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Items: 1 to 50 of 81

1.

Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities.

Zuñiga C, Li CT, Yu G, Al-Bassam MM, Li T, Jiang L, Zaramela LS, Guarnieri M, Betenbaugh MJ, Zengler K.

Nat Microbiol. 2019 Oct 7. doi: 10.1038/s41564-019-0567-6. [Epub ahead of print]

PMID:
31591554
2.

Utilizing genome-scale models to optimize nutrient supply for sustained algal growth and lipid productivity.

Li CT, Yelsky J, Chen Y, Zuñiga C, Eng R, Jiang L, Shapiro A, Huang KW, Zengler K, Betenbaugh MJ.

NPJ Syst Biol Appl. 2019 Sep 24;5:33. doi: 10.1038/s41540-019-0110-7. eCollection 2019.

3.

Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates.

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.

Nat Microbiol. 2019 Sep 23. doi: 10.1038/s41564-019-0564-9. [Epub ahead of print]

PMID:
31548686
4.

Functional and Proteomic Analysis of Streptococcus pyogenes Virulence Upon Loss of Its Native Cas9 Nuclease.

Gao NJ, Al-Bassam MM, Poudel S, Wozniak JM, Gonzalez DJ, Olson J, Zengler K, Nizet V, Valderrama JA.

Front Microbiol. 2019 Aug 22;10:1967. doi: 10.3389/fmicb.2019.01967. eCollection 2019.

5.

Modelling approaches for studying the microbiome.

Kumar M, Ji B, Zengler K, Nielsen J.

Nat Microbiol. 2019 Aug;4(8):1253-1267. doi: 10.1038/s41564-019-0491-9. Epub 2019 Jul 23. Review.

PMID:
31337891
6.

EcoFABs: advancing microbiome science through standardized fabricated ecosystems.

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.

Nat Methods. 2019 Jul;16(7):567-571. doi: 10.1038/s41592-019-0465-0. No abstract available.

7.

Establishing microbial composition measurement standards with reference frames.

Morton JT, Marotz C, Washburne A, Silverman J, Zaramela LS, Edlund A, Zengler K, Knight R.

Nat Commun. 2019 Jun 20;10(1):2719. doi: 10.1038/s41467-019-10656-5.

8.

The impact of skin care products on skin chemistry and microbiome dynamics.

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.

BMC Biol. 2019 Jun 12;17(1):47. doi: 10.1186/s12915-019-0660-6.

9.

Quorum sensing between bacterial species on the skin protects against epidermal injury in atopic dermatitis.

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.

Sci Transl Med. 2019 May 1;11(490). pii: eaat8329. doi: 10.1126/scitranslmed.aat8329.

PMID:
31043573
10.

Mast cell recruitment is modulated by the hairless skin microbiome.

Wu CC, Kim JN, Wang Z, Chang YL, Zengler K, Di Nardo A.

J Allergy Clin Immunol. 2019 Jul;144(1):330-333.e6. doi: 10.1016/j.jaci.2019.02.033. Epub 2019 Mar 27. No abstract available.

PMID:
30928651
11.

Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen.

Liu JK, Lloyd C, Al-Bassam MM, Ebrahim A, Kim JN, Olson C, Aksenov A, Dorrestein P, Zengler K.

PLoS Comput Biol. 2019 Mar 7;15(3):e1006848. doi: 10.1371/journal.pcbi.1006848. eCollection 2019 Mar.

12.

A Novel Sparse Compositional Technique Reveals Microbial Perturbations.

Martino C, Morton JT, Marotz CA, Thompson LR, Tripathi A, Knight R, Zengler K.

mSystems. 2019 Feb 12;4(1). pii: e00016-19. doi: 10.1128/mSystems.00016-19. eCollection 2019 Jan-Feb.

13.

The nonlesional skin surface distinguishes atopic dermatitis with food allergy as a unique endotype.

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 Jr, Crumrine D, Cole RN, Elias P, Zengler K, Seibold MA, Berdyshev E, Goleva E.

