-
1
-
-
55049125445
-
Comparative genomics: the bacterial pan-genome
-
Tettelin H., Riley D., Cattuto C., Medini D. Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol 2008, 11:472-477.
-
(2008)
Curr Opin Microbiol
, vol.11
, pp. 472-477
-
-
Tettelin, H.1
Riley, D.2
Cattuto, C.3
Medini, D.4
-
2
-
-
27444438599
-
The microbial pan-genome
-
Medini D., Donati C., Tettelin H., Masignani V., Rappuoli R. The microbial pan-genome. Curr Opin Genet Dev 2005, 15:589-594.
-
(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
-
3
-
-
84893456850
-
A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species
-
Ramasamy D., Mishra A.K., Lagier J.C., Padhmanabhan R., Rossi M., Sentausa E., et al. A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol 2014, 64:384-391.
-
(2014)
Int J Syst Evol Microbiol
, vol.64
, pp. 384-391
-
-
Ramasamy, D.1
Mishra, A.K.2
Lagier, J.C.3
Padhmanabhan, R.4
Rossi, M.5
Sentausa, E.6
-
4
-
-
25444524604
-
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome"
-
Tettelin H., Masignani V., Cieslewicz M.J., Donati C., Medini D., Ward N.L., et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A 2005, 102:13950-13955.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 13950-13955
-
-
Tettelin, H.1
Masignani, V.2
Cieslewicz, M.J.3
Donati, C.4
Medini, D.5
Ward, N.L.6
-
5
-
-
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., Hu F.Z., Janto B., Boissy R., Hayes J., Keefe R., 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 2007, 8:R103.
-
(2007)
Genome Biol
, vol.8
, pp. R103
-
-
Hogg, J.S.1
Hu, F.Z.2
Janto, B.3
Boissy, R.4
Hayes, J.5
Keefe, R.6
-
6
-
-
79953902020
-
Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model
-
Boissy R., Ahmed A., Janto B., Earl J., Hall B.G., Hogg J.S., et al. Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model. BMC Genomics 2011, 12:187.
-
(2011)
BMC Genomics
, vol.12
, pp. 187
-
-
Boissy, R.1
Ahmed, A.2
Janto, B.3
Earl, J.4
Hall, B.G.5
Hogg, J.S.6
-
7
-
-
79952797542
-
Defining pathogenic bacterial species in the genomic era
-
Georgiades K., Raoult D. Defining pathogenic bacterial species in the genomic era. Front Microbiol 2010, 1:151.
-
(2010)
Front Microbiol
, vol.1
, pp. 151
-
-
Georgiades, K.1
Raoult, D.2
-
8
-
-
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 2009, 10:385.
-
(2009)
BMC Genomics
, vol.10
, pp. 385
-
-
Snipen, L.1
Almoy, T.2
Ussery, D.W.3
-
9
-
-
77958479691
-
Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept
-
Lefebure T., Bitar P.D., Suzuki H., Stanhope M.J. Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept. Genome Biol Evol 2010, 2:646-655.
-
(2010)
Genome Biol Evol
, vol.2
, pp. 646-655
-
-
Lefebure, T.1
Bitar, P.D.2
Suzuki, H.3
Stanhope, M.J.4
-
10
-
-
84879295485
-
The rhizome of the multidrug-resistant Enterobacter aerogenes genome reveals how new "killer bugs" are created because of a sympatric lifestyle
-
Diene S.M., Merhej V., Henry M., El Filali A., Roux V., Robert C., et al. The rhizome of the multidrug-resistant Enterobacter aerogenes genome reveals how new "killer bugs" are created because of a sympatric lifestyle. Mol Biol Evol 2013 Feb, 30(2):369-383.
-
(2013)
Mol Biol Evol
, vol.30
, Issue.2
, pp. 369-383
-
-
Diene, S.M.1
Merhej, V.2
Henry, M.3
El Filali, A.4
Roux, V.5
Robert, C.6
-
12
-
-
70350244424
-
Universal species concept: pipe dream or a step toward unifying biology?
-
Staley J.T. Universal species concept: pipe dream or a step toward unifying biology?. J Ind Microbiol Biotechnol 2009, 36:1331-1336.
-
(2009)
J Ind Microbiol Biotechnol
, vol.36
, pp. 1331-1336
-
-
Staley, J.T.1
-
13
-
-
33845890829
-
Genomics and the bacterial species problem
-
Doolittle W.F., Papke R.T. Genomics and the bacterial species problem. Genome Biol 2006, 7:116.
-
(2006)
Genome Biol
, vol.7
, pp. 116
-
-
Doolittle, W.F.1
Papke, R.T.2
-
14
-
-
23944437942
-
Opinion: Re-evaluating prokaryotic species
-
Gevers D., Cohan F.M., Lawrence J.G., Spratt B.G., Coenye T., Feil E.J., et al. Opinion: Re-evaluating prokaryotic species. Nat Rev Microbiol 2005, 3:733-739.
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 733-739
-
-
Gevers, D.1
Cohan, F.M.2
Lawrence, J.G.3
Spratt, B.G.4
Coenye, T.5
Feil, E.J.6
-
15
-
-
33750810896
-
The tree of one percent
-
Dagan T., Martin W. The tree of one percent. Genome Biol 2006, 7:118.
-
(2006)
Genome Biol
, vol.7
, pp. 118
-
-
Dagan, T.1
Martin, W.2
-
16
-
-
53849104729
-
The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates
-
Rasko D.A., Rosovitz M.J., Myers G.S., Mongodin E.F., Fricke W.F., Gajer P., et al. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol 2008, 190:6881-6893.
-
(2008)
J Bacteriol
, vol.190
, pp. 6881-6893
-
-
Rasko, D.A.1
Rosovitz, M.J.2
Myers, G.S.3
Mongodin, E.F.4
Fricke, W.F.5
Gajer, P.6
-
17
-
-
84866662453
-
Genotyping of invasive Kingella kingae isolates reveals predominant clones and association with specific clinical syndromes
-
Amit U., Porat N., Basmaci R., Bidet P., Bonacorsi S., Dagan R., et al. Genotyping of invasive Kingella kingae isolates reveals predominant clones and association with specific clinical syndromes. Clin Infect Dis 2012, 55:1074-1079.
