-
1
-
-
84865543577
-
Computational methods for gene finding in prokaryotes
-
In: Gusev, M. (ed.). Ohrid, Macedonia, Springer
-
Angelova, M. et al. (2010) Computational methods for gene finding in prokaryotes. In: Gusev, M. (ed.) ICT Innovations 2010. Ohrid, Macedonia, Springer, pp. 11-20.
-
(2010)
ICT Innovations 2010
, pp. 11-20
-
-
Angelova, M.1
-
2
-
-
84952009484
-
Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
-
Bradley, P. et al. (2015) Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat. Commun., 6, 10063.
-
(2015)
Nat. Commun.
, vol.6
, pp. 10063
-
-
Bradley, P.1
-
3
-
-
84938841197
-
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
-
Brettin, T. et al. (2015) RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci. Rep., 5, 8365.
-
(2015)
Sci. Rep.
, vol.5
, pp. 8365
-
-
Brettin, T.1
-
4
-
-
84997283916
-
Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary
-
Brynildsrud, O. et al. (2016) Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary. Genome Biol., 17, 238.
-
(2016)
Genome Biol.
, vol.17
, pp. 238
-
-
Brynildsrud, O.1
-
5
-
-
84862081029
-
Existing classes of antibiotics are probably the best we will ever have
-
Cormican, M. and Vellinga, A. (2012) Existing classes of antibiotics are probably the best we will ever have. Brit. Med. J., 344, e3369.
-
(2012)
Brit. Med. J.
, vol.344
, pp. e3369
-
-
Cormican, M.1
Vellinga, A.2
-
6
-
-
85068579878
-
PanX: Pan-genome analysis and exploration
-
Ding, W. et al. (2018) panX: pan-genome analysis and exploration. Nucleic Acids Res., 46, e5.
-
(2018)
Nucleic Acids Res.
, vol.46
, pp. e5
-
-
Ding, W.1
-
7
-
-
80055082271
-
Accelerated profile HMM searches
-
Eddy, S.R. (2011) Accelerated profile HMM searches. PLoS Comput. Biol., 7, e1002195.
-
(2011)
PLoS Comput. Biol.
, vol.7
, pp. e1002195
-
-
Eddy, S.R.1
-
8
-
-
84870431038
-
CD-HIT: Accelerated for clustering the next-generation sequencing data
-
Fu, L. et al. (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics, 28, 3150-3152.
-
(2012)
Bioinformatics
, vol.28
, pp. 3150-3152
-
-
Fu, L.1
-
9
-
-
84897134429
-
Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing
-
Gordon, N.C. et al. (2014) Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing. J. Clin.Microbiol., 52, 1182-1191.
-
(2014)
J. Clin.Microbiol.
, vol.52
, pp. 1182-1191
-
-
Gordon, N.C.1
-
10
-
-
85017376495
-
Evolview v2: An online visualization and management tool for customized and annotated phylogenetic trees
-
He, Z. et al. (2016) Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees. Nucleic Acids Res., 44, W236-W241.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. W236-W241
-
-
He, Z.1
-
11
-
-
84936803320
-
Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health
-
Holt, K.E. et al. (2015) Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc. Natl. Acad. Sci. USA, 112, E3574-E3581.
-
(2015)
Proc. Natl. Acad. Sci. USA
, vol.112
, pp. E3574-E3581
-
-
Holt, K.E.1
-
12
-
-
84976905626
-
EggNOG 4.5: A hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
-
Huerta-Cepas, J. et al. (2016) eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res., 44, D286-D293.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D286-D293
-
-
Huerta-Cepas, J.1
-
13
-
-
77952299957
-
Prodigal: Prokaryotic gene recognition and translation initiation site identification
-
Hyatt, D. et al. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, 11, 119.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 119
-
-
Hyatt, D.1
-
14
-
-
85016050964
-
CARD 2017: Expansion and model-centric curation of the comprehensive antibiotic resistance database
-
Jia, B et al. (2017) CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database.Nucleic Acids Res., 45, D566-D573
-
(2017)
Nucleic Acids Res.
, vol.45
, pp. D566-D573
-
-
Jia, B.1
-
15
-
-
85028975787
-
Pan-genome analysis of Bacillus for microbiome profiling
-
Kim, Y. et al. (2017) Pan-genome analysis of Bacillus for microbiome profiling. Sci. Rep., 7, 10984.
-
(2017)
Sci. Rep.
, vol.7
, pp. 10984
-
-
Kim, Y.1
-
16
-
-
84858006569
-
Comparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera
-
Lukjancenko, O. et al. (2012) Comparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera. Microb. Ecol., 63, 651-673.
-
(2012)
Microb. Ecol.
, vol.63
, pp. 651-673
-
-
Lukjancenko, O.1
-
17
-
-
84983353060
-
Whole-genome sequencing for detecting antimicrobial resistance in nontyphoidal Salmonella
-
McDermott, P.F. et al. (2016) Whole-genome sequencing for detecting antimicrobial resistance in nontyphoidal Salmonella. Antimicrob. Agents Chemother., 60, 5515-5520.
-
(2016)
Antimicrob. Agents Chemother.
