Evolvability and hierarchy in rewired bacterial gene networks

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482

Emergence of Scaling in Random Networks

Barabási, A.-L., & Albert, R. (1999) · Science · doi:10.1126/science.286.5439.509 · Cited by 36,135

A Simple Sequentially Rejective Multiple Test Procedure

(1979) · Scandinavian Journal of Statistics · doi:10.2307/4615733 · Cited by 21,526

Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments

Smyth, G. K. (2004) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1027 · Cited by 11,829

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

Error and attack tolerance of complex networks

Albert, R., Jeong, H., & Barabási, A.-L. (2000) · Nature · doi:10.1038/35019019 · Cited by 7,534

Error and attack tolerance of complex networksPreprint

Albert, R., Jeong, H., & Barabási, A.-Ĺ. (2000) · Cited by 6,554

The Evolutionary Fate and Consequences of Duplicate Genes

Lynch, M., & Conery, J. S. (2000) · Science · doi:10.1126/science.290.5494.1151 · Cited by 4,988

A synthetic oscillatory network of transcriptional regulators

Elowitz, M., & Leibler, S. (2000) · Nature · doi:10.1038/35002125 · Cited by 4,812

Construction of a genetic toggle switch in Escherichia coli

Gardner, T. S., Cantor, C. R., & Collins, J. J. (2000) · Nature · doi:10.1038/35002131 · Cited by 4,310

Network motifs in the transcriptional regulation network of Escherichia coli

Shen-Orr, S. S., Milo, R., Mangan, S., & Alon, U. S. (2002) · Nature Genetics · doi:10.1038/ng881 · Cited by 2,970

Structure and evolution of transcriptional regulatory networks

Babu, M. M., Luscombe, N. M., Aravind, L., Gerstein, M., & Teichmann, S. A. (2004) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2004.05.004 · Cited by 780

Optimality and evolutionary tuning of the expression level of a protein

Dekel, E., & Alon, U. (2005) · Nature · doi:10.1038/nature03842 · Cited by 766

A comprehensive library of fluorescent transcriptional reporters for Escherichia coli

Zaslaver, A., Bren, A., Ronen, M., Itzkovitz, S., Kikoin, I., Shavit, S., Liebermeister, W., Surette, M. G., & Alon, U. S. (2006) · Nature Methods · doi:10.1038/nmeth895 · Cited by 748

Engineered gene circuits

Hasty, J., McMillen, D. R., & Collins, J. J. (2002) · Nature · doi:10.1038/nature01257 · Cited by 744

EcoCyc: a comprehensive database resource for Escherichia coli

Keseler, I. M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki108 · Cited by 737

Mapping Pathways and Phenotypes by Systematic Gene Overexpression

Sopko, R., Huang, D., Preston, N., Chua, G., Papp, B., Kafadar, K. A., Snyder, M., Oliver, S. G., Cyert, M., Hughes, T. R., et al. (2006) · Molecular Cell · doi:10.1016/j.molcel.2005.12.011 · Cited by 665

Topological and causal structure of the yeast transcriptional regulatory network

Guelzim, N., Bottani, S., Bourgine, P., & Képès, F. (2002) · Nature Genetics · doi:10.1038/ng873 · Cited by 608

Genetic analysis of Salmonella enteritidis biofilm formation: critical role of cellulose

Solano, C., García, B., Valle, J., Berasain, C., Ghigo, J., Gamazo, C., & Lasa, Í. (2002) · Molecular Microbiology · doi:10.1046/j.1365-2958.2002.02802.x · Cited by 551

Identifying global regulators in transcriptional regulatory networks in bacteria

Martínez‐Antonio, A., & Collado‐Vides, J. (2003) · Current Opinion in Microbiology · doi:10.1016/j.mib.2003.09.002 · Cited by 547

Isolation of an Escherichia coli K-12 Mutant Strain Able To Form Biofilms on Inert Surfaces: Involvement of a New ompR Allele That Increases Curli Expression

Vidal, O., Longin, R., Prigent‐Combaret, C., Dorel, C., Hooreman, M., & Lejeune, P. (1998) · Journal of Bacteriology · doi:10.1128/jb.180.9.2442-2449.1998 · Cited by 509

Gene regulatory network growth by duplication

Teichmann, S. A., & Babu, M. M. (2004) · Nature Genetics · doi:10.1038/ng1340 · Cited by 502

Curli Fibers Are Highly Conserved between Salmonella typhimurium and Escherichia coli with Respect to Operon Structure and Regulation

Römling, U., Zhao, B., Hammar, M., Sierralta, W. D., & Normark, S. J. (1998) · Journal of Bacteriology · doi:10.1128/jb.180.3.722-731.1998 · Cited by 467

Complex Regulatory Network Controls Initial Adhesion and Biofilm Formation in Escherichia coli via Regulation of the csgD Gene

Prigent‐Combaret, C., Brombacher, E., Vidal, O., Ambert, A., Lejeune, P., Landini, P., & Dorel, C. (2001) · Journal of Bacteriology · doi:10.1128/jb.183.24.7213-7223.2001 · Cited by 410

RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions

Salgado, H. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj156 · Cited by 368

Evolution of transcription factors and the gene regulatory network in Escherichia coli

Babu, M. M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg210 · Cited by 354

The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12

Pérez‐Rueda, E. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.8.1838 · Cited by 322

From acids to osmZ: multiple factors influence synthesis of the OmpF and OmpC porins in Escherichia coli

Pratt, L. A., Hsing, W., Gibson, K. E., & Silhavy, T. J. (1996) · Molecular Microbiology · doi:10.1111/j.1365-2958.1996.tb02532.x · Cited by 318

