Identity and Function of a Large Gene Network Underlying Mutagenic Repair of DNA Breaks

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

Escherichia coli and Salmonella :cellular and molecular biology

Neidhardt, F. C. (1996) · ASM Press eBooks · Cited by 8,197

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

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

Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., & Mori, H. (2006) · Molecular Systems Biology · doi:10.1038/msb4100050 · Cited by 7,858

Stochastic Gene Expression in a Single Cell

Elowitz, M. B., Levine, A. J., Siggia, E. D., & Swain, P. S. (2002) · Science · doi:10.1126/science.1070919 · Cited by 5,441

A short course in bacterial genetics

Miller, J. H. (1992) · Cited by 4,391

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

Szklarczyk, D., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A. C., Mínguez, P., Doerks, T., Stark, M., Muller, J., Bork, P., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq973 · Cited by 3,469

Integration of biological networks and gene expression data using Cytoscape

Cline, M. S., Smoot, M., Cerami, E., Kuchinsky, A., Landys, N., Workman, C., Christmas, R., Avila-Campilo, I., Creech, M., Gross, B., et al. (2007) · Nature Protocols · doi:10.1038/nprot.2007.324 · Cited by 2,507

Mutational Processes Molding the Genomes of 21 Breast Cancers

Nik-Zainal, S., Alexandrov, L. B., Wedge, D. C., Van Loo, P., Greenman, C. D., Raine, K., Jones, D., Hinton, J., Marshall, J., Stebbings, L. A., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.024 · Cited by 1,909

Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria

Postma, P. W., Lengeler, J. W., & Jacobson, G. R. (1993) · Microbiological Reviews · doi:10.1128/mr.57.3.543-594.1993 · Cited by 1,802

Stress-induced mutagenesis: Stress diversity facilitates the persistence of mutator genes

Lukačišinová, M., Novak, S., & Paixão, T. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005609 · Cited by 24

Design of microbial catalysts for two-stage processes

Shabestary, K., Klamt, S., Link, H., Mahadevan, R., Steuer, R., & Hudson, E. P. (2024) · Nature Reviews Bioengineering · doi:10.1038/s44222-024-00225-x · Cited by 23

Antibody Profiling of Kawasaki Disease Using Escherichia coli Proteome Microarrays

Kuo, H., Huang, Y., Chung, F.-H., Chen, P.-C., Sung, T., Chen, Y.-W., Hsieh, K., Chen, C., & Syu, G. (2017) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra117.000198 · Cited by 23

Roles of Nucleoid-Associated Proteins in Stress-Induced Mutagenic Break Repair in StarvingEscherichia coli

Moore, J. M., Magnan, D. R., Mojica, A. K., Núñez, M. A. B., Bates, D. B., Rosenberg, S. M., & Hastings, P. J. (2015) · Genetics · doi:10.1534/genetics.115.178970 · Cited by 22

Evolution of Escherichia coli for maximum HOCl resistance through constitutive expression of the OxyR regulon

Gundlach, J., & Winter, J. (2014) · Microbiology · doi:10.1099/mic.0.074815-0 · Cited by 21

Sequence-Specific Peptide Nucleic Acid-Based Antisense Inhibitors of TEM-1 β-Lactamase and Mechanism of Adaptive Resistance

Courtney, C. M., & Chatterjee, A. (2015) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.5b00042 · Cited by 21

Suppression of antibiotic resistance evolution by single-gene deletion

Horinouchi, T., Maeda, T., Kotani, H., & Furusawa, C. (2020) · Scientific Reports · doi:10.1038/s41598-020-60663-6 · Cited by 22

DNA Data Storage.

