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    Karsten Zengler

    TitleAssociate Professor
    SchoolUniversity of California, San Diego
    DepartmentPediatrics
    Address9500 Gilman Drive #0760
    CA La Jolla 92093
    Phone858-534-5758
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      Collapse Research 
      Collapse Research Activities and Funding
      Transcriptional response of a skin microbiome transplant
      NIH/NIAMS R21AR071731Apr 1, 2017 - Mar 31, 2018
      Role: Principal Investigator
      Establishing a Skin Microbiome Transplant
      NIH/NIAMS R21AR067547Aug 1, 2015 - May 31, 2017
      Role: Principal Investigator

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      Collapse Bibliographic 
      Collapse Publications
      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. Zuniga C, Levering J, Antoniewicz MR, Guarnieri MT, Betenbaugh MJ, Zengler K. Predicting dynamic metabolic demands in the photosynthetic eukaryote Chlorella vulgaris. Plant Physiol. 2017 Sep 26. PMID: 28951490.
        View in: PubMed
      2. Zuñiga C, Zaramela L, Zengler K. Elucidation of complexity and prediction of interactions in microbial communities. Microb Biotechnol. 2017 Sep 19. PMID: 28925555.
        View in: PubMed
      3. Wankel SD, Ziebis W, Buchwald C, Charoenpong C, de Beer D, Dentinger J, Xu Z, Zengler K. Evidence for fungal and chemodenitrification based N2O flux from nitrogen impacted coastal sediments. Nat Commun. 2017 Jun 05; 8:15595. PMID: 28580932.
        View in: PubMed
      4. Nakatsuji T, Chen TH, Narala S, Chun KA, Two AM, Yun T, Shafiq F, Kotol PF, Bouslimani A, Melnik AV, Latif H, Kim JN, Lockhart A, Artis K, David G, Taylor P, Streib J, Dorrestein PC, Grier A, Gill SR, Zengler K, Hata TR, Leung DY, Gallo RL. Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis. Sci Transl Med. 2017 Feb 22; 9(378). PMID: 28228596.
        View in: PubMed
      5. Levering J, Dupont CL, Allen AE, Palsson BO, Zengler K. Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels. mSystems. 2017 Jan-Feb; 2(1). PMID: 28217746.
        View in: PubMed
      6. Bosch TC, Zengler K, Naik S, Biedermann T, Kong HH, Loser K, Brüggeman H, Calleawert C, Lambert J, Van de Wiele T. FRT - FONDATION RENE TOURAINE: An International Foundation For Dermatology. Exp Dermatol. 2016 Nov; 25(11):917-932. PMID: 27792248.
        View in: PubMed
      7. Zuñiga C, Li CT, Huelsman T, Levering J, Zielinski DC, McConnell BO, Long CP, Knoshaug EP, Guarnieri MT, Antoniewicz MR, Betenbaugh MJ, Zengler K. Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions. Plant Physiol. 2016 Sep; 172(1):589-602. PMID: 27372244.
        View in: PubMed
      8. Movahedi NS, Embree M, Nagarajan H, Zengler K, Chitsaz H. Efficient Synergistic Single-Cell Genome Assembly. Front Bioeng Biotechnol. 2016; 4:42. PMID: 27243002; PMCID: PMC4876485.
      9. Levering J, Broddrick J, Dupont CL, Peers G, Beeri K, Mayers J, Gallina AA, Allen AE, Palsson BO, Zengler K. Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom. PLoS One. 2016; 11(5):e0155038. PMID: 27152931; PMCID: PMC4859558.
      10. Embree M, Liu JK, Al-Bassam MM, Zengler K. Networks of energetic and metabolic interactions define dynamics in microbial communities. Proc Natl Acad Sci U S A. 2015 Dec 15; 112(50):15450-5. PMID: 26621749; PMCID: PMC4687543.
      11. Levering J, Broddrick J, Zengler K. Engineering of oleaginous organisms for lipid production. Curr Opin Biotechnol. 2015 Dec; 36:32-9. PMID: 26319892.
