Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection

Molecular cloning: A laboratory manual

Deininger, P. L. (1990) · Analytical Biochemistry · doi:10.1016/0003-2697(90)90595-z · Cited by 84,684

One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products.

Datsenko, K., & Wanner, B. (2000) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.120163297 · Cited by 15,902

The River Continuum Concept

Vannote, R. L., Minshall, G. W., Cummins, K. W., Sedell, J. R., & Cushing, C. E. (1980) · Canadian Journal of Fisheries and Aquatic Sciences · doi:10.1139/f80-017 · Cited by 9,984

The complete genome sequence of Escherichia coli K-12.

Blattner, F., Plunkett, G., Bloch, C., Perna, N., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C., Mayhew, G., et al. (1997) · Science · doi:10.1126/science.277.5331.1453 · Cited by 7,996

Forage Fiber Analysis (Apparatus, reagents, procedures and some applications)

Goering, H. K. (1970) · Medical Entomology and Zoology · Cited by 5,738

Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter

Guzman, L., Belin, D., Carson, M. J., & Beckwith, J. (1995) · Journal of Bacteriology · doi:10.1128/jb.177.14.4121-4130.1995 · Cited by 4,942

Functional profiling of the Saccharomyces cerevisiae genome

Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., et al. (2002) · Nature · doi:10.1038/nature00935 · Cited by 4,316

Handbook of applied hydrology

Chow, V. T. (2010) · Cited by 3,340

The physical map of the whole E. coli chromosome: Application of a new strategy for rapid analysis and sorting of a large genomic library

Kohara, Y., Akiyama, K., & Isono, K. (1987) · Cell · doi:10.1016/0092-8674(87)90503-4 · Cited by 1,754

VASCULAR PLANT BREAKDOWN IN FRESHWATER ECOSYSTEMS

Webster, J. R., & Benfield, E. F. (1986) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.es.17.110186.003031 · Cited by 1,583

A human gut microbial gene catalogue established by metagenomic sequencing

MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624

A Common Mechanism of Cellular Death Induced by Bactericidal Antibiotics

Kohanski, M. A., Dwyer, D. J., Hayete, B., Lawrence, C. A., & Collins, J. J. (2007) · Cell · doi:10.1016/j.cell.2007.06.049 · Cited by 2,982

The re-emergence of natural products for drug discovery in the genomics era

Harvey, A. L., Edrada‐Ebel, R., & Quinn, R. J. (2015) · Nature Reviews Drug Discovery · doi:10.1038/nrd4510 · Cited by 2,654

Antibacterial drug discovery in the resistance era

Brown, E. D., & Wright, G. D. (2016) · Nature · doi:10.1038/nature17042 · Cited by 2,315

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

Taniguchi, Y., Choi, P. J., Li, G.-W., Chen, H., Babu, M., Hearn, J., Emili, A., & Xie, X. S. (2010) · Science · doi:10.1126/science.1188308 · Cited by 1,982

Persister cells

Lewis, K. (2010) · Annual Review of Microbiology · doi:10.1146/annurev.micro.112408.134306 · Cited by 1,858

The Challenge of Efflux-Mediated Antibiotic Resistance in Gram-Negative Bacteria

Li, X.-Z., Plésiat, P., & Nikaido, H. (2015) · Clinical Microbiology Reviews · doi:10.1128/cmr.00117-14 · Cited by 1,648

A genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic information

Feist, A. M., Henry, C. S., Reed, J. L., Krummenacker, M., Joyce, A. R., Karp, P. D., Broadbelt, L. J., Vassily Hatzimanikatis, A., & Palsson, B. Ø. (2007) · Molecular Systems Biology · doi:10.1038/msb4100155 · Cited by 1,408

Persistent bacterial infections and persister cells

Fisher, R. A., Gollan, B., & Helaine, S. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.42 · Cited by 1,243

Strains, functions and dynamics in the expanded Human Microbiome Project

Lloyd-Price, J., Mahurkar, A., Rahnavard, G., Crabtree, J., Orvis, J., Hall, A. B., Brady, A., Creasy, H. H., McCracken, C., Giglio, M. G., et al. (2017) · Nature · doi:10.1038/nature23889 · Cited by 1,267

