The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

By David A. Rasko, M. J. Rosovitz, G. Myers, E. Mongodin, W. F. Fricke, Pawel Gajer, J. Crabtree, M. Sebaihia, N. Thomson, R. Chaudhuri and 3 more. Journal of Bacteriology, 2008

877 citations recorded by the source corpus.

Subfields: Endocrinology, Food Science

View Paper: https://www.semanticscholar.org/paper/fbd9ea9a6c019485f14f9fbd004fad656ce7cebd

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Endocrinology

1. Frederick M. Cohan
2. B. B. Finlay
3. Bob Mau
4. Nicole T. Perna
5. Aaron E. Darling
6. E. Denamur

In Food Science

1. Aaron E. Darling
2. Bob Mau
3. Nicole T. Perna
4. B. B. Finlay
5. E. Denamur

Citations in the corpus

• BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons (2011, neutral): “coli HS CP000802 [28]”
• The population genetics of commensal Escherichia coli (2010, background): “Hence, each strain or group of strains contains some genes sampled from a pool that currently contains up to 8,000 genes (excluding insertion sequences, phage and phage-like elements, as well as core genes) but that keeps increasing with the number of strains studie”
• PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies (2012, neutral): “9-941 0 0 0 0 0 0 0 0 0 Escherichia coli K12 Escherichia coli APEC O1 10 (38) 10 0 0 10 0 0 10 0 0 Escherichia coli K12 Escherichia coli HS 3 (39) 2 0 1 3 1 0 3 1 0 Escherichia coli K12 Escherichia coli O157:H7 EDL933 18 (36) 17 0 1 15 0 3 18 0 0”
• VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences (2020, background): “Finally, hokC may indicate mechanisms of virally encoded virulence [84].”
• Molecular mechanisms of Escherichia coli pathogenicity (2012, background): “coli isolates are thought to have a core genome of approximately 2,200 genes and a pan-genome of approximately 13,000 gene”
• Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. (2011, background): “The problem is that the taxa recognized as species by bacterial systematics are extremely broadly defined, with enormous levels of divergence in physiology, genome content, and most importantly, ecology (Welch et al., 2002; Whittam & Bumbaugh, 2002; Tettelin et al., 2005; Lefébure & Stanhope, 2007; ”
• progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement (2010, background): “included in the protein-based study [56], so organism sampling”
• PGAP: pan-genomes analysis pipeline (2011, neutral): “PGAP’s performance has been evaluated on 11 Streptococcus pyogenes strains.”
• The healthy human microbiome (2016, neutral): “coli species pangenome level [126].”