-
1
-
-
84856023505
-
Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle
-
Sobetzko P, Travers A, Muskhelishvili G. 2012. Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle. Proc. Natl. Acad. Sci. U. S. A. 109:E42–E50. http://dx.doi.org/10.1073/pnas.1108229109.
-
(2012)
Proc. Natl. Acad. Sci. U. S. A
, vol.109
, pp. E42-E50
-
-
Sobetzko, P.1
Travers, A.2
Muskhelishvili, G.3
-
2
-
-
77954242830
-
Spatial organization of the flow of genetic information in bacteria
-
Montero Llopis P, Jackson AF, Sliusarenko O, Surovtsev I, Heinritz J, Emonet T, Jacobs-Wagner C. 2010. Spatial organization of the flow of genetic information in bacteria. Nature 466:77–81. http://dx.doi.org/10.1038/nature09152.
-
(2010)
Nature
, vol.466
, pp. 77-81
-
-
Montero Llopis, P.1
Jackson, A.F.2
Sliusarenko, O.3
Surovtsev, I.4
Heinritz, J.5
Emonet, T.6
Jacobs-Wagner, C.7
-
4
-
-
25444524604
-
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial “pan-genome
-
Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, MargarityRos I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O’Connor KJ, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc. Natl. Acad. Sci. U. S. A. 102:13950-13955. http://dx.doi.org/10.1073/pnas.0506758102.
-
(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
Angiuoli, S.V.7
Crabtree, J.8
Jones, A.L.9
Durkin, A.S.10
Deboy, R.T.11
Davidsen, T.M.12
Mora, M.13
Scarselli, M.14
Margarityros, I.15
Peterson, J.D.16
Hauser, C.R.17
Sundaram, J.P.18
Nelson, W.C.19
Madupu, R.20
Brinkac, L.M.21
Dodson, R.J.22
Rosovitz, M.J.23
Sullivan, S.A.24
Daugherty, S.C.25
Haft, D.H.26
Selengut, J.27
Gwinn, M.L.28
Zhou, L.29
Zafar, N.30
Khouri, H.31
Radune, D.32
Dimitrov, G.33
Watkins, K.34
O’Connor, K.J.35
Smith, S.36
Utterback, T.R.37
White, O.38
Rubens, C.E.39
Grandi, G.40
Madoff, L.C.41
Kasper, D.L.42
Telford, J.L.43
Wessels, M.R.44
Rappuoli, R.45
Fraser, C.M.46
more..
-
5
-
-
33644700003
-
Toward automatic reconstruction of a highly resolved tree of life
-
Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283–1287. http://dx.doi.org/10.1126/science.1123061.
-
(2006)
Science
, vol.311
, pp. 1283-1287
-
-
Ciccarelli, F.D.1
Doerks, T.2
Von Mering, C.3
Creevey, C.J.4
Snel, B.5
Bork, P.6
-
6
-
-
3042849253
-
Biased biological functions of horizontally transferred genes in prokaryotic genomes
-
Nakamura Y, Itoh T, Matsuda H, Gojobori T. 2004. Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat. Genet. 36:760–766. http://dx.doi.org/10.1038/ng1381.
-
(2004)
Nat. Genet
, vol.36
, pp. 760-766
-
-
Nakamura, Y.1
Itoh, T.2
Matsuda, H.3
Gojobori, T.4
-
7
-
-
84868289569
-
Gene location and DNA density determine transcription factor distributions in Escherichia coli
-
Kuhlman TE, Cox EC. 2012. Gene location and DNA density determine transcription factor distributions in Escherichia coli. Mol. Syst. Biol. 8:610. http://dx.doi.org/10.1038/msb.2012.42.
-
(2012)
Mol. Syst. Biol
, vol.8
, pp. 610
-
-
Kuhlman, T.E.1
Cox, E.C.2
-
8
-
-
36249021315
-
Genome-wide experimental determination of barriers to horizontal gene transfer
-
Sorek R, Zhu Y, Creevey CJ, Francino MP, Bork P, Rubin EM. 2007. Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318:1449-1452. http://dx.doi.org/10.1126/science.1147112.
-
(2007)
Science
, vol.318
, pp. 1449-1452
-
-
Sorek, R.1
Zhu, Y.2
Creevey, C.J.3
Francino, M.P.4
Bork, P.5
Rubin, E.M.6
-
9
-
-
28444475529
-
Adaptive evolution of bacterial metabolic networks by horizontal gene transfer
-
Pál C, Papp B, Lercher MJ. 2005. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat. Genet. 37:1372–1375. http://dx.doi.org/10.1038/ng1686.