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

Touchon, M., Hoede, C., Tenaillon, O., Barbe, V., Baeriswyl, S., Bidet, P., Bingen, É., Bonacorsi, S., Bouchier, C., Bouvet, O. M. M., et al. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000344 · Cited by 1,248

A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011

Orth, J. D., Conrad, T. M., Na, J., Lerman, J. A., Nam, H., Feist, A. M., & Palsson, B. Ø. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.65 · Cited by 1,006

Antibiotics induce redox-related physiological alterations as part of their lethality

Dwyer, D. J., Belenky, P. A., Yang, J. H., MacDonald, I. C., Martell, J. D., Takahashi, N. K., Chan, C. T. Y., Lobritz, M. A., Braff, D., Schwarz, E. G., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1401876111 · Cited by 938

Genomically Recoded Organisms Expand Biological Functions

Lajoie, M. J., Rovner, A. J., Goodman, D. B., Aerni, H. R., Haimovich, A. D., Kuznetsov, G., Mercer, J. A. M., Wang, H. H., Carr, P. A., Mosberg, J. A., et al. (2013) · Science · doi:10.1126/science.1241459 · Cited by 874

Evolution by gene loss

Albalat, R., & Cañestro, C. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.39 · Cited by 775

Constraint-based models predict metabolic and associated cellular functions

Bordbar, A., Monk, J. M., King, Z. A., & Palsson, B. Ø. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3643 · Cited by 844

Drug combinations: a strategy to extend the life of antibiotics in the 21st century

Tyers, M., & Wright, G. D. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0141-x · Cited by 849

Metabolic engineering of Escherichia coli for 1-butanol production

Atsumi, S., Cann, A. F., Connor, M. R., Shen, C. R., Smith, K. M., Brynildsen, M. P., Chou, K., Hanai, T., & Liao, J. C. (2007) · Metabolic Engineering · doi:10.1016/j.ymben.2007.08.003 · Cited by 823

The Molecular Diversity of Adaptive Convergence

Tenaillon, O., Rodríguez-Verdugo, A., Gaut, R. L., McDonald, P., Bennett, A. F., Long, A. D., & Gaut, B. S. (2012) · Science · doi:10.1126/science.1212986 · Cited by 815

Ciprofloxacin Causes Persister Formation by Inducing the TisB toxin in Escherichia coli

Dörr, T., Vulić, M., & Lewis, K. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000317 · Cited by 781

Overflow metabolism in Escherichia coli results from efficient proteome allocation

Basan, M., Hui, S., Okano, H., Zhang, Z., Shen, Y., Williamson, J. R., & Hwa, T. (2015) · Nature · doi:10.1038/nature15765 · Cited by 785

The quantitative and condition-dependent Escherichia coli proteome

Schmidt, A., Kochanowski, K., Vedelaar, S. R., Ahrné, E., Volkmer, B., Callipo, L., Knoops, K., Bauer, M., Aebersold, R. H., & Heinemann, M. (2015) · Nature Biotechnology · doi:10.1038/nbt.3418 · Cited by 759

Precise and reliable gene expression via standard transcription and translation initiation elements

Mutalik, V. K., Guimaraes, J. C., Cambray, G., Lam, C. S. C., Christoffersen, M. J., Mai, Q.-A., Tran, A. B., Paull, M. L., Keasling, J. D., Arkin, A. P., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2404 · Cited by 772

Lysine Succinylation Is a Frequently Occurring Modification in Prokaryotes and Eukaryotes and Extensively Overlaps with Acetylation

Weinert, B. T., Scholz, C. W., Wagner, S., Iešmantavičius, V., Su, D., Daniel, J. A., & Choudhary, C. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.07.024 · Cited by 774

Function and Biogenesis of Lipopolysaccharides

Bertani, B., & Ruiz, N. (2018) · EcoSal Plus · doi:10.1128/ecosalplus.esp-0001-2018 · Cited by 742