-
(2012)
Clin Infect Dis
, vol.55
, pp. 1074-1079
-
-
Amit, U.1
Porat, N.2
Basmaci, R.3
Bidet, P.4
Bonacorsi, S.5
Dagan, R.6
-
18
-
-
84858166692
-
Potential serodiagnostic markers for Q fever identified in Coxiella burnetii by immunoproteomic and protein microarray approaches
-
Xiong X., Wang X., Wen B., Graves S., Stenos J. Potential serodiagnostic markers for Q fever identified in Coxiella burnetii by immunoproteomic and protein microarray approaches. BMC Microbiol 2012, 12:35.
-
(2012)
BMC Microbiol
, vol.12
, pp. 35
-
-
Xiong, X.1
Wang, X.2
Wen, B.3
Graves, S.4
Stenos, J.5
-
19
-
-
33745833651
-
Molecular characterization of Coxiella burnetii isolates by infrequent restriction site-PCR and MLVA typing
-
Arricau-Bouvery N., Hauck Y., Bejaoui A., Frangoulidis D., Bodier C.C., Souriau A., et al. Molecular characterization of Coxiella burnetii isolates by infrequent restriction site-PCR and MLVA typing. BMC Microbiol 2006, 6:38.
-
(2006)
BMC Microbiol
, vol.6
, pp. 38
-
-
Arricau-Bouvery, N.1
Hauck, Y.2
Bejaoui, A.3
Frangoulidis, D.4
Bodier, C.C.5
Souriau, A.6
-
20
-
-
79953678082
-
Molecular epidemiology of Coxiella burnetii from ruminants in Q fever outbreak, the Netherlands
-
Roest H.I., Ruuls R.C., Tilburg J.J., Nabuurs-Franssen M.H., Klaassen C.H., Vellema P., et al. Molecular epidemiology of Coxiella burnetii from ruminants in Q fever outbreak, the Netherlands. Emerg Infect Dis 2011, 17:668-675.
-
(2011)
Emerg Infect Dis
, vol.17
, pp. 668-675
-
-
Roest, H.I.1
Ruuls, R.C.2
Tilburg, J.J.3
Nabuurs-Franssen, M.H.4
Klaassen, C.H.5
Vellema, P.6
-
21
-
-
84857412615
-
Genotypic diversity of Coxiella burnetii in the 2007-2010 Q fever outbreak episodes in The Netherlands
-
Tilburg J.J., Rossen J.W., van Hannen E.J., Melchers W.J., Hermans M.H., van de Bovenkamp J., et al. Genotypic diversity of Coxiella burnetii in the 2007-2010 Q fever outbreak episodes in The Netherlands. J Clin Microbiol 2012, 50:1076-1078.
-
(2012)
J Clin Microbiol
, vol.50
, pp. 1076-1078
-
-
Tilburg, J.J.1
Rossen, J.W.2
van Hannen, E.J.3
Melchers, W.J.4
Hermans, M.H.5
van de Bovenkamp, J.6
-
22
-
-
84873467253
-
A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak
-
Reuter S., Harrison T.G., Koser C.U., Ellington M.J., Smith G.P., Parkhill J., et al. A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak. BMJ Open 2013, 3.
-
(2013)
BMJ Open
, vol.3
-
-
Reuter, S.1
Harrison, T.G.2
Koser, C.U.3
Ellington, M.J.4
Smith, G.P.5
Parkhill, J.6
-
23
-
-
70349304423
-
Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae
-
Chun J., Grim C.J., Hasan N.A., Lee J.H., Choi S.Y., Haley B.J., et al. Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae. Proc Natl Acad Sci U S A 2009, 106:15442-15447.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 15442-15447
-
-
Chun, J.1
Grim, C.J.2
Hasan, N.A.3
Lee, J.H.4
Choi, S.Y.5
Haley, B.J.6
-
24
-
-
80052150179
-
Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany
-
Rasko D.A., Webster D.R., Sahl J.W., Bashir A., Boisen N., Scheutz F., et al. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 2011, 365:709-717. 10.1056/NEJMoa1106920.
-
(2011)
N Engl J Med
, vol.365
, pp. 709-717
-
-
Rasko, D.A.1
Webster, D.R.2
Sahl, J.W.3
Bashir, A.4
Boisen, N.5
Scheutz, F.6
-
25
-
-
34447332244
-
A fast and flexible approach to oligonucleotide probe design for genomes and gene families
-
Feng S., Tillier E.R. A fast and flexible approach to oligonucleotide probe design for genomes and gene families. Bioinformatics 2007, 23:1195-1202.
-
(2007)
Bioinformatics
, vol.23
, pp. 1195-1202
-
-
Feng, S.1
Tillier, E.R.2
-
26
-
-
79961082938
-
Design and verification of a pangenome microarray oligonucleotide probe set for Dehalococcoides spp
-
Hug L.A., Salehi M., Nuin P., Tillier E.R., Edwards E.A. Design and verification of a pangenome microarray oligonucleotide probe set for Dehalococcoides spp. Appl Environ Microbiol 2011, 77:5361-5369.
-
(2011)
Appl Environ Microbiol
, vol.77
, pp. 5361-5369
-
-
Hug, L.A.1
Salehi, M.2
Nuin, P.3
Tillier, E.R.4
Edwards, E.A.5
-
27
-
-
70449432929
-
Efficient oligonucleotide probe selection for pan-genomic tiling arrays
-
Phillippy A.M., Deng X., Zhang W., Salzberg S.L. Efficient oligonucleotide probe selection for pan-genomic tiling arrays. BMC Bioinformatics 2009, 10:293.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 293
-
-
Phillippy, A.M.1
Deng, X.2
Zhang, W.3
Salzberg, S.L.4
-
28
-
-
80055035226
-
Genomotyping of Coxiella burnetii using microarrays reveals a conserved genomotype for hard tick isolates
-
Leroy Q., Armougom F., Barbry P., Raoult D. Genomotyping of Coxiella burnetii using microarrays reveals a conserved genomotype for hard tick isolates. PLoS One 2011, 6:e25781.
-
(2011)
PLoS One
, vol.6
, pp. e25781
-
-
Leroy, Q.1
Armougom, F.2
Barbry, P.3
Raoult, D.4
-
29
-
-
77951977661
-
Review of microarray studies for host-intracellular pathogen interactions
-
Leroy Q., Raoult D. Review of microarray studies for host-intracellular pathogen interactions. J Microbiol Methods 2010, 81:81-95.