-
(2005)
Nat. Genet
, vol.37
, pp. 1372-1375
-
-
Pál, C.1
Papp, B.2
Lercher, M.J.3
-
10
-
-
59249089471
-
Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
-
Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, Calteau A, Chiapello H, Clermont O, Cruveiller S, Danchin A, Diard M, Dossat C, Karoui ME, Frapy E, Garry L, Ghigo JM, Gilles AM, Johnson J, Le Bouguénec C, Lescat M, Mangenot S, Martinez-Jéhanne V, Matic I, Nassif X, Oztas S, Petit MA, Pichon C, Rouy Z, Ruf CS, Schneider D, Tourret J, Vacherie B, Vallenet D, Médigue C, Rocha EP, Denamur E. 2009. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 5:e1000344. http://dx.doi.org/10.1371/journal.pgen.1000344.
-
(2009)
Plos Genet
, vol.5
, pp. 10003
-
-
Touchon, M.1
Hoede, C.2
Tenaillon, O.3
Barbe, V.4
Baeriswyl, S.5
Bidet, P.6
Bingen, E.7
Bonacorsi, S.8
Bouchier, C.9
Bouvet, O.10
Calteau, A.11
Chiapello, H.12
Clermont, O.13
Cruveiller, S.14
Danchin, A.15
Diard, M.16
Dossat, C.17
Karoui, M.E.18
Frapy, E.19
Garry, L.20
Ghigo, J.M.21
Gilles, A.M.22
Johnson, J.23
Le Bouguénec, C.24
Lescat, M.25
Mangenot, S.26
Martinez-Jéhanne, V.27
Matic, I.28
Nassif, X.29
Oztas, S.30
Petit, M.A.31
Pichon, C.32
Rouy, Z.33
Ruf, C.S.34
Schneider, D.35
Tourret, J.36
Vacherie, B.37
Vallenet, D.38
Médigue, C.39
Rocha, E.P.40
Denamur, E.41
more..
-
12
-
-
0942279509
-
Chromosomal constraints in Gram-positive bacteria revealed by artificial inversions
-
Campo N, Dias MJ, Daveran-Mingot ML, Ritzenthaler P, Le Bourgeois P. 2004. Chromosomal constraints in Gram-positive bacteria revealed by artificial inversions. Mol. Microbiol. 51:511–522. http://dx.doi.org/10.1046/j.1365-2958.2003.03847.x.
-
(2004)
Mol. Microbiol
, vol.51
, pp. 511-522
-
-
Campo, N.1
Dias, M.J.2
Daveran-Mingot, M.L.3
Ritzenthaler, P.4
Le Bourgeois, P.5
-
13
-
-
37749029027
-
Chromosome structuring limits genome plasticity in Escherichia coli
-
Esnault E, Valens M, Espéli O, Boccard F. 2007. Chromosome structuring limits genome plasticity in Escherichia coli. PLoS Genet. 3:e226. http://dx.doi.org/10.1371/journal.pgen.0030226.
-
(2007)
Plos Genet
, vol.3
-
-
Esnault, E.1
Valens, M.2
Espéli, O.3
Boccard, F.4
-
14
-
-
84896298536
-
Bacterial genome instability
-
Darmon E, Leach DR. 2014. Bacterial genome instability. Microbiol. Mol. Biol. Rev. 78:1–39. http://dx.doi.org/10.1128/MMBR.00035-13.
-
(2014)
Microbiol. Mol. Biol. Rev
, vol.78
, pp. 1-39
-
-
Darmon, E.1
Leach, D.R.2
-
15
-
-
48249144818
-
Dynamics of genome rearrangement in bacterial populations
-
Darling AE, Miklós I, Ragan MA. 2008. Dynamics of genome rearrangement in bacterial populations. PLoS Genet. 4:e1000128. http://dx.doi.org/10.1371/journal.pgen.1000128.
-
(2008)
Plos Genet
, vol.4
-
-
Darling, A.E.1
Miklós, I.2
Ragan, M.A.3
-
16
-
-
84862542765
-
Coordinated phenotype switching with large-scale chromosome flip-flop inversion observed in bacteria
-
Cui L, Neoh HM, Iwamoto A, Hiramatsu K. 2012. Coordinated phenotype switching with large-scale chromosome flip-flop inversion observed in bacteria. Proc. Natl. Acad. Sci. U. S. A. 109:E1647–E1656. http://dx.doi.org/10.1073/pnas.1204307109.
