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Karsten Zengler

Title(s)Associate Professor, Pediatrics
SchoolAcademic Aff
Address9500 Gilman Drive #0760
La Jolla CA 92093
Phone858-534-5758
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    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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    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity. bioRxiv. 2020 Aug 18. Martino C, Kellman BP, Sandoval DR, Clausen TM, Marotz CA, Song SJ, Wandro S, Zaramela LS, Salido Benítez RA, Zhu Q, Armingol E, Vázquez-Baeza Y, McDonald D, Sorrentino JT, Taylor B, Belda-Ferre P, Liang C, Zhang Y, Schifanella L, Klatt NR, Havulinna AS, Jousilahti P, Huang S, Haiminen N, Parida L, Kim HC, Swafford AD, Zengler K, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Esko JD, Lewis NE, Knight R. PMID: 32839779.
      View in: PubMed   Mentions:
    2. Linking metabolic phenotypes to pathogenic traits among "Candidatus Liberibacter asiaticus" and its hosts. NPJ Syst Biol Appl. 2020 Aug 04; 6(1):24. Zuñiga C, Peacock B, Liang B, McCollum G, Irigoyen SC, Tec-Campos D, Marotz C, Weng NC, Zepeda A, Vidalakis G, Mandadi KK, Borneman J, Zengler K. PMID: 32753656.
      View in: PubMed   Mentions:    Fields:    
    3. Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth. Nat Commun. 2020 Jul 30; 11(1):3803. Zuñiga C, Li T, Guarnieri MT, Jenkins JP, Li CT, Bingol K, Kim YM, Betenbaugh MJ, Zengler K. PMID: 32732991.
      View in: PubMed   Mentions:    Fields:    
    4. Modeling of nitrogen fixation and polymer production in the heterotrophic diazotroph Azotobacter vinelandii DJ. Metab Eng Commun. 2020 Dec; 11:e00132. Campos DT, Zuñiga C, Passi A, Del Toro J, Tibocha-Bonilla JD, Zepeda A, Betenbaugh MJ, Zengler K. PMID: 32551229.
      View in: PubMed   Mentions:
    5. Transcriptional profiling of lung macrophages identifies a predictive signature for inflammatory lung disease in preterm infants. Commun Biol. 2020 May 22; 3(1):259. Sahoo D, Zaramela LS, Hernandez GE, Mai U, Taheri S, Dang D, Stouch AN, Medal RM, McCoy AM, Aschner JL, Blackwell TS, Zengler K, Prince LS. PMID: 32444859.
      View in: PubMed   Mentions:
    6. Dynamic resource allocation drives growth under nitrogen starvation in eukaryotes. NPJ Syst Biol Appl. 2020 May 15; 6(1):14. Tibocha-Bonilla JD, Kumar M, Richelle A, Godoy-Silva RD, Zengler K, Zuñiga C. PMID: 32415097.
      View in: PubMed   Mentions: 2     Fields:    
    7. Genomic and Transcriptomic Evidence Supports Methane Metabolism in Archaeoglobi. mSystems. 2020 Mar 17; 5(2). Liu YF, Chen J, Zaramela LS, Wang LY, Mbadinga SM, Hou ZW, Wu XL, Gu JD, Zengler K, Mu BZ. PMID: 32184369.
      View in: PubMed   Mentions:
    8. Interplay of Staphylococcal and Host Proteases Promotes Skin Barrier Disruption in Netherton Syndrome. Cell Rep. 2020 Mar 03; 30(9):2923-2933.e7. Williams MR, Cau L, Wang Y, Kaul D, Sanford JA, Zaramela LS, Khalil S, Butcher AM, Zengler K, Horswill AR, Dupont CL, Hovnanian A, Gallo RL. PMID: 32130897.