Buko, T., Tuczko, N., & Ishikawa, T. (2023) · BioTech · doi:10.3390/biotech12020044 · Cited by 21

Spontaneous Phage Resistance in Avian Pathogenic Escherichia coli

Sørensen, P. E., Baig, S., Stegger, M., Ingmer, H., Garmyn, A., & Butaye, P. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.782757 · Cited by 23

Integrative genomics would strengthen AMR understanding through ONE health approach

Liu, C. S. C., & Pandey, R. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e34719 · Cited by 23

Development of a stress-induced mutagenesis module for autonomous adaptive evolution of Escherichia coli to improve its stress tolerance

Zhu, L., Li, Y., & Cai, Z. (2015) · Biotechnology for Biofuels · doi:10.1186/s13068-015-0276-1 · Cited by 22

Outlining Core Pathways of Amyloid Toxicity in Bacteria with the RepA-WH1 Prionoid

Molina-García, L., Álamo, M. M., Botías, P., Martín‐Moldes, Z., Fernández, M., Sánchez-Gorostiaga, A., Valle, A. A.-D., Nogales, J., García‐Cantalejo, J., & Giraldo, R. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00539 · Cited by 21

The genome as a developmental organ

Lamm, E. (2014) · The Journal of Physiology · doi:10.1113/jphysiol.2014.271734 · Cited by 20

In Darwinian evolution, feedback from natural selection leads to biased mutations

Caporale, L. H., & Doyle, J. C. (2013) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.12235 · Cited by 20

Opposing effects of final population density and stress on Escherichia coli mutation rate

Krašovec, R., Richards, H., Gifford, D. R., Belavkin, R. V., Channon, A., Aston, E., McBain, A. J., & Cg, K. (2018) · The ISME Journal · doi:10.1038/s41396-018-0237-3 · Cited by 16

Metabolic stress constrains microbial L-cysteine production in Escherichia coli by accelerating transposition through mobile genetic elements

Heieck, K., Arnold, N. D., & Brück, T. (2023) · Microbial Cell Factories · doi:10.1186/s12934-023-02021-5 · Cited by 19

Optimal cancer evasion in a dynamic immune microenvironment generates diverse post-escape tumor antigenicity profiles

George, J. T., & Levine, H. (2023) · eLife · doi:10.7554/elife.82786 · Cited by 18

A New Criterion for Demarcating Life from Non-Life

van Hateren, J. H. (2013) · Origins of Life and Evolution of Biospheres · doi:10.1007/s11084-013-9352-3 · Cited by 19

Combining genetic and evolutionary engineering to establish C4metabolism in C3plants

Li, Y., Heckmann, D., Lercher, M. J., & Maurino, V. G. (2016) · Journal of Experimental Botany · doi:10.1093/jxb/erw333 · Cited by 18

Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF

Gao, A., Vasilyev, N., Luciano, D. J., Levenson-Palmer, R., Richards, J., Marsiglia, W. M., Traaseth, N. J., Belasco, J. G., & Serganov, A. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky327 · Cited by 18

Central metabolism is a key player in E. coli biofilm stimulation by sub-MIC antibiotics

Yaeger, L. N., French, S., Brown, E. D., Côté, J., & Burrows, L. L. (2023) · PLoS Genetics · doi:10.1371/journal.pgen.1011013 · Cited by 18

The Small RNA GcvB Promotes Mutagenic Break Repair by Opposing the Membrane Stress Response

Barreto, B., Rogers, E. J., Xia, J., Frisch, R. L., Richters, M. M., Fitzgerald, D. M., & Rosenberg, S. M. (2016) · Journal of Bacteriology · doi:10.1128/jb.00555-16 · Cited by 18

Heterogeneous survival upon disinfection underlies evolution of increased tolerance

Nordholt, N., Sobisch, L., Gödt, A., Lewerenz, D., & Schreiber, F. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.03276-22 · Cited by 19

Role of RelA-synthesized (p)ppGpp and ROS-induced mutagenesis in de novo acquisition of antibiotic resistance in E. coli

Qi, W., Jonker, M. J., de Leeuw, W. C., Brul, S., & ter Kuile, B. H. (2024) · iScience · doi:10.1016/j.isci.2024.109579 · Cited by 16

