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Singer, Steven

TitleGeological Staff Scientist
InstitutionLawrence Berkeley National Lab
DepartmentBiological Systems & Eng
Address1 Cyclotron Road
Berkeley CA 94720
Phone510/486-5556
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. 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 S, Spatafora JW, Wang M, Veneault-Fourrey C, Henrissat B, Grigoriev IV, Martin FM, Perotto S. Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists. New Phytol. 2018 Feb; 217(3):1213-1229. PMID: 29315638.
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    2. Amaike Campen S, Lynn J, Sibert SJ, Srikrishnan S, Phatale P, Feldman T, Guenther JM, Hiras J, Tran YTA, Singer S, Adams PD, Sale KL, Simmons BA, Baker SE, Magnuson JK, Gladden JM. Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger. PLoS One. 2017; 12(12):e0189604. PMID: 29281693.
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    3. Mohamed ET, Wang S, Lennen RM, Herrgård MJ, Simmons BA, Singer S, Feist AM. Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution. Microb Cell Fact. 2017 Nov 16; 16(1):204. PMID: 29145855.
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    4. 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 S. Xylose induces cellulase production in Thermoascus aurantiacus. Biotechnol Biofuels. 2017; 10:271. PMID: 29167701.
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    5. 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 S. A bacterial pioneer produces cellulase complexes that persist through community succession. Nat Microbiol. 2018 Jan; 3(1):99-107. PMID: 29109478.
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    6. 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 S, Magnuson JK, Arkin AP, Skerker JM, Gladden JM. Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts. Biotechnol Biofuels. 2017; 10:241. PMID: 29075325.
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    7. Sitepu IR, Garay LA, Enriquez L, Fry R, Butler JH, Lopez JM, Kanti A, Faulina SA, Nugroho AJ, Simmons BA, Singer S, Simmons CW, Boundy-Mills K. 1-Ethyl-3-methylimidazolium tolerance and intracellular lipid accumulation of 38 oleaginous yeast species. Appl Microbiol Biotechnol. 2017 Dec; 101(23-24):8621-8631. PMID: 29051987.
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    8. 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, Balvociute 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 S, 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. Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software. Nat Methods. 2017 Nov; 14(11):1063-1071. PMID: 28967888.
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    9. Jiménez DJ, Dini-Andreote F, DeAngelis KM, Singer S, Salles JF, van Elsas JD. Ecological Insights into the Dynamics of Plant Biomass-Degrading Microbial Consortia. Trends Microbiol. 2017 Oct; 25(10):788-796. PMID: 28648267.
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    10. Metreveli E, Kachlishvili E, Singer S, Elisashvili V. 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. Bioresour Technol. 2017 Oct; 241:652-660. PMID: 28609753.
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    11. Wu YW, Higgins B, Yu C, Reddy AP, Ceballos S, Joh LD, Simmons BA, Singer S, VanderGheynst JS. Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis. mSystems. 2016 Nov-Dec; 1(6). PMID: 27981239.
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    12. Yu C, Simmons BA, Singer S, Thelen MP, VanderGheynst JS. Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts. Appl Microbiol Biotechnol. 2016 Dec; 100(24):10237-10249. PMID: 27838839.
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    13. Kothari A, Charrier M, Wu YW, Malfatti S, Zhou CE, Singer S, Dugan L, Mukhopadhyay A. Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization. FEMS Microbiol Lett. 2016 10; 363(20). PMID: 27664055.
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    14. 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 S. Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis. MBio. 2016 08 23; 7(4). PMID: 27555310; PMCID: PMC4999548.
    15. Pace S, Ceballos SJ, Harrold D, Stannard W, Simmons BA, Singer S, Thelen MP, VanderGheynst JS. Enrichment of microbial communities tolerant to the ionic liquids tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate. Appl Microbiol Biotechnol. 2016 Jun; 100(12):5639-52. PMID: 27102129.
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    16. 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 S, Banfield JF. Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage. Front Microbiol. 2016; 7:238. PMID: 26973616; PMCID: PMC4776211.
    17. Yu C, Reddy AP, Simmons CW, Simmons BA, Singer S, VanderGheynst JS. Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions. Biotechnol Biofuels. 2015; 8:206. PMID: 26633993; PMCID: PMC4667496.
