-
1
-
-
79955559191
-
Genome sequencing of environmental escherichia coli expands understanding of the ecology and speciation of the model bacterial species
-
COI: 1:CAS:528:DC%2BC3MXlslyqtLw%3D
-
Luo, C. et al. Genome sequencing of environmental escherichia coli expands understanding of the ecology and speciation of the model bacterial species. Proc. Natl Acad. Sci. 108, 7200–7205 (2011)
-
(2011)
Proc. Natl Acad. Sci.
, vol.108
, pp. 7200-7205
-
-
Luo, C.1
-
2
-
-
84859499489
-
Population genomics of early events in the ecological differentiation of bacteria
-
COI: 1:CAS:528:DC%2BC38XkvV2rs7w%3D
-
Shapiro, B. J. et al. Population genomics of early events in the ecological differentiation of bacteria. Science 336, 48–51 (2012)
-
(2012)
Science
, vol.336
, pp. 48-51
-
-
Shapiro, B.J.1
-
3
-
-
33846555715
-
DNA-DNA hybridization values and their relationship to whole-genome sequence similarities
-
COI: 1:CAS:528:DC%2BD2sXitFGgs78%3D
-
Goris, J. et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57, 81–91 (2007)
-
(2007)
Int. J. Syst. Evol. Microbiol.
, vol.57
, pp. 81-91
-
-
Goris, J.1
-
4
-
-
14044262978
-
Genomic insights that advance the species definition for prokaryotes
-
COI: 1:CAS:528:DC%2BD2MXhvFKiurc%3D
-
Konstantinidis, K. T. & Tiedje, J. M. Genomic insights that advance the species definition for prokaryotes. Proc. Natl Acad. Sci. USA 102, 2567–2572 (2005)
-
(2005)
Proc. Natl Acad. Sci. U.S.A.
, vol.102
, pp. 2567-2572
-
-
Konstantinidis, K.T.1
Tiedje, J.M.2
-
5
-
-
84906272014
-
Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences
-
COI: 1:CAS:528:DC%2BC2cXhtlGnt7vI
-
Yarza, P. et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat. Rev. Microbiol. 12, 635 (2014)
-
(2014)
Nat. Rev. Microbiol.
, vol.12
, pp. 635
-
-
Yarza, P.1
-
6
-
-
84883464181
-
Accurate and universal delineation of prokaryotic species
-
COI: 1:CAS:528:DC%2BC3sXhtFOht7vJ
-
Mende, D. R., Sunagawa, S., Zeller, G. & Bork, P. Accurate and universal delineation of prokaryotic species. Nat. Methods 10, 881 (2013)
-
(2013)
Nat. Methods
, vol.10
, pp. 881
-
-
Mende, D.R.1
Sunagawa, S.2
Zeller, G.3
Bork, P.4
-
7
-
-
84946034354
-
Microbial species delineation using whole genome sequences
-
COI: 1:CAS:528:DC%2BC2MXhs1Kgsr%2FM
-
Varghese, N. J. et al. Microbial species delineation using whole genome sequences. Nucl. Acids Res. 43, 6761–6771 (2015)
-
(2015)
Nucl. Acids Res.
, vol.43
, pp. 6761-6771
-
-
Varghese, N.J.1
-
8
-
-
24944433946
-
Updating prokaryotic taxonomy
-
Rosselló-Mora, R. Updating prokaryotic taxonomy. J. Bacteriol. 187, 6255–6257 (2005)
-
(2005)
J. Bacteriol.
, vol.187
, pp. 6255-6257
-
-
Rosselló-Mora, R.1
-
9
-
-
77950235480
-
The phylogenomic species concept
-
Staley, J. The phylogenomic species concept. Microbiol. Today 36, 80–83 (2009)
-
(2009)
Microbiol. Today
, vol.36
, pp. 80-83
-
-
Staley, J.1
-
10
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
COI: 1:CAS:528:DyaK2sXlvFyhu7w%3D
-
Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25, 3389–3402 (1997)
-
(1997)
Nucl. Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
-
11
-
-
84958251714
-
Edit distance cannot be computed in strongly subquadratic time (Unless SETH is false)
-
Eds Servedio, R. & Rubinfeld, R., ACM, Portland, Oregon, United States
-
Backurs, A. & Indyk, P. Edit distance cannot be computed in strongly subquadratic time (unless SETH is false). In Proc. forty-seventh annual ACM symposium on Theory of computing (Eds Servedio, R. & Rubinfeld, R.) 51–58 (ACM, Portland, Oregon, United States 2015)
-
(2015)
Proc. Forty-Seventh Annual ACM Symposium on Theory of Computing
, pp. 51-58
-
-
Backurs, A.1
Indyk, P.2
-
12
-
-
0036226603
-
BLAT—the BLAST-like alignment tool
-
COI: 1:CAS:528:DC%2BD38XivVemtLw%3D
-
Kent, W. J. BLAT—the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002)
-
(2002)
Genome Res.