-
(2012)
Proc. Natl. Acad. Sci. U. S. A
, vol.109
, pp. E1647-E1656
-
-
Cui, L.1
Neoh, H.M.2
Iwamoto, A.3
Hiramatsu, K.4
-
17
-
-
0034568798
-
Evidence for symmetric chromosomal inversions around the replication origin in bacteria
-
1:Research0011
-
Eisen JA, Heidelberg JF, White O, Salzberg SL. 2000. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biol. 1:Research0011. http://dx.doi.org/10.1186/gb-2000-1-6-research0011.
-
(2000)
Genome Biol
-
-
Eisen, J.A.1
Heidelberg, J.F.2
White, O.3
Salzberg, S.L.4
-
18
-
-
84885390505
-
The evolution of genomic instability in the obligate endosymbionts of whiteflies
-
Sloan DB, Moran NA. 2013. The evolution of genomic instability in the obligate endosymbionts of whiteflies. Genome Biol. Evol. 5:783–793. http://dx.doi.org/10.1093/gbe/evt044.
-
(2013)
Genome Biol. Evol
, vol.5
, pp. 783-793
-
-
Sloan, D.B.1
Moran, N.A.2
-
19
-
-
84880888580
-
Comparison of the complete genome sequence of two closely related isolates of “Candidatus Phytoplasma australiense” reveals genome plasticity
-
Andersen MT, Liefting LW, Havukkala I, Beever RE. 2013. Comparison of the complete genome sequence of two closely related isolates of “Candidatus Phytoplasma australiense” reveals genome plasticity. BMC Genomics 14:529. http://dx.doi.org/10.1186/1471-2164-14-529.
-
(2013)
BMC Genomics
, vol.14
, pp. 529
-
-
Andersen, M.T.1
Liefting, L.W.2
Havukkala, I.3
Beever, R.E.4
-
20
-
-
84895810887
-
Phylo SI: A new genomewide approach for prokaryotic phylogeny
-
Shifman A, Ninyo N, Gophna U, Snir S. 2014. Phylo SI: a new genomewide approach for prokaryotic phylogeny. Nucleic Acids Res. 42: 2391–2404. http://dx.doi.org/10.1093/nar/gkt1138.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 2391-2404
-
-
Shifman, A.1
Ninyo, N.2
Gophna, U.3
Snir, S.4
-
21
-
-
84879171367
-
Short and long-term genome stability analysis of prokaryotic genomes
-
Brilli M, Liò P, Lacroix V, Sagot MF. 2013. Short and long-term genome stability analysis of prokaryotic genomes. BMC Genomics 14:309. http://dx.doi.org/10.1186/1471-2164-14-309.
-
(2013)
BMC Genomics
, vol.14
, pp. 309
-
-
Brilli, M.1
Liò, P.2
Lacroix, V.3
Sagot, M.F.4
-
22
-
-
0036709941
-
Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?
-
Rocha E. 2002. Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes? Trends Microbiol. 10:393–395. http://dx.doi.org/10.1016/S0966-842X(02)02420-4.
-
(2002)
Trends Microbiol
, vol.10
, pp. 393-395
-
-
Rocha, E.1
-
23
-
-
33947177875
-
Comparative analysis of eubacterial DNA polymerase III alpha subunits
-
Zhao XQ, Hu JF, Yu J. 2006. Comparative analysis of eubacterial DNA polymerase III alpha subunits. Genomics Proteomics Bioinformatics 4:203–211. http://dx.doi.org/10.1016/S1672-0229(07)60001-1.
-
(2006)
Genomics Proteomics Bioinformatics
, vol.4
, pp. 203-211
-
-
Zhao, X.Q.1
Hu, J.F.2
Yu, J.3
-
24
-
-
84855498305
-
On the molecular mechanism of GC content variation among eubacterial genomes
-
Wu H, Zhang Z, Hu S, Yu J. 2012. On the molecular mechanism of GC content variation among eubacterial genomes. Biol. Direct 7:2. http://dx.doi.org/10.1186/1745-6150-7-2.
-
(2012)
Biol. Direct
, vol.7
, pp. 2
-
-
Wu, H.1
Zhang, Z.2
Hu, S.3
Yu, J.4
-
25
-
-
3142679507
-
The replication-related organization of bacterial genomes
-
Rocha EP. 2004. The replication-related organization of bacterial genomes. Microbiology 150:1609-1627. http://dx.doi.org/10.1099/mic.0.26974-0.