Protective role of the RpoE (σE) and Cpx envelope stress responses against gentamicin killing of nongrowingEscherichia coliincubated under aerobic, phosphate starvation conditions

Moreau, P. L. (2014) · FEMS Microbiology Letters · doi:10.1111/1574-6968.12534 · Cited by 15

An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes inEscherichia coli

Nehring, R. B., Gu, F., Lin, H., Gibson, J. L., Blythe, M., Wilson, R., Núñez, M. A. B., Hastings, P. J., Louis, E. J., Frisch, R. L., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1131 · Cited by 15

Proline mitigates antibiotic resistance evolution induced by ciprofloxacin at environmental concentrations

Wang, H., Wu, X., Xu, J., Lü, Z., Hu, B., Hu, B., & Lü, H. (2025) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2025.137561 · Cited by 15

Analysis of differentially upregulated proteins in ptsHIcrr− and rppH− mutants in Escherichia coli during an adaptive laboratory evolution experiment

Aguilar, C., Martínez-Batallar, G., Flores, N., Moreno, F., Encarnación‐Guevara, S., Escalante, A., & Bolívar, F. G. (2018) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-018-9397-3 · Cited by 14

Escherichia coli mutation rates and spectra with combinations of environmental limitations

Maharjan, R. P., & Ferenci, T. (2018) · Microbiology · doi:10.1099/mic.0.000727 · Cited by 11

Pseudouridines of tRNA Anticodon Stem-Loop Have Unexpected Role in Mutagenesis in Pseudomonas sp.

Tagel, M., Ilves, H., Leppik, M., Jürgenstein, K., Rèmme, J., & Kivisaar, M. (2020) · Microorganisms · doi:10.3390/microorganisms9010025 · Cited by 12

Mutational heterogeneity: A key ingredient of bet‐hedging and evolutionary divergence?

Ferenci, T., & Maharjan, R. P. (2014) · BioEssays · doi:10.1002/bies.201400153 · Cited by 14

Role of yqiC in the Pathogenicity of Salmonella and Innate Immune Responses of Human Intestinal Epithelium

Wang, K.-C., Huang, C.-H., Ding, S.-M., Chen, C.-K., Fang, H.-W., Huang, M.-T., & Fang, S. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01614 · Cited by 13

The road not taken: Could stress-specific mutations lead to different evolutionary paths?

Agashe, D. (2017) · PLoS Biology · doi:10.1371/journal.pbio.2002862 · Cited by 13

Engineered RecA Constructs Reveal the Minimal SOS Activation Complex

Cory, M. B., Li, A., Hurley, C. M., Hostetler, Z. M., Venkatesh, Y., Jones, C. M., Petersson, E. J., & Kohli, R. M. (2022) · Biochemistry · doi:10.1021/acs.biochem.2c00505 · Cited by 12

The response of Escherichia coli to the alkylating agents chloroacetaldehyde and styrene oxide

Muenter, M., Aiken, A., Akanji, J. O., Baig, S., Bellou, S., Carlson, A., Conway, C., Cowell, C. M., DeLateur, N. A., Hester, A., et al. (2019) · Mutation Research/Genetic Toxicology and Environmental Mutagenesis · doi:10.1016/j.mrgentox.2019.02.001 · Cited by 12

Stress-Induced Mutation Rates Show a Sigmoidal and Saturable Increase Due to the RpoS Sigma Factor in Escherichia coli

Maharjan, R. P., & Ferenci, T. (2014) · Genetics · doi:10.1534/genetics.114.170258 · Cited by 12

Evolutionary innovation using EDGE, a system for localized elevated mutagenesis

Yi, X., Kazlauskas, R. J., & Travisano, M. (2020) · PLoS ONE · doi:10.1371/journal.pone.0232330 · Cited by 11

Multi-omic based production strain improvement (MOBpsi) for bio-manufacturing of toxic chemicals

