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Bacteria

  • 1.
    Tang J, Brynildsen M. Genome-wide mapping of fluoroquinolone-stabilized DNA gyrase cleavage sites displays drug specific effects that correlate with bacterial persistence. Nucleic Acids Res. 2023;51(3):1208–1228. PMCID: PMC9943676
    Reference Link
  • 1.
    Rossine F, Vercelli G, Tarnita C, Gregor T. Structured foraging of soil predators unveils functional responses to bacterial defenses. Proc Natl Acad Sci U S A. 2022;119(52):e2210995119. PMCID: PMC9907142
    Reference Link
  • 1.
    Martínez-Calvo A, Bhattacharjee T, Bay K, Luu H, Hancock A, Wingreen N, Datta S. Morphological instability and roughening of growing 3D bacterial colonies. Proc Natl Acad Sci U S A. 2022;119(43):e2208019119. PMCID: PMC9618147
    Reference Link
  • 1.
    Ellison C, Fei C, Dalia T, Wingreen N, Dalia A, Shaevitz J, Gitai Z. Subcellular localization of type IV pili regulates bacterial multicellular development. Nat Commun. 2022;13(1):6334. PMCID: PMC9596432
    Reference Link
  • 1.
    Zeng X, Xing X, Gupta M, Keber F, Lopez J, Lee Y-C, Roichman A, Wang L, Neinast M, Donia M, Wühr M, Jang C, Rabinowitz J. Gut bacterial nutrient preferences quantified in vivo. Cell. 2022;185(18):3441–3456.e19. PMCID: PMC9450212
    Reference Link
  • 1.
    Ruiz N, Silhavy T. How Escherichia coli Became the Flagship Bacterium of Molecular Biology. J Bacteriol. 2022;204(9):e0023022. PMCID: PMC9487582
    Reference Link
  • 1.
    Bridges A, Prentice J, Wingreen N, Bassler B. Signal Transduction Network Principles Underlying Bacterial Collective Behaviors. Annu Rev Microbiol. 2022;76:235–257. PMCID: PMC9463083
    Reference Link
  • 1.
    Tsitsiklis A, Osborne C, Kamm J, Williamson K, Kalantar K, Dudas G, Caldera S, Lyden A, Tan M, Neff N, Soesanto V, Harris K, Ambroggio L, Maddux A, Carpenter T, Reeder R, Locandro C, Simões E, Leroue M, Hall M, Zuppa A, Carcillo J, Meert K, Sapru A, Pollack M, McQuillen P, Notterman D, Dean M, Zinter M, Wagner B, DeRisi J, Mourani P, Langelier C. Lower respiratory tract infections in children requiring mechanical ventilation: a multicentre prospective surveillance study incorporating airway metagenomics. Lancet Microbe. 2022;3(4):e284-e293. PMCID: PMC9446282
    Reference Link
  • 1.
    Lopez J, Wingreen N. Noisy metabolism can promote microbial cross-feeding. Elife. 2022;11. PMCID: PMC8983042
    Reference Link
  • 1.
    Murawski A, Rittenbach K, DeCoste C, Laevsky G, Brynildsen M. Counting Chromosomes in Individual Bacteria to Quantify Their Impacts on Persistence. Methods Mol Biol. 2021;2357:125–146. PMCID: 7136161
    Reference Link
  • 1.
    Yang J, Sanfilippo J, Abbasi N, Gitai Z, Bassler B, Stone H. Evidence for biosurfactant-induced flow in corners and bacterial spreading in unsaturated porous media. Proc Natl Acad Sci U S A. 2021;118(38). PMCID: PMC8463848
    Reference Link
  • 1.
    López J, Duran L, Avalos J. Physiological limitations and opportunities in microbial metabolic engineering. Nat Rev Microbiol. 2022;20(1):35–48. PMCID: 5812522
    Reference Link
  • 1.
    Narla A, Borenstein D, Wingreen N. A biophysical limit for quorum sensing in biofilms. Proc Natl Acad Sci U S A. 2021;118(21). PMCID: PMC8166027
    Reference Link
  • 1.
    Covington B, Xu F, Seyedsayamdost M. A Natural Product Chemist’s Guide to Unlocking Silent Biosynthetic Gene Clusters. Annu Rev Biochem. 2021;90:763–788. PMCID: PMC9148385
    Reference Link
  • 1.
    Valastyan J, Kraml C, Pelczer I, Ferrante T, Bassler B. Saccharomyces cerevisiae Requires To Produce 4-Hydroxy-5-Methylfuran-3(2H)-One, a Mimic of the Bacterial Quorum-Sensing Autoinducer AI-2. mBio. 2021;12(2). PMCID: PMC8092285
    Reference Link
  • 1.
