thorne PG, Johnson JP, Foster A, Shikhare ID, Klingeman DM, Brown SD, Davison BH, Lynd LR, Hogsett DA.

Biotechnol Biofuels. 2016 Jun 16;9:125. doi: 10.1186/s13068-016-0536-8. eCollection 2016.

19.

Replicates, Read Numbers, and Other Important Experimental Design Considerations for Microbial RNA-seq Identified Using Bacillus thuringiensis Datasets.

Manga P, Klingeman DM, Lu TY, Mehlhorn TL, Pelletier DA, Hauser LJ, Wilson CM, Brown SD.

Front Microbiol. 2016 May 31;7:794. doi: 10.3389/fmicb.2016.00794. eCollection 2016.

20.

Near-Complete Genome Sequence of Clostridium paradoxum Strain JW-YL-7.

Lancaster WA, Utturkar SM, Poole FL, Klingeman DM, Elias DA, Adams MW, Brown SD.

Genome Announc. 2016 May 5;4(3). pii: e00229-16. doi: 10.1128/genomeA.00229-16.

21.

Dramatic performance of Clostridium thermocellum explained by its wide range of cellulase modalities.

Xu Q, Resch MG, Podkaminer K, Yang S, Baker JO, Donohoe BS, Wilson C, Klingeman DM, Olson DG, Decker SR, Giannone RJ, Hettich RL, Brown SD, Lynd LR, Bayer EA, Himmel ME, Bomble YJ.

Sci Adv. 2016 Feb 5;2(2):e1501254. doi: 10.1126/sciadv.1501254. eCollection 2016 Feb.

22.

Draft Genome Sequence of Streptomyces vitaminophilus ATCC 31673, a Producer of Pyrrolomycin Antibiotics, Some of Which Contain a Nitro Group.

Mahan KM, Klingeman DM, Hettich RL, Parry RJ, Graham DE.

Genome Announc. 2016 Jan 21;4(1). pii: e01582-15. doi: 10.1128/genomeA.01582-15.

23.

Clostridium thermocellum DSM 1313 transcriptional responses to redox perturbation.

Sander K, Wilson CM, Rodriguez M Jr, Klingeman DM, Rydzak T, Davison BH, Brown SD.

Biotechnol Biofuels. 2015 Dec 12;8:211. doi: 10.1186/s13068-015-0394-9. eCollection 2015.

24.

Draft Genome Sequences of Four Streptomyces Isolates from the Populus trichocarpa Root Endosphere and Rhizosphere.

Klingeman DM, Utturkar S, Lu TY, Schadt CW, Pelletier DA, Brown SD.

Genome Announc. 2015 Nov 12;3(6). pii: e01344-15. doi: 10.1128/genomeA.01344-15.

25.

Near-Complete Genome Sequence of the Cellulolytic Bacterium Bacteroides (Pseudobacteroides) cellulosolvens ATCC 35603.

Dassa B, Utturkar S, Hurt RA, Klingeman DM, Keller M, Xu J, Reddy YH, Borovok I, Rozman Grinberg I, Lamed R, Zhivin O, Bayer EA, Brown SD.

Genome Announc. 2015 Sep 24;3(5). pii: e01022-15. doi: 10.1128/genomeA.01022-15.

26.

Genome-scale resources for Thermoanaerobacterium saccharolyticum.

Currie DH, Raman B, Gowen CM, Tschaplinski TJ, Land ML, Brown SD, Covalla SF, Klingeman DM, Yang ZK, Engle NL, Johnson CM, Rodriguez M, Shaw AJ, Kenealy WR, Lynd LR, Fong SS, Mielenz JR, Davison BH, Hogsett DA, Herring CD.

BMC Syst Biol. 2015 Jun 26;9:30. doi: 10.1186/s12918-015-0159-x.

27.

Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies.

Utturkar SM, Klingeman DM, Bruno-Barcena JM, Chinn MS, Grunden AM, Köpke M, Brown SD.

Sci Data. 2015 Apr 14;2:150014. doi: 10.1038/sdata.2015.14. eCollection 2015.

28.

Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum.

Chou WC, Ma Q, Yang S, Cao S, Klingeman DM, Brown SD, Xu Y.