      View in: PubMed   Mentions: 1     Fields:    
    9. Blockade of IL-17 signaling reverses alcohol-induced liver injury and excessive alcohol drinking in mice. JCI Insight. 2020 02 13; 5(3). Xu J, Ma HY, Liu X, Rosenthal S, Baglieri J, McCubbin R, Sun M, Koyama Y, Geoffroy CG, Saijo K, Shang L, Nishio T, Maricic I, Kreifeldt M, Kusumanchi P, Roberts A, Zheng B, Kumar V, Zengler K, Pizzo DP, Hosseini M, Contet C, Glass CK, Liangpunsakul S, Tsukamoto H, Gao B, Karin M, Brenner DA, Koob GF, Kisseleva T. PMID: 32051339.
      View in: PubMed   Mentions:    Fields:    
    10. Author Correction: Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities. Nat Microbiol. 2019 Dec; 4(12):2578. Zuñiga C, Li CT, Yu G, Al-Bassam MM, Li T, Jiang L, Zaramela LS, Guarnieri M, Betenbaugh MJ, Zengler K. PMID: 31690826.
      View in: PubMed   Mentions:    Fields:    
    11. Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities. Nat Microbiol. 2019 12; 4(12):2184-2191. Zuñiga C, Li CT, Yu G, Al-Bassam MM, Li T, Jiang L, Zaramela LS, Guarnieri M, Betenbaugh MJ, Zengler K. PMID: 31591554.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCellsPHPublic Health
    12. Utilizing genome-scale models to optimize nutrient supply for sustained algal growth and lipid productivity. NPJ Syst Biol Appl. 2019; 5:33. Li CT, Yelsky J, Chen Y, Zuñiga C, Eng R, Jiang L, Shapiro A, Huang KW, Zengler K, Betenbaugh MJ. PMID: 31583115.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    13. Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates. Nat Microbiol. 2019 12; 4(12):2082-2089. Zaramela LS, Martino C, Alisson-Silva F, Rees SD, Diaz SL, Chuzel L, Ganatra MB, Taron CH, Secrest P, Zuñiga C, Huang J, Siegel D, Chang G, Varki A, Zengler K. PMID: 31548686.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    14. Functional and Proteomic Analysis of Streptococcus pyogenes Virulence Upon Loss of Its Native Cas9 Nuclease. Front Microbiol. 2019; 10:1967. Gao NJ, Al-Bassam MM, Poudel S, Wozniak JM, Gonzalez DJ, Olson J, Zengler K, Nizet V, Valderrama JA. PMID: 31507572.
      View in: PubMed   Mentions:
    15. Modelling approaches for studying the microbiome. Nat Microbiol. 2019 08; 4(8):1253-1267. Kumar M, Ji B, Zengler K, Nielsen J. PMID: 31337891.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    16. EcoFABs: advancing microbiome science through standardized fabricated ecosystems. Nat Methods. 2019 07; 16(7):567-571. Zengler K, Hofmockel K, Baliga NS, Behie SW, Bernstein HC, Brown JB, Dinneny JR, Floge SA, Forry SP, Hess M, Jackson SA, Jansson C, Lindemann SR, Pett-Ridge J, Maranas C, Venturelli OS, Wallenstein MD, Shank EA, Northen TR. PMID: 31227812.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    17. Establishing microbial composition measurement standards with reference frames. Nat Commun. 2019 06 20; 10(1):2719. Morton JT, Marotz C, Washburne A, Silverman J, Zaramela LS, Edlund A, Zengler K, Knight R. PMID: 31222023.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCellsPHPublic Health