-
(2010)
J Microbiol Methods
, vol.81
, pp. 81-95
-
-
Leroy, Q.1
Raoult, D.2
-
30
-
-
59549102977
-
PanCGH: a genotype-calling algorithm for pangenome CGH data
-
Bayjanov J.R., Wels M., Starrenburg M., van Hylckama Vlieg J.E., Siezen R.J., et al. PanCGH: a genotype-calling algorithm for pangenome CGH data. Bioinformatics 2009, 25:309-314.
-
(2009)
Bioinformatics
, vol.25
, pp. 309-314
-
-
Bayjanov, J.R.1
Wels, M.2
Starrenburg, M.3
van Hylckama Vlieg, J.E.4
Siezen, R.J.5
-
31
-
-
77952858385
-
PanCGHweb: a web tool for genotype calling in pangenome CGH data
-
Bayjanov J.R., Siezen R.J., van Hijum S.A. PanCGHweb: a web tool for genotype calling in pangenome CGH data. Bioinformatics 2010, 26:1256-1257.
-
(2010)
Bioinformatics
, vol.26
, pp. 1256-1257
-
-
Bayjanov, J.R.1
Siezen, R.J.2
van Hijum, S.A.3
-
32
-
-
0025183708
-
Basic local alignment search tool
-
Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
33
-
-
33644787447
-
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
-
Chen F., Mackey A.J., Stoeckert C.J., Roos D.S. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res 2006, 34:D363-D368.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. D363-D368
-
-
Chen, F.1
Mackey, A.J.2
Stoeckert, C.J.3
Roos, D.S.4
-
34
-
-
80055122428
-
Unity in variety-the pan-genome of the Chlamydiae
-
Collingro A., Tischler P., Weinmaier T., Penz T., Heinz E., Brunham R.C., et al. Unity in variety-the pan-genome of the Chlamydiae. Mol Biol Evol 2011, 28:3253-3270.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 3253-3270
-
-
Collingro, A.1
Tischler, P.2
Weinmaier, T.3
Penz, T.4
Heinz, E.5
Brunham, R.C.6
-
35
-
-
77952260431
-
Legionella pneumophila pangenome reveals strain-specific virulence factors
-
D'Auria G., Jimenez-Hernandez N., Peris-Bondia F., Moya A., Latorre A. Legionella pneumophila pangenome reveals strain-specific virulence factors. BMC Genomics 2010, 11:181.
-
(2010)
BMC Genomics
, vol.11
, pp. 181
-
-
D'Auria, G.1
Jimenez-Hernandez, N.2
Peris-Bondia, F.3
Moya, A.4
Latorre, A.5
-
36
-
-
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 2011, 62:487-504.
-
(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
-
37
-
-
0035162592
-
The COG database: new developments in phylogenetic classification of proteins from complete genomes
-
Tatusov R.L., Natale D.A., Garkavtsev I.V., Tatusova T.A., Shankavaram U.T., Rao B.S., et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 2001, 29:22-28.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 22-28
-
-
Tatusov, R.L.1
Natale, D.A.2
Garkavtsev, I.V.3
Tatusova, T.A.4
Shankavaram, U.T.5
Rao, B.S.6
-
38
-
-
0035166973
-
The InterPro database, an integrated documentation resource for protein families, domains and functional sites
-
Apweiler R., Attwood T.K., Bairoch A., Bateman A., Birney E., Biswas M., et al. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res 2001, 29:37-40.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 37-40
-
-
Apweiler, R.1
Attwood, T.K.2
Bairoch, A.3
Bateman, A.4
Birney, E.5
Biswas, M.6
-
39
-
-
0032919364
-
KEGG: Kyoto Encyclopedia of Genes and Genomes
-
Ogata H., Goto S., Sato K., Fujibuchi W., Bono H., Kanehisa M. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 1999, 27:29-34.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 29-34
-
-
Ogata, H.1
Goto, S.2
Sato, K.3
Fujibuchi, W.4
Bono, H.5
Kanehisa, M.6
-
40
-
-
84876978729
-
P2RP: a web-based framework for the identification and analysis of regulatory proteins in prokaryotic genomes
-
Barakat M., Ortet P., Whitworth D.E. P2RP: a web-based framework for the identification and analysis of regulatory proteins in prokaryotic genomes. BMC Genomics 2013, 14:269.
-
(2013)
BMC Genomics
, vol.14
, pp. 269
-
-
Barakat, M.1
Ortet, P.2
Whitworth, D.E.3
-
41
-
-
77956193448
-
ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement
-
Darling A.E., Mau B., Perna N.T. ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 2010, 5:e11147.
-
(2010)
PLoS One
, vol.5
, pp. e11147
-
-
Darling, A.E.1
Mau, B.2
Perna, N.T.3
-
42
-
-
79957613599
-
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
-
Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28:2731-2739.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 2731-2739
-
-
Tamura, K.1
Peterson, D.2
Peterson, N.3
Stecher, G.4
Nei, M.5
Kumar, S.6
-
43
-
-
0037100671
-
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
-
Katoh K., Misawa K., Kuma K., Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002, 30:3059-3066.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3059-3066
-
-
Katoh, K.1
Misawa, K.2
Kuma, K.3
Miyata, T.4
-
44
-
-
84873085208
-
Progressive genome-wide introgression in agricultural Campylobacter coli
-
Sheppard S.K., Didelot X., Jolley K.A., Darling A.E., Pascoe B., Meric G., et al. Progressive genome-wide introgression in agricultural Campylobacter coli. Mol Ecol 2013, 22:1051-1064.
-
(2013)
Mol Ecol
, vol.22
, pp. 1051-1064
-
-
Sheppard, S.K.1
Didelot, X.2
Jolley, K.A.3
Darling, A.E.4
Pascoe, B.5
Meric, G.6
-
45
-
-
84872185929
-
Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis
-
Cui Y., Yu C., Yan Y., Li D., Li Y., Jombart T., et al. Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proc Natl Acad Sci U S A 2013, 110:577-582.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. 577-582
-
-
Cui, Y.1
Yu, C.2
Yan, Y.3
Li, D.4
Li, Y.5
Jombart, T.6
-
46
-
-
58149183697
-
ARDB-Antibiotic Resistance Genes Database
-
Liu B., Pop M. ARDB-Antibiotic Resistance Genes Database. Nucleic Acids Res 2009, 37:D443-D447.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. D443-D447
-
-
Liu, B.1
Pop, M.2
-
47
-
-
84886790064
-
Resistome analysis of Mycobacterium tuberculosis: identification of aminoglycoside 2'-Nacetyltransferase (AAC) as co-target for drug desigining
-
Joshi R.S., Jamdhade M.D., Sonawane M.S., Giri A.P. Resistome analysis of Mycobacterium tuberculosis: identification of aminoglycoside 2'-Nacetyltransferase (AAC) as co-target for drug desigining. Bioinformation 2013, 9:174-181.
