-
1
-
-
25444524604
-
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pangenome"
-
Tettelin, H. et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pangenome". Proc Natl Acad Sci USA 102, 13950-5 (2005).
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 13950-13955
-
-
Tettelin, H.1
-
2
-
-
53849104729
-
The pangenome structure of Escherichia coli: Comparative genomic analysis of E. Coli commensal and pathogenic isolates
-
Rasko, D. A. et al. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol 190, 6881-93 (2008).
-
(2008)
J Bacteriol
, vol.190
, pp. 6881-6893
-
-
Rasko, D.A.1
-
3
-
-
84880437408
-
Lactobacillus paracasei comparative genomics: Towards species pan-genome definition and exploitation of diversity
-
Smokvina, T. et al. Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity. Plos One 8, e68731 (2013).
-
(2013)
Plos One
, vol.8
-
-
Smokvina, T.1
-
4
-
-
36549029848
-
Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains
-
Hogg, J. S. et al. Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains. Genome Biol 8, R103 (2007).
-
(2007)
Genome Biol
, vol.8
, pp. R103
-
-
Hogg, J.S.1
-
5
-
-
69549105878
-
Microbial comparative pan-genomics using binomial mixture models
-
Snipen, L., Almoy, T. & Ussery, D. W. Microbial comparative pan-genomics using binomial mixture models. BMC Genomics 10, 385 (2009).
-
(2009)
BMC Genomics
, vol.10
, pp. 385
-
-
Snipen, L.1
Almoy, T.2
Ussery, D.W.3
-
6
-
-
36549020646
-
Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: Insights into the pneumococcal supragenome
-
Hiller, N. L. et al. Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome. J Bacteriol 189, 8186-95 (2007).
-
(2007)
J Bacteriol
, vol.189
, pp. 8186-8195
-
-
Hiller, N.L.1
-
7
-
-
77949412186
-
Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium
-
Eppinger, M. et al. Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium. J Bacteriol 192, 1685-99 (2010).
-
(2010)
J Bacteriol
, vol.192
, pp. 1685-1699
-
-
Eppinger, M.1
-
8
-
-
34548846699
-
Evolution of the core and pan-genome of Streptococcus: Positive selection, recombination, and genome composition
-
Lefebure, T. & Stanhope, M. J. Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol 8, R71 (2007).
-
(2007)
Genome Biol
, vol.8
, pp. R71
-
-
Lefebure, T.1
Stanhope, M.J.2
-
9
-
-
77958580152
-
Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species
-
Donati, C. et al. Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol 11, R107 (2010).
-
(2010)
Genome Biol
, vol.11
, pp. R107
-
-
Donati, C.1
-
10
-
-
80052889924
-
The Salmonella enterica pan-genome
-
Jacobsen, A., Hendriksen, R. S., Aaresturp, F. M., Ussery, D. W. & Friis, C. The Salmonella enterica pan-genome. Microb Ecol 62, 487-504 (2011).
-
(2011)
Microb Ecol
, vol.62
, pp. 487-504
-
-
Jacobsen, A.1
Hendriksen, R.S.2
Aaresturp, F.M.3
Ussery, D.W.4
Friis, C.5
-
11
-
-
84999254709
-
Patterns and implications of gene gain and loss in the evolution of Prochlorococcus
-
Kettler, G. C. et al. Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. Plos Genet 3, e231 (2007).
-
(2007)
Plos Genet
, vol.3
, pp. e231
-
-
Kettler, G.C.1
-
12
-
-
61349194462
-
Estimating the size of the bacterial pan-genome
-
Lapierre, P. & Gogarten, J. P. Estimating the size of the bacterial pan-genome. Trends Genet 25, 107-10 (2009).
-
(2009)
Trends Genet
, vol.25
, pp. 107-110
-
-
Lapierre, P.1
Gogarten, J.P.2
-
13
-
-
84890551700
-
Complete genome sequence of Cannes 8 virus, a new member of the proposed family "marseilleviridae"
-
Aherfi, S. et al. Complete genome sequence of Cannes 8 virus, a new member of the proposed family "Marseilleviridae". Virus Genes 47, 550-5 (2013).