Webb, J. P., Paiva, A. C., Rossoni, L., Alstrom-Moore, A., Springthorpe, V., Vaud, S., Yeh, V., Minde, D., Langer, S., Walker, H. J., et al. (2022) · Metabolic Engineering · doi:10.1016/j.ymben.2022.03.004 · Cited by 13

Atypical Role for PhoU in Mutagenic Break Repair under Stress in Escherichia coli

Gibson, J. L., Lombardo, M., Aponyi, I., Cruz, D. V., Ray, M. P., & Rosenberg, S. M. (2015) · PLoS ONE · doi:10.1371/journal.pone.0123315 · Cited by 11

Isolating the Escherichia coli Transcriptomic Response to Superoxide Generation from Cadmium Chalcogenide Quantum Dots

Aunins, T. R., Eller, K. A., Courtney, C. M., Levy, M., Goodman, S. M., Nagpal, P., & Chatterjee, A. (2019) · ACS Biomaterials Science & Engineering · doi:10.1021/acsbiomaterials.9b01087 · Cited by 10

An essential protease, FtsH , influences daptomycin resistance acquisition inEnterococcus faecalis

Nair, Z. J., Gao, I. H., Firras, A., Chong, K. K. L., Hill, E. D., Choo, P. Y., Colomer‐Winter, C., Chen, Q., Manzano, C., Pethe, K., et al. (2024) · Molecular Microbiology · doi:10.1111/mmi.15253 · Cited by 9

Rapid identification of key antibiotic resistance genes in E. coli using high-resolution genome-scale CRISPRi screening

Choe, D., Lee, E., Kim, K., Hwang, S., Jeong, K. J., Palsson, B. Ø., Cho, B., & Cho, S. (2025) · iScience · doi:10.1016/j.isci.2025.112435 · Cited by 9

Serving Two Masters: Effect of Escherichia coli Dual Resistance on Antibiotic Susceptibility

Jeje, O., Ewunkem, A. J., Jeffers-Francis, L. K., & Graves, J. L. (2023) · Antibiotics · doi:10.3390/antibiotics12030603 · Cited by 9

Markovian language model of the DNA and its information content

Srivastava, S., & Baptista, M. S. (2016) · Royal Society Open Science · doi:10.1098/rsos.150527 · Cited by 9

Virus–Host Interaction Gets Curiouser and Curiouser. PART II: Functional Transcriptomics of the E. coli DksA-Deficient Cell upon Phage P1vir Infection

Cech, G. M., Szalewska-Pałasz, A., Potrykus, K., & Kłoska, A. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22116159 · Cited by 9

Integration Host Factor IHF facilitates homologous recombination and mutagenic processes in Pseudomonas putida

Mikkel, K., Tagel, M., Ukkivi, K., Ilves, H., & Kivisaar, M. (2019) · DNA repair · doi:10.1016/j.dnarep.2019.102745 · Cited by 8

Genotoxic Agents Produce Stressor-Specific Spectra of Spectinomycin Resistance Mutations Based on Mechanism of Action and Selection in Bacillus subtilis

Korry, B. J., Lee, S. Y. E., Chakrabarti, A. K., Choi, A. H., Ganser, C., Machan, J. T., & Belenky, P. A. (2021) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00891-21 · Cited by 8

Systems Biology

Konieczny, L., Roterman-Konieczna, I., & Spólnik, P. (2023) · Springer eBooks · doi:10.1007/978-3-031-31557-2 · Cited by 11

Development of a 3-hydroxypropionate resistantEscherichia colistrain

Liu, M., Han, X., Xian, M., Ding, Y., Liu, H., & Zhao, G. (2015) · Bioengineered · doi:10.1080/21655979.2015.1122143 · Cited by 8

Accumulation of deleterious mutations during bacterial range expansionsPreprint

Bosshard, L., Dupanloup, I., Tenaillon, O., Bruggmann, R., Ackermann, M., Peischl, S., & Excoffier, L. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/093658 · Cited by 9