-
(2013)
Bioinformation
, vol.9
, pp. 174-181
-
-
Joshi, R.S.1
Jamdhade, M.D.2
Sonawane, M.S.3
Giri, A.P.4
-
48
-
-
78649565669
-
Comparative genomics of the bacterial genus Listeria: genome evolution is characterized by limited gene acquisition and limited gene loss
-
den Bakker H.C., Cummings C.A., Ferreira V., Vatta P., Orsi R.H., Degoricija L., et al. Comparative genomics of the bacterial genus Listeria: genome evolution is characterized by limited gene acquisition and limited gene loss. BMC Genomics 2010, 11:688.
-
(2010)
BMC Genomics
, vol.11
, pp. 688
-
-
den Bakker, H.C.1
Cummings, C.A.2
Ferreira, V.3
Vatta, P.4
Orsi, R.H.5
Degoricija, L.6
-
49
-
-
34547579396
-
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats
-
Grissa I., Vergnaud G., Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 2007, 35:W52-W57.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. W52-W57
-
-
Grissa, I.1
Vergnaud, G.2
Pourcel, C.3
-
50
-
-
79959979274
-
PHAST: a fast phage search tool
-
Zhou Y., Liang Y., Lynch K.H., Dennis J.J., Wishart D.S. PHAST: a fast phage search tool. Nucleic Acids Res 2011, 39:W347-W352.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. W347-W352
-
-
Zhou, Y.1
Liang, Y.2
Lynch, K.H.3
Dennis, J.J.4
Wishart, D.S.5
-
51
-
-
40549120596
-
The RAST Server: rapid annotations using subsystems technology
-
Aziz R.K., Bartels D., Best A.A., DeJongh M., Disz T., Edwards R.A., et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008, 9:75.
-
(2008)
BMC Genomics
, vol.9
, pp. 75
-
-
Aziz, R.K.1
Bartels, D.2
Best, A.A.3
DeJongh, M.4
Disz, T.5
Edwards, R.A.6
-
52
-
-
33644873699
-
ISfinder: the reference centre for bacterial insertion sequences
-
Siguier P., Perochon J., Lestrade L., Mahillon J., Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006, 34:D32-D36.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. D32-D36
-
-
Siguier, P.1
Perochon, J.2
Lestrade, L.3
Mahillon, J.4
Chandler, M.5
-
53
-
-
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 2012, 40:e172.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. e172
-
-
Fouts, D.E.1
Brinkac, L.2
Beck, E.3
Inman, J.4
Sutton, G.5
-
54
-
-
84856571322
-
PGAP: pan-genomes analysis pipeline
-
Zhao Y., Wu J., Yang J., Sun S., Xiao J., Yu J. PGAP: pan-genomes analysis pipeline. Bioinformatics 2012, 28:416-418.
-
(2012)
Bioinformatics
, vol.28
, pp. 416-418
-
-
Zhao, Y.1
Wu, J.2
Yang, J.3
Sun, S.4
Xiao, J.5
Yu, J.6
-
55
-
-
77956552653
-
Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions
-
Laing C., Buchanan C., Taboada E.N., Zhang Y., Kropinski A., Villegas A., et al. Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions. BMC Bioinformatics 2010, 11:461.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 461
-
-
Laing, C.1
Buchanan, C.2
Taboada, E.N.3
Zhang, Y.4
Kropinski, A.5
Villegas, A.6
-
56
-
-
84892872968
-
Toxin-antitoxin systems: biology, identification, and application
-
Unterholzner S.J., Poppenberger B., Rozhon W. Toxin-antitoxin systems: biology, identification, and application. Mob Genet Elements 2013, 3:e26219.
-
(2013)
Mob Genet Elements
, vol.3
, pp. e26219
-
-
Unterholzner, S.J.1
Poppenberger, B.2
Rozhon, W.3
-
57
-
-
84875235726
-
Connection of toxin-antitoxin modules to inoculation eschar and arthropod vertical transmission in Rickettsiales
-
Socolovschi C., Audoly G., Raoult D. Connection of toxin-antitoxin modules to inoculation eschar and arthropod vertical transmission in Rickettsiales. Comp Immunol Microbiol Infect Dis 2013, 36:199-209.
-
(2013)
Comp Immunol Microbiol Infect Dis
, vol.36
, pp. 199-209
-
-
Socolovschi, C.1
Audoly, G.2
Raoult, D.3
-
58
-
-
84882967629
-
Postgenomic analysis of bacterial pathogens repertoire reveals genome reduction rather than virulence factors
-
Merhej V., Georgiades K., Raoult D. Postgenomic analysis of bacterial pathogens repertoire reveals genome reduction rather than virulence factors. Brief Funct Genomics 2013, 12:291-304.
-
(2013)
Brief Funct Genomics
, vol.12
, pp. 291-304
-
-
Merhej, V.1
Georgiades, K.2
Raoult, D.3
-
59
-
-
79952808907
-
Genomes of the most dangerous epidemic bacteria have a virulence repertoire characterized by fewer genes but more toxin-antitoxin modules
-
Georgiades K., Raoult D. Genomes of the most dangerous epidemic bacteria have a virulence repertoire characterized by fewer genes but more toxin-antitoxin modules. PLoS One 2011, 6:e17962.
-
(2011)
PLoS One
, vol.6
, pp. e17962
-
-
Georgiades, K.1
Raoult, D.2
-
60
-
-
84897462030
-
Comparative genomics evidence that only protein toxins are tagging bad bugs
-
Georgiades K., Raoult D. Comparative genomics evidence that only protein toxins are tagging bad bugs. Front Cell Infect Microbiol 2011, 1:7.
-
(2011)
Front Cell Infect Microbiol
, vol.1
, pp. 7
-
-
Georgiades, K.1
Raoult, D.2
-
61
-
-
0035860458
-
Mechanisms of evolution in Rickettsia conorii and R. prowazekii
-
Ogata H., Audic S., Renesto-Audiffren P., Fournier P.E., Barbe V., Samson D., et al. Mechanisms of evolution in Rickettsia conorii and R. prowazekii. Science 2001, 293:2093-2098.