        View in: PubMed
      12. Islam MA, Zengler K, Edwards EA, Mahadevan R, Stephanopoulos G. Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model. Integr Biol (Camb). 2015 Aug; 7(8):869-82. PMID: 25994252.
        View in: PubMed
      13. Latif H, Sahin M, Tarasova J, Tarasova Y, Portnoy VA, Nogales J, Zengler K. Adaptive Evolution of Thermotoga maritima Reveals Plasticity of the ABC Transporter Network. Appl Environ Microbiol. 2015 Aug 15; 81(16):5477-85. PMID: 26048924; PMCID: PMC4510162.
      14. Latif H, Szubin R, Tan J, Brunk E, Lechner A, Zengler K, Palsson BO. A streamlined ribosome profiling protocol for the characterization of microorganisms. Biotechniques. 2015 Jun; 58(6):329-32. PMID: 26054770.
        View in: PubMed
      15. Tan J, Zuniga C, Zengler K. Unraveling interactions in microbial communities - from co-cultures to microbiomes. J Microbiol. 2015 May; 53(5):295-305. PMID: 25935300.
        View in: PubMed
      16. Patil SA, Gildemyn S, Pant D, Zengler K, Logan BE, Rabaey K. A logical data representation framework for electricity-driven bioproduction processes. Biotechnol Adv. 2015 Nov 01; 33(6 Pt 1):736-44. PMID: 25765230.
        View in: PubMed
      17. Liu JK, O'Brien EJ, Lerman JA, Zengler K, Palsson BO, Feist AM. Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. BMC Syst Biol. 2014 Sep 18; 8:110. PMID: 25227965; PMCID: PMC4177180.
      18. Chen P, Torralba M, Tan J, Embree M, Zengler K, Stärkel P, van Pijkeren JP, DePew J, Loomba R, Ho SB, Bajaj JS, Mutlu EA, Keshavarzian A, Tsukamoto H, Nelson KE, Fouts DE, Schnabl B. Supplementation of saturated long-chain fatty acids maintains intestinal eubiosis and reduces ethanol-induced liver injury in mice. Gastroenterology. 2015 Jan; 148(1):203-214.e16. PMID: 25239591; PMCID: PMC4274236.
      19. Feist AM, Nagarajan H, Rotaru AE, Tremblay PL, Zhang T, Nevin KP, Lovley DR, Zengler K. Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens. PLoS Comput Biol. 2014 Apr; 10(4):e1003575. PMID: 24762737; PMCID: PMC3998878.
      20. Federowicz S, Kim D, Ebrahim A, Lerman J, Nagarajan H, Cho BK, Zengler K, Palsson B. Determining the control circuitry of redox metabolism at the genome-scale. PLoS Genet. 2014 Apr; 10(4):e1004264. PMID: 24699140; PMCID: PMC3974632.
      21. Embree M, Qiu Y, Shieu W, Nagarajan H, O'Neil R, Lovley D, Zengler K. The iron stimulon and fur regulon of Geobacter sulfurreducens and their role in energy metabolism. Appl Environ Microbiol. 2014 May; 80(9):2918-27. PMID: 24584254; PMCID: PMC3993298.
      22. Cho BK, Kim D, Knight EM, Zengler K, Palsson BO. Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states. BMC Biol. 2014 Jan 24; 12:4. PMID: 24461193; PMCID: PMC3923258.
      23. Latif H, Zeidan AA, Nielsen AT, Zengler K. Trash to treasure: production of biofuels and commodity chemicals via syngas fermenting microorganisms. Curr Opin Biotechnol. 2014 Jun; 27:79-87. PMID: 24863900.
        View in: PubMed
      24. Nagarajan H, Sahin M, Nogales J, Latif H, Lovley DR, Ebrahim A, Zengler K. Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii. Microb Cell Fact. 2013 Nov 25; 12:118. PMID: 24274140; PMCID: PMC4222884.
      25. Embree M, Nagarajan H, Movahedi N, Chitsaz H, Zengler K. Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community. ISME J. 2014 Apr; 8(4):757-67. PMID: 24152715; PMCID: PMC3960532.