    18. The impact of skin care products on skin chemistry and microbiome dynamics. BMC Biol. 2019 06 12; 17(1):47. Bouslimani A, da Silva R, Kosciolek T, Janssen S, Callewaert C, Amir A, Dorrestein K, Melnik AV, Zaramela LS, Kim JN, Humphrey G, Schwartz T, Sanders K, Brennan C, Luzzatto-Knaan T, Ackermann G, McDonald D, Zengler K, Knight R, Dorrestein PC. PMID: 31189482.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    19. Quorum sensing between bacterial species on the skin protects against epidermal injury in atopic dermatitis. Sci Transl Med. 2019 05 01; 11(490). Williams MR, Costa SK, Zaramela LS, Khalil S, Todd DA, Winter HL, Sanford JA, O'Neill AM, Liggins MC, Nakatsuji T, Cech NB, Cheung AL, Zengler K, Horswill AR, Gallo RL. PMID: 31043573.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    20. Mast cell recruitment is modulated by the hairless skin microbiome. J Allergy Clin Immunol. 2019 07; 144(1):330-333.e6. Wu CC, Kim JN, Wang Z, Chang YL, Zengler K, Di Nardo A. PMID: 30928651.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    21. Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen. PLoS Comput Biol. 2019 03; 15(3):e1006848. Liu JK, Lloyd C, Al-Bassam MM, Ebrahim A, Kim JN, Olson C, Aksenov A, Dorrestein P, Zengler K. PMID: 30845144.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    22. The nonlesional skin surface distinguishes atopic dermatitis with food allergy as a unique endotype. Sci Transl Med. 2019 02 20; 11(480). Leung DYM, Calatroni A, Zaramela LS, LeBeau PK, Dyjack N, Brar K, David G, Johnson K, Leung S, Ramirez-Gama M, Liang B, Rios C, Montgomery MT, Richers BN, Hall CF, Norquest KA, Jung J, Bronova I, Kreimer S, Talbot CC, Crumrine D, Cole RN, Elias P, Zengler K, Seibold MA, Berdyshev E, Goleva E. PMID: 30787169.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    23. A Novel Sparse Compositional Technique Reveals Microbial Perturbations. mSystems. 2019 Jan-Feb; 4(1). Martino C, Morton JT, Marotz CA, Thompson LR, Tripathi A, Knight R, Zengler K. PMID: 30801021.
      View in: PubMed   Mentions:
    24. Anaerobic degradation of hexadecane and phenanthrene coupled to sulfate reduction by enriched consortia from northern Gulf of Mexico seafloor sediment. Sci Rep. 2019 02 04; 9(1):1239. Shin B, Kim M, Zengler K, Chin KJ, Overholt WA, Gieg LM, Konstantinidis KT, Kostka JE. PMID: 30718896.
      View in: PubMed   Mentions:    Fields:    
    25. A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. PLoS Comput Biol. 2019 01; 15(1):e1006644. Seif Y, Monk JM, Mih N, Tsunemoto H, Poudel S, Zuniga C, Broddrick J, Zengler K, Palsson BO. PMID: 30625152.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    26. GABA-modulating bacteria of the human gut microbiota. Nat Microbiol. 2019 03; 4(3):396-403. Strandwitz P, Kim KH, Terekhova D, Liu JK, Sharma A, Levering J, McDonald D, Dietrich D, Ramadhar TR, Lekbua A, Mroue N, Liston C, Stewart EJ, Dubin MJ, Zengler K, Knight R, Gilbert JA, Clardy J, Lewis K. PMID: 30531975.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    27. Optimization of carbon and energy utilization through differential translational efficiency. Nat Commun. 2018 10 26; 9(1):4474. Al-Bassam MM, Kim JN, Zaramela LS, Kellman BP, Zuniga C, Wozniak JM, Gonzalez DJ, Zengler K. PMID: 30367068.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    28. Group B Streptococcus Biofilm Regulatory Protein A Contributes to Bacterial Physiology and Innate Immune Resistance. J Infect Dis. 2018 10 05; 218(10):1641-1652. Patras KA, Derieux J, Al-Bassam MM, Adiletta N, Vrbanac A, Lapek JD, Zengler K, Gonzalez DJ, Nizet V. PMID: 29868829.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    29. Advances in metabolic modeling of oleaginous microalgae. Biotechnol Biofuels. 2018; 11:241. Tibocha-Bonilla JD, Zuñiga C, Godoy-Silva RD, Zengler K. PMID: 30202436.
      View in: PubMed   Mentions:
    30. Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry. mBio. 2018 07 17; 9(4). Zhalnina K, Zengler K, Newman D, Northen TR. PMID: 30018110.