Potential roles of gut microbiome and metabolites in modulating ALS in mice

Blacher, E., Bashiardes, S., Shapiro, H., Rothschild, D., Mor, U., Dori-Bachash, M., Kleimeyer, C., Moresi, C., Harnik, Y., Zur, M., et al. (2019) · Nature · doi:10.1038/s41586-019-1443-5 · Cited by 700

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

Goodman, A. L., McNulty, N. P., Zhao, Y., Leip, D., Mitra, R. D., Lozupone, C., Knight, R. D., & Gordon, J. I. (2009) · Cell Host & Microbe · doi:10.1016/j.chom.2009.08.003 · Cited by 713

Cytoplasmic steps of peptidoglycan biosynthesis

Barreteau, H., Kovač, A., Boniface, A., Sova, M., Gobec, S., & Blanot, D. (2008) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2008.00104.x · Cited by 727

Phenotypic Landscape of a Bacterial Cell

Nichols, R. J., Sen, Ś., Choo, Y. J., Beltrão, P., Zietek, M., Chaba, R., Lee, S., Kazmierczak, K. M., Lee, K. J., Wong, A., et al. (2010) · Cell · doi:10.1016/j.cell.2010.11.052 · Cited by 723

A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria

Peters, J. M., Colavin, A., Shi, H., Czarny, T. L., Larson, M. H., Wong, S. S., Hawkins, J. S., Lu, C. H. S., Koo, B., Marta, E., et al. (2016) · Cell · doi:10.1016/j.cell.2016.05.003 · Cited by 701

Revenge of the phages: defeating bacterial defences

Samson, J. E., Magadán, A. H., Sabri, M., & Moineau, S. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro3096 · Cited by 727

Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli

Yosef, I., Goren, M. G., & Qimron, U. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks216 · Cited by 655

Cryptic prophages help bacteria cope with adverse environments

Wang, X., Kim, Y., Ma, Q., Hong, S. H., Pokusaeva, K., Sturino, J. M., & Wood, T. K. (2010) · Nature Communications · doi:10.1038/ncomms1146 · Cited by 677

Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations

Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., et al. (2007) · Science · doi:10.1126/science.1132067 · Cited by 683

Critical role of gut microbiota in the production of biologically active, free catecholamines in the gut lumen of mice

Asano, Y., Hiramoto, T., Nishino, R., Aiba, Y., Kimura, T., Yoshihara, K., Koga, Y., & Sudo, N. (2012) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00341.2012 · Cited by 659

Bacterial charity work leads to population-wide resistance

Lee, H. H., Molla, M. N., Cantor, C. R., & Collins, J. J. (2010) · Nature · doi:10.1038/nature09354 · Cited by 638

Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis

Koo, B., Kritikos, G., Farelli, J. D., Todor, H., Tong, K., Kimsey, H. H., Wapinski, I. N., Galardini, M., Cabal, A., Peters, J. M., et al. (2017) · Cell Systems · doi:10.1016/j.cels.2016.12.013 · Cited by 584

Contribution of bacterial outer membrane vesicles to innate bacterial defense

Manning, A. J., & Kuehn, M. J. (2011) · BMC Microbiology · doi:10.1186/1471-2180-11-258 · Cited by 623

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutantsPreprint

Langridge, G. C., Phan, M.-D., Turner, D., Perkins, T. T., Parts, L., Haase, J., Charles, I., Maskell, D. J., Peters, S. E., Dougan, G., et al. (2009) · Genome Research · doi:10.1101/gr.097097.109 · Cited by 641

A semi-synthetic organism with an expanded genetic alphabet

Malyshev, D. A., Dhami, K., Lavergne, T., Chen, T., Dai, N., Foster, J. M., Junior, I. R. C., & Romesberg, F. E. (2014) · Nature · doi:10.1038/nature13314 · Cited by 614

The biomass objective function

Feist, A. M., & Palsson, B. Ø. (2010) · Current Opinion in Microbiology · doi:10.1016/j.mib.2010.03.003 · Cited by 629

Escherichia coli K-12: a cooperatively developed annotation snapshot--2005

Riley, M. A. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj405 · Cited by 609

Toxicity Mechanisms in Escherichia coli Vary for Silver Nanoparticles and Differ from Ionic Silver