    Sivaloganathan D, Brynildsen M. Phagosome-Bacteria Interactions from the Bottom Up. Annu Rev Chem Biomol Eng. 2021;12:309–331. PMID: 33781082
    Reference Link
  • 1.
    Shim S, Khodaparast S, Lai C-Y, Yan J, Ault J, Rallabandi B, Shardt O, Stone H. CO-Driven diffusiophoresis for maintaining a bacteria-free surface. Soft Matter. 2021;17(9):2568–2576. PMID: 33514979
    Reference Link
  • 1.
    Duddy O, Bassler B. Quorum sensing across bacterial and viral domains. PLoS Pathog. 2021;17(1):e1009074. PMCID: PMC7790227
    Reference Link
  • 1.
    Li Z, Liu B, Li S, King C, Gitai Z, Wingreen N. Modeling microbial metabolic trade-offs in a chemostat. PLoS Comput Biol. 2020;16(8):e1008156. PMCID: PMC7482850
    Reference Link
  • 1.
    Doane M, Morris M, Papudeshi B, Allen L, Pande D, Haggerty J, Johri S, Turnlund A, Peterson M, Kacev D, Nosal A, Ramirez D, Hovel K, Ledbetter J, Alker A, Avalos J, Baker K, Bhide S, Billings E, Byrum S, Clemens M, Demery A, Lima L, Gomez O, Gutierrez O, Hinton S, Kieu D, Kim A, Loaiza R, Martinez A, McGhee J, Nguyen K, Parlan S, Pham A, Price-Waldman R, Edwards R, Dinsdale E. The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge. Microbiome. 2020;8(1):93. PMCID: PMC7293782
    Reference Link
  • 1.
    Javdan B, Lopez J, Chankhamjon P, Lee Y-C, Hull R, Wu Q, Wang X, Chatterjee S, Donia M. Personalized Mapping of Drug Metabolism by the Human Gut Microbiome. Cell. 2020;181(7):1661–1679.e22. PMCID: PMC8591631
    Reference Link
  • 1.
    Wu L, Shen M, Li J, Huang S, Li Z, Yan Z, Peng Y. Cooperation between partial-nitrification, complete ammonia oxidation (comammox), and anaerobic ammonia oxidation (anammox) in sludge digestion liquid for nitrogen removal. Environ Pollut. 2019;254(Pt A):112965. PMID: 31401520
    Reference Link
  • 1.
    Simsek A, Braeutigam A, Koch M, Shaevitz J, Huang Y, Gompper G, Sabass B. Substrate-rigidity dependent migration of an idealized twitching bacterium. Soft Matter. 2019;15(30):6224–6236. PMID: 31334524
    Reference Link
  • 1.
    Yan J, Bassler B. Surviving as a Community: Antibiotic Tolerance and Persistence in Bacterial Biofilms. Cell Host Microbe. 2019;26(1):15–21. PMCID: PMC6629468
    Reference Link
  • 1.
    Sanfilippo J, Lorestani A, Koch M, Bratton B, Siryaporn A, Stone H, Gitai Z. Microfluidic-based transcriptomics reveal force-independent bacterial rheosensing. Nat Microbiol. 2019;4(8):1274–1281. PMCID: PMC6656604
    Reference Link
  • 1.
    Balaban N, Helaine S, Lewis K, Ackermann M, Aldridge B, Andersson D, Brynildsen M, Bumann D, Camilli A, Collins J, Dehio C, Fortune S, Ghigo J-M, Hardt W-D, Harms A, Heinemann M, Hung D, Jenal U, Levin B, Michiels J, Storz G, Tan M-W, Tenson T, Van Melderen L, Zinkernagel A. Definitions and guidelines for research on antibiotic persistence. Nat Rev Microbiol. 2019;17(7):441–448. PMCID: PMC7136161
    Reference Link
  • 1.
    Xu F, Wu Y, Zhang C, Davis K, Moon K, Bushin L, Seyedsayamdost M. A genetics-free method for high-throughput discovery of cryptic microbial metabolites. Nat Chem Biol. 2019;15(2):161–168. PMCID: PMC6339573
    Reference Link
  • 1.
    Seyedsayamdost M. Toward a global picture of bacterial secondary metabolism. J Ind Microbiol Biotechnol. 2019;46(3-4):301–311. PMCID: PMC6779422
    Reference Link
  • 1.
    Tuttle R, Demko A, Patin N, Kapono C, Donia M, Dorrestein P, Jensen P. Detection of Natural Products and Their Producers in Ocean Sediments. Appl Environ Microbiol. 2019;85(8). PMCID: PMC6450032
    Reference Link
  • 1.
    Braffman N, Piscotta F, Hauver J, Campbell E, Link J, Darst S. Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin. Proc Natl Acad Sci U S A. 2019;116(4):1273–1278. PMCID: PMC6347699
    Reference Link
  • 1.