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
13
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
COI: 1:CAS:528:DC%2BC3cXht1WhtbzM
-
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010)
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
14
-
-
84925021592
-
Fast and sensitive protein alignment using DIAMOND
-
COI: 1:CAS:528:DC%2BC2cXhvFKlsrzN
-
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59 (2015)
-
(2015)
Nat. Methods
, vol.12
, pp. 59
-
-
Buchfink, B.1
Xie, C.2
Huson, D.H.3
-
15
-
-
73149098333
-
Shifting the genomic gold standard for the prokaryotic species definition
-
COI: 1:CAS:528:DC%2BD1MXhsFGlsbbK
-
Richter, M. & Rosselló-Móra, R. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl Acad. Sci. 106, 19126–19131 (2009)
-
(2009)
Proc. Natl Acad. Sci.
, vol.106
, pp. 19126-19131
-
-
Richter, M.1
Rosselló-Móra, R.2
-
16
-
-
84976491899
-
The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes
-
Rodriguez-R, L. M. & Konstantinidis, K. T. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Prepr. 4, e1900v1 (2016)
-
(2016)
PeerJ Prepr.
, vol.4
, pp. e1900v1
-
-
Rodriguez-R, L.M.1
Konstantinidis, K.T.2
-
17
-
-
84960373245
-
OrthoANI: an improved algorithm and software for calculating average nucleotide identity
-
COI: 1:CAS:528:DC%2BC28XhvVyksr3O
-
Lee, I., Kim, Y. O., Park, S. -C. & Chun, J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int. J. Syst. Evol. Microbiol. 66, 1100–1103 (2016)
-
(2016)
Int. J. Syst. Evol. Microbiol.
, vol.66
, pp. 1100-1103
-
-
Lee, I.1
Kim, Y.O.2
Park, S.C.3
Chun, J.4
-
18
-
-
85012917775
-
A large-scale evaluation of algorithms to calculate average nucleotide identity
-
COI: 1:CAS:528:DC%2BC2sXivFalt7c%3D
-
Yoon, S. -H., Ha, S. -m, Lim, J., Kwon, S. & Chun, J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110, 1281–1286 (2017)
-
(2017)
Antonie Van Leeuwenhoek
, vol.110
, pp. 1281-1286
-
-
Yoon, S.H.1
Ha, S.2
Lim, J.3
Kwon, S.4
Chun, J.5
-
19
-
-
72949101201
-
A phylogeny-driven genomic encyclopaedia of bacteria and archaea
-
COI: 1:CAS:528:DC%2BD1MXhs1SktbbM
-
Wu, D. et al. A phylogeny-driven genomic encyclopaedia of bacteria and archaea. Nature 462, 1056–1060 (2009)
-
(2009)
Nature
, vol.462
, pp. 1056-1060
-
-
Wu, D.1
-
20
-
-
85024405108
-
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
-
Mukherjee, S. et al. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nat. Biotechnol. 7, 676–683 (2017)
-
(2017)
Nat. Biotechnol.
, vol.7
, pp. 676-683
-
-
Mukherjee, S.1
-
22
-
-
85019066712
-
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
-
COI: 1:CAS:528:DC%2BC2sXhtFyjsrvI
-
Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27, 722–736 (2017)
-
(2017)
Genome Res.
, vol.27
, pp. 722-736
-
-
Koren, S.1
-
23
-
-
84930851165
-
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
-
COI: 1:CAS:528:DC%2BC2MXhtFaiurzN
-
Berlin, K. et al. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat. Biotechnol. 33, 623–630 (2015)
-
(2015)
Nat. Biotechnol.
, vol.33
, pp. 623-630
-
-
Berlin, K.1
-
24
-
-
85018448144
-
A fast approximate algorithm for mapping long reads to large reference databases
-
Springer, Hong Kong
-
Jain, C., Dilthey, A., Koren, S., Aluru, S. & Phillippy, A. M. A fast approximate algorithm for mapping long reads to large reference databases. In International Conference on Research in Computational Molecular Biology (Springer, Hong Kong, 2017)
-
(2017)
International Conference on Research in Computational Molecular Biology
-
-
Jain, C.1
Dilthey, A.2
Koren, S.3
Aluru, S.4
Phillippy, A.M.5
-
25
-
-
84978998700
-
Mash: fast genome and metagenome distance estimation using minhash
-
Ondov, B. D. et al. Mash: fast genome and metagenome distance estimation using minhash. Genome Biol. 17, 132 (2016)
-
(2016)
Genome Biol.
, vol.17
-
-
Ondov, B.D.1
-
26
-
-
85034643980
-
dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
-
COI: 1:CAS:528:DC%2BC2sXhvVeiur7K
-
Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J 11, 2864–2868 (2017)
-
(2017)
The ISME Journal
, vol.11
, Issue.12
, pp. 2864-2868
-
-
Olm, M.R.1
Brown, C.T.2
Brooks, B.3
Banfield, J.F.4
-
27
-
-
85029026923
-
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
-
COI: 1:CAS:528:DC%2BC2sXhvV2isLnK
-
Parks, D. H. et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat. Microbiol. 2, 1533 (2017)
-
(2017)
Nat. Microbiol.