The origin of genetic and metabolic systems: Evolutionary structuralinsights

Deng, S. (2023) · Heliyon · doi:10.1016/j.heliyon.2023.e14466 · Cited by 7

A Small-Molecule Inducible Synthetic Circuit for Control of the SOS Gene Network without DNA Damage

Kubiak, J. M., Culyba, M. J., Liu, M. Y., Mo, C. Y., Goulian, M., & Kohli, R. M. (2017) · ACS Synthetic Biology · doi:10.1021/acssynbio.7b00108 · Cited by 7

Intrinsic estimates of fitness affect the causal structure of evolutionary change

van Hateren, J. H. (2014) · Biology & Philosophy · doi:10.1007/s10539-014-9463-x · Cited by 7

Monitoring Intraspecies Competition in a Bacterial Cell Population by Cocultivation of Fluorescently Labelled Strains

Stannek, L., Egelkamp, R., Gunka, K., & Commichau, F. M. (2014) · Journal of Visualized Experiments · doi:10.3791/51196 · Cited by 7

Evolutionary dynamics and information hierarchies in biological systems

Walker, S. I., Callahan, B. J., Arya, G., Barry, J. D., Tanmoy Bhattacharya, A., Grigoryev, S. A., Pellegrini, M. A., Rippe, K., & Rosenberg, S. M. (2013) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.12140 · Cited by 7

DNA damage-signaling, homologous recombination and genetic mutation induced by 5-azacytidine and DNA-protein crosslinks in Escherichia coli

Klaric, J. A., Glass, D. J., Perr, E., Reuven, A. D., Towne, M. J., & Lovett, S. T. (2021) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2021.111742 · Cited by 8

The F plasmid conjutome: the repertoire of E. coli proteins translocated through an F-encoded type IV secretion system

Mamun, A. A. M. A., Kissoon, K., Li, Y. G., Hancock, E., & Christie, P. J. (2024) · mSphere · doi:10.1128/msphere.00354-24 · Cited by 6

Basic Nitrogenous Heterocyclic Rings at the 7-Position of Fluoroquinolones Foster Their Induction of Antibiotic Resistance in Escherichia coli

Yang, Q. X., Kaw, H. Y., Yu, J., Ma, X., Yang, K., Zhu, L., & Wang, W. (2025) · Environmental Science & Technology · doi:10.1021/acs.est.4c11346 · Cited by 6

Novel heterologous bacterial system reveals enhanced susceptibility to DNA damage mediated by yqgF, a nearly ubiquitous and often essential gene

McClung, D. J., Calixto, A., Mosera, M. N., Kumar, R., Neidle, E. L., & Elliott, K. T. (2016) · Microbiology · doi:10.1099/mic.0.000355 · Cited by 6

Evolutionary feedback from the environment shapes mechanisms that generate genome variation

Caporale, L. H. (2024) · The Journal of Physiology · doi:10.1113/jp284411 · Cited by 6

Toxin-Antitoxin Systems and Bacterial Persistence (Review)

Zamakhaev, M. V., Гончаренко, А. В., & Shumkov, M. S. (2019) · Applied Biochemistry and Microbiology · doi:10.1134/s0003683819060140 · Cited by 7

Genome-wide DNA polymorphisms of Citrus unshiu Marc. cv. Miyagawa-wase cultivated in different regions based on whole-genome re-sequencing

Eun, C., & Kim, I.-J. (2021) · Plant Biotechnology Reports · doi:10.1007/s11816-021-00696-z · Cited by 5

Double‐Strand‐Break Repair, Mutagenesis, and Stress

Rogers, E. J., Correa, R., Barreto, B., Núñez, M. A. B., Minnick, P. J., Cruz, D. V., Xia, J., Hastings, P. J., & Rosenberg, S. M. (2016) · Wiley eBooks · doi:10.1002/9781119004813.ch15 · Cited by 5