    18. Wu YW, Simmons BA, Singer S. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2016 Feb 15; 32(4):605-7. PMID: 26515820.
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    19. Hiras J, Wu YW, Eichorst SA, Simmons BA, Singer S. Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage. ISME J. 2016 Apr; 10(4):833-45. PMID: 26325358; PMCID: PMC4796922 [Available on 04/01/17].
    20. Merkley ED, Wrighton KC, Castelle CJ, Anderson BJ, Wilkins MJ, Shah V, Arbour T, Brown JN, Singer S, Smith RD, Lipton MS. Changes in protein expression across laboratory and field experiments in Geobacter bemidjiensis. J Proteome Res. 2015 Mar 06; 14(3):1361-75. PMID: 25496566.
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    21. Simmons CW, Reddy AP, D'haeseleer P, Khudyakov J, Billis K, Pati A, Simmons BA, Singer S, Thelen MP, VanderGheynst JS. Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw. Biotechnol Biofuels. 2014; 7(1):495. PMID: 25648696; PMCID: PMC4296540.
    22. Sitepu IR, Shi S, Simmons BA, Singer S, Boundy-Mills K, Simmons CW. Yeast tolerance to the ionic liquid 1-ethyl-3-methylimidazolium acetate. FEMS Yeast Res. 2014 Dec; 14(8):1286-94. PMID: 25348480.
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    23. Woebken D, Burow LC, Behnam F, Mayali X, Schintlmeister A, Fleming ED, Prufert-Bebout L, Singer S, Cortés AL, Hoehler TM, Pett-Ridge J, Spormann AM, Wagner M, Weber PK, Bebout BM. Revisiting N2 fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach. ISME J. 2015 Feb; 9(2):485-96. PMID: 25303712; PMCID: PMC4303640.
    24. Eichorst SA, Joshua C, Sathitsuksanoh N, Singh S, Simmons BA, Singer S. Substrate-Specific Development of Thermophilic Bacterial Consortia by Using Chemically Pretreated Switchgrass. Appl Environ Microbiol. 2014 Dec; 80(23):7423-32. PMID: 25261509; PMCID: PMC4249183.
    25. Wu YW, Tang YH, Tringe SG, Simmons BA, Singer S. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome. 2014; 2:26. PMID: 25136443; PMCID: PMC4129434.
    26. Ruegg TL, Kim EM, Simmons BA, Keasling JD, Singer S, Lee TS, Thelen MP. An auto-inducible mechanism for ionic liquid resistance in microbial biofuel production. Nat Commun. 2014 Mar 26; 5:3490. PMID: 24667370.
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    27. Gladden JM, Park JI, Bergmann J, Reyes-Ortiz V, D'haeseleer P, Quirino BF, Sale KL, Simmons BA, Singer S. Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community. Biotechnol Biofuels. 2014 Jan 29; 7(1):15. PMID: 24479406; PMCID: PMC3923250.
    28. Simmons CW, Reddy AP, Vandergheynst JS, Simmons BA, Singer S. Bacillus coagulans tolerance to 1-ethyl-3-methylimidazolium-based ionic liquids in aqueous and solid-state thermophilic culture. Biotechnol Prog. 2014 Mar-Apr; 30(2):311-6. PMID: 24376258.
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    29. Bergmann JC, Costa OY, Gladden JM, Singer S, Heins R, D'haeseleer P, Simmons BA, Quirino BF. Discovery of two novel ß-glucosidases from an Amazon soil metagenomic library. FEMS Microbiol Lett. 2014 Feb; 351(2):147-55. PMID: 24236615.
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    30. Cheng X, Hiras J, Deng K, Bowen B, Simmons BA, Adams PD, Singer S, Northen TR. High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal ß-glucosidase production. Front Microbiol. 2013; 4:365. PMID: 24367356; PMCID: PMC3854461.
    31. Bi C, Su P, Müller J, Yeh YC, Chhabra SR, Beller HR, Singer S, Hillson NJ. Development of a broad-host synthetic biology toolbox for Ralstonia eutropha and its application to engineering hydrocarbon biofuel production. Microb Cell Fact. 2013 Nov 13; 12:107. PMID: 24219429; PMCID: PMC3831590.