    Shaevitz J. Microbiology: Peeling Back the Layers of Bacterial Envelope Mechanics. Curr Biol. 2018;28(20):R1210-R1211. PMID: 30352194
    Reference Link
  • 1.
    Brynildsen M. Nitric Oxide Stress as a Metabolic Flux. Adv Microb Physiol. 2018;73:63–76. PMID: 30262110
    Reference Link
  • 1.
    Eickhoff M, Bassler B. SnapShot: Bacterial Quorum Sensing. Cell. 2018;174(5):1328–1328.e1. PMID: 30142348
    Reference Link
  • 1.
    Mao D, Okada B, Wu Y, Xu F, Seyedsayamdost M. Recent advances in activating silent biosynthetic gene clusters in bacteria. Curr Opin Microbiol. 2018;45:156–163. PMCID: PMC6281788
    Reference Link
  • 1.
    Rowland E, Snowden C, Cristea I. Protein lipoylation: an evolutionarily conserved metabolic regulator of health and disease. Curr Opin Chem Biol. 2018;42:76–85. PMCID: PMC5965299
    Reference Link
  • 1.
    Wang J, Yan C, Li Y, Hirata K, Yamamoto M, Yan N, Hu Q. Crystal structure of a bacterial homologue of SWEET transporters. Cell Res. 2014;24(12):1486–9. PMCID: PMC4260346
    Reference Link
  • 1.
    Yan N. Structural Biology of the Major Facilitator Superfamily Transporters. Annu Rev Biophys. 2015;44:257–83. PMID: 26098515
    Reference Link
  • 1.
    Carabetta V, Cristea I. Regulation, Function, and Detection of Protein Acetylation in Bacteria. J Bacteriol. 2017;199(16). PMCID: PMC5527388
    Reference Link
  • 1.
    Barrett T, Mok W, Brynildsen M. Biased inheritance protects older bacteria from harm. Science. 2017;356(6335):247–248. PMID: 28428383
    Reference Link
  • 1.
    Khodaparast S, Kim M, Silpe J, Stone H. Bubble-Driven Detachment of Bacteria from Confined Microgeometries. Environ Sci Technol. 2017;51(3):1340–1347. PMID: 28075119
    Reference Link
  • 1.
    Guo C-J, Chang F-Y, Wyche T, Backus K, Acker T, Funabashi M, Taketani M, Donia M, Nayfach S, Pollard K, Craik C, Cravatt B, Clardy J, Voigt C, Fischbach M. Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases. Cell. 2017;168(3):517–526.e18. PMCID: PMC5302092
    Reference Link
  • 1.
    Mok W, Brynildsen M. An Orphan Riboswitch Unveils Guanidine Regulation in Bacteria. Mol Cell. 2017;65(2):205–206. PMID: 28107646
    Reference Link
  • 1.
    Bitbol A-F, Dwyer R, Colwell L, Wingreen N. Inferring interaction partners from protein sequences. Proc Natl Acad Sci U S A. 2016;113(43):12180–12185. PMCID: PMC5087060
    Reference Link
  • 1.
    Orman M, Mok W, Brynildsen M. Aminoglycoside-enabled elucidation of bacterial persister metabolism. Curr Protoc Microbiol. 2015;36:17.9.1–17.9.14. PMCID: PMC4380151
    Reference Link
  • 1.
    Seyedsayamdost M, Case R, Kolter R, Clardy J. The Jekyll-and-Hyde chemistry of Phaeobacter gallaeciensis. Nat Chem. 2011;3(4):331–5. PMCID: PMC3376411
    Reference Link
  • 1.
    Link J. Biosynthesis: Leading the way to RiPPs. Nat Chem Biol. 2015;11(8):551–2. PMCID: PMC4794250
    Reference Link
  • 1.
    Henry T, Brynildsen M. Quantifying Current Events Identifies a Novel Endurance Regulator. Trends Microbiol. 2016;24(5):324–326. PMCID: PMC4841710
    Reference Link
  • 1.
    Kwan J, Tianero M, Donia M, Wyche T, Bugni T, Schmidt E. Host control of symbiont natural product chemistry in cryptic populations of the tunicate Lissoclinum patella. PLoS One. 2014;9(5):e95850. PMCID: PMC4008419
    Reference Link
  • 1.
    Williams B, Van Benschoten A, Cimermancic P, Donia M, Zimmermann M, Taketani M, Ishihara A, Kashyap P, Fraser J, Fischbach M. Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine. Cell Host Microbe. 2014;16(4):495–503. PMCID: PMC4260654
    Reference Link
  • 1.
    Donia M, Cimermancic P, Schulze C, Brown L, Martin J, Mitreva M, Clardy J, Linington R, Fischbach M. A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics. Cell. 2014;158(6):1402–1414. PMCID: PMC4164201
    Reference Link

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