Azithromycin represses evolution of ceftazidime/avibactam resistance by translational repression of rpoS in Pseudomonas aeruginosa

Xu, C., Feng, J., Zhou, Y., Ren, H., Pan, X., Chen, S., Liu, X., Li, G., Li, J., Geng, B., et al. (2025) · Journal of Bacteriology · doi:10.1128/jb.00552-24 · Cited by 4

Thermally adapted Escherichia coli keeps transcriptomic response during temperature upshift exposure

Pérez-Morales, G., Martínez-Conde, K. V., Caspeta, L., Merino, E., Cevallos, M. A., Gosset, G., & Martı́nez, A. (2025) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-025-13495-1 · Cited by 4

Consequences of benzalkonium chloride tolerance for selection dynamics and de novo resistance evolution driven by antibiotics

Kanaris, O., Sobisch, L., Gödt, A., Schreiber, F., & Nordholt, N. (2026) · npj Antimicrobials and Resistance · doi:10.1038/s44259-025-00170-8 · Cited by 4

Unraveling the potential impact of climate change on the evolution and acceleration of antimicrobial resistance: mechanisms, consequences, and control strategies

Nahiduzzaman, F., Akhi, M. A. J., Zarin, T., Chouhan, C. S., Rahman, M. A., Rahman, A. K. M. A., Khatun, M. M., Islam, M. A., Danishuddin, & Haque, M. A. (2026) · Environmental Reviews · doi:10.1139/er-2025-0165 · Cited by 4

Harnessing halophyte adaptations for salinity resilient agriculture through genetic mechanisms and crop improvement

Sasipriya, S., Hiremata, V., Bandhavi, R. D., Kumar, M. R., & Reddy, S. (2026) · Discover Plants. · doi:10.1007/s44372-026-00685-y · Cited by 5

Suppressors of dGTP Starvation in Escherichia coli

Itsko, M., & Schaaper, R. M. (2017) · Journal of Bacteriology · doi:10.1128/jb.00142-17 · Cited by 4

ArsR Family Regulator MSMEG_6762 Mediates the Programmed Cell Death by Regulating the Expression of HNH Nuclease in Mycobacteria

Duan, X., Huang, X. S., Xu, J., Li, X., Niu, J., Du, X., Wang, X., Li, J., Kelly, M., Guo, J., et al. (2022) · Microorganisms · doi:10.3390/microorganisms10081535 · Cited by 4

Competition for nutritional resources masks the true frequency of bacterial mutants

Neves, H., Machado, G. T., Ramos, T. C. D. S., Yang, H. M., Yagil, E., & Spira, B. (2020) · BMC Biology · doi:10.1186/s12915-020-00913-1 · Cited by 4

Label-free affinity screening, design and synthesis of inhibitors targeting the Mycobacterium tuberculosis L-alanine dehydrogenase

Kim, H.-B., Bacik, J. P., Wu, R., Jha, R. K., Hebron, M. L., Triandafillou, C. G., McCown, J., Baek, N., Kim, J., Kim, Y. J., et al. (2022) · PLoS ONE · doi:10.1371/journal.pone.0277670 · Cited by 4

A novel papillation assay for the identification of genes affecting mutation rate in Pseudomonas putida and other pseudomonads

Tagel, M., Tavita, K., Hõrak, R., Kivisaar, M., & Ilves, H. (2016) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2016.06.002 · Cited by 3

The Long Hunt for pssR —Looking for a Phospholipid Synthesis Transcriptional Regulator, Finding the Ribosome

Bartoli, J., My, L., Belmudes, L., Couté, Y., Viala, J. P. M., & Bouveret, E. (2017) · Journal of Bacteriology · doi:10.1128/jb.00202-17 · Cited by 3

Rapid evolution of acetic acid-detoxifying Escherichia coli under phosphate starvation conditions requires activation of the cryptic PhnE permease and induction of translesion synthesis DNA polymerases