-
(2001)
Science
, vol.293
, pp. 2093-2098
-
-
Ogata, H.1
Audic, S.2
Renesto-Audiffren, P.3
Fournier, P.E.4
Barbe, V.5
Samson, D.6
-
62
-
-
84870821244
-
Antivirulence genes: insights into pathogen evolution through gene loss
-
Bliven K.A., Maurelli A.T. Antivirulence genes: insights into pathogen evolution through gene loss. Infect Immun 2012, 80:4061-4070.
-
(2012)
Infect Immun
, vol.80
, pp. 4061-4070
-
-
Bliven, K.A.1
Maurelli, A.T.2
-
63
-
-
84884238012
-
The intrinsic resistome of bacterial pathogens
-
Olivares J., Bernardini A., Garcia-Leon G., Corona F., Sanchez B., Martinez J.L. The intrinsic resistome of bacterial pathogens. Front Microbiol 2013, 4:103.
-
(2013)
Front Microbiol
, vol.4
, pp. 103
-
-
Olivares, J.1
Bernardini, A.2
Garcia-Leon, G.3
Corona, F.4
Sanchez, B.5
Martinez, J.L.6
-
64
-
-
84878908205
-
The culturable soil antibiotic resistome: a community of multi-drug resistant bacteria
-
Walsh F., Duffy B. The culturable soil antibiotic resistome: a community of multi-drug resistant bacteria. PLoS One 2013, 8:e65567.
-
(2013)
PLoS One
, vol.8
, pp. e65567
-
-
Walsh, F.1
Duffy, B.2
-
65
-
-
79952393752
-
Core and panmetabolism in Escherichia coli
-
Vieira G., Sabarly V., Bourguignon P.Y., Durot M., Le F.F., Mornico D., et al. Core and panmetabolism in Escherichia coli. J Bacteriol 2011, 193:1461-1472.
-
(2011)
J Bacteriol
, vol.193
, pp. 1461-1472
-
-
Vieira, G.1
Sabarly, V.2
Bourguignon, P.Y.3
Durot, M.4
Le, F.F.5
Mornico, D.6
-
66
-
-
79955837064
-
Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti
-
Galardini M., Mengoni A., Brilli M., Pini F., Fioravanti A., Lucas S., et al. Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti. BMC Genomics 2011, 12:235.
-
(2011)
BMC Genomics
, vol.12
, pp. 235
-
-
Galardini, M.1
Mengoni, A.2
Brilli, M.3
Pini, F.4
Fioravanti, A.5
Lucas, S.6
-
67
-
-
77954289636
-
Listeria monocytogenes σB has a small core regulon and a conserved role in virulence but makes differential contributions to stress tolerance across a diverse collection of strains
-
Oliver H.F., Orsi R.H., Wiedmann M., Boor K.J. Listeria monocytogenes σB has a small core regulon and a conserved role in virulence but makes differential contributions to stress tolerance across a diverse collection of strains. Appl Environ Microbiol 2010, 76:4216-4232.
-
(2010)
Appl Environ Microbiol
, vol.76
, pp. 4216-4232
-
-
Oliver, H.F.1
Orsi, R.H.2
Wiedmann, M.3
Boor, K.J.4
-
68
-
-
80055121868
-
Insight into cross-talk between intra-amoebal pathogens
-
Gimenez G., Bertelli C., Moliner C., Robert C., Raoult D., Fournier P.E., et al. Insight into cross-talk between intra-amoebal pathogens. BMC Genomics 2011, 12:542.
-
(2011)
BMC Genomics
, vol.12
, pp. 542
-
-
Gimenez, G.1
Bertelli, C.2
Moliner, C.3
Robert, C.4
Raoult, D.5
Fournier, P.E.6
-
69
-
-
77953346772
-
The Genus Escherichia
-
Springer-Verlag, New York, [Chapter 3.3.3]
-
Welch Rodney A. The Genus Escherichia. The Prokaryotes 2006, vol. 6:60-71. Springer-Verlag, New York, [Chapter 3.3.3].
-
(2006)
The Prokaryotes
, vol.6
, pp. 60-71
-
-
Welch, R.A.1
-
70
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar R.C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26(19):2460-2461.
-
(2010)
Bioinformatics
, vol.26
, Issue.19
, pp. 2460-2461
-
-
Edgar, R.C.1
-
71
-
-
66749136930
-
Massive comparative genomic analysis reveals convergent evolution of specialized bacteria
-
Merhej V., Royer-Carenzi M., Pontarotti P., Raoult D. Massive comparative genomic analysis reveals convergent evolution of specialized bacteria. Biol Direct 2009, 4:13.
-
(2009)
Biol Direct
, vol.4
, pp. 13
-
-
Merhej, V.1
Royer-Carenzi, M.2
Pontarotti, P.3
Raoult, D.4
-
72
-
-
79551682170
-
Gene gain and loss events in Rickettsia and Orientia species
-
Georgiades K., Merhej V., El K.K., Raoult D., Pontarotti P. Gene gain and loss events in Rickettsia and Orientia species. Biol Direct 2011, 6:6.
-
(2011)
Biol Direct
, vol.6
, pp. 6
-
-
Georgiades, K.1
Merhej, V.2
El, K.K.3
Raoult, D.4
Pontarotti, P.5
-
73
-
-
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., Worsham P.L., Nikolich M.P., Riley D.R., Sebastian Y., Mou S., 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 2010, 192:1685-1699.
-
(2010)
J Bacteriol
, vol.192
, pp. 1685-1699
-
-
Eppinger, M.1
Worsham, P.L.2
Nikolich, M.P.3
Riley, D.R.4
Sebastian, Y.5
Mou, S.6
-
74
-
-
0035224746
-
Design of a compartmentalized shotgun assembler for the human genome
-
Huson D.H., Reinert K., Kravitz S.A., Remington K.A., Delcher A.L., Dew I.M., et al. Design of a compartmentalized shotgun assembler for the human genome. Bioinformatics 2001, 17(Suppl. 1):S132-S139.