    32. Reddy AP, Simmons CW, D'haeseleer P, Khudyakov J, Burd H, Hadi M, Simmons BA, Singer S, Thelen MP, Vandergheynst JS. Discovery of microorganisms and enzymes involved in high-solids decomposition of rice straw using metagenomic analyses. PLoS One. 2013; 8(10):e77985. PMID: 24205054; PMCID: PMC3808287.
    33. Everroad RC, Woebken D, Singer S, Burow LC, Kyrpides N, Woyke T, Goodwin L, Detweiler A, Prufert-Bebout L, Pett-Ridge J. Draft Genome Sequence of an Oscillatorian Cyanobacterium, Strain ESFC-1. Genome Announc. 2013 Aug 01; 1(4). PMID: 23908279; PMCID: PMC3731833.
    34. D'haeseleer P, Gladden JM, Allgaier M, Chain PS, Tringe SG, Malfatti SA, Aldrich JT, Nicora CD, Robinson EW, Paša-Tolic L, Hugenholtz P, Simmons BA, Singer S. Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. PLoS One. 2013; 8(7):e68465. PMID: 23894306.
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    35. Eichorst SA, Varanasi P, Stavila V, Zemla M, Auer M, Singh S, Simmons BA, Singer S. Community dynamics of cellulose-adapted thermophilic bacterial consortia. Environ Microbiol. 2013 Sep; 15(9):2573-87. PMID: 23763762.
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    36. Müller J, MacEachran D, Burd H, Sathitsuksanoh N, Bi C, Yeh YC, Lee TS, Hillson NJ, Chhabra SR, Singer S, Beller HR. Engineering of Ralstonia eutropha H16 for autotrophic and heterotrophic production of methyl ketones. Appl Environ Microbiol. 2013 Jul; 79(14):4433-9. PMID: 23686271; PMCID: PMC3697500.
    37. Yeh YC, Müller J, Bi C, Hillson NJ, Beller HR, Chhabra SR, Singer S. Functionalizing bacterial cell surfaces with a phage protein. Chem Commun (Camb). 2013 Jan 30; 49(9):910-2. PMID: 23247551.
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    38. Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer S, Eisen JA, Banfield JF. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun. 2013; 4:2120. PMID: 23979677; PMCID: PMC3903129.
    39. 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 S. Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics. ISME J. 2013 Apr; 7(4):817-29. PMID: 23190731; PMCID: PMC3603402.
    40. McClendon SD, Batth T, Petzold CJ, Adams PD, Simmons BA, Singer S. Thermoascus aurantiacus is a promising source of enzymes for biomass deconstruction under thermophilic conditions. Biotechnol Biofuels. 2012 Jul 28; 5(1):54. PMID: 22839529; PMCID: PMC3507748.
    41. Park JI, Steen EJ, Burd H, Evans SS, Redding-Johnson AM, Batth T, Benke PI, D'haeseleer P, Sun N, Sale KL, Keasling JD, Lee TS, Petzold CJ, Mukhopadhyay A, Singer S, Simmons BA, Gladden JM. A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels. PLoS One. 2012; 7(5):e37010. PMID: 22649505; PMCID: PMC3359315.
    42. Wheeler KE, Erickson BK, Mueller R, Singer S, Verberkmoes NC, Hwang M, Thelen MP, Hettich RL. Metal affinity enrichment increases the range and depth of proteome identification for extracellular microbial proteins. J Proteome Res. 2012 Feb 03; 11(2):861-70. PMID: 22191549.
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    43. Woebken D, Burow LC, Prufert-Bebout L, Bebout BM, Hoehler TM, Pett-Ridge J, Spormann AM, Weber PK, Singer S. Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis. ISME J. 2012 Jul; 6(7):1427-39. PMID: 22237543; PMCID: PMC3379636.
    44. Singer S. Targeted isolation of proteins from natural microbial communities living in an extreme environment. Methods Mol Biol. 2012; 881:63-72. PMID: 22639210.
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    45. Gladden JM, Eichorst SA, Hazen TC, Simmons BA, Singer S. Substrate perturbation alters the glycoside hydrolase activities and community composition of switchgrass-adapted bacterial consortia. Biotechnol Bioeng. 2012 May; 109(5):1140-5. PMID: 22125273.