-
(2013)
Virus Genes
, vol.47
, pp. 550-555
-
-
Aherfi, S.1
-
14
-
-
80053384429
-
Whole-genome sequencing of multiple Arabidopsis thaliana populations
-
Cao, J. et al. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 43, 956-63 (2011).
-
(2011)
Nat Genet
, vol.43
, pp. 956-963
-
-
Cao, J.1
-
15
-
-
84880511242
-
Pan genome of the phytoplankton Emiliania underpins its global distribution
-
Read, B. A. et al. Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature 499, 209-13 (2013).
-
(2013)
Nature
, vol.499
, pp. 209-213
-
-
Read, B.A.1
-
16
-
-
84923019049
-
De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits
-
Li, Y. H. et al. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat Biotechnol 32, 1045-52 (2014).
-
(2014)
Nat Biotechnol
, vol.32
, pp. 1045-1052
-
-
Li, Y.H.1
-
17
-
-
84860591356
-
Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments
-
Dunn, B., Richter, C., Kvitek, D. J., Pugh, T. & Sherlock, G. Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments. Genome Res 22, 908-24 (2012).
-
(2012)
Genome Res
, vol.22
, pp. 908-924
-
-
Dunn, B.1
Richter, C.2
Kvitek, D.J.3
Pugh, T.4
Sherlock, G.5
-
18
-
-
27444438599
-
The microbial pan-genome
-
Medini, D., Donati, C., Tettelin, H., Masignani, V. & Rappuoli, R. The microbial pan-genome. Curr Opin Genet Dev. 15, 589-94 (2005).
-
(2005)
Curr Opin Genet Dev.
, vol.15
, pp. 589-594
-
-
Medini, D.1
Donati, C.2
Tettelin, H.3
Masignani, V.4
Rappuoli, R.5
-
19
-
-
84916892245
-
Ten years of pan-genome analyses
-
Vernikos, G., Medini, D., Riley, D. R. & Tettelin, H. Ten years of pan-genome analyses. Curr Opin Microbiol. 23, 148-54 (2015).
-
(2015)
Curr Opin Microbiol.
, vol.23
, pp. 148-154
-
-
Vernikos, G.1
Medini, D.2
Riley, D.R.3
Tettelin, H.4
-
20
-
-
79251574138
-
The bacterial pan-genome: A new paradigm in microbiology
-
Mira, A., Martin-Cuadrado, A. B., D'Auria, G. & Rodriguez-Valera, F. The bacterial pan-genome:a new paradigm in microbiology. Int Microbiol. 13, 45-57 (2010).
-
(2010)
Int Microbiol.
, vol.13
, pp. 45-57
-
-
Mira, A.1
Martin-Cuadrado, A.B.2
D'Auria, G.3
Rodriguez-Valera, F.4
-
21
-
-
84925669449
-
A brief review of software tools for pangenomics
-
Xiao, J., Zhang, Z., Wu, J. & Yu, J. A brief review of software tools for pangenomics. Genomics Proteomics Bioinformatics. 13, 73-6 (2015).
-
(2015)
Genomics Proteomics Bioinformatics.
, vol.13
, pp. 73-76
-
-
Xiao, J.1
Zhang, Z.2
Wu, J.3
Yu, J.4
-
22
-
-
33646569665
-
Post-genomic vaccine development
-
Serruto, D. & Rappuoli, R. Post-genomic vaccine development. FEBS Lett. 580, 2985-92 (2006).
-
(2006)
FEBS Lett.
, vol.580
, pp. 2985-2992
-
-
Serruto, D.1
Rappuoli, R.2
-
23
-
-
21644481459
-
Identification of a universal Group B streptococcus vaccine by multiple genome screen
-
Maione, D. et al. Identification of a universal Group B streptococcus vaccine by multiple genome screen. Science. 309, 148-50 (2005).