Nucleic Acids Res. 2015 May 26;43(10):e67. doi: 10.1093/nar/gkv177. Epub 2015 Mar 12.

29.

Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences.

Utturkar SM, Klingeman DM, Land ML, Schadt CW, Doktycz MJ, Pelletier DA, Brown SD.

Bioinformatics. 2014 Oct;30(19):2709-16. doi: 10.1093/bioinformatics/btu391. Epub 2014 Jun 14.

30.

Draft Genome Sequence of Rhodococcus rhodochrous Strain ATCC 21198.

Shields-Menard SA, Brown SD, Klingeman DM, Indest K, Hancock D, Wewalwela JJ, French WT, Donaldson JR.

Genome Announc. 2014 Feb 13;2(1). pii: e00054-14. doi: 10.1128/genomeA.00054-14.

31.

Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass.

Wilson CM, Rodriguez M Jr, Johnson CM, Martin SL, Chu TM, Wolfinger RD, Hauser LJ, Land ML, Klingeman DM, Syed MH, Ragauskas AJ, Tschaplinski TJ, Mielenz JR, Brown SD.

Biotechnol Biofuels. 2013 Dec 2;6(1):179. doi: 10.1186/1754-6834-6-179.

32.

Draft Genome Sequence for Caulobacter sp. Strain OR37, a Bacterium Tolerant to Heavy Metals.

Utturkar SM, Bollmann A, Brzoska RM, Klingeman DM, Epstein SE, Palumbo AV, Brown SD.

Genome Announc. 2013 Jun 27;1(3). pii: e00322-13. doi: 10.1128/genomeA.00322-13.

33.

Draft Genome Sequence for Ralstonia sp. Strain OR214, a Bacterium with Potential for Bioremediation.

Utturkar SM, Bollmann A, Brzoska RM, Klingeman DM, Epstein SE, Palumbo AV, Brown SD.

Genome Announc. 2013 Jun 27;1(3). pii: e00321-13. doi: 10.1128/genomeA.00321-13.

34.

Genome Sequences of Industrially Relevant Saccharomyces cerevisiae Strain M3707, Isolated from a Sample of Distillers Yeast and Four Haploid Derivatives.

Brown SD, Klingeman DM, Johnson CM, Clum A, Aerts A, Salamov A, Sharma A, Zane M, Barry K, Grigoriev IV, Davison BH, Lynd LR, Gilna P, Hau H, Hogsett DA, Froehlich AC.

Genome Announc. 2013 Jun 27;1(3). pii: e00323-13. doi: 10.1128/genomeA.00323-13.

35.

Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides.

Brown SD, Utturkar SM, Klingeman DM, Johnson CM, Martin SL, Land ML, Lu TY, Schadt CW, Doktycz MJ, Pelletier DA.

J Bacteriol. 2012 Nov;194(21):5991-3. doi: 10.1128/JB.01243-12.

36.

Draft genome sequences for two metal-reducing Pelosinus fermentans strains isolated from a Cr(VI)-contaminated site and for type strain R7.

Brown SD, Podar M, Klingeman DM, Johnson CM, Yang ZK, Utturkar SM, Land ML, Mosher JJ, Hurt RA Jr, Phelps TJ, Palumbo AV, Arkin AP, Hazen TC, Elias DA.

J Bacteriol. 2012 Sep;194(18):5147-8. doi: 10.1128/JB.01174-12.

37.

Draft genome sequences for Clostridium thermocellum wild-type strain YS and derived cellulose adhesion-defective mutant strain AD2.

Brown SD, Lamed R, Morag E, Borovok I, Shoham Y, Klingeman DM, Johnson CM, Yang Z, Land ML, Utturkar SM, Keller M, Bayer EA.

J Bacteriol. 2012 Jun;194(12):3290-1. doi: 10.1128/JB.00473-12.

38.

Draft genome sequence for Microbacterium laevaniformans strain OR221, a bacterium tolerant to metals, nitrate, and low pH.

Brown SD, Palumbo AV, Panikov N, Ariyawansa T, Klingeman DM, Johnson CM, Land ML, Utturkar SM, Epstein SS.