      26. Rodionov DA, Rodionova IA, Li X, Ravcheev DA, Tarasova Y, Portnoy VA, Zengler K, Osterman AL. Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima. Front Microbiol. 2013; 4:244. PMID: 23986752; PMCID: PMC3750489.
      27. Latif H, Lerman JA, Portnoy VA, Tarasova Y, Nagarajan H, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Lee DH, Qiu Y, Zengler K. The genome organization of Thermotoga maritima reflects its lifestyle. PLoS Genet. 2013 Apr; 9(4):e1003485. PMID: 23637642; PMCID: PMC3636130.
      28. Qiu Y, Nagarajan H, Embree M, Shieu W, Abate E, Juárez K, Cho BK, Elkins JG, Nevin KP, Barrett CL, Lovley DR, Palsson BO, Zengler K. Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks. Nat Commun. 2013; 4:1755. PMID: 23612296.
        View in: PubMed
      29. Nakatsuji T, Chiang HI, Jiang SB, Nagarajan H, Zengler K, Gallo RL. The microbiome extends to subepidermal compartments of normal skin. Nat Commun. 2013; 4:1431. PMID: 23385576; PMCID: PMC3655727.
      30. Nagarajan H, Embree M, Rotaru AE, Shrestha PM, Feist AM, Palsson BØ, Lovley DR, Zengler K. Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association. Nat Commun. 2013; 4:2809. PMID: 24264237.
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      31. Gong Y, Ebrahim A, Feist AM, Embree M, Zhang T, Lovley D, Zengler K. Sulfide-driven microbial electrosynthesis. Environ Sci Technol. 2013 Jan 02; 47(1):568-73. PMID: 23252645.
        View in: PubMed
      32. Alain K, Harder J, Widdel F, Zengler K. Anaerobic utilization of toluene by marine alpha- and gammaproteobacteria reducing nitrate. Microbiology. 2012 Dec; 158(Pt 12):2946-57. PMID: 23038808.
        View in: PubMed
      33. Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BO. In silico method for modelling metabolism and gene product expression at genome scale. Nat Commun. 2012 Jul 03; 3:929. PMID: 22760628; PMCID: PMC3827721.
      34. Zengler K, Palsson BO. A road map for the development of community systems (CoSy) biology. Nat Rev Microbiol. 2012 03 27; 10(5):366-72. PMID: 22450377.
        View in: PubMed
      35. Ravcheev DA, Li X, Latif H, Zengler K, Leyn SA, Korostelev YD, Kazakov AE, Novichkov PS, Osterman AL, Rodionov DA. Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex. J Bacteriol. 2012 Mar; 194(5):1145-57. PMID: 22210771; PMCID: PMC3294762.
      36. Cho BK, Federowicz S, Park YS, Zengler K, Palsson BØ. Deciphering the transcriptional regulatory logic of amino acid metabolism. Nat Chem Biol. 2011 Nov 13; 8(1):65-71. PMID: 22082910; PMCID: PMC3777760.
      37. Cho BK, Palsson B, Zengler K. Deciphering the regulatory codes in bacterial genomes. Biotechnol J. 2011 Sep; 6(9):1052-63. PMID: 21845736.
        View in: PubMed
      38. Portnoy VA, Bezdan D, Zengler K. Adaptive laboratory evolution--harnessing the power of biology for metabolic engineering. Curr Opin Biotechnol. 2011 Aug; 22(4):590-4. PMID: 21497080.
        View in: PubMed
      39. Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen FC, Fleming RM, Hsiung CA, De Keersmaecker SC, Liao YC, Marchal K, Mo ML, Özdemir E, Raghunathan A, Reed JL, Shin SI, Sigurbjörnsdóttir S, Steinmann J, Sudarsan S, Swainston N, Thijs IM, Zengler K, Palsson BO, Adkins JN, Bumann D. A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst Biol. 2011 Jan 18; 5:8. PMID: 21244678; PMCID: PMC3032673.
      40. Tremblay PL, Summers ZM, Glaven RH, Nevin KP, Zengler K, Barrett CL, Qiu Y, Palsson BO, Lovley DR. A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution. Environ Microbiol. 2011 Jan; 13(1):13-23. PMID: 20636372.