-
(2005)
Science.
, vol.309
, pp. 148-150
-
-
Maione, D.1
-
24
-
-
84871199596
-
PanOCT: Automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species
-
Fouts, D. E., Brinkac, L., Beck, E., Inman, J. & Sutton, G. PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species. Nucleic Acids Res. 40, e172 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. e172
-
-
Fouts, D.E.1
Brinkac, L.2
Beck, E.3
Inman, J.4
Sutton, G.5
-
25
-
-
77956552653
-
Pan-genome sequence analysis using Panseq: An online tool for the rapid analysis of core and accessory genomic regions
-
Laing, C. et al. Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions. BMC Bioinformatics. 11, 461 (2010).
-
(2010)
BMC Bioinformatics.
, vol.11
, pp. 461
-
-
Laing, C.1
-
26
-
-
84897951003
-
PanGP: A tool for quickly analyzing bacterial pan-genome profile
-
Zhao, Y. et al. PanGP: a tool for quickly analyzing bacterial pan-genome profile. Bioinformatics. 30, 1297-9 (2014).
-
(2014)
Bioinformatics.
, vol.30
, pp. 1297-1299
-
-
Zhao, Y.1
-
27
-
-
84947793096
-
Roary: Rapid large-scale prokaryote pan genome analysis
-
Page, A. J. et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 31, 3691-3 (2015).
-
(2015)
Bioinformatics.
, vol.31
, pp. 3691-3693
-
-
Page, A.J.1
-
28
-
-
84856571322
-
PGAP: Pan-genomes analysis pipeline
-
Zhao, Y. et al. PGAP: pan-genomes analysis pipeline. Bioinformatics. 28, 416-8 (2012).
-
(2012)
Bioinformatics.
, vol.28
, pp. 416-418
-
-
Zhao, Y.1
-
29
-
-
84891760995
-
ITEP: An integrated toolkit for exploration of microbial pan-genomes
-
Benedict, M. N., Henriksen, J. R., Metcalf, W. W., Whitaker, R. J. & Price, N. D. ITEP: an integrated toolkit for exploration of microbial pan-genomes. BMC Genomics. 15, 8 (2014).
-
(2014)
BMC Genomics.
, vol.15
, pp. 8
-
-
Benedict, M.N.1
Henriksen, J.R.2
Metcalf, W.W.3
Whitaker, R.J.4
Price, N.D.5
-
30
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-7 (2004).
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
31
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 26, 2460-1 (2010).
-
(2010)
Bioinformatics.
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
32
-
-
33745634395
-
Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 22, 1658-9 (2006).
-
(2006)
Bioinformatics.
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
33
-
-
0141519279
-
OrthoMCL: Identification of ortholog groups for eukaryotic genomes
-
Li, L., Stoeckert, C. J. Jr. &Roos, D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178-89 (2003).
-
(2003)
Genome Res.
, vol.13
, pp. 2178-2189
-
-
Li, L.1
Stoeckert, C.J.2
Roos, D.S.3
-
34
-
-
13144252236
-
Multi locus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms
-
Maiden, M. C. et al. Multi locus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95, 3140-5 (1998).
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 3140-3145
-
-
Maiden, M.C.1
-
35
-
-
84930606850
-
Inferring horizontal gene transfer
-
Ravenhall, M., Skunca, N., Lassalle, F. & Dessimoz, C. Inferring horizontal gene transfer. Plos Comput Biol. 11, e1004095 (2015).
-
(2015)
Plos Comput Biol.
, vol.11
-
-
Ravenhall, M.1
Skunca, N.2
Lassalle, F.3
Dessimoz, C.4
-
36
-
-
67149096084
-
In silico prediction of horizontal gene transfer events in Lactobacillus bulgaricus and Streptococcus thermophilus reveals protocooperation in yogurt manufacturing
-
Liu, M., Siezen, R. J. & Nauta, A. In silico prediction of horizontal gene transfer events in Lactobacillus bulgaricus and Streptococcus thermophilus reveals protocooperation in yogurt manufacturing. Appl Environ Microbiol. 75, 4120-9 (2009).