Moreau, P. L. (2017) · FEMS Microbiology Letters · doi:10.1093/femsle/fnx031 · Cited by 3

Control of glutamate homeostasis in the Gram-positive model organism Bacillus subtilis

Stannek, L. (2015) · eDiss (Georg-August-Universität Göttingen) · doi:10.53846/goediss-5321 · Cited by 3

Inducible genome-wide mutagenesis for improvement of pDNA production by E. coli

Li, Z., Sun, G., Al’Abri, I. S., Zhou, Y., & Crook, N. (2025) · Microbial Cell Factories · doi:10.1186/s12934-025-02821-x · Cited by 2

Escherichia coli K-12 Transcriptomics for Assessing the Mechanism of Action of High-Power Ultrasound

Spiteri, D., Griffin, S., Karatzas, K. A. G., Scerri, C. A., & Valdramidis, V. (2023) · Microorganisms · doi:10.3390/microorganisms11112768 · Cited by 2

Pathogen-encoded Rum DNA polymerase drives rapid bacterial drug resistance

Jaszczur, M. M., Pham, P., Ojha, D., Pham, C. Q., McDonald, J. P., Woodgate, R., & Goodman, M. F. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae899 · Cited by 2

Evaluation of the Escherichia coli HK82 and BS87 strains as tools for AlkB studies

Mielecki, D., Sikora, A., Wrzesiński, M., Nieminuszczy, J., Detman, A., Żuchniewicz, K., Gromadka, R., & Grzesiuk, E. (2015) · DNA repair · doi:10.1016/j.dnarep.2015.12.010 · Cited by 2

Information—its Role and Meaning in Organisms

Konieczny, L., Roterman‐Konieczna, I., & Spólnik, P. (2013) · Springer eBooks · doi:10.1007/978-3-319-01336-7_3 · Cited by 2

Mutagenesis Associated with DNA-Damage-Stress Response

Skopec, R. (2016) · Journal of Analytical Oncology · doi:10.6000/1927-7229.2016.05.01.4 · Cited by 2

Errors in mutagenesis and the benefit of cell-to-cell signalling in the evolution of stress-induced mutagenesis

Dellus-Gur, E., Ram, Y., & Hadany, L. (2017) · Royal Society Open Science · doi:10.1098/rsos.170529 · Cited by 2

Information: Its Role and Meaning in Organisms

Konieczny, L., Roterman‐Konieczna, I., & Spólnik, P. (2023) · Springer eBooks · doi:10.1007/978-3-031-31557-2_3 · Cited by 3

Mutagenesis Associated with Repair of DNA Double-Strand Breaks Under Stress

Shee, C., Hastings, P. J., & Rosenberg, S. M. (2013) · Springer eBooks · doi:10.1007/978-1-4614-6280-4_2 · Cited by 3

Evolutionary Change Is Naturally Biological and Purposeful

Shapiro, J. A. (2023) · The MIT Press eBooks · doi:10.7551/mitpress/14642.003.0018 · Cited by 2

Site-specific adaptation mechanisms of an oral pathobiont in the oral and gut mucosaePreprint

Guo, Y., Kitamoto, S., Caballero-Flores, G. G., Watanabe, D., Sugihara, K., Núñez, G., Alteri, C. J., Inohara, N., & Kamada, N. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.13.476151 · Cited by 2

An essential protease, FtsH, influences daptomycin resistance acquisition in Enterococcus faecalisPreprint

Nair, Z. J., Gao, I. H., Firras, A., Chong, K. K. L., Choo, P. Y., Pethe, K., & Kline, K. A. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.31.551240 · Cited by 2

Function-specific epistasis shapes evolutionary trajectories towards antibiotic resistance

Petrungaro, G., Fink, T., Fernando, B., Ansmann, G., & Bollenbach, T. (2026) · Nature Communications · doi:10.1038/s41467-026-76025-1 · Cited by 1