      View in: PubMed   Mentions: 1     Fields:    Translation:PHPublic Health
    31. The social network of microorganisms - how auxotrophies shape complex communities. Nat Rev Microbiol. 2018 06; 16(6):383-390. Zengler K, Zaramela LS. PMID: 29599459.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    32. ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions. PLoS One. 2018; 13(5):e0197272. Latif H, Federowicz S, Ebrahim A, Tarasova J, Szubin R, Utrilla J, Zengler K, Palsson BO. PMID: 29771928.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    33. Genome Sequence of the Oleaginous Green Alga, Chlorella vulgaris UTEX 395. Front Bioeng Biotechnol. 2018; 6:37. Guarnieri MT, Levering J, Henard CA, Boore JL, Betenbaugh MJ, Zengler K, Knoshaug EP. PMID: 29675409.
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    34. The Role of Intestinal C-type Regenerating Islet Derived-3 Lectins for Nonalcoholic Steatohepatitis. Hepatol Commun. 2018 04; 2(4):393-406. Bluemel S, Wang L, Martino C, Lee S, Wang Y, Williams B, Horvath A, Stadlbauer V, Zengler K, Schnabl B. PMID: 29619418.
      View in: PubMed   Mentions:
    35. Improving saliva shotgun metagenomics by chemical host DNA depletion. Microbiome. 2018 02 27; 6(1):42. Marotz CA, Sanders JG, Zuniga C, Zaramela LS, Knight R, Zengler K. PMID: 29482639.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    36. Metabolic capability and in situ activity of microorganisms in an oil reservoir. Microbiome. 2018 01 05; 6(1):5. Liu YF, Galzerani DD, Mbadinga SM, Zaramela LS, Gu JD, Mu BZ, Zengler K. PMID: 29304850.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    37. Predicting Dynamic Metabolic Demands in the Photosynthetic Eukaryote Chlorella vulgaris. Plant Physiol. 2018 01; 176(1):450-462. Zuñiga C, Levering J, Antoniewicz MR, Guarnieri MT, Betenbaugh MJ, Zengler K. PMID: 28951490.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    38. Elucidation of complexity and prediction of interactions in microbial communities. Microb Biotechnol. 2017 11; 10(6):1500-1522. Zuñiga C, Zaramela L, Zengler K. PMID: 28925555.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    39. Evidence for fungal and chemodenitrification based N2O flux from nitrogen impacted coastal sediments. Nat Commun. 2017 06 05; 8:15595. Wankel SD, Ziebis W, Buchwald C, Charoenpong C, de Beer D, Dentinger J, Xu Z, Zengler K. PMID: 28580932.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    40. Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis. Sci Transl Med. 2017 02 22; 9(378). 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. PMID: 28228596.
      View in: PubMed   Mentions: 70     Fields:    Translation:HumansAnimalsCellsCTClinical Trials
    41. Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels. mSystems. 2017 Jan-Feb; 2(1). Levering J, Dupont CL, Allen AE, Palsson BO, Zengler K. PMID: 28217746.
      View in: PubMed   Mentions:
    42. FRT - FONDATION RENE TOURAINE: An International Foundation For Dermatology. Exp Dermatol. 2016 11; 25(11):917-932. Bosch TC, Zengler K, Naik S, Biedermann T, Kong HH, Loser K, Brüggeman H, Calleawert C, Lambert J, Van de Wiele T. PMID: 27792248.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    43. 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 09; 172(1):589-602. Zuñiga C, Li CT, Huelsman T, Levering J, Zielinski DC, McConnell BO, Long CP, Knoshaug EP, Guarnieri MT, Antoniewicz MR, Betenbaugh MJ, Zengler K. PMID: 27372244.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    44. Efficient Synergistic Single-Cell Genome Assembly. Front Bioeng Biotechnol. 2016; 4:42. Movahedi NS, Embree M, Nagarajan H, Zengler K, Chitsaz H. PMID: 27243002.