Sci Transl Med. 2019 Feb 20;11(480). pii: eaav2685. doi: 10.1126/scitranslmed.aav2685.

PMID:
30787169
14.

Anaerobic degradation of hexadecane and phenanthrene coupled to sulfate reduction by enriched consortia from northern Gulf of Mexico seafloor sediment.

Shin B, Kim M, Zengler K, Chin KJ, Overholt WA, Gieg LM, Konstantinidis KT, Kostka JE.

Sci Rep. 2019 Feb 4;9(1):1239. doi: 10.1038/s41598-018-36567-x.

15.

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types.

Seif Y, Monk JM, Mih N, Tsunemoto H, Poudel S, Zuniga C, Broddrick J, Zengler K, Palsson BO.

PLoS Comput Biol. 2019 Jan 9;15(1):e1006644. doi: 10.1371/journal.pcbi.1006644. eCollection 2019 Jan.

16.

GABA-modulating bacteria of the human gut microbiota.

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.

Nat Microbiol. 2019 Mar;4(3):396-403. doi: 10.1038/s41564-018-0307-3. Epub 2018 Dec 10.

17.

Optimization of carbon and energy utilization through differential translational efficiency.

Al-Bassam MM, Kim JN, Zaramela LS, Kellman BP, Zuniga C, Wozniak JM, Gonzalez DJ, Zengler K.

Nat Commun. 2018 Oct 26;9(1):4474. doi: 10.1038/s41467-018-06993-6.

18.

Advances in metabolic modeling of oleaginous microalgae.

Tibocha-Bonilla JD, Zuñiga C, Godoy-Silva RD, Zengler K.

Biotechnol Biofuels. 2018 Sep 5;11:241. doi: 10.1186/s13068-018-1244-3. eCollection 2018. Review.

19.

Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry.

Zhalnina K, Zengler K, Newman D, Northen TR.

MBio. 2018 Jul 17;9(4). pii: e01175-18. doi: 10.1128/mBio.01175-18.

20.

Group B Streptococcus Biofilm Regulatory Protein A Contributes to Bacterial Physiology and Innate Immune Resistance.

Patras KA, Derieux J, Al-Bassam MM, Adiletta N, Vrbanac A, Lapek JD, Zengler K, Gonzalez DJ, Nizet V.

J Infect Dis. 2018 Oct 5;218(10):1641-1652. doi: 10.1093/infdis/jiy341.

21.

ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions.

Latif H, Federowicz S, Ebrahim A, Tarasova J, Szubin R, Utrilla J, Zengler K, Palsson BO.

PLoS One. 2018 May 17;13(5):e0197272. doi: 10.1371/journal.pone.0197272. eCollection 2018.

22.

Genome Sequence of the Oleaginous Green Alga, Chlorella vulgaris UTEX 395.

Guarnieri MT, Levering J, Henard CA, Boore JL, Betenbaugh MJ, Zengler K, Knoshaug EP.

Front Bioeng Biotechnol. 2018 Apr 5;6:37. doi: 10.3389/fbioe.2018.00037. eCollection 2018. No abstract available.

23.

The Role of Intestinal C-type Regenerating Islet Derived-3 Lectins for Nonalcoholic Steatohepatitis.

Bluemel S, Wang L, Martino C, Lee S, Wang Y, Williams B, Horvath A, Stadlbauer V, Zengler K, Schnabl B.

Hepatol Commun. 2018 Feb 28;2(4):393-406. doi: 10.1002/hep4.1165. eCollection 2018 Apr.

24.

The social network of microorganisms - how auxotrophies shape complex communities.

Zengler K, Zaramela LS.

Nat Rev Microbiol. 2018 Jun;16(6):383-390. doi: 10.1038/s41579-018-0004-5. Review.

25.

Improving saliva shotgun metagenomics by chemical host DNA depletion.

Marotz CA, Sanders JG, Zuniga C, Zaramela LS, Knight R, Zengler K.