-
(2004)
Microbiology
, vol.150
, pp. 1609-1627
-
-
Rocha, E.P.1
-
26
-
-
0344668838
-
Gene essentiality determines chromosome organisation in bacteria
-
Rocha EP, Danchin A. 2003. Gene essentiality determines chromosome organisation in bacteria. Nucleic Acids Res. 31:6570-6577. http://dx.doi.org/10.1093/nar/gkg859.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 6570-6577
-
-
Rocha, E.P.1
Danchin, A.2
-
27
-
-
65549146767
-
Population genomics and the bacterial species concept
-
Riley MA, Lizotte-Waniewski M. 2009. Population genomics and the bacterial species concept. Methods Mol. Biol. 532:367–377. http://dx.doi.org/10.1007/978-1-60327-853-9_21.
-
(2009)
Methods Mol. Biol
, vol.532
, pp. 367-377
-
-
Riley, M.A.1
Lizotte-Waniewski, M.2
-
28
-
-
2942679276
-
Small change: Keeping pace with microevolution
-
Feil EJ. 2004. Small change: keeping pace with microevolution. Nat. Rev. Microbiol. 2:483–495. http://dx.doi.org/10.1038/nrmicro904.
-
(2004)
Nat. Rev. Microbiol
, vol.2
, pp. 483-495
-
-
Feil, E.J.1
-
29
-
-
80052939924
-
Use of a coenzyme by the glmS ribozymeriboswitch suggests primordial expansion of RNA chemistry by small molecules
-
Ferré-D’Amaré AR. 2011. Use of a coenzyme by the glmS ribozymeriboswitch suggests primordial expansion of RNA chemistry by small molecules. Philos. Trans. R. Soc. Lond. B Biol. Sci. 366:2942–2948. http://dx.doi.org/10.1098/rstb.2011.0131.
-
(2011)
Philos. Trans. R. Soc. Lond. B Biol. Sci
, vol.366
, pp. 2942-2948
-
-
Ferré-D’amaré, A.R.1
-
30
-
-
78149403030
-
Origin and evolution of the ribosome
-
Fox GE. 2010. Origin and evolution of the ribosome. Cold Spring Harb. Perspect. Bi o l2: a003483. http://dx.doi.org/10.1101/cshperspect.a003483.
-
(2010)
Cold Spring Harb. Perspect. Bi O
, vol.12
-
-
Fox, G.E.1
-
31
-
-
84055224165
-
Similarity of genes horizontally acquired by Escherichia coli and Salmonella enterica is evidence of a supraspecies pangenome
-
Karberg KA, Olsen GJ, Davis JJ. 2011. Similarity of genes horizontally acquired by Escherichia coli and Salmonella enterica is evidence of a supraspecies pangenome. Proc. Natl. Acad. Sci. U. S. A. 108:20154–20159. http://dx.doi.org/10.1073/pnas.1109451108.
-
(2011)
Proc. Natl. Acad. Sci. U. S. A
, vol.108
, pp. 20154-20159
-
-
Karberg, K.A.1
Olsen, G.J.2
Davis, J.J.3
-
32
-
-
84862827380
-
Codon deviation coefficient: A novel measure for estimating codon usage bias and its statistical significance
-
Zhang Z, Li J, Cui P, Ding F, Li A, Townsend JP, Yu J. 2012. Codon deviation coefficient: a novel measure for estimating codon usage bias and its statistical significance. BMC Bioinformatics 13:43. http://dx.doi.org/10.1186/1471-2105-13-43.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 43
-
-
Zhang, Z.1
Li, J.2
Cui, P.3
Ding, F.4
Li, A.5
Townsend, J.P.6
Yu, J.7
-
33
-
-
28444475529
-
Adaptive evolution of bacterial metabolic networks by horizontal gene transfer
-
Pál C, Papp B, Lercher MJ. 2005. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat. Genet. 37:1372–1375. http://dx.doi.org/10.1038/ng1686.
-
(2005)
Nat. Genet
, vol.37
, pp. 1372-1375
-
-
Pál, C.1
Papp, B.2
Lercher, M.J.3
-
34
-
-
84880798154
-
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
-
Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10:563–569. http://dx.doi.org/10.1038/nmeth.2474.
-
(2013)
Nat. Methods
, vol.10
, pp. 563-569
-
-
Chin, C.S.1
Alexander, D.H.2
Marks, P.3
Klammer, A.A.4
Drake, J.5
Heiner, C.6
Clum, A.7
Copeland, A.8
Huddleston, J.9
Eichler, E.E.10
Turner, S.W.11
Korlach, J.12
-
35
-
-
84856571322
-
PGAP: Pan-genomes analysis pipeline
-
Zhao Y, Wu J, Yang J, Sun S, Xiao J, Yu J. 2012. PGAP: pan-genomes analysis pipeline. Bioinformatics 28:416–418. http://dx.doi.org/10.1093/bioinformatics/bts416.
-
(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
|