      View in: PubMed   Mentions:
    45. Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom. PLoS One. 2016; 11(5):e0155038. Levering J, Broddrick J, Dupont CL, Peers G, Beeri K, Mayers J, Gallina AA, Allen AE, Palsson BO, Zengler K. PMID: 27152931.
      View in: PubMed   Mentions: 19     Fields:    Translation:AnimalsCells
    46. 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. Embree M, Liu JK, Al-Bassam MM, Zengler K. PMID: 26621749.
      View in: PubMed   Mentions: 30     Fields:    Translation:Cells
    47. Engineering of oleaginous organisms for lipid production. Curr Opin Biotechnol. 2015 Dec; 36:32-9. Levering J, Broddrick J, Zengler K. PMID: 26319892.
      View in: PubMed   Mentions: 9     Fields:    
    48. Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model. Integr Biol (Camb). 2015 Aug; 7(8):869-82. Islam MA, Zengler K, Edwards EA, Mahadevan R, Stephanopoulos G. PMID: 25994252.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    49. Adaptive Evolution of Thermotoga maritima Reveals Plasticity of the ABC Transporter Network. Appl Environ Microbiol. 2015 Aug 15; 81(16):5477-85. Latif H, Sahin M, Tarasova J, Tarasova Y, Portnoy VA, Nogales J, Zengler K. PMID: 26048924.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    50. A streamlined ribosome profiling protocol for the characterization of microorganisms. Biotechniques. 2015 Jun; 58(6):329-32. Latif H, Szubin R, Tan J, Brunk E, Lechner A, Zengler K, Palsson BO. PMID: 26054770.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    51. Unraveling interactions in microbial communities - from co-cultures to microbiomes. J Microbiol. 2015 May; 53(5):295-305. Tan J, Zuniga C, Zengler K. PMID: 25935300.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    52. A logical data representation framework for electricity-driven bioproduction processes. Biotechnol Adv. 2015 Nov 01; 33(6 Pt 1):736-44. Patil SA, Gildemyn S, Pant D, Zengler K, Logan BE, Rabaey K. PMID: 25765230.
      View in: PubMed   Mentions: 8     Fields:    
    53. Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. BMC Syst Biol. 2014 Sep 18; 8:110. Liu JK, O'Brien EJ, Lerman JA, Zengler K, Palsson BO, Feist AM. PMID: 25227965.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    54. 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. 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. PMID: 25239591.
      View in: PubMed   Mentions: 73     Fields:    Translation:AnimalsCells
    55. Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens. PLoS Comput Biol. 2014 Apr; 10(4):e1003575. Feist AM, Nagarajan H, Rotaru AE, Tremblay PL, Zhang T, Nevin KP, Lovley DR, Zengler K. PMID: 24762737.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    56. Determining the control circuitry of redox metabolism at the genome-scale. PLoS Genet. 2014 Apr; 10(4):e1004264. Federowicz S, Kim D, Ebrahim A, Lerman J, Nagarajan H, Cho BK, Zengler K, Palsson B. PMID: 24699140.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    57. The iron stimulon and fur regulon of Geobacter sulfurreducens and their role in energy metabolism. Appl Environ Microbiol. 2014 May; 80(9):2918-27. Embree M, Qiu Y, Shieu W, Nagarajan H, O'Neil R, Lovley D, Zengler K. PMID: 24584254.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    58. Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states. BMC Biol. 2014 Jan 24; 12:4. Cho BK, Kim D, Knight EM, Zengler K, Palsson BO. PMID: 24461193.
      View in: PubMed   Mentions: 34     Fields:    Translation:Cells
    59. Trash to treasure: production of biofuels and commodity chemicals via syngas fermenting microorganisms. Curr Opin Biotechnol. 2014 Jun; 27:79-87. Latif H, Zeidan AA, Nielsen AT, Zengler K. PMID: 24863900.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    60. Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii. Microb Cell Fact. 2013 Nov 25; 12:118. Nagarajan H, Sahin M, Nogales J, Latif H, Lovley DR, Ebrahim A, Zengler K. PMID: 24274140.