Microbiome. 2018 Feb 27;6(1):42. doi: 10.1186/s40168-018-0426-3.

26.

Metabolic capability and in situ activity of microorganisms in an oil reservoir.

Liu YF, Galzerani DD, Mbadinga SM, Zaramela LS, Gu JD, Mu BZ, Zengler K.

Microbiome. 2018 Jan 5;6(1):5. doi: 10.1186/s40168-017-0392-1.

27.

Predicting Dynamic Metabolic Demands in the Photosynthetic Eukaryote Chlorella vulgaris.

Zuñiga C, Levering J, Antoniewicz MR, Guarnieri MT, Betenbaugh MJ, Zengler K.

Plant Physiol. 2018 Jan;176(1):450-462. doi: 10.1104/pp.17.00605. Epub 2017 Sep 26.

28.

Elucidation of complexity and prediction of interactions in microbial communities.

Zuñiga C, Zaramela L, Zengler K.

Microb Biotechnol. 2017 Nov;10(6):1500-1522. doi: 10.1111/1751-7915.12855. Epub 2017 Sep 19. Review.

29.

Evidence for fungal and chemodenitrification based N2O flux from nitrogen impacted coastal sediments.

Wankel SD, Ziebis W, Buchwald C, Charoenpong C, de Beer D, Dentinger J, Xu Z, Zengler K.

Nat Commun. 2017 Jun 5;8:15595. doi: 10.1038/ncomms15595.

30.

Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis.

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.

Sci Transl Med. 2017 Feb 22;9(378). pii: eaah4680. doi: 10.1126/scitranslmed.aah4680.

31.

Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels.

Levering J, Dupont CL, Allen AE, Palsson BO, Zengler K.

mSystems. 2017 Feb 14;2(1). pii: e00142-16. doi: 10.1128/mSystems.00142-16. eCollection 2017 Jan-Feb.

32.

FRT - FONDATION RENE TOURAINE: An International Foundation For Dermatology.

Bosch TC, Zengler K, Naik S, Biedermann T, Kong HH, Loser K, Brüggeman H, Calleawert C, Lambert J, Van de Wiele T.

Exp Dermatol. 2016 Nov;25(11):917-932. doi: 10.1111/exd.13160. No abstract available.

PMID:
27792248
33.

Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions.

Zuñiga C, Li CT, Huelsman T, Levering J, Zielinski DC, McConnell BO, Long CP, Knoshaug EP, Guarnieri MT, Antoniewicz MR, Betenbaugh MJ, Zengler K.

Plant Physiol. 2016 Sep;172(1):589-602. doi: 10.1104/pp.16.00593. Epub 2016 Jul 2.

34.

Efficient Synergistic Single-Cell Genome Assembly.

Movahedi NS, Embree M, Nagarajan H, Zengler K, Chitsaz H.

Front Bioeng Biotechnol. 2016 May 23;4:42. doi: 10.3389/fbioe.2016.00042. eCollection 2016.

35.

Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom.

Levering J, Broddrick J, Dupont CL, Peers G, Beeri K, Mayers J, Gallina AA, Allen AE, Palsson BO, Zengler K.

PLoS One. 2016 May 6;11(5):e0155038. doi: 10.1371/journal.pone.0155038. eCollection 2016.

36.

Networks of energetic and metabolic interactions define dynamics in microbial communities.

Embree M, Liu JK, Al-Bassam MM, Zengler K.

Proc Natl Acad Sci U S A. 2015 Dec 15;112(50):15450-5. doi: 10.1073/pnas.1506034112. Epub 2015 Nov 30.

37.

Engineering of oleaginous organisms for lipid production.

Levering J, Broddrick J, Zengler K.

Curr Opin Biotechnol. 2015 Dec;36:32-9. doi: 10.1016/j.copbio.2015.08.001. Epub 2015 Aug 28. Review.

PMID:
26319892
38.

Adaptive Evolution of Thermotoga maritima Reveals Plasticity of the ABC Transporter Network.