-
(2001)
Bioinformatics
, vol.17
, pp. S132-S139
-
-
Huson, D.H.1
Reinert, K.2
Kravitz, S.A.3
Remington, K.A.4
Delcher, A.L.5
Dew, I.M.6
-
75
-
-
2942538300
-
Versatile and open software for comparing large genomes
-
Kurtz S., Phillippy A., Delcher A.L., Smoot M., Shumway M., Antonescu C., et al. Versatile and open software for comparing large genomes. Genome Biol 2004, 5:R12.
-
(2004)
Genome Biol
, vol.5
, pp. R12
-
-
Kurtz, S.1
Phillippy, A.2
Delcher, A.L.3
Smoot, M.4
Shumway, M.5
Antonescu, C.6
-
76
-
-
84884555902
-
A genomic redefinition of species
-
Scortichini M., Marcelletti S., Ferrante P., Firrao G. A genomic redefinition of species. PLoS One 2013, 8:e75794.
-
(2013)
PLoS One
, vol.8
, pp. e75794
-
-
Scortichini, M.1
Marcelletti, S.2
Ferrante, P.3
Firrao, G.4
-
77
-
-
84873728531
-
Rapid detection of Bacillus anthracis spores using a super-paramagnetic lateral-flow immunological detection system
-
Wang D.B., Tian B., Zhang Z.P., Deng J.Y., Cui Z.Q., Yang R.F., et al. Rapid detection of Bacillus anthracis spores using a super-paramagnetic lateral-flow immunological detection system. Biosens Bioelectron 2012, pii: S0956-5663(12)00782-8. 10.1016/j.bios.2012.10.088.
-
(2012)
Biosens Bioelectron
-
-
Wang, D.B.1
Tian, B.2
Zhang, Z.P.3
Deng, J.Y.4
Cui, Z.Q.5
Yang, R.F.6
-
78
-
-
77950421915
-
Genome analysis of microorganisms living in amoebae reveals a melting pot of evolution
-
Moliner C., Fournier P.E., Raoult D. Genome analysis of microorganisms living in amoebae reveals a melting pot of evolution. FEMS Microbiol Rev 2010, 34:281-294.
-
(2010)
FEMS Microbiol Rev
, vol.34
, pp. 281-294
-
-
Moliner, C.1
Fournier, P.E.2
Raoult, D.3
-
79
-
-
77958580152
-
Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species
-
Donati C., Hiller N.L., Tettelin H., Muzzi A., Croucher N.J., Angiuoli S.V., et al. Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol 2010, 11:R107.
-
(2010)
Genome Biol
, vol.11
, pp. R107
-
-
Donati, C.1
Hiller, N.L.2
Tettelin, H.3
Muzzi, A.4
Croucher, N.J.5
Angiuoli, S.V.6
-
80
-
-
77649189114
-
Development of pooled suppression subtractive hybridization to analyze the pangenome of Staphylococcus aureus
-
Gerrish R.S., Gill A.L., Fowler V.G., Gill S.R. Development of pooled suppression subtractive hybridization to analyze the pangenome of Staphylococcus aureus. J Microbiol Methods 2010, 81:56-60.
-
(2010)
J Microbiol Methods
, vol.81
, pp. 56-60
-
-
Gerrish, R.S.1
Gill, A.L.2
Fowler, V.G.3
Gill, S.R.4
-
81
-
-
34249276425
-
Gain and loss of multiple genes during the evolution of Helicobacter pylori
-
Gressmann H., Linz B., Ghai R., Pleissner K.P., Schlapbach R., Yamaoka Y., et al. Gain and loss of multiple genes during the evolution of Helicobacter pylori. PLoS Genet 2005, 1:e43.
-
(2005)
PLoS Genet
, vol.1
, pp. e43
-
-
Gressmann, H.1
Linz, B.2
Ghai, R.3
Pleissner, K.P.4
Schlapbach, R.5
Yamaoka, Y.6
-
82
-
-
72449152187
-
Genomic taxonomy of Vibrios
-
Thompson C.C., Vicente A.C., Souza R.C., Vasconcelos A.T., Vesth T., Alves N., et al. Genomic taxonomy of Vibrios. BMC Evol Biol 2009, 9:258.
-
(2009)
BMC Evol Biol
, vol.9
, pp. 258
-
-
Thompson, C.C.1
Vicente, A.C.2
Souza, R.C.3
Vasconcelos, A.T.4
Vesth, T.5
Alves, N.6
-
83
-
-
79953234204
-
Mycobacterial species as case-study of comparative genome analysis
-
Zakham F., Belayachi L., Ussery D., Akrim M., Benjouad A., El A.R., et al. Mycobacterial species as case-study of comparative genome analysis. Cell Mol Biol (Noisy-le-grand) 2011, 57(Suppl.):OL1462-OL1469.
-
(2011)
Cell Mol Biol (Noisy-le-grand)
, vol.57
, pp. OL1462-OL1469
-
-
Zakham, F.1
Belayachi, L.2
Ussery, D.3
Akrim, M.4
Benjouad, A.5
El, A.R.6
-
84
-
-
79960939630
-
The genomics of Acinetobacter baumannii: insights into genome plasticity, antimicrobial resistance and pathogenicity
-
Imperi F., Antunes L.C., Blom J., Villa L., Iacono M., Visca P., et al. The genomics of Acinetobacter baumannii: insights into genome plasticity, antimicrobial resistance and pathogenicity. IUBMB Life 2011, 63:1068-1074.
-
(2011)
IUBMB Life
, vol.63
, pp. 1068-1074
-
-
Imperi, F.1
Antunes, L.C.2
Blom, J.3
Villa, L.4
Iacono, M.5
Visca, P.6
-
85
-
-
77956600970
-
Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification
-
Deng X., Phillippy A.M., Li Z., Salzberg S.L., Zhang W. Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification. BMC Genomics 2010, 11:500.
-
(2010)
BMC Genomics
, vol.11
, pp. 500
-
-
Deng, X.1
Phillippy, A.M.2
Li, Z.3
Salzberg, S.L.4
Zhang, W.5
-
86
-
-
84872467231
-
Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome
-
Kuenne C., Billion A., Mraheil M.A., Strittmatter A., Daniel R., Goesmann A., et al. Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome. BMC Genomics 2013, 14:47.
-
(2013)
BMC Genomics
, vol.14
, pp. 47
-
-
Kuenne, C.1
Billion, A.2
Mraheil, M.A.3
Strittmatter, A.4
Daniel, R.5
Goesmann, A.6
-
87
-
-
84859103889
-
Pseudomonas aeruginosa genomic structure and diversity
-
Klockgether J., Cramer N., Wiehlmann L., Davenport C.F., Tummler B. Pseudomonas aeruginosa genomic structure and diversity. Front Microbiol 2011, 2:150.
