-
1
-
-
43849099955
-
Microbiology in the post-genomic era
-
Medini, D. et al. Microbiology in the post-genomic era. Nat. Rev. Microbiol. 6, 419-430 (2008).
-
(2008)
Nat. Rev. Microbiol
, vol.6
, pp. 419-430
-
-
Medini, D.1
-
2
-
-
80054924581
-
Bacterial epidemiology and biology-lessons from genome sequencing
-
Parkhill, J. & Wren, B.W. Bacterial epidemiology and biology-lessons from genome sequencing. Genome Biol. 12, 230 (2011).
-
(2011)
Genome Biol
, vol.12
, pp. 230
-
-
Parkhill, J.1
Wren, B.W.2
-
3
-
-
84861125187
-
Genome-scale genetic manipulation methods for exploring bacterial molecular biology
-
Gagarinova, A. & Emili, A. Genome-scale genetic manipulation methods for exploring bacterial molecular biology. Mol. Biosyst. 8, 1626-1638 (2012).
-
(2012)
Mol. Biosyst
, vol.8
, pp. 1626-1638
-
-
Gagarinova, A.1
Emili, A.2
-
4
-
-
84865179264
-
High-throughput bacterial genome sequencing: An embarrassment of choice, a world of opportunity
-
Loman, N.J. et al. High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat. Rev. Microbiol. 10, 599-606 (2012).
-
(2012)
Nat. Rev. Microbiol
, vol.10
, pp. 599-606
-
-
Loman, N.J.1
-
5
-
-
84865363124
-
The limitations of draft assemblies for understanding prokaryotic adaptation and evolution
-
Ricker, N., Qian, H. & Fulthorpe, R.R. The limitations of draft assemblies for understanding prokaryotic adaptation and evolution. Genomics 100, 167-175 (2012).
-
(2012)
Genomics
, vol.100
, pp. 167-175
-
-
Ricker, N.1
Qian, H.2
Fulthorpe, R.R.3
-
6
-
-
33748876971
-
Insertion sequences in prokaryotic genomes
-
Siguier, P., Filée, J. & Chandler, M. Insertion sequences in prokaryotic genomes. Curr. Opin. Microbiol. 9, 526-531 (2006).
-
(2006)
Curr. Opin. Microbiol
, vol.9
, pp. 526-531
-
-
Siguier, P.1
Filée, J.2
Chandler, M.3
-
7
-
-
76949108806
-
The phasevarion: Phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes
-
Srikhanta, Y.N., Fox, K.L. & Jennings, M.P. The phasevarion: phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes. Nat. Rev. Microbiol. 8, 196-206 (2010).
-
(2010)
Nat. Rev. Microbiol
, vol.8
, pp. 196-206
-
-
Srikhanta, Y.N.1
Fox, K.L.2
Jennings, M.P.3
-
8
-
-
84855906559
-
Prokaryote genome fluidity: Toward a system approach of the mobilome
-
Toussaint, A. & Chandler, M. Prokaryote genome fluidity: toward a system approach of the mobilome. Methods Mol. Biol. 804, 57-80 (2012).
-
(2012)
Methods Mol. Biol.
, vol.804
, pp. 57-80
-
-
Toussaint, A.1
Chandler, M.2
-
9
-
-
76749117156
-
Assembly complexity of prokaryotic genomes using short reads
-
Kingsford, C., Schatz, M.C. & Pop, M. Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics 11, 21 (2010).
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 21
-
-
Kingsford, C.1
Schatz, M.C.2
Pop, M.3
-
10
-
-
84857893016
-
GAGE: A critical evaluation of genome assemblies and assembly algorithms
-
Salzberg, S.L. et al. GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res. 22, 557-567 (2012).
-
(2012)
Genome Res
, vol.22
, pp. 557-567
-
-
Salzberg, S.L.1
-
11
-
-
0036889014
-
The value of complete microbial genome sequencing (you get what you pay for)
-
Fraser, C.M., Eisen, J.A., Nelson, K.E., Paulsen, I.T. & Salzberg, S.L. The value of complete microbial genome sequencing (you get what you pay for). J. Bacteriol. 184, 6403-6405 (2002).
-
(2002)
J. Bacteriol
, vol.184
, pp. 6403-6405
-
-
Fraser, C.M.1
Eisen, J.A.2
Nelson, K.E.3
Paulsen, I.T.4
Salzberg, S.L.5
-
12
-
-
84869814079
-
Mind the gap: Upgrading genomes with Pacific Biosciences RS long-read sequencing technology
-
English, A.C. et al. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS ONE 7, e47768 (2012).
-
(2012)
PLoS ONE
, vol.7
-
-
English, A.C.1
-
13
-
-
80052150179
-
Origins of the E. Coli strain causing an outbreak of hemolytic-uremic syndrome in Germany
-
Rasko, D.A. et al. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N. Engl. J. Med. 365, 709-717 (2011).