J Bacteriol. 2012 Jun;194(12):3279-80. doi: 10.1128/JB.00474-12.

39.

Draft genome sequence of Rhizobium sp. strain PDO1-076, a bacterium isolated from Populus deltoides.

Brown SD, Klingeman DM, Lu TY, Johnson CM, Utturkar SM, Land ML, Schadt CW, Doktycz MJ, Pelletier DA.

J Bacteriol. 2012 May;194(9):2383-4. doi: 10.1128/JB.00198-12.

40.

Ethanol-tolerant gene identification in Clostridium thermocellum using pyro-resequencing for metabolic engineering.

Yang S, Klingeman DM, Brown SD.

Methods Mol Biol. 2012;834:111-36. doi: 10.1007/978-1-61779-483-4_9.

PMID:
22144357
41.

Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum.

Brown SD, Guss AM, Karpinets TV, Parks JM, Smolin N, Yang S, Land ML, Klingeman DM, Bhandiwad A, Rodriguez M Jr, Raman B, Shao X, Mielenz JR, Smith JC, Keller M, Lynd LR.

Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13752-7. doi: 10.1073/pnas.1102444108. Epub 2011 Aug 8.

42.

Draft genome sequence of the thermoalkaliphilic Caldalkalibacillus thermarum strain TA2.A1.

Kalamorz F, Keis S, McMillan DG, Olsson K, Stanton JA, Stockwell P, Black MA, Klingeman DM, Land ML, Han CS, Martin SL, Becher SA, Peddie CJ, Morgan HW, Matthies D, Preiss L, Meier T, Brown SD, Cook GM.

J Bacteriol. 2011 Aug;193(16):4290-1. doi: 10.1128/JB.05035-11. Epub 2011 Jun 17.

43.

Shewanella oneidensis MR-1 sensory box protein involved in aerobic and anoxic growth.

Sundararajan A, Kurowski J, Yan T, Klingeman DM, Joachimiak MP, Zhou J, Naranjo B, Gralnick JA, Fields MW.

Appl Environ Microbiol. 2011 Jul;77(13):4647-56. doi: 10.1128/AEM.03003-10. Epub 2011 May 20.

44.

Complete genome sequence of the cellulolytic thermophile Caldicellulosiruptor obsidiansis OB47T.

Elkins JG, Lochner A, Hamilton-Brehm SD, Davenport KW, Podar M, Brown SD, Land ML, Hauser LJ, Klingeman DM, Raman B, Goodwin LA, Tapia R, Meincke LJ, Detter JC, Bruce DC, Han CS, Palumbo AV, Cottingham RW, Keller M, Graham DE.

J Bacteriol. 2010 Nov;192(22):6099-100. doi: 10.1128/JB.00950-10. Epub 2010 Sep 17.

45.

Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae.

Yang S, Land ML, Klingeman DM, Pelletier DA, Lu TY, Martin SL, Guo HB, Smith JC, Brown SD.

Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10395-400. doi: 10.1073/pnas.0914506107. Epub 2010 May 19.

46.

Improved genome annotation for Zymomonas mobilis.

Yang S, Pappas KM, Hauser LJ, Land ML, Chen GL, Hurst GB, Pan C, Kouvelis VN, Typas MA, Pelletier DA, Klingeman DM, Chang YJ, Samatova NF, Brown SD.

Nat Biotechnol. 2009 Oct;27(10):893-4. doi: 10.1038/nbt1009-893. No abstract available.

PMID:
19816441
47.

Generation and validation of a Shewanella oneidensis MR-1 clone set for protein expression and phage display.

Gao H, Pattison D, Yan T, Klingeman DM, Wang X, Petrosino J, Hemphill L, Wan X, Leaphart AB, Weinstock GM, Palzkill T, Zhou J.

PLoS One. 2008 Aug 20;3(8):e2983. doi: 10.1371/journal.pone.0002983.

49.

Global transcriptome analysis of Shewanella oneidensis MR-1 exposed to different terminal electron acceptors.

Beliaev AS, Klingeman DM, Klappenbach JA, Wu L, Romine MF, Tiedje JM, Nealson KH, Fredrickson JK, Zhou J.

J Bacteriol. 2005 Oct;187(20):7138-45.

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