, vol.2
, pp. 1533
-
-
Parks, D.H.1
-
28
-
-
3543051830
-
Mauve: multiple alignment of conserved genomic sequence with rearrangements
-
COI: 1:CAS:528:DC%2BD2cXlvFWjtb8%3D
-
Darling, A. C., Mau, B., Blattner, F. R. & Perna, N. T. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394–1403 (2004)
-
(2004)
Genome Res.
, vol.14
, pp. 1394-1403
-
-
Darling, A.C.1
Mau, B.2
Blattner, F.R.3
Perna, N.T.4
-
29
-
-
0038752612
-
Genome sequence of bacillus cereus and comparative analysis with bacillus anthracis
-
Natalia, I. et al. Genome sequence of bacillus cereus and comparative analysis with bacillus anthracis. Nature 423, 87 (2003)
-
(2003)
Nature
, vol.423
, pp. 87
-
-
Natalia, I.1
-
30
-
-
2942538300
-
Versatile and open software for comparing large genomes
-
Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004)
-
(2004)
Genome Biol.
, vol.5
-
-
Kurtz, S.1
-
31
-
-
84893511241
-
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
-
COI: 1:CAS:528:DC%2BC2cXhtlClsr7I
-
Kim, M., Oh, H. -S., Park, S. -C. & Chun, J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int. J. Syst. Evol. Microbiol. 64, 346–351 (2014)
-
(2014)
Int. J. Syst. Evol. Microbiol.
, vol.64
, pp. 346-351
-
-
Kim, M.1
Oh, H.S.2
Park, S.C.3
Chun, J.4
-
32
-
-
84856582558
-
Bacterial species may exist, metagenomics reveal
-
COI: 1:CAS:528:DC%2BC38XksVamsr0%3D
-
Caro-Quintero, A. & Konstantinidis, K. T. Bacterial species may exist, metagenomics reveal. Environ. Microbiol. 14, 347–355 (2012)
-
(2012)
Environ. Microbiol.
, vol.14
, pp. 347-355
-
-
Caro-Quintero, A.1
Konstantinidis, K.T.2
-
33
-
-
59849086092
-
The bacterial species challenge: making sense of genetic and ecological diversity
-
COI: 1:CAS:528:DC%2BD1MXhtlert7w%3D
-
Fraser, C., Alm, E. J., Polz, M. F., Spratt, B. G. & Hanage, W. P. The bacterial species challenge: making sense of genetic and ecological diversity. Science 323, 741–746 (2009)
-
(2009)
Science
, vol.323
, pp. 741-746
-
-
Fraser, C.1
Alm, E.J.2
Polz, M.F.3
Spratt, B.G.4
Hanage, W.P.5
-
34
-
-
0035527404
-
Bacterial species and speciation
-
COI: 1:STN:280:DC%2BD38zntVOmtg%3D%3D
-
Cohan, F. M. Bacterial species and speciation. Syst. Biol. 50, 513–524 (2001)
-
(2001)
Syst. Biol.
, vol.50
, pp. 513-524
-
-
Cohan, F.M.1
-
35
-
-
33751217150
-
The bacterial species definition in the genomic era
-
Konstantinidis, K. T., Ramette, A. & Tiedje, J. M. The bacterial species definition in the genomic era. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361, 1929–1940 (2006)
-
(2006)
Philos. Trans. R. Soc. Lond. B Biol. Sci.
, vol.361
, pp. 1929-1940
-
-
Konstantinidis, K.T.1
Ramette, A.2
Tiedje, J.M.3
-
36
-
-
57549111277
-
The dynamic genetic repertoire of microbial communities
-
Wilmes, P., Simmons, S. L., Denef, V. J. & Banfield, J. F. The dynamic genetic repertoire of microbial communities. FEMS Microbiol. Rev. 33, 109–132 (2008)
-
(2008)
FEMS Microbiol. Rev.
, vol.33
, pp. 109-132
-
-
Wilmes, P.1
Simmons, S.L.2
Denef, V.J.3
Banfield, J.F.4
-
38
-
-
33750998520
-
Toward a more robust assessment of intraspecies diversity, using fewer genetic markers
-
COI: 1:CAS:528:DC%2BD28Xht1Gksr3P
-
Konstantinidis, K. T., Ramette, A. & Tiedje, J. M. Toward a more robust assessment of intraspecies diversity, using fewer genetic markers. Appl. Environ. Microbiol. 72, 7286–7293 (2006)
-
(2006)
Appl. Environ. Microbiol.
, vol.72
, pp. 7286-7293
-
-
Konstantinidis, K.T.1
Ramette, A.2
Tiedje, J.M.3
-
39
-
-
77956519355
-
genoPlotR: comparative gene and genome visualization in R
-
COI: 1:CAS:528:DC%2BC3cXhtFGhu7zN
-
Guy, L., Roat Kultima, J. & Andersson, S. G. genoPlotR: comparative gene and genome visualization in R. Bioinformatics 26, 2334–2335 (2010)
-
(2010)
Bioinformatics
, vol.26
, pp. 2334-2335
-
-
Guy, L.1
Roat Kultima, J.2
Andersson, S.G.3
|