-
(2011)
N. Engl. J. Med
, vol.365
, pp. 709-717
-
-
Rasko, D.A.1
-
14
-
-
84863664355
-
A hybrid approach for the automated finishing of bacterial genomes
-
Bashir, A. et al. A hybrid approach for the automated finishing of bacterial genomes. Nat. Biotechnol. 30, 701-707 (2012).
-
(2012)
Nat. Biotechnol
, vol.30
, pp. 701-707
-
-
Bashir, A.1
-
15
-
-
84863651532
-
Hybrid error correction and de novo assembly of single-molecule sequencing reads
-
Koren, S. et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat. Biotechnol. 30, 693-700 (2012).
-
(2012)
Nat. Biotechnol
, vol.30
, pp. 693-700
-
-
Koren, S.1
-
16
-
-
84868327508
-
Finished bacterial genomes from shotgun sequence data
-
Ribeiro, F.J. et al. Finished bacterial genomes from shotgun sequence data. Genome Res. 22, 2270-2277 (2012).
-
(2012)
Genome Res
, vol.22
, pp. 2270-2277
-
-
Ribeiro, F.J.1
-
17
-
-
33947398002
-
Minimus: A fast, lightweight genome assembler
-
Sommer, D.D., Delcher, A.L., Salzberg, S.L. & Pop, M. Minimus: a fast, lightweight genome assembler. BMC Bioinformatics 8, 64 (2007).
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 64
-
-
Sommer, D.D.1
Delcher, A.L.2
Salzberg, S.L.3
Pop, M.4
-
18
-
-
80051972336
-
Next generation sequence assembly with AMOS
-
Treangen, T.J., Sommer, D.D., Angly, F.E., Koren, S. & Pop, M. Next generation sequence assembly with AMOS. Curr. Protoc. Bioinformatics 33, 118 (2011).
-
(2011)
Curr. Protoc. Bioinformatics
, vol.33
, pp. 118
-
-
Treangen, T.J.1
Sommer, D.D.2
Angly, F.E.3
Koren, S.4
Pop, M.5
-
19
-
-
15444350252
-
The complete genome sequence of Escherichia coli K-12
-
Blattner, F.R. et al. The complete genome sequence of Escherichia coli K-12. Science 277, 1453-1462 (1997).
-
(1997)
Science
, vol.277
, pp. 1453-1462
-
-
Blattner, F.R.1
-
20
-
-
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
-
21
-
-
80053364713
-
Complete genome sequence of Meiothermus ruber type strain (21T)
-
Tindall, B.J. et al. Complete genome sequence of Meiothermus ruber type strain (21T). Stand. Genomic Sci. 3, 26-36 (2010).
-
(2010)
Stand. Genomic Sci
, vol.3
, pp. 26-36
-
-
Tindall, B.J.1
-
22
-
-
77957104084
-
Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3T)
-
Han, C. et al. Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3T). Stand. Genomic Sci. 1, 54-62 (2009).
-
(2009)
Stand. Genomic Sci
, vol.1
, pp. 54-62
-
-
Han, C.1
-
23
-
-
79954672317
-
Genome structural variation discovery and genotyping
-
Alkan, C., Coe, B.P. & Eichler, E.E. Genome structural variation discovery and genotyping. Nat. Rev. Genet. 12, 363-376 (2011).
-
(2011)
Nat. Rev. Genet
, vol.12
, pp. 363-376
-
-
Alkan, C.1
Coe, B.P.2
Eichler, E.E.3
-
24
-
-
84858123725
-
Advances in BAC-based physical mapping and map integration strategies in plants
-
184854
-
Ariyadasa, R. & Stein, N. Advances in BAC-based physical mapping and map integration strategies in plants. J. Biomed. Biotechnol. 2012, 184854 (2012).
-
(2012)
J. Biomed. Biotechnol
-
-
Ariyadasa, R.1
Stein, N.2
-
25
-
-
66049147797
-
Comparative analysis of Alu repeats in primate genomes
-
Liu, G.E., Alkan, C., Jiang, L., Zhao, S. & Eichler, E.E. Comparative analysis of Alu repeats in primate genomes. Genome Res. 19, 876-885 (2009).
-
(2009)
Genome Res
, vol.19
, pp. 876-885
-
-
Liu, G.E.1
Alkan, C.2
Jiang, L.3
Zhao, S.4
Eichler, E.E.5
-
26
-
-
77956125365
-
A flexible and efficient template format for circular consensus sequencing and SNP detection
-
Travers, K.J., Chin, C.S., Rank, D.R., Eid, J.S. & Turner, S.W. A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res. 38, e159 (2010).
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Travers, K.J.1
Chin, C.S.2
Rank, D.R.3
Eid, J.S.4
Turner, S.W.5
-
27
-
-
0031955518
-
Base-calling of automated sequencer traces using phred I. Accuracy assessment
-
Ewing, B., Hillier, L., Wendl, M.C. & Green, P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175-185 (1998).
-
(1998)
Genome Res
, vol.8
, pp. 175-185
-
-
Ewing, B.1
Hillier, L.2
Wendl, M.C.3
Green, P.4
-
28
-
-
0032519307
-
Automating the identification of DNA variations using quality-based fluorescence re-sequencing: Analysis of the human mitochondrial genome
-
Rieder, M.J., Taylor, S.L., Tobe, V.O. & Nickerson, D.A. Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genome. Nucleic Acids Res. 26, 967-973 (1998).