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    46. Burow LC, Woebken D, Bebout BM, McMurdie PJ, Singer S, Pett-Ridge J, Prufert-Bebout L, Spormann AM, Weber PK, Hoehler TM. Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay. ISME J. 2012 Apr; 6(4):863-74. PMID: 22011721; PMCID: PMC3309353.
    47. Gladden JM, Allgaier M, Miller CS, Hazen TC, VanderGheynst JS, Hugenholtz P, Simmons BA, Singer S. Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass. Appl Environ Microbiol. 2011 Aug 15; 77(16):5804-12. PMID: 21724886; PMCID: PMC3165268.
    48. Miller CS, Baker BJ, Thomas BC, Singer S, Banfield JF. EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biol. 2011; 12(5):R44. PMID: 21595876; PMCID: PMC3219967.
    49. Reddy AP, Allgaier M, Singer S, Hazen TC, Simmons BA, Hugenholtz P, VanderGheynst JS. Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction. Biotechnol Bioeng. 2011 Sep; 108(9):2088-98. PMID: 21520015.
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    50. Casey CP, Johnson JB, Jiao X, Beetner SE, Singer S. Chain mechanism for exchange of D2 with a ruthenium hydride. Chem Commun (Camb). 2010 Nov 14; 46(42):7915-7. PMID: 20856982.
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    51. Singer S, Erickson BK, VerBerkmoes NC, Hwang M, Shah MB, Hettich RL, Banfield JF, Thelen MP. Posttranslational modification and sequence variation of redox-active proteins correlate with biofilm life cycle in natural microbial communities. ISME J. 2010 Nov; 4(11):1398-409. PMID: 20485387.
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    52. Erickson BK, Mueller RS, VerBerkmoes NC, Shah M, Singer S, Thelen MP, Banfield JF, Hettich RL. Computational prediction and experimental validation of signal peptide cleavages in the extracellular proteome of a natural microbial community. J Proteome Res. 2010 May 07; 9(5):2148-59. PMID: 20218729.
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    53. Goltsman DS, Denef VJ, Singer S, VerBerkmoes NC, Lefsrud M, Mueller RS, Dick GJ, Sun CL, Wheeler KE, Zemla A, Baker BJ, Hauser L, Land M, Shah MB, Thelen MP, Hettich RL, Banfield JF. Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms. Appl Environ Microbiol. 2009 Jul; 75(13):4599-615. PMID: 19429552; PMCID: PMC2704813.
    54. Singer S, Chan CS, Zemla A, VerBerkmoes NC, Hwang M, Hettich RL, Banfield JF, Thelen MP. Characterization of cytochrome 579, an unusual cytochrome isolated from an iron-oxidizing microbial community. Appl Environ Microbiol. 2008 Jul; 74(14):4454-62. PMID: 18469132; PMCID: PMC2493166.
    55. Jeans C, Singer S, Chan CS, Verberkmoes NC, Shah M, Hettich RL, Banfield JF, Thelen MP. Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community. ISME J. 2008 May; 2(5):542-50. PMID: 18463612.
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    56. Singer S, Hirst MB, Ludden PW. CO-dependent H2 evolution by Rhodospirillum rubrum: role of CODH:CooF complex. Biochim Biophys Acta. 2006 Dec; 1757(12):1582-91. PMID: 17123462.
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    57. Jeon WB, Singer S, Ludden PW, Rubio LM. New insights into the mechanism of nickel insertion into carbon monoxide dehydrogenase: analysis of Rhodospirillum rubrum carbon monoxide dehydrogenase variants with substituted ligands to the [Fe3S4] portion of the active-site C-cluster. J Biol Inorg Chem. 2005 Dec; 10(8):903-12. PMID: 16283394.
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    58. Casey CP, Johnson JB, Singer S, Cui Q. Hydrogen elimination from a hydroxycyclopentadienyl ruthenium(II) hydride: study of hydrogen activation in a ligand-metal bifunctional hydrogenation catalyst. J Am Chem Soc. 2005 Mar 09; 127(9):3100-9. PMID: 15740149.
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    59. Rubio LM, Singer S, Ludden PW. Purification and characterization of NafY (apodinitrogenase gamma subunit) from Azotobacter vinelandii. J Biol Chem. 2004 May 07; 279(19):19739-46. PMID: 14996831; PMCID: PMC1249483.
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