      View in: PubMed   Mentions: 26     Fields:    Translation:Cells
    61. Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community. ISME J. 2014 Apr; 8(4):757-67. Embree M, Nagarajan H, Movahedi N, Chitsaz H, Zengler K. PMID: 24152715.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    62. Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima. Front Microbiol. 2013; 4:244. Rodionov DA, Rodionova IA, Li X, Ravcheev DA, Tarasova Y, Portnoy VA, Zengler K, Osterman AL. PMID: 23986752.
      View in: PubMed   Mentions:
    63. The genome organization of Thermotoga maritima reflects its lifestyle. PLoS Genet. 2013 Apr; 9(4):e1003485. Latif H, Lerman JA, Portnoy VA, Tarasova Y, Nagarajan H, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Lee DH, Qiu Y, Zengler K. PMID: 23637642.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    64. The microbiome extends to subepidermal compartments of normal skin. Nat Commun. 2013; 4:1431. Nakatsuji T, Chiang HI, Jiang SB, Nagarajan H, Zengler K, Gallo RL. PMID: 23385576.
      View in: PubMed   Mentions: 80     Fields:    Translation:HumansCells
    65. Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks. Nat Commun. 2013; 4:1755. 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. PMID: 23612296.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    66. Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association. Nat Commun. 2013; 4:2809. Nagarajan H, Embree M, Rotaru AE, Shrestha PM, Feist AM, Palsson BØ, Lovley DR, Zengler K. PMID: 24264237.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    67. Sulfide-driven microbial electrosynthesis. Environ Sci Technol. 2013 Jan 02; 47(1):568-73. Gong Y, Ebrahim A, Feist AM, Embree M, Zhang T, Lovley D, Zengler K. PMID: 23252645.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    68. Anaerobic utilization of toluene by marine alpha- and gammaproteobacteria reducing nitrate. Microbiology. 2012 Dec; 158(Pt 12):2946-2957. Alain K, Harder J, Widdel F, Zengler K. PMID: 23038808.
      View in: PubMed   Mentions:
    69. In silico method for modelling metabolism and gene product expression at genome scale. Nat Commun. 2012 Jul 03; 3:929. Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BO. PMID: 22760628.
      View in: PubMed   Mentions: 71     Fields:    Translation:Cells
    70. A road map for the development of community systems (CoSy) biology. Nat Rev Microbiol. 2012 03 27; 10(5):366-72. Zengler K, Palsson BO. PMID: 22450377.
      View in: PubMed   Mentions: 45     Fields:    Translation:PHPublic Health
    71. Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex. J Bacteriol. 2012 Mar; 194(5):1145-57. Ravcheev DA, Li X, Latif H, Zengler K, Leyn SA, Korostelev YD, Kazakov AE, Novichkov PS, Osterman AL, Rodionov DA. PMID: 22210771.
      View in: PubMed   Mentions: 51     Fields:    Translation:Cells
    72. Deciphering the transcriptional regulatory logic of amino acid metabolism. Nat Chem Biol. 2011 Nov 13; 8(1):65-71. Cho BK, Federowicz S, Park YS, Zengler K, Palsson BØ. PMID: 22082910.
      View in: PubMed   Mentions: 34     Fields:    Translation:Cells
    73. Deciphering the regulatory codes in bacterial genomes. Biotechnol J. 2011 Sep; 6(9):1052-63. Cho BK, Palsson B, Zengler K. PMID: 21845736.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    74. Adaptive laboratory evolution--harnessing the power of biology for metabolic engineering. Curr Opin Biotechnol. 2011 Aug; 22(4):590-4. Portnoy VA, Bezdan D, Zengler K. PMID: 21497080.
      View in: PubMed   Mentions: 33     Fields:    Translation:AnimalsCells
    75. 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. 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. PMID: 21244678.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansCells
    76. 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. Tremblay PL, Summers ZM, Glaven RH, Nevin KP, Zengler K, Barrett CL, Qiu Y, Palsson BO, Lovley DR. PMID: 20636372.