Ivask, A., Badawy, A. M. E., Kaweeteerawat, C., Boren, D., Fischer, H., Ji, Z., Chang, C. H., Liu, R., Tolaymat, T. M., Telesca, D., et al. (2013) · ACS Nano · doi:10.1021/nn4044047 · Cited by 618

Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28

Smargon, A. A., Cox, D. B. T., Pyzocha, N. K., Zheng, K., Slaymaker, I. M., Gootenberg, J. S., Abudayyeh, O. A., Essletzbichler, P., Shmakov, S., Makarova, K. S., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2016.12.023 · Cited by 575

E. coli genome manipulation by P1 transduction.

Thomason, L., Costantino, N., & Court, D. (2007) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb0117s79 · Cited by 654

Mistranslation of Membrane Proteins and Two-Component System Activation Trigger Antibiotic-Mediated Cell Death

Kohanski, M. A., Dwyer, D. J., Wierzbowski, J., Cottarel, G., & Collins, J. J. (2008) · Cell · doi:10.1016/j.cell.2008.09.038 · Cited by 576

Mutant phenotypes for thousands of bacterial genes of unknown function

Price, M. N., Wetmore, K. M., Waters, R. J., Callaghan, M., Ray, J., Liu, H., Kuehl, J. V., Melnyk, R. A., Lamson, J. S., Suh, Y., et al. (2018) · Nature · doi:10.1038/s41586-018-0124-0 · Cited by 576

A Map of Protein-Metabolite Interactions Reveals Principles of Chemical Communication

Piazza, I., Kochanowski, K., Cappelletti, V., Fuhrer, T., Noor, Ε., Sauer, U., & Picotti, P. (2018) · Cell · doi:10.1016/j.cell.2017.12.006 · Cited by 555

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

Feist, A. M., & Palsson, B. Ø. (2008) · Nature Biotechnology · doi:10.1038/nbt1401 · Cited by 545

EcoCyc: fusing model organism databases with systems biology

Keseler, I. M., Mackie, A. M., Peralta-Gil, M., Santos-Zavaleta, A., Gama‐Castro, S., Bonavides-Martínez, C., Fulcher, C. A., Huerta, A. M., Kothari, A., Krummenacker, M., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1027 · Cited by 542

Spatiotemporal microbial evolution on antibiotic landscapes

Baym, M., Lieberman, T. D., Kelsic, E. D., Chait, R., Gross, R., Yelin, I., & Kishony, R. (2016) · Science · doi:10.1126/science.aag0822 · Cited by 548

A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: From biofuels and chemicals, to biocatalysis and bioremediation

Nicolaou, S. A., Gaida, S. M., & Papoutsakis, E. T. (2010) · Metabolic Engineering · doi:10.1016/j.ymben.2010.03.004 · Cited by 537

SOS Response Induces Persistence to Fluoroquinolones in Escherichia coli

Dörr, T., Lewis, K., & Vulić, M. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000760 · Cited by 553

Conversion of Escherichia coli to Generate All Biomass Carbon from CO2

Gleizer, S., Ben-Nissan, R., Bar‐On, Y. M., Antonovsky, N., Noor, Ε., Zohar, Y., Jona, G., Krieger, E., Shamshoum, M., Bar‐Even, A., et al. (2019) · Cell · doi:10.1016/j.cell.2019.11.009 · Cited by 528

Bacterial lipids: Metabolism and membrane homeostasis

Parsons, J. B., & Rock, C. O. (2013) · Progress in Lipid Research · doi:10.1016/j.plipres.2013.02.002 · Cited by 543

DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements: Table 1.