-
(2011)
Front Microbiol
, vol.2
, pp. 150
-
-
Klockgether, J.1
Cramer, N.2
Wiehlmann, L.3
Davenport, C.F.4
Tummler, B.5
-
88
-
-
77950649022
-
Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island
-
van S.W., Top J., Riley D.R., Boekhorst J., Vrijenhoek J.E., Schapendonk C.M., et al. Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island. BMC Genomics 2010, 11:239.
-
(2010)
BMC Genomics
, vol.11
, pp. 239
-
-
van, S.W.1
Top, J.2
Riley, D.R.3
Boekhorst, J.4
Vrijenhoek, J.E.5
Schapendonk, C.M.6
-
89
-
-
78650114015
-
Analysis of ultra low genome conservation in Clostridium difficile
-
Scaria J., Ponnala L., Janvilisri T., Yan W., Mueller L.A., Chang Y.F. Analysis of ultra low genome conservation in Clostridium difficile. PLoS One 2010, 5:e15147.
-
(2010)
PLoS One
, vol.5
, pp. e15147
-
-
Scaria, J.1
Ponnala, L.2
Janvilisri, T.3
Yan, W.4
Mueller, L.A.5
Chang, Y.F.6
-
90
-
-
73349110129
-
Analysis of the pan genome of Campylobacter jejuni isolates recovered from poultry by pulsed-field gel electrophoresis, multilocus sequence typing (MLST), and repetitive sequence polymerase chain reaction (rep-PCR) reveals different discriminatory capabilities
-
Wilson M.K., Lane A.B., Law B.F., Miller W.G., Joens L.A., Konkel M.E., et al. Analysis of the pan genome of Campylobacter jejuni isolates recovered from poultry by pulsed-field gel electrophoresis, multilocus sequence typing (MLST), and repetitive sequence polymerase chain reaction (rep-PCR) reveals different discriminatory capabilities. Microb Ecol 2009, 58:843-855.
-
(2009)
Microb Ecol
, vol.58
, pp. 843-855
-
-
Wilson, M.K.1
Lane, A.B.2
Law, B.F.3
Miller, W.G.4
Joens, L.A.5
Konkel, M.E.6
-
91
-
-
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 2010, 13:45-57.
-
(2010)
Int Microbiol
, vol.13
, pp. 45-57
-
-
Mira, A.1
Martin-Cuadrado, A.B.2
D'Auria, G.3
Rodriguez-Valera, F.4
-
92
-
-
78049389005
-
Comparative genomic characterization of Actinobacillus pleuropneumoniae
-
Xu Z., Chen X., Li L., Li T., Wang S., Chen H., et al. Comparative genomic characterization of Actinobacillus pleuropneumoniae. J Bacteriol 2010, 192:5625-5636.
-
(2010)
J Bacteriol
, vol.192
, pp. 5625-5636
-
-
Xu, Z.1
Chen, X.2
Li, L.3
Li, T.4
Wang, S.5
Chen, H.6
-
93
-
-
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 2007, 8:R71.
-
(2007)
Genome Biol
, vol.8
, pp. R71
-
-
Lefebure, T.1
Stanhope, M.J.2
-
94
-
-
80054862901
-
Comparative genomic analysis of Streptococcus suis reveals significant genomic diversity among different serotypes
-
Zhang A., Yang M., Hu P., Wu J., Chen B., Hua Y., et al. Comparative genomic analysis of Streptococcus suis reveals significant genomic diversity among different serotypes. BMC Genomics 2011, 12:523.
-
(2011)
BMC Genomics
, vol.12
, pp. 523
-
-
Zhang, A.1
Yang, M.2
Hu, P.3
Wu, J.4
Chen, B.5
Hua, Y.6
-
95
-
-
79960451405
-
Identification of the pangenome and its components in 14 distinct Aggregatibacter actinomycetemcomitans strains by comparative genomic analysis
-
Kittichotirat W., Bumgarner R.E., Asikainen S., Chen C. Identification of the pangenome and its components in 14 distinct Aggregatibacter actinomycetemcomitans strains by comparative genomic analysis. PLoS One 2011, 6:e22420.
-
(2011)
PLoS One
, vol.6
, pp. e22420
-
-
Kittichotirat, W.1
Bumgarner, R.E.2
Asikainen, S.3
Chen, C.4
-
96
-
-
67649397594
-
Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04
-
Barrangou R., Briczinski E.P., Traeger L.L., Loquasto J.R., Richards M., Horvath P., et al. Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04. J Bacteriol 2009, 191:4144-4151.
-
(2009)
J Bacteriol
, vol.191
, pp. 4144-4151
-
-
Barrangou, R.1
Briczinski, E.P.2
Traeger, L.L.3
Loquasto, J.R.4
Richards, M.5
Horvath, P.6
-
97
-
-
77954582930
-
Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence
-
Remenant B., Coupat-Goutaland B., Guidot A., Cellier G., Wicker E., Allen C., et al. Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence. BMC Genomics 2010, 11:379.
-
(2010)
BMC Genomics
, vol.11
, pp. 379
-
-
Remenant, B.1
Coupat-Goutaland, B.2
Guidot, A.3
Cellier, G.4
Wicker, E.5
Allen, C.6
-
98
-
-
84873608021
-
Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core
-
Mann R.A., Smits T.H., Buhlmann A., Blom J., Goesmann A., Frey J.E., et al. Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core. PLoS One 2013, 8:e55644.
-
(2013)
PLoS One
, vol.8
, pp. e55644
-
-
Mann, R.A.1
Smits, T.H.2
Buhlmann, A.3
Blom, J.4
Goesmann, A.5
Frey, J.E.6
-
99
-
-
84872282918
-
The pan-genome of the animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the biovar ovis and equi strains
-
Soares S.C., Silva A., Trost E., Blom J., Ramos R., Carneiro A., et al. The pan-genome of the animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the biovar ovis and equi strains. PLoS One 2013, 8:e53818.
-
(2013)
PLoS One
, vol.8
, pp. e53818
-
-
Soares, S.C.1
Silva, A.2
Trost, E.3
Blom, J.4
Ramos, R.5
Carneiro, A.6
-
100
-
-
84867018919
-
Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation
-
Broadbent J.R., Neeno-Eckwall E.C., Stahl B., Tandee K., Cai H., Morovic W., et al. Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation. BMC Genomics 2012, 13:533.