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 967-973
-
-
Rieder, M.J.1
Taylor, S.L.2
Tobe, V.O.3
Nickerson, D.A.4
-
29
-
-
84871392152
-
Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene
-
Loomis, E.W. et al. Sequencing the unsequenceable: expanded CGG-repeat alleles of the fragile X gene. Genome Res. 23, 121-128 (2013).
-
(2013)
Genome Res
, vol.23
, pp. 121-128
-
-
Loomis, E.W.1
-
30
-
-
84863886793
-
Improving genome assemblies by sequencing PCR products with PacBio
-
Zhang, X. et al. Improving genome assemblies by sequencing PCR products with PacBio. Biotechniques 53, 61-62 (2012).
-
(2012)
Biotechniques
, vol.53
, pp. 61-62
-
-
Zhang, X.1
-
31
-
-
84864518203
-
Pacific Biosciences sequencing technology for genotyping and variation discovery in human data
-
Carneiro, M.O. et al. Pacific Biosciences sequencing technology for genotyping and variation discovery in human data. BMC Genomics 13, 375 (2012).
-
(2012)
BMC Genomics
, vol.13
, pp. 375
-
-
Carneiro, M.O.1
-
32
-
-
70349866672
-
Genome project standards in a new era of sequencing
-
Chain, P.S.G. et al. Genome project standards in a new era of sequencing. Science 326, 236-237 (2009).
-
(2009)
Science
, vol.326
, pp. 236-237
-
-
Chain, P.S.G.1
-
33
-
-
84871222928
-
The methylomes of six bacteria
-
Murray, I.A. et al. The methylomes of six bacteria. Nucleic Acids Res. 40, 11450-11462 (2012).
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 11450-11462
-
-
Murray, I.A.1
-
34
-
-
77949512406
-
Tablet-next generation sequence assembly visualization
-
Milne, I. et al. Tablet-next generation sequence assembly visualization. Bioinformatics 26, 401-402 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 401-402
-
-
Milne, I.1
-
35
-
-
34249734822
-
A rapid and sensitive tool for creating dotplots on genome scale
-
Krumsiek, J., Arnold, R. & Rattei, T. Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics 23, 1026-1028 (2007).
-
(2007)
Bioinformatics
, vol.23
, pp. 1026-1028
-
-
Krumsiek, J.1
Arnold, R.2
Gepard, R.T.3
-
36
-
-
84866266717
-
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): Application and theory
-
Chaisson, M.J. & Tesler, G. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics 13, 238 (2012).
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 238
-
-
Chaisson, M.J.1
Tesler, G.2
-
37
-
-
0036203448
-
Multiple sequence alignment using partial order graphs
-
Lee, C., Grasso, C. & Sharlow, M.F. Multiple sequence alignment using partial order graphs. Bioinformatics 18, 452-464 (2002).
-
(2002)
Bioinformatics
, vol.18
, pp. 452-464
-
-
Lee, C.1
Grasso, C.2
Sharlow, M.F.3
-
38
-
-
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, 1792-1797 (2004).
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
39
-
-
65449134298
-
A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads
-
Rausch, T. et al. A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. Bioinformatics 25, 1118-1124 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1118-1124
-
-
Rausch, T.1
-
40
-
-
0029933276
-
An improved sequence assembly program
-
Huang, X. An improved sequence assembly program. Genomics 33, 21-31 (1996).
-
(1996)
Genomics
, vol.33
, pp. 21-31
-
-
Huang, X.1
-
41
-
-
78649358717
-
Quake quality-aware detection and correction of sequencing errors
-
Kelley, D.R., Schatz, M.C. & Salzberg, S.L. Quake: quality-aware detection and correction of sequencing errors. Genome Biol. 11, R116 (2010).
-
(2010)
Genome Biol
, vol.11
-
-
Kelley, D.R.1
Schatz, M.C.2
Salzberg, S.L.3
-
42
-
-
0034708758
-
A whole-genome assembly of Drosophila
-
Myers, E.W. et al. A whole-genome assembly of Drosophila. Science 287, 2196-2204 (2000).
-
(2000)
Science
, vol.287
, pp. 2196-2204
-
-
Myers, E.W.1
-
43
-
-
58149234737
-
Real-time DNA sequencing from single polymerase molecules
-
Eid, J. et al. Real-time DNA sequencing from single polymerase molecules. Science 323, 133-138 (2009).
-
(2009)
Science
, vol.323
, pp. 133-138
-
-
Eid, J.1
-
44
-
-
77957051540
-
Real-time DNA sequencing from single polymerase molecules
-
Korlach, J. et al. Real-time DNA sequencing from single polymerase molecules. Methods Enzymol. 472, 431-455 (2010).
-
(2010)
Methods Enzymol
, vol.472
, pp. 431-455
-
-
Korlach, J.1
|