      View in: PubMed   Mentions: 19     Fields:    Translation:CellsPHPublic Health
    77. The challenges of integrating multi-omic data sets. Nat Chem Biol. 2010 Nov; 6(11):787-9. Palsson B, Zengler K. PMID: 20976870.
      View in: PubMed   Mentions: 43     Fields:    Translation:Cells
    78. Structural and operational complexity of the Geobacter sulfurreducens genome. Genome Res. 2010 Sep; 20(9):1304-11. Qiu Y, Cho BK, Park YS, Lovley D, Palsson BØ, Zengler K. PMID: 20592237.
      View in: PubMed   Mentions: 41     Fields:    Translation:Cells
    79. 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. Klimes A, Franks AE, Glaven RH, Tran H, Barrett CL, Qiu Y, Zengler K, Lovley DR. PMID: 20629752.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    80. 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. Nagarajan H, Butler JE, Klimes A, Qiu Y, Zengler K, Ward J, Young ND, Methé BA, Palsson BØ, Lovley DR, Barrett CL. PMID: 20544019.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    81. Central role of the cell in microbial ecology. Microbiol Mol Biol Rev. 2009 Dec; 73(4):712-29. Zengler K. PMID: 19946138.
      View in: PubMed   Mentions: 15     Fields:    Translation:CellsPHPublic Health
    82. The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol. 2009 Nov; 27(11):1043-9. Cho BK, Zengler K, Qiu Y, Park YS, Knight EM, Barrett CL, Gao Y, Palsson BØ. PMID: 19881496.
      View in: PubMed   Mentions: 130     Fields:    Translation:Cells
    83. Targeted access to the genomes of low-abundance organisms in complex microbial communities. Appl Environ Microbiol. 2007 May; 73(10):3205-14. Podar M, Abulencia CB, Walcher M, Hutchison D, Zengler K, Garcia JA, Holland T, Cotton D, Hauser L, Keller M. PMID: 17369337.
      View in: PubMed   Mentions: 71     Fields:    Translation:CellsPHPublic Health
    84. 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. Kevbrin VV, Zengler K, Lysenko AM, Wiegel J. PMID: 16142505.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    85. High-throughput cultivation of microorganisms using microcapsules. Methods Enzymol. 2005; 397:124-30. Zengler K, Walcher M, Clark G, Haller I, Toledo G, Holland T, Mathur EJ, Woodnutt G, Short JM, Keller M. PMID: 16260288.
      View in: PubMed   Mentions: 15     Fields:    Translation:CellsPHPublic Health
    86. Tapping into microbial diversity. Nat Rev Microbiol. 2004 Feb; 2(2):141-50. Keller M, Zengler K. PMID: 15040261.
      View in: PubMed   Mentions: 55     Fields:    Translation:CellsPHPublic Health
    87. Cultivating the uncultured. Proc Natl Acad Sci U S A. 2002 Nov 26; 99(24):15681-6. Zengler K, Toledo G, Rappe M, Elkins J, Mathur EJ, Short JM, Keller M. PMID: 12438682.
      View in: PubMed   Mentions: 152     Fields:    Translation:CellsPHPublic Health
    88. Methane formation from long-chain alkanes by anaerobic microorganisms. Nature. 1999 Sep 16; 401(6750):266-9. Zengler K, Richnow HH, Rosselló-Mora R, Michaelis W, Widdel F. PMID: 10499582.
      View in: PubMed   Mentions: 87     Fields:    Translation:CellsPHPublic Health
    89. 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. Champion KM, Zengler K, Rabus R. PMID: 10941798.
      View in: PubMed   Mentions: 14     Fields:    Translation:CellsPHPublic Health
    90. 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. Harms G, Zengler K, Rabus R, Aeckersberg F, Minz D, Rosselló-Mora R, Widdel F. PMID: 10049854.
      View in: PubMed   Mentions: 27     Fields:    Translation:CellsPHPublic Health
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