-
(2012)
BMC Genomics
, vol.13
, pp. 533
-
-
Broadbent, J.R.1
Neeno-Eckwall, E.C.2
Stahl, B.3
Tandee, K.4
Cai, H.5
Morovic, W.6
-
101
-
-
84866555340
-
Pan-genomic analysis provides insights into the genomic variation and evolution of Salmonella Paratyphi A
-
Liang W., Zhao Y., Chen C., Cui X., Yu J., Xiao J., et al. Pan-genomic analysis provides insights into the genomic variation and evolution of Salmonella Paratyphi A. PLoS One 2012, 7:e45346.
-
(2012)
PLoS One
, vol.7
, pp. e45346
-
-
Liang, W.1
Zhao, Y.2
Chen, C.3
Cui, X.4
Yu, J.5
Xiao, J.6
-
102
-
-
84864523777
-
Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways
-
Borneman A.R., McCarthy J.M., Chambers P.J., Bartowsky E.J. Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways. BMC Genomics 2012, 13:373.
-
(2012)
BMC Genomics
, vol.13
, pp. 373
-
-
Borneman, A.R.1
McCarthy, J.M.2
Chambers, P.J.3
Bartowsky, E.J.4
-
103
-
-
84871029413
-
Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates
-
Conlan S., Mijares L.A., Becker J., Blakesley R.W., Bouffard G.G., Brooks S., et al. Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates. Genome Biol 2012, 13:R64.
-
(2012)
Genome Biol
, vol.13
, pp. R64
-
-
Conlan, S.1
Mijares, L.A.2
Becker, J.3
Blakesley, R.W.4
Bouffard, G.G.5
Brooks, S.6
-
104
-
-
84863991677
-
Pangenomic study of Corynebacterium diphtheriae that provides insights into the genomic diversity of pathogenic isolates from cases of classical diphtheria, endocarditis, and pneumonia
-
Trost E., Blom J., Soares S.C., Huang I.H., Al-Dilaimi A., Schroder J., et al. Pangenomic study of Corynebacterium diphtheriae that provides insights into the genomic diversity of pathogenic isolates from cases of classical diphtheria, endocarditis, and pneumonia. J Bacteriol 2012, 194:3199-3215.
-
(2012)
J Bacteriol
, vol.194
, pp. 3199-3215
-
-
Trost, E.1
Blom, J.2
Soares, S.C.3
Huang, I.H.4
Al-Dilaimi, A.5
Schroder, J.6
-
105
-
-
67649653746
-
Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens
-
Silby M.W., Cerdeno-Tarraga A.M., Vernikos G.S., Giddens S.R., Jackson R.W., Preston G.M., et al. Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol 2009, 10:R51.
-
(2009)
Genome Biol
, vol.10
, pp. R51
-
-
Silby, M.W.1
Cerdeno-Tarraga, A.M.2
Vernikos, G.S.3
Giddens, S.R.4
Jackson, R.W.5
Preston, G.M.6
-
106
-
-
79952329442
-
Novel pan-genomic analysis approach in target selection for multiplex PCR identification and detection of Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia cepacia complex species: a proof-of-concept study
-
Ho C.C., Lau C.C., Martelli P., Chan S.Y., Tse C.W., Wu A.K., et al. Novel pan-genomic analysis approach in target selection for multiplex PCR identification and detection of Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia cepacia complex species: a proof-of-concept study. J Clin Microbiol 2009, 49:814-821.
-
(2009)
J Clin Microbiol
, vol.49
, pp. 814-821
-
-
Ho, C.C.1
Lau, C.C.2
Martelli, P.3
Chan, S.Y.4
Tse, C.W.5
Wu, A.K.6
-
107
-
-
77955869456
-
The genus Burkholderia: analysis of 56 genomic sequences
-
Ussery D.W., Kiil K., Lagesen K., Sicheritz-Ponten T., Bohlin J., Wassenaar T.M. The genus Burkholderia: analysis of 56 genomic sequences. Genome Dyn 2009, 6:140-157.
-
(2009)
Genome Dyn
, vol.6
, pp. 140-157
-
-
Ussery, D.W.1
Kiil, K.2
Lagesen, K.3
Sicheritz-Ponten, T.4
Bohlin, J.5
Wassenaar, T.M.6
-
108
-
-
78049490714
-
Comparative genomics of the genus Bifidobacterium
-
Bottacini F., Medini D., Pavesi A., Turroni F., Foroni E., Riley D., et al. Comparative genomics of the genus Bifidobacterium. Microbiology 2010, 156:3243-3254.
-
(2010)
Microbiology
, vol.156
, pp. 3243-3254
-
-
Bottacini, F.1
Medini, D.2
Pavesi, A.3
Turroni, F.4
Foroni, E.5
Riley, D.6
-
109
-
-
78049442430
-
Characterizing the metabolism of Dehalococcoides with a constraint-based model
-
Ahsanul I.M., Edwards E.A., Mahadevan R. Characterizing the metabolism of Dehalococcoides with a constraint-based model. PLoS Comput Biol 2010, 6.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Ahsanul, I.M.1
Edwards, E.A.2
Mahadevan, R.3
-
110
-
-
84859974349
-
Comparative genomics of Mycoplasma: analysis of conserved essential genes and diversity of the pan-genome
-
Liu W., Fang L., Li M., Li S., Guo S., Luo R., et al. Comparative genomics of Mycoplasma: analysis of conserved essential genes and diversity of the pan-genome. PLoS One 2012, 7:e35698.
-
(2012)
PLoS One
, vol.7
, pp. e35698
-
-
Liu, W.1
Fang, L.2
Li, M.3
Li, S.4
Guo, S.5
Luo, R.6
-
111
-
-
84866309633
-
Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass
-
Blumer-Schuette S.E., Giannone R.J., Zurawski J.V., Ozdemir I., Ma Q., Yin Y., et al. Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass. J Bacteriol 2012, 194:4015-4028.
-
(2012)
J Bacteriol
, vol.194
, pp. 4015-4028
-
-
Blumer-Schuette, S.E.1
Giannone, R.J.2
Zurawski, J.V.3
Ozdemir, I.4
Ma, Q.5
Yin, Y.6
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