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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
....g., NCBI Sequence Read Archive [SRA]) of short-read sequences of bacterial pathogens that have been deposited since the recent drop in price of high-throughput sequencing (https://www..gov/sequencingcostsdata/). In October 2019, SRA contained genomic sequence reads from 430,417 Salmonella, Escherichia...
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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
...–54. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215: 403–410. Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF. 2009. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461: 1243...
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Method: Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing
- Ole Skovgaard,
- Mads Bak,
- Anders Løbner-Olesen,
- and Niels Tommerup
Genome Res. August 2011 21: 1388-1393; Published in Advance May 9, 2011, doi:10.1101/gr.117416.110
..., Glasner JD, Rode CK, Mayhew GF, et al. 1997. The complete sequence of Escherichia coli K-12. Science 277: 1453–1462. Bremer H, ChurchwardG. 1977. An examination of the Cooper-Helmstetter theory of DNA replication in bacteria and its underlying assumptions. J Theor Biol 69: 645–654. Clark DJ, Maaløe O...
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LETTER: Principles of transcriptional regulation and evolution of the metabolic system in E. coli
- Aswin S.N. Seshasayee,
- Gillian M. Fraser,
- M. Madan Babu,
- and Nicholas M. Luscombe
Genome Res. January 2009 19: 79-91; Published in Advance October 3, 2008, doi:10.1101/gr.079715.108
...to investigate the evolutionary trends and transcriptional control of metabolism in Escherichia coli K12. Globally, the regulatory system is organized in a clear hierarchy of general and specific transcription factors (TFs) that control differing ranges of metabolic functions. Further, catabolic, anabolic...
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METHODS: Shotgun Optical Maps of the Whole Escherichia coli O157:H7 Genome
- Alex Lim,
- Eileen T. Dimalanta,
- Konstantinos D. Potamousis,
- Galex Yen,
- Jennifer Apodoca,
- Chunhong Tao,
- Jieyi Lin,
- Rong Qi,
- John Skiadas,
- Arvind Ramanathan,
- Nicole T. Perna,
- Guy Plunkett III,
- Valerie Burland,
- Bob Mau,
- Jeremiah Hackett,
- Frederick R. Blattner,
- Thomas S. Anantharaman,
- Bhubaneswar Mishra,
- and David C. Schwartz
Genome Res. September 1, 2001 11: 1584-1593; Published in Advance August 16, 2001, doi:10.1101/gr.172101
.... ( 1997 ) The complete sequence of Escherichia coli K-12. Science 277 : 1453 – 1462 . ↵ Cai W. , Jing J. , Irvin B. , Ohler L. , Rose E. , Shizuya H. , Kim U. , Simon M. , Anantharaman T. , Mishra B. , et al. ( 1998 ) High-resolution restriction maps of bacterial artificial chromosomes constructed...
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Research: Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome
- Vera B. Kaiser,
- Lana Talmane,
- Yatendra Kumar,
- Fiona Semple,
- Marie MacLennan,
- Deciphering Developmental Disorders Study,
- David R. FitzPatrick,
- Martin S. Taylor,
- and Colin A. Semple
Genome Res. November 2021 31: 1994-2007; Published in Advance August 20, 2021, doi:10.1101/gr.275407.121
...in spermatogonia, potentially altering neurodevelopmental regulatory architecture. Local chromatin structure in spermatogonia is thus pervasive in shaping both evolution and disease.Mutation is the ultimate source of genetic variation, and inherited variation must invariably arise in the germline. It is well...
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Research: Global fitness landscapes of the Shine-Dalgarno sequence
- Syue-Ting Kuo,
- Ruey-Lin Jahn,
- Yuan-Ju Cheng,
- Yi-Lan Chen,
- Yun-Ju Lee,
- Florian Hollfelder,
- Jin-Der Wen,
- and Hsin-Hung David Chou
Genome Res. May 2020 30: 711-723; Published in Advance May 18, 2020, doi:10.1101/gr.260182.119
...great sequence diversity, questioning how SD functions. Here, we determined the molecular fitness (i.e., translation efficiency) of 49 synthetic 9-nt SD genotypes in three distinct mRNA contexts in Escherichia coli. We uncovered generic principles governing the SD fitness landscapes: (1) Guanine...
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Method: Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
- Arkarachai Fungtammasan,
- Guruprasad Ananda,
- Suzanne E. Hile,
- Marcia Shu-Wei Su,
- Chen Sun,
- Robert Harris,
- Paul Medvedev,
- Kristin Eckert,
- and Kateryna D. Makova
Genome Res. May 2015 25: 736-749; Published in Advance March 30, 2015, doi:10.1101/gr.185892.114
...because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied...
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Research: Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation
- Wesley A. Brashear,
- Terje Raudsepp,
- and William J. Murphy
Genome Res. December 2018 28: 1841-1851; Published in Advance October 31, 2018, doi:10.1101/gr.237586.118
...greater than 30 were kept and represented those mate pairs most likely to be derived from the Y Chromosome.Sequenced Illumina libraries were trimmed using TrimGalore!, a wrapper tool around Cutadapt (Martin 2011), and were assessed for quality using FastQC. Trimmed libraries were mapped to the Escherichia...
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Methods: Reconstructing ancestral gene content by coevolution
- Tamir Tuller,
- Hadas Birin,
- Uri Gophna,
- Martin Kupiec,
- and Eytan Ruppin
Genome Res. January 2010 20: 122-132; Published in Advance November 30, 2009, doi:10.1101/gr.096115.109
...was obtained from recently published manuscripts (Gavin et al. 2006; Krogan et al. 2006; Reguly et al. 2006) and from public databases (Xenarios et al. 2002; Christie et al. 2004). High-throughput mass spectrometry data (Gavin et al. 2006; Krogan et al. 2006) was translated into binary protein...

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