Latif H, Sahin M, Tarasova J, Tarasova Y, Portnoy VA, Nogales J, Zengler K.

Appl Environ Microbiol. 2015 Aug 15;81(16):5477-85. doi: 10.1128/AEM.01365-15. Epub 2015 Jun 5.

39.

Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model.

Islam MA, Zengler K, Edwards EA, Mahadevan R, Stephanopoulos G.

Integr Biol (Camb). 2015 Aug;7(8):869-82. doi: 10.1039/c5ib00095e.

PMID:
25994252
40.

Unraveling interactions in microbial communities - from co-cultures to microbiomes.

Tan J, Zuniga C, Zengler K.

J Microbiol. 2015 May;53(5):295-305. doi: 10.1007/s12275-015-5060-1. Epub 2015 May 3. Review.

PMID:
25935300
41.

A logical data representation framework for electricity-driven bioproduction processes.

Patil SA, Gildemyn S, Pant D, Zengler K, Logan BE, Rabaey K.

Biotechnol Adv. 2015 Nov 1;33(6 Pt 1):736-44. doi: 10.1016/j.biotechadv.2015.03.002. Epub 2015 Mar 10. Review.

PMID:
25765230
42.

Supplementation of saturated long-chain fatty acids maintains intestinal eubiosis and reduces ethanol-induced liver injury in mice.

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.

Gastroenterology. 2015 Jan;148(1):203-214.e16. doi: 10.1053/j.gastro.2014.09.014. Epub 2014 Sep 16.

43.

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale.

Liu JK, O'Brien EJ, Lerman JA, Zengler K, Palsson BO, Feist AM.

BMC Syst Biol. 2014 Sep 18;8:110. doi: 10.1186/s12918-014-0110-6.

44.

Trash to treasure: production of biofuels and commodity chemicals via syngas fermenting microorganisms.

Latif H, Zeidan AA, Nielsen AT, Zengler K.

Curr Opin Biotechnol. 2014 Jun;27:79-87. doi: 10.1016/j.copbio.2013.12.001. Epub 2013 Dec 28. Review.

PMID:
24863900
45.

Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens.

Feist AM, Nagarajan H, Rotaru AE, Tremblay PL, Zhang T, Nevin KP, Lovley DR, Zengler K.

PLoS Comput Biol. 2014 Apr 24;10(4):e1003575. doi: 10.1371/journal.pcbi.1003575. eCollection 2014 Apr.

46.

Determining the control circuitry of redox metabolism at the genome-scale.

Federowicz S, Kim D, Ebrahim A, Lerman J, Nagarajan H, Cho BK, Zengler K, Palsson B.

PLoS Genet. 2014 Apr 3;10(4):e1004264. doi: 10.1371/journal.pgen.1004264. eCollection 2014 Apr.

47.

The iron stimulon and fur regulon of Geobacter sulfurreducens and their role in energy metabolism.

Embree M, Qiu Y, Shieu W, Nagarajan H, O'Neil R, Lovley D, Zengler K.

Appl Environ Microbiol. 2014 May;80(9):2918-27. doi: 10.1128/AEM.03916-13. Epub 2014 Feb 28.

48.

Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states.

Cho BK, Kim D, Knight EM, Zengler K, Palsson BO.

BMC Biol. 2014 Jan 24;12:4. doi: 10.1186/1741-7007-12-4.

49.

A streamlined ribosome profiling protocol for the characterization of microorganisms.

Latif H, Szubin R, Tan J, Brunk E, Lechner A, Zengler K, Palsson BO.

Biotechniques. 2015 Jun 1;58(6):329-32. doi: 10.2144/000114302. eCollection 2015 Jun.

50.

Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii.

Nagarajan H, Sahin M, Nogales J, Latif H, Lovley DR, Ebrahim A, Zengler K.

Microb Cell Fact. 2013 Nov 25;12:118. doi: 10.1186/1475-2859-12-118.

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