        View in: PubMed
      41. Palsson B, Zengler K. The challenges of integrating multi-omic data sets. Nat Chem Biol. 2010 Nov; 6(11):787-9. PMID: 20976870.
        View in: PubMed
      42. Qiu Y, Cho BK, Park YS, Lovley D, Palsson BØ, Zengler K. Structural and operational complexity of the Geobacter sulfurreducens genome. Genome Res. 2010 Sep; 20(9):1304-11. PMID: 20592237; PMCID: PMC2928509.
      43. Klimes A, Franks AE, Glaven RH, Tran H, Barrett CL, Qiu Y, Zengler K, Lovley DR. Production of pilus-like filaments in Geobacter sulfurreducens in the absence of the type IV pilin protein PilA. FEMS Microbiol Lett. 2010 Sep 01; 310(1):62-8. PMID: 20629752.
        View in: PubMed
      44. Nagarajan H, Butler JE, Klimes A, Qiu Y, Zengler K, Ward J, Young ND, Methé BA, Palsson BØ, Lovley DR, Barrett CL. De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads. PLoS One. 2010 Jun 08; 5(6):e10922. PMID: 20544019; PMCID: PMC2882325.
      45. Zengler K. Central role of the cell in microbial ecology. Microbiol Mol Biol Rev. 2009 Dec; 73(4):712-29. PMID: 19946138; PMCID: PMC2786577.
      46. Cho BK, Zengler K, Qiu Y, Park YS, Knight EM, Barrett CL, Gao Y, Palsson BØ. The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol. 2009 Nov; 27(11):1043-9. PMID: 19881496; PMCID: PMC3832199.
      47. Podar M, Abulencia CB, Walcher M, Hutchison D, Zengler K, Garcia JA, Holland T, Cotton D, Hauser L, Keller M. Targeted access to the genomes of low-abundance organisms in complex microbial communities. Appl Environ Microbiol. 2007 May; 73(10):3205-14. PMID: 17369337; PMCID: PMC1907129.
      48. Kevbrin VV, Zengler K, Lysenko AM, Wiegel J. Anoxybacillus kamchatkensis sp. nov., a novel thermophilic facultative aerobic bacterium with a broad pH optimum from the Geyser valley, Kamchatka. Extremophiles. 2005 Oct; 9(5):391-8. PMID: 16142505.
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      49. Zengler K, Walcher M, Clark G, Haller I, Toledo G, Holland T, Mathur EJ, Woodnutt G, Short JM, Keller M. High-throughput cultivation of microorganisms using microcapsules. Methods Enzymol. 2005; 397:124-30. PMID: 16260288.
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      50. Keller M, Zengler K. Tapping into microbial diversity. Nat Rev Microbiol. 2004 Feb; 2(2):141-50. PMID: 15040261.
        View in: PubMed
      51. Zengler K, Toledo G, Rappe M, Elkins J, Mathur EJ, Short JM, Keller M. Cultivating the uncultured. Proc Natl Acad Sci U S A. 2002 Nov 26; 99(24):15681-6. PMID: 12438682; PMCID: PMC137776.
      52. Zengler K, Richnow HH, Rosselló-Mora R, Michaelis W, Widdel F. Methane formation from long-chain alkanes by anaerobic microorganisms. Nature. 1999 Sep 16; 401(6750):266-9. PMID: 10499582.
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      53. Champion KM, Zengler K, Rabus R. Anaerobic degradation of ethylbenzene and toluene in denitrifying strain EbN1 proceeds via independent substrate-induced pathways. J Mol Microbiol Biotechnol. 1999 Aug; 1(1):157-64. PMID: 10941798.
        View in: PubMed
      54. Harms G, Zengler K, Rabus R, Aeckersberg F, Minz D, Rosselló-Mora R, Widdel F. Anaerobic oxidation of o-xylene, m-xylene, and homologous alkylbenzenes by new types of sulfate-reducing bacteria. Appl Environ Microbiol. 1999 Mar; 65(3):999-1004. PMID: 10049854; PMCID: PMC91135.
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