-
(2009)
Appl Environ Microbiol.
, vol.75
, pp. 4120-4129
-
-
Liu, M.1
Siezen, R.J.2
Nauta, A.3
-
37
-
-
84928746540
-
Divergences in gene repertoire among the reference Prevotella genomes derived from distinct body sites of human
-
Gupta, V. K., Chaudhari, N. M., Iskepalli, S. & Dutta, C. Divergences in gene repertoire among the reference Prevotella genomes derived from distinct body sites of human. BMC Genomics. 16, 153 (2015).
-
(2015)
BMC Genomics.
, vol.16
, pp. 153
-
-
Gupta, V.K.1
Chaudhari, N.M.2
Iskepalli, S.3
Dutta, C.4
-
38
-
-
83855165692
-
Extreme genome reduction in symbiotic bacteria
-
McCutcheon, J. P. & Moran, N. A. Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol. 10, 13-26 (2011).
-
(2011)
Nat Rev Microbiol.
, vol.10
, pp. 13-26
-
-
McCutcheon, J.P.1
Moran, N.A.2
-
39
-
-
9744258014
-
Genome reduction in prokaryotic obligatory intracellular parasites of humans: A comparative analysis
-
Sakharkar, K. R., Dhar, P. K. & Chow, V. T. Genome reduction in prokaryotic obligatory intracellular parasites of humans: a comparative analysis. Int J Syst Evol Microbiol. 54, 1937-41 (2004).
-
(2004)
Int J Syst Evol Microbiol.
, vol.54
, pp. 1937-1941
-
-
Sakharkar, K.R.1
Dhar, P.K.2
Chow, V.T.3
-
40
-
-
84937941206
-
Genomics of Streptococcus salivarius, a major human commensal
-
Delorme, C., Abraham, A. L., Renault, P. & Guedon, E. Genomics of Streptococcus salivarius, a major human commensal. Infection, Genetics and Evolution. 33, 381-392 (2015).
-
(2015)
Infection, Genetics and Evolution.
, vol.33
, pp. 381-392
-
-
Delorme, C.1
Abraham, A.L.2
Renault, P.3
Guedon, E.4
-
41
-
-
84872264616
-
-
(Accessed: 3rd November 2015)
-
NCBI taxonomy database. Available at: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id= 342023. (Accessed: 3rd November 2015).
-
NCBI Taxonomy Database
-
-
-
42
-
-
84872264616
-
-
(Accessed: 3rd November 2015)
-
NCBI taxonomy database. Available at: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id= 301447. (Accessed: 3rd November 2015).
-
NCBI Taxonomy Database
-
-
-
43
-
-
0037397627
-
Streptococcus pyogenes expressing M and M-like surface proteins are phagocytosed but survive inside human neutrophils
-
Staali, L., Morgelin, M., Bjorck, L. & Tapper, H. Streptococcus pyogenes expressing M and M-like surface proteins are phagocytosed but survive inside human neutrophils. Cell Microbiol. 5, 253-65 (2003).
-
(2003)
Cell Microbiol.
, vol.5
, pp. 253-265
-
-
Staali, L.1
Morgelin, M.2
Bjorck, L.3
Tapper, H.4
-
44
-
-
85027933961
-
Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance
-
Davies, M. R. et al. Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance. Nat Genet. 47, 84-7 (2014).
-
(2014)
Nat Genet.
, vol.47
, pp. 84-87
-
-
Davies, M.R.1
-
45
-
-
80051918561
-
PGAT: A multi strain analysis resource for microbial genomes
-
Brittnacher, M. J. et al. PGAT: a multi strain analysis resource for microbial genomes. Bioinformatics. 27, 2429-30 (2011).
-
(2011)
Bioinformatics.
, vol.27
, pp. 2429-2430
-
-
Brittnacher, M.J.1
|