The DOI matches its Crossref record; 195 of the 196 references it cites were found in a registry or an index.
Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection
Open accessAbstract
We have systematically made a set of precisely defined, single-gene deletions of all nonessential genes in Escherichia coli K-12. Open-reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a one-step method for inactivation of chromosomal genes and primers designed to create in-frame deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in high-throughput studies, two independent mutants were saved for every deleted gene. These mutants-the 'Keio collection'-provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome-wide testing of mutational effects in a common strain background, E. coli K-12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase (http://ecoli.aist-nara.ac.jp/).
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“The CyDisCo has been exploited as an efficient route for the production of scFv and Fab fragments derived from known antibodies of different classes and from different organisms (human, mouse and humanized) in the cytoplasm of the KEIO (collection parental K12) E. coli strain in shake flasks [127].”
From Evolution of Escherichia coli Expression System in Producing Antibody Recombinant Fragments (2020) · cites this paper as [127]
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“Single molecule sensitivity was confirmed by abrupt photobleaching of membrane-bound YFPs expressed at low level (Fig. S14) (8, 18, 23).”
From Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells (2010) · cites this paper as [23]
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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
Self-citationVannote, 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
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
Chow, V. T. (2010) · Cited by 3,340
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
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Research works printed but not linked: 4
- Fraenkel DG (1996) Glycolysis. In Escherichia coli and Salmonella Cellular and Molecular Biology, Neidhardt FC, Curtiss III R, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE (eds), 2 edn, pp 189–198. Washington, DC: ASM Press
- Holden C (2002) Cell biology: alliance launched to modelE. coli. Science297: 1459–1460
- Neidhardt FC (1996) The enteric bacterial cell and the age of bacteria. In Escherichia coli and Salmonella Cellular and Molecular Biology, Neidhardt FC, Curtiss III R, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M and Umbarger HE (eds), 2 edn, pp 1–4. Washington, DC: ASM Press
- Wanner BL (1994) Gene expression in bacteria using TnphoA and TnphoA′ elements to make and switch phoA gene, lacZ (op), and lacZ (pr) fusions. In Methods in Molecular Genetics, Adolph KW (ed), Vol. 3, pp 291–310. Orlando: Academic Press
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Haeusser, D. P., Hoashi, M., Weaver, A., Brown, N., Pan, J., Sawitzke, J., Thomason, L., Court, D., & Margolin, W. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004217 · Cited by 88
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Roberts, C. A., Al-Tameemi, H. M., Mashruwala, A. A., Rosario-Cruz, Z., Chauhan, U., Sause, W. E., Torres, V. J., Belden, W. J., & Boyd, J. M. (2017) · Infection and Immunity · doi:10.1128/iai.00100-17 · Cited by 84
Zhang, J., Li, X., Olmedo, M., Holdorf, A. D., Shang, Y., Artal-Sanz, M., Yilmaz, L. S., & Walhout, A. J. M. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.07.010 · Cited by 77
Pony, P., Rapisarda, C., Terradot, L., Marza, E., & Fronzes, R. (2020) · Nature Communications · doi:10.1038/s41467-020-15214-y · Cited by 82
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Metadata
- Authors
- Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., & Mori, H.
- Affiliations
- Institute for Advanced Biosciences, Keio University (JP)
- Japan Science and Technology Agency (JP)
- Purdue University West Lafayette (US)
- Corresponding author
- Wanner, Barry L
- Mori, Hirotada
- Venue
- Molecular Systems Biology
- Published
- 2006-02-21
- Volume
- 2
- Issue
- 1
- Pages
- 2006.0008-2006.0008
- ISSN
- 1744-4292 (ISSN-L)
- PMC
- PMC1681482
- OpenAlex
- W2111967267
- Cited by
- 7,858
- References
- 196
- Citations by year
- 2026: 331 · 2025: 452 · 2024: 489 · 2023: 429 · 2022: 458 · 2021: 490 · 2020: 502 · 2019: 451 · 2018: 454 · 2017: 464 · 2016: 394 · 2015: 435 · 2014: 451 · 2013: 415 · 2012: 376
- FWCI
- 117.12
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Molecular Systems Biology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Keio University
- National Institutes of Health
- National Institute of General Medical Sciences (GM 62662, R01GM062662)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Keywords
- Keio collection, Escherichia coli K-12, single gene deletion, non-essential genes, kanamycin resistance cassette, gene inactivation, gene function analysis, gene regulatory networks, essential genes
- MeSH terms
- Escherichia coli, Mutation, Gene Deletion, Internet, Organisms, Genetically Modified
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