Regulation in the rpoS regulon of Escherichia coli

Loewen, P. C., Hu, B., Strutinsky, J., & Sparling, R. (1998) · Canadian Journal of Microbiology · doi:10.1139/cjm-44-8-707 · Cited by 290

Evolutionary Dynamics of Prokaryotic Transcriptional Regulatory Networks

Babu, M. M., Teichmann, S. A., & Aravind, L. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.02.019 · Cited by 267

Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states

Fong, S. S., Joyce, A. R., & Palsson, B. Ø. (2005) · Genome Research · doi:10.1101/gr.3832305 · Cited by 265

RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12

Salgado, H. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.72 · Cited by 256

rpoS regulation of acid, heat, and salt tolerance in Escherichia coli O157:H7

Cheville, A. M., Arnold, K. W., Buchrieser, C., Cheng, C.-M., & Kaspar, C. W. (1996) · Applied and Environmental Microbiology · doi:10.1128/aem.62.5.1822-1824.1996 · Cited by 253

Bacterial regulatory networks are extremely flexible in evolution

Lozada-Chávez, I. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl423 · Cited by 219

Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements

Teichmann, S. A., Park, J. M., & Chothia, C. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.25.14658 · Cited by 168

The integration host factor (IHF) integrates stationary‐phase and virulence gene expression in Salmonella enterica serovar Typhimurium

Mangan, M. W., Lucchini, S., Danino, V., Cróinı́n, T. Ó., Hinton, J. C. D., & Dorman, C. J. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05062.x · Cited by 160

Regulation in the rpoS regulon of Escherichia coli

Loewen, P. C., Hu, B., Strutinsky, J., & Sparling, R. (1998) · Canadian Journal of Microbiology · doi:10.1139/w98-069 · Cited by 137

Engineering Gene Networks to Emulate Drosophila Embryonic Pattern Formation

Isalan, M., Lemerle, C., & Serrano, L. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030064 · Cited by 118

A regulator of the flagellar regulon of Escherichia coli, flhD, also affects cell division

Prüß, B. M., & Matsumura, P. (1996) · Journal of Bacteriology · doi:10.1128/jb.178.3.668-674.1996 · Cited by 113

The nIpD gene is located in an operon with rpoS on the Escherichia coli chromosome and encodes a novel lipoprotein with a potential function in ceil wall formation

Lange, R., & Hengge‐Aronis, R. (1994) · Molecular Microbiology · doi:10.1111/j.1365-2958.1994.tb00466.x · Cited by 105

On the Nature of Gene Innovation: Duplication Patterns in Microbial Genomes

Hooper, S. D. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg101 · Cited by 103

Mutational activation of the Cpx signal transduction pathway of Escherichia coli suppresses the toxicity conferred by certain envelope‐associated stresses

Cosma, C. L., Danese, P. N., Carlson, J. H., Silhavy, T. J., & Snyder, W. B. (1995) · Molecular Microbiology · doi:10.1111/j.1365-2958.1995.mmi_18030491.x · Cited by 94

Inducible Acid Tolerance Mechanisms in Enteric Bacteria

Foster, J. W., & Moreno, M. S. (2007) · Novartis Foundation symposium · doi:10.1002/9780470515631.ch5 · Cited by 70

Evolutionary Potential of a Duplicated Repressor-Operator Pair: Simulating Pathways Using Mutation Data

Poelwijk, F. J., Kiviet, D. J., & Tans, S. J. (2005) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020058 · Cited by 44

Localized transfection on arrays of magnetic beads coated with PCR products

Isalan, M., Santori, M. I., González, C., & Serrano, L. G. (2005) · Nature Methods · doi:10.1038/nmeth732 · Cited by 34

Isolation and characterization of the Escherichia coli htrD gene, whose product is required for growth at high temperatures

Delaney, J. M., Ang, D., & Georgopoulos, C. P. (1992) · Journal of Bacteriology · doi:10.1128/jb.174.4.1240-1247.1992 · Cited by 22

A census of human transcription factors: function, expression and evolution

Vaquerizas, J. M., Kummerfeld, S. K., Teichmann, S. A., & Luscombe, N. M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2538 · Cited by 1,573

A synchronized quorum of genetic clocks

Danino, T., Mondragón-Palomino, O., Tsimring, L. S., & Hasty, J. (2010) · Nature · doi:10.1038/nature08753 · Cited by 1,002

A brief history of synthetic biology

Cameron, D. E., Bashor, C. J., & Collins, J. J. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3239 · Cited by 988

Adaptive laboratory evolution—Principles and applications for biotechnology

Dragosits, M., & Mattanovich, D. (2013) · Microbial Cell Factories · doi:10.1186/1475-2859-12-64 · Cited by 827

Evolution of Two-Component Signal Transduction Systems

Capra, E. J., & Laub, M. T. (2012) · Annual Review of Microbiology · doi:10.1146/annurev-micro-092611-150039 · Cited by 705

Genome rewired

Bennett, M. R., & Hasty, J. (2008) · Nature · doi:10.1038/452824a · Cited by 13

Rewiring E. coli

Doerr, A. J. (2008) · Nature Methods · doi:10.1038/nmeth0608-464b

The propagation of perturbations in rewired bacterial gene networks

Baumstark, R., Hänzelmann, S., Tsuru, S., Schaerli, Y., Francesconi, M., Mancuso, F. M., Castelo, R., & Isalan, M. (2015) · Nature Communications · doi:10.1038/ncomms10105 · Cited by 22

Don’t Try This at Home

Ray, L. B. (2008) · Science Signaling · doi:10.1126/stke.116ec137

Evolution of gene regulatory networks in a bacterial experimental system: Identifying general principles governing regulator rewiring from two contrasting mutational pathways

Shepherd, M., Pierce, A., Jackson, R. W., Hurst, L. D., & Taylor, T. (2021)