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Method: Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts
- Irmgard U. Haussmann,
- Thomas C. Dix,
- David W.J. McQuarrie,
- Veronica Dezi,
- Abdullah I. Hans,
- Roland Arnold,
- and Matthias Soller
Genome Res. December 2024 34: 2279-2292; Published in Advance December 3, 2024, doi:10.1101/gr.279479.124
...-target cleavage needs to be tested. Of note, the effect of structural constraints is stronger in cold-blooded animals likely reflecting that the optimal temperature for Escherichia coli is 37°C. In this context, it would be worth exploring how much longer the sgRNA can be to still support Cas9 DNA scission...
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Method: Memory-bound k-mer selection for large and evolutionarily diverse reference libraries
- Ali Osman Berk Şapcı and
- Siavash Mirarab
Genome Res. September 2024 34: 1455-1467; Published in Advance August 29, 2024, doi:10.1101/gr.279339.124
...sampling will have little representation, whereas highly sampled groups (e.g., Escherichia coli) will dominate. We partially address this challenge by imposing a size constraint on hash table size for each internal node during traversal to avoid having bloated nodes that starve sister taxa. Although...
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Research: Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage
- Kavitha Uthanumallian,
- Andrea Del Cortona,
- Susana M. Coelho,
- Olivier De Clerck,
- Sebastian Duchene,
- and Heroen Verbruggen
Genome Res. August 2024 34: 1130-1139; Published in Advance August 29, 2024, doi:10.1101/gr.279002.124
....2.1067 ↵Akashi H. 1997. Codon bias evolution in Drosophila: population genetics of mutation-selection drift. Gene 205: 269–278. doi:10.1016/S0378-1119(97)00400-9 ↵Balbi KJ, Rocha EPC, Feil EJ. 2009. The temporal dynamics of slightly deleterious mutations in Escherichia coli and Shigella spp. Mol Biol Evol 26...
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Research: Genome-wide promoter assembly in E. coli measured at single-base resolution
- Jordan John,
- Javaid Jabbar,
- Nitika Badjatia,
- Matthew J. Rossi,
- William K.M. Lai,
- and B. Franklin Pugh
Genome Res. May 2022 32: 878-892; Published in Advance April 28, 2022, doi:10.1101/gr.276544.121
...of the epigenomic organization of the Escherichia coli transcription machinery and nucleoid structural proteins at the time when cells are growing exponentially and upon rapid reprogramming (acute heat shock). We examined the site specificity of three sigma factors (RpoD/σ70, RpoH/σ32, and RpoN/σ54), RNA polymerase...
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Research: Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains
- Stephen J. Salipante,
- David J. Roach,
- Jacob O. Kitzman,
- Matthew W. Snyder,
- Bethany Stackhouse,
- Susan M. Butler-Wu,
- Choli Lee,
- Brad T. Cookson,
- and Jay Shendure
Genome Res. January 2015 25: 119-128; Published in Advance November 4, 2014, doi:10.1101/gr.180190.114
...blood- or urine-derived isolates of extraintestinal pathogenic (ExPEC) Escherichia coli, a common agent of sepsis and community-acquired urinary tract infections, obtained during the course of routine clinical care at a single institution. We find that ExPEC E. coli are highly genomically heterogeneous...
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Research: Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains
- Yoko Arimizu,
- Yumi Kirino,
- Mitsuhiko P. Sato,
- Koichi Uno,
- Toshio Sato,
- Yasuhiro Gotoh,
- Frédéric Auvray,
- Hubert Brugere,
- Eric Oswald,
- Jacques G. Mainil,
- Kelly S. Anklam,
- Dörte Döpfer,
- Shuji Yoshino,
- Tadasuke Ooka,
- Yasuhiro Tanizawa,
- Yasukazu Nakamura,
- Atsushi Iguchi,
- Tomoko Morita-Ishihara,
- Makoto Ohnishi,
- Koichi Akashi,
- Tetsuya Hayashi,
- and Yoshitoshi Ogura
Genome Res. September 2019 29: 1495-1505; Published in Advance August 22, 2019, doi:10.1101/gr.249268.119
...Large-scale analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains Yoko Arimizu1,2, Yumi Kirino3, Mitsuhiko P. Sato1, Koichi Uno4, Toshio Sato4, Yasuhiro Gotoh1, Frédéric...
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Research: Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131
- Teemu Kallonen,
- Hayley J. Brodrick,
- Simon R. Harris,
- Jukka Corander,
- Nicholas M. Brown,
- Veronique Martin,
- Sharon J. Peacock,
- and Julian Parkhill
Genome Res. August 2017 27: 1437-1449; Published in Advance July 18, 2017, doi:10.1101/gr.216606.116
...-dependent selection occurring outside of the hospital, most probably in the commensal niche, and that drug resistance is not a primary determinant of success in this niche. [Supplemental material is available for this article.] Escherichia coli is a common commensal of the gastrointestinal tract of humans and other...
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Resource: The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity
- Zhemin Zhou,
- Nabil-Fareed Alikhan,
- Khaled Mohamed,
- Yulei Fan,
- the Agama Study Group,
- and Mark Achtman
Genome Res. January 2020 30: 138-152; Published in Advance December 6, 2019, doi:10.1101/gr.251678.119
...://github.com/zheminzhou/EToKi) of useful modules (Supplemental Fig. S2B–E) that facilitate genomic assemblies (EToKi modules prepare and assemble), MLST (MLSType), calling nonrepetitive SNPs against a reference (EToKi modules align and phylo), or predicting serotypes of Escherichia coli from assemblies (EBEis).EnteroBase performs daily...
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LETTER: Selection-driven transcriptome polymorphism in Escherichia coli/Shigella species
- Tony Le Gall,
- Pierre Darlu,
- Patricia Escobar-Páramo,
- Bertrand Picard,
- and Erick Denamur
Genome Res. February 2005 15: 260-268; doi:10.1101/gr.2405905
...Selection-driven transcriptome polymorphism in Escherichia coli/Shigella species Tony Le Gall 1 , 2 , Pierre Darlu 3 , Patricia Escobar-Páramo 1 , Bertrand Picard 2 , and Erick Denamur 1 , 4 1 Institut National de la...
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LETTER: Transcription of foreign DNA in Escherichia coli
- René L. Warren,
- John D. Freeman,
- Roger C. Levesque,
- Duane E. Smailus,
- Stephane Flibotte,
- and Robert A. Holt
Genome Res. November 2008 18: 1798-1805; Published in Advance August 13, 2008, doi:10.1101/gr.080358.108
...Transcription of foreign DNA in Escherichia coli René L. Warren 1 , John D. Freeman 1 , Roger C. Levesque 2 , Duane E. Smailus 1 , Stephane Flibotte 1 , and Robert A. Holt 1 , 3 1 BC Cancer Agency, Canada...

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