Nutrients drive the antibiotic-specific evolution of resistance in Pseudomonas aeruginosa

Kok, M., Zwep, L. B., Jansen, R. S., Hankemeier, T., & van Hasselt, J. G. C. (2025) · Research in Microbiology · doi:10.1016/j.resmic.2025.104323 · Cited by 1

Origins of cancer symposium 2016: exploring tumor complexity

Harlow, M. L., Lee, K., & Winn, M. E. (2016) · Genes & Cancer · doi:10.18632/genesandcancer.119 · Cited by 1

Transposon insertion sequencing reveals novel hypermutator genes in Acinetobacter baumannii

Short, F. L., Maharjan, R. P., Li, L., Afrin, N., Delgado, N. N., Boinett, C. J., Parkhill, J., Cain, A. K., & Paulsen, I. T. (2025) · mBio · doi:10.1128/mbio.00966-25 · Cited by 1

How a Large Gene Network Couples Mutagenic DNA Break Repair to Stress inEscherichia Coli

Rogers, E. J., Hastings, P. J., Núñez, M. A. B., & Rosenberg, S. M. (2016) · doi:10.1002/9781119004813.ch54 · Cited by 1

Usefulness of a Concept Called Autonomous SelectionPreprint

Solon, I. S. (2019) · Preprints.org · doi:10.20944/preprints201907.0285.v1

Trade-Offs, Trade-Ups, and High Mutational Parallelism Underlie Microbial Adaptation to Extreme Feast/FaminePreprint

Behringer, M. G., Ho, W.-C., Miller, S. F., Worthan, S. B., Cen, Z., Stikeleather, R., & Lynch, M. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.04.560893 · Cited by 1

Role of RelA-synthesized (p)ppGpp in de novo acquisition of antibiotic resistance in E. coliPreprint

ter Kuile, B. H., Qi, W., Jonker, M. J., de Leeuw, W. C., & Brul, S. (2023) · Research Square · doi:10.21203/rs.3.rs-3404172/v1 · Cited by 1

Discovery of a DNA damage response in Acinetobacter baumannii and analysis of translesion synthesis DNA polymerases of both A. baumannii and Escherichia coli

Norton, M. (2013) · doi:10.17760/d20003375

Epigenetic Psychiatry: Potential of the Pre-Emptive Adaptation

Skopec, R. (2016) · Translational Biomedicine · doi:10.21767/2172-0479.100082

Epigenetic psychiatry: potential of the pre-emptive adaptation

Skopec, R. (2017) · Global Vaccines and Immunology · doi:10.15761/gvi.1000124

Cellular adaptation through fitness-directed transcriptional tuningPreprint

Freddolino, P. L., Yang, J., & Tavazoie, S. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/137810

Roles of Nucleoid-Associated Proteins in Stress-Induced Mutagenic Break Repair in StarvingEscherichia coli

Moore, J. M., Magnan, D. R., Mojica, A. K., Núñez, M. A. B., Bates, D. B., Rosenberg, S. M., & Hastings, P. J. (2015) · Genetics · doi:10.1534/genetics.115.178970 · Cited by 22

Impact of a stress-inducible switch to mutagenic repair of DNA breaks on mutation in Escherichia coli

Shee, C., Gibson, J. L., Darrow, M. C., González, C., & Rosenberg, S. M. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1104681108 · Cited by 120

Sewing Up DNA Repair

Riddihough, G. (2012) · Science Signaling · doi:10.1126/scisignal.2003855

Separate DNA Pol II- and Pol IV-Dependent Pathways of Stress-Induced Mutation during Double-Strand-Break Repair in Escherichia coli Are Controlled by RpoS

(2010)

Mutagenesis Associated with Repair of DNA Double-Strand Breaks Under Stress

Shee, C., Hastings, P. J., & Rosenberg, S. M. (2013) · Springer eBooks · doi:10.1007/978-1-4614-6280-4_2 · Cited by 3