Luo, H., Lin, Y., Gao, F., Zhang, C., & Zhang, R. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1131 · Cited by 528

Quantifying changes in the thiol redox proteome upon oxidative stress in vivo

Leichert, L. I. O., Gehrke, F., Gudiseva, H. V., Blackwell, T. W., Ilbert, M., Walker, A. K., Strahler, J. R., Andrews, P., & Jakob, U. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0707723105 · Cited by 514

Modular cell biology: retroactivity and insulation

Del Vecchio, D., Ninfa, A. J., & Sontag, E. D. (2008) · Molecular Systems Biology · doi:10.1038/msb4100204 · Cited by 519

Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

Harcombe, W. R., Riehl, W. J., Dukovski, I., Granger, B. R., Betts, A., Lang, A., Bonilla, G. M., Kar, A., Leiby, N., Mehta, P., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.03.070 · Cited by 535

Repeatability and Contingency in the Evolution of a Key Innovation in Phage Lambda

Meyer, J. R., Dobias, D. T., Weitz, J. S., Barrick, J. E., Quick, R. T., & Lenski, R. E. (2012) · Science · doi:10.1126/science.1214449 · Cited by 518

DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes

Zhang, R., & Lin, Y. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn858 · Cited by 503

Highly accurate genome sequences of Escherichia coli K‐12 strains MG1655 and W3110

Hayashi, K., Morooka, N., Yamamoto, Y., Fujita, K., Isono, K., Choi, S., Ohtsubo, E., Baba, T., Wanner, B. L., Mori, H., et al. (2006) · Molecular Systems Biology · doi:10.1038/msb4100049 · Cited by 503

Oxidation of the Guanine Nucleotide Pool Underlies Cell Death by Bactericidal Antibiotics

Foti, J. J., Devadoss, B., Winkler, J. A., Collins, J. J., & Walker, G. C. (2012) · Science · doi:10.1126/science.1219192 · Cited by 493

SEDS proteins are a widespread family of bacterial cell wall polymerases

Meeske, A. J., Riley, E. P., Robins, W. P., Uehara, T., Mekalanos, J. J., Kahne, D. E., Walker, S., Kruse, A. C., Bernhardt, T. G., & Rudner, D. Z. (2016) · Nature · doi:10.1038/nature19331 · Cited by 493

Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit

Gupta, A., Reizman, I., Reisch, C. R., & Prather, K. L. J. (2017) · Nature Biotechnology · doi:10.1038/nbt.3796 · Cited by 492

The Yeast Deletion Collection: A Decade of Functional Genomics

Giaever, G. N., & Nislow, C. (2014) · Genetics · doi:10.1534/genetics.114.161620 · Cited by 500

GTPase activity–coupled treadmilling of the bacterial tubulin FtsZ organizes septal cell wall synthesis

Yang, X., Lyu, Z., Miguel, A. V., McQuillen, R. J., Huang, K. C., & Xiao, J. (2017) · Science · doi:10.1126/science.aak9995 · Cited by 483

Personalized Mapping of Drug Metabolism by the Human Gut Microbiome

Javdan, B., Lopez, J. G., Chankhamjon, P., Lee, Y.-C. J., Hull, R., Wu, Q., Wang, X., Chatterjee, S., & Donia, M. S. (2020) · Cell · doi:10.1016/j.cell.2020.05.001 · Cited by 492

Biocontainment of genetically modified organisms by synthetic protein design

Mandell, D. J., Lajoie, M. J., Mee, M. T., Takeuchi, R., Kuznetsov, G., Norville, J. E., Gregg, C. J., Stoddard, B. L., & Church, G. M. (2015) · Nature · doi:10.1038/nature14121 · Cited by 487

Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons

Wetmore, K. M., Price, M. N., Waters, R. J., Lamson, J. S., He, J., Hoover, C. A., Blow, M. J., Bristow, J. D., Butland, G. P., Arkin, A. P., et al. (2015) · mBio · doi:10.1128/mbio.00306-15 · Cited by 480

Lysine Acetylation Is a Highly Abundant and Evolutionarily Conserved Modification in Escherichia Coli

Zhang, J., Sprung, R. W., Pei, J., Tan, X., Kim, S., Zhu, H., Liu, C., Grishin, N. V., & Zhao, Y. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800187-mcp200 · Cited by 474

Indole is an inter-species biofilm signal mediated by SdiA

Lee, J., Jayaraman, A., & Wood, T. K. (2007) · BMC Microbiology · doi:10.1186/1471-2180-7-42 · Cited by 471

Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production

Brynildsen, M. P., Winkler, J. A., Spina, C. S., MacDonald, I. C., & Collins, J. J. (2013) · Nature Biotechnology · doi:10.1038/nbt.2458 · Cited by 466

Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli

Dwyer, D. J., Kohanski, M. A., Hayete, B., & Collins, J. J. (2007) · Molecular Systems Biology · doi:10.1038/msb4100135 · Cited by 470

Translation Elongation Factor EF-P Alleviates Ribosome Stalling at Polyproline Stretches

Ude, S., Lassak, J., Starosta, A. L., Kraxenberger, T., Wilson, D. N., & Jung, K. (2012) · Science · doi:10.1126/science.1228985 · Cited by 460

Siderophores from Neighboring Organisms Promote the Growth of Uncultured Bacteria

Donofrio, A. E., Crawford, J. M., Stewart, E. J., Witt, K., Gavrish, E., Epstein, S. S., Clardy, J., & Lewis, K. (2010) · Chemistry & Biology · doi:10.1016/j.chembiol.2010.02.010 · Cited by 457

Enzyme clustering accelerates processing of intermediates through metabolic channeling

Castellana, M., Wilson, M. Z., Xu, Y., Joshi, P., Cristea, I. M., Rabinowitz, J. D., Gitai, Z., & Wingreen, N. S. (2014) · Nature Biotechnology · doi:10.1038/nbt.3018 · Cited by 447

Second Messenger-Mediated Adjustment of Bacterial Swimming Velocity

Boehm, A., Kaiser, M., Li, H., Spangler, C., Kasper, C. A., Ackermann, M., Kaever, V., Sourjik, V., Röth, V., & Jenal, U. (2010) · Cell · doi:10.1016/j.cell.2010.01.018 · Cited by 441

Toxin-Antitoxin Systems Influence Biofilm and Persister Cell Formation and the General Stress Response

Wang, X., & Wood, T. K. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.05068-11 · Cited by 431

Regulation of glycogen metabolism in yeast and bacteria

Wilson, W. A., Roach, P. J., Montero, M., Baroja‐Fernández, E., Muñoz, F. J., Eydallin, G., Viale, A. M., & Pozueta‐Romero, J. (2010) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2010.00220.x · Cited by 423

The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal

Deana, A., Čelešnik, H., & Belasco, J. G. (2008) · Nature · doi:10.1038/nature06475 · Cited by 418

CRISPR adaptation biases explain preference for acquisition of foreign DNA

Levy, A., Goren, M. G., Yosef, I., Auster, O., Manor, M., Amitai, G., Edgar, R., Qimron, U., & Sorek, R. (2015) · Nature · doi:10.1038/nature14302 · Cited by 408

Expanding metabolism for biosynthesis of nonnatural alcohols

Zhang, K., Sawaya, M. R., Eisenberg, D. S., & Liao, J. C. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0807157106 · Cited by 412

Selective small-molecule inhibition of an RNA structural element

Howe, J. A., Wang, H., Fischmann, T. O., Balibar, C. J., Xiao, L., Galgoci, A. M., Malinverni, J. C., Mayhood, T., Villafania, A., Nahvi, A., et al. (2015) · Nature · doi:10.1038/nature15542 · Cited by 407

Bacterial Retrons Function In Anti-Phage Defense

Millman, A., Bernheim, A. G., Stokar-Avihail, A., Fedorenko, T., Voichek, M., Leavitt, A., Oppenheimer‐Shaanan, Y., & Sorek, R. (2020) · Cell · doi:10.1016/j.cell.2020.09.065 · Cited by 411

'Deadman' and 'Passcode' microbial kill switches for bacterial containment

Chan, C. T. Y., Lee, J. W., Cameron, D. E., Bashor, C. J., & Collins, J. J. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1979 · Cited by 406

Biosynthesis of Pantothenic Acid and Coenzyme A

Leonardi, R., & Jackowski, S. (2007) · EcoSal Plus · doi:10.1128/ecosalplus.3.6.3.4 · Cited by 404

Synthetic non-oxidative glycolysis enables complete carbon conservation

Bogorad, I. W., Lin, T., & Liao, J. C. (2013) · Nature · doi:10.1038/nature12575 · Cited by 403

Large-scale identification of protein–protein interaction of Escherichia coli K-12