, vol.60
, pp. 5515-5520
-
-
McDermott, P.F.1
-
18
-
-
2942511249
-
Structure of the multidrug resistance efflux transporter EmrE from Escherichia coli
-
Ma, C. and Chang, G. (2004) Structure of the multidrug resistance efflux transporter EmrE from Escherichia coli. Proc. Natl. Acad. Sci. USA, 101, 2852-2857.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 2852-2857
-
-
Ma, C.1
Chang, G.2
-
19
-
-
27444438599
-
The microbial pan-genome
-
Medini, D. et al. (2005) The microbial pan-genome. Curr. Opin. Genet. Dev., 15, 589-594.
-
(2005)
Curr. Opin. Genet. Dev.
, vol.15
, pp. 589-594
-
-
Medini, D.1
-
20
-
-
0033815868
-
Regulation of transcription of the mph(A) gene for macrolide 2 '-phosphotransferase i in Escherichia coli: Characterization of the regulatory gene mphR(A)
-
Noguchi, N. et al. (2000) Regulation of transcription of the mph(A) gene for macrolide 2 '-phosphotransferase I in Escherichia coli: characterization of the regulatory gene mphR(A). J. Bacteriol., 182, 5052-5058.
-
(2000)
J. Bacteriol.
, vol.182
, pp. 5052-5058
-
-
Noguchi, N.1
-
21
-
-
84987804431
-
Mechanisms of polymyxin resistance: Acquired and intrinsic resistance in bacteria
-
Olaitan, A.O. et al. (2014) Mechanisms of polymyxin resistance: acquired and intrinsic resistance in bacteria. Front. Microbiol., 5, 643.
-
(2014)
Front. Microbiol.
, vol.5
, pp. 643
-
-
Olaitan, A.O.1
-
22
-
-
84947793096
-
Roary: Rapid large-scale prokaryote pan genome analysis
-
Page, A.J. et al. (2015) Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics, 31, 3691-3693.
-
(2015)
Bioinformatics
, vol.31
, pp. 3691-3693
-
-
Page, A.J.1
-
23
-
-
53849104729
-
The pangenome structure of Escherichia coli: Comparative genomic analysis of E. coli commensal and pathogenic isolates
-
Rasko, D.A. et al. (2008) The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J. Bacteriol., 190, 6881-6893.
-
(2008)
J. Bacteriol.
, vol.190
, pp. 6881-6893
-
-
Rasko, D.A.1
-
24
-
-
84875164559
-
The true cost of antimicrobial resistance
-
Smith, R. and Coast, J. (2013) The true cost of antimicrobial resistance. BMJ-Brit. Med. J., 346, f1493.
-
(2013)
BMJ-Brit. Med. J.
, vol.346
, pp. f1493
-
-
Smith, R.1
Coast, J.2
-
25
-
-
84888796738
-
Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data
-
Stoesser, N. et al. (2013) Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. J. Antimicrob. Chemother., 68, 2234-2244.
-
(2013)
J. Antimicrob. Chemother.
, vol.68
, pp. 2234-2244
-
-
Stoesser, N.1
-
26
-
-
25444524604
-
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial 'pan-genome'
-
Tettelin, H. et al. (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial 'pan-genome'. Proc. Natl. Acad. Sci. USA, 102, 13950-13955.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 13950-13955
-
-
Tettelin, H.1
-
27
-
-
55049125445
-
Comparative genomics: The bacterial pan-genome
-
Tettelin, H. et al. (2008) Comparative genomics: the bacterial pan-genome. Curr. Opin. Microbiol., 11, 472-477.
-
(2008)
Curr. Opin. Microbiol.
, vol.11
, pp. 472-477
-
-
Tettelin, H.1
-
28
-
-
84943793968
-
WGS accurately predicts antimicrobial resistance in Escherichia coli
-
Tyson, G.H. et al. (2015) WGS accurately predicts antimicrobial resistance in Escherichia coli. J. Antimicrob. Chemother., 70, 2763-2769.
-
(2015)
J. Antimicrob. Chemother.
, vol.70
, pp. 2763-2769
-
-
Tyson, G.H.1
-
29
-
-
84891776599
-
PATRIC, the bacterial bioinformatics database and analysis resource
-
Wattam, A.R. et al. (2014) PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res., 42, D581-D591.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D581-D591
-
-
Wattam, A.R.1
-
30
-
-
85016046470
-
Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center
-
Wattam, A.R. et al. (2017) Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res., 45, D535-D542.
-
(2017)
Nucleic Acids Res.
, vol.45
, pp. D535-D542
-
-
Wattam, A.R.1
-
31
-
-
85040796775
-
EzTree: An automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes
-
Wu, Y.W. (2018) ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes. BMC Genomics, 19, 921.
-
(2018)
BMC Genomics
, vol.19
, pp. 921
-
-
Wu, Y.W.1
-
32
-
-
0028986717
-
Emre, an Escherichia-Coli 12-Kda multidrug transporter, exchanges toxic cations and H and is soluble in organic-solvents
-
Yerushalmi, H. et al. (1995) Emre, an Escherichia-Coli 12-Kda multidrug transporter, exchanges toxic cations and H and is soluble in organic-solvents. J. Biol. Chem., 270, 6856-6863.
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 6856-6863
-
-
Yerushalmi, H.1
-
33
-
-
84897951003
-
PanGP: A tool for quickly analyzing bacterial pan-genome profile
-
Zhao, Y. et al. (2014) PanGP: a tool for quickly analyzing bacterial pan-genome profile. Bioinformatics, 30, 1297-1299.
-
(2014)
Bioinformatics
, vol.30
, pp. 1297-1299
-
-
Zhao, Y.1
|