Arifuzzaman, M., Maeda, M., Itoh, A., Nishikata, K., Takita, C., Saito, R., Ara, T., Nakahigashi, K., Huang, H.-C., Hirai, A., et al. (2006) · Genome Research · doi:10.1101/gr.4527806 · Cited by 403

Growth of E. coli on formate and methanol via the reductive glycine pathway

Kim, S., Lindner, S. N., Aslan, S., Yishai, O., Wenk, S., Schann, K., & Bar‐Even, A. (2020) · Nature Chemical Biology · doi:10.1038/s41589-020-0473-5 · Cited by 385

ATP-Dependent Dynamic Protein Aggregation Regulates Bacterial Dormancy Depth Critical for Antibiotic Tolerance

Pu, Y., Li, Y., Jin, X., Tian, T., Ma, Q., Zhao, Z., Lin, S.-Y., Chen, Z., Li, B., Yao, G., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.10.022 · Cited by 387

Escherichia coli as a host for metabolic engineering

Pontrelli, S., Chiu, T., Lan, E. I., Chen, F. Y.-H., Chang, P., & Liao, J. C. (2018) · Metabolic Engineering · doi:10.1016/j.ymben.2018.04.008 · Cited by 397

Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the keto-acid pathways

Shen, C. R., & Liao, J. C. (2008) · Metabolic Engineering · doi:10.1016/j.ymben.2008.08.001 · Cited by 391

Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins

Hu, P., Janga, S. C., Babu, M., Díaz-Mejía, J. J., Butland, G., Yang, W., Pogoutse, O., Guo, X., Phanse, S., Wong, P., et al. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000096 · Cited by 387

Consequences of Membrane Protein Overexpression in Escherichia coli

Wagner, S., Baars, L., Ytterberg, A. J., Klußmeier, A., Wagner, C., Nord, O., Nygren, P., van Wijk, K. J., & Gier, J. D. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m600431-mcp200 · Cited by 384

Regulation of Peptidoglycan Synthesis by Outer-Membrane Proteins

Typas, A., Banzhaf, M., van Saparoea, H. B. V. D. B., Verheul, J., Biboy, J., Nichols, R. J., Zietek, M., Beilharz, K., Kannenberg, K., von Rechenberg, M., et al. (2010) · Cell · doi:10.1016/j.cell.2010.11.038 · Cited by 397

Antibiotic-resistant bacteria show widespread collateral sensitivity to antimicrobial peptides

Lázár, V., Martins, A., Spohn, R., Daruka, L., Grézal, G., Fekete, G., Számel, M., Jangir, P. K., Kintses, B., Csörgő, B., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0164-0 · Cited by 379

The Complete Genome Sequence of Escherichia coli DH10B: Insights into the Biology of a Laboratory Workhorse

Durfee, T., Nelson, R., Baldwin, S., Plunkett, G., Burland, V., Mau, B., Petrosino, J. F., Qin, X., Muzny, D. M., Ayele, M., et al. (2008) · Journal of Bacteriology · doi:10.1128/jb.01695-07 · Cited by 369

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol 2:2006.0008

Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., & Mori, H. (2006)

The Applications of Systematic In-Frame, Single-Gene Knockout Mutant Collection of Escherichia coli K-12

Baba, T., Huan, H.-C., Datsenko, K. A., Wanner, B. L., & Mori, H. (2008) · Methods in molecular biology · doi:10.1007/978-1-59745-321-9_12 · Cited by 45

Update on the Keio collection of Escherichia coli single‐gene deletion mutants

Yamamoto, N., Nakahigashi, K., Nakamichi, T., Yoshino, M., Takai, Y., Touda, Y., Furubayashi, A., Kinjo, S., Dose, H., Hasegawa, M. L., et al. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.92 · Cited by 273

The Construction of Systematic In-Frame, Single-Gene Knockout Mutant Collection in Escherichia coli K-12

Baba, T., & Mori, H. (2008) · Methods in molecular biology · doi:10.1007/978-1-59745-321-9_11 · Cited by 48

Checks and Balances with Use of the Keio Collection for Phenotype Testing

Aedo, S. J., Ma, H. R., & Brynildsen, M. P. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9142-6_9 · Cited by 10