-
1
-
-
0346434985
-
-
Alberts B, Bray D, Lewis J, Raff M, Roberts K and Watson J D 2008 Molecular Biology of the Cell (New York: Garland)
-
(2008)
Molecular Biology of the Cell
-
-
Alberts, B.1
Bray, D.2
Lewis, J.3
Raff, M.4
Roberts, K.5
Watson, J.D.6
-
2
-
-
0037381991
-
Increased bending rigidity of single DNA molecules by H-NS, a temperature and osmolarity sensor
-
Amit R, Oppenheim A B and Stavans J 2003 Increased bending rigidity of single DNA molecules by H-NS, a temperature and osmolarity sensor Biophys. J. 84 246773 (Pubitemid 36373568)
-
(2003)
Biophysical Journal
, vol.84
, Issue.4
, pp. 2467-2473
-
-
Amit, R.1
Oppenheim, A.B.2
Stavans, J.3
-
3
-
-
34848860442
-
Time scale of entropic segregation of flexible polymers in confinement: Implications for chromosome segregation in filamentous bacteria
-
DOI 10.1103/PhysRevE.76.031901
-
Arnold A and Jun S 2007 Time scale of entropic segregation of flexible polymers in confinement: implications for chromosome segregation in filamentous bacteria Phys. Rev. E 76 031901 (Pubitemid 47507103)
-
(2007)
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics
, vol.76
, Issue.3
, pp. 031901
-
-
Arnold, A.1
Jun, S.2
-
4
-
-
84863531078
-
-
(submitted)
-
Barbieri M, Chotalia M, Fraser J, Lavitas L-M, Dostie J, Pombo A and Nicodemi M 2011 Complexity of chromatin folding: the strings and binders switch model (submitted)
-
(2011)
Complexity of Chromatin Folding: The Strings and Binders Switch Model
-
-
Barbieri, M.1
Chotalia, M.2
Fraser, J.3
Lavitas, L.-M.4
Dostie, J.5
Pombo, A.6
Nicodemi, M.7
-
5
-
-
74149085645
-
Coordination of genomic structure and transcription by the main bacterial nucleoid-associated protein HU
-
10.1038/embor.2009.232 1469-221X
-
Berger M, Farcas A, Geertz M, Zhelyazkova P, Brix K, Travers A and Muskhelishvili G 2010 Coordination of genomic structure and transcription by the main bacterial nucleoid-associated protein HU EMBO Rep. 11 5964
-
(2010)
EMBO Rep.
, vol.11
, Issue.1
, pp. 59-64
-
-
Berger, M.1
Farcas, A.2
Geertz, M.3
Zhelyazkova, P.4
Brix, K.5
Travers, A.6
Muskhelishvili, G.7
-
6
-
-
52949111871
-
Spatial organization of a replicating bacterial chromosome
-
10.1073/pnas.0804982105 0027-8424
-
Berlatzky I A, Rouvinski A and Ben-Yehuda S 2008 Spatial organization of a replicating bacterial chromosome Proc. Natl Acad. Sci. USA 105 1413640
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, Issue.37
, pp. 14136-14140
-
-
Berlatzky, I.A.1
Rouvinski, A.2
Ben-Yehuda, S.3
-
7
-
-
0033954256
-
The Protein Data Bank
-
Berman H M, Westbrook J, Feng Z, Gilliland G, Bhat T N, Weissig H, Shindyalov I N and Bourne P E 2000 The protein data bank Nucl. Acids Res. 28 23542 (Pubitemid 30047768)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
8
-
-
33745612978
-
Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome
-
DOI 10.1038/sj.embor.7400729, PII 7400729
-
Blot N, Mavathur R, Geertz M, Travers A and Muskhelishvili G 2006 Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome Embo. Rep. 7 71015 (Pubitemid 43986268)
-
(2006)
EMBO Reports
, vol.7
, Issue.7
, pp. 710-715
-
-
Blot, N.1
Mavathur, R.2
Geertz, M.3
Travers, A.4
Muskhelishvili, G.5
-
9
-
-
34948885665
-
Effects of Fis on Escherichia coli gene expression during different growth stages
-
DOI 10.1099/mic.0.2007/008565-0
-
Bradley M D, Beach M B, de Koning A P J, Pratt T S and Osuna R 2007 Effects of Fis on Escherichia coli gene expression during different growth stages Microbiology 153 292240 (Pubitemid 47517054)
-
(2007)
Microbiology
, vol.153
, Issue.9
, pp. 2922-2940
-
-
Bradley, M.D.1
Beach, M.B.2
De Koning, A.P.J.3
Pratt, T.S.4
Osuna, R.5
-
11
-
-
78149484750
-
A geometrical model for DNA organization in bacteria
-
10.1371/journal.pone.0013806 1932-6203 e13806
-
Buenemann M and Lenz P 2010 A geometrical model for DNA organization in bacteria PLoS One 5 e13806
-
(2010)
PLoS One
, vol.5
, Issue.11
-
-
Buenemann, M.1
Lenz, P.2
-
12
-
-
51849083802
-
Fractional langevin equation: Overdamped, underdamped, and critical behaviors
-
10.1103/PhysRevE.78.031112 1539-3755 E 031112
-
Burov S and Barkai E 2008 Fractional langevin equation: overdamped, underdamped, and critical behaviors Phys. Rev. E 78 031112
-
(2008)
Phys. Rev.
, vol.78
, Issue.3
-
-
Burov, S.1
Barkai, E.2
-
13
-
-
79952370252
-
Spiral architecture of the nucleoid in
-
Butan C, Hartnell L M, Fenton A K, Bliss D, Sockett R E, Subramaniam S and Milne J L S 2011 Spiral architecture of the nucleoid in Bdellovibrio bacteriovorus J. Bacteriol. 193 134150
-
(2011)
Bdellovibrio Bacteriovorus J. Bacteriol.
, vol.193
, pp. 1341-1350
-
-
Butan, C.1
Hartnell, L.M.2
Fenton, A.K.3
Bliss, D.4
Sockett, R.E.5
Subramaniam, S.6
Milne, J.L.S.7
-
14
-
-
67649394401
-
Active transcription of rRNA operons condenses the nucleoid in Escherichia coli: Examining the effect of transcription on nucleoid structure in the absence of transertion
-
10.1128/JB.01707-08 0021-9193
-
Cabrera J E, Cagliero C, Quan S, Squires C L and Jin D J 2009 Active transcription of rRNA operons condenses the nucleoid in Escherichia coli: examining the effect of transcription on nucleoid structure in the absence of transertion J. Bacteriol. 191 41805
-
(2009)
J. Bacteriol.
, vol.191
, Issue.13
, pp. 4180-4185
-
-
Cabrera, J.E.1
Cagliero, C.2
Quan, S.3
Squires, C.L.4
Jin, D.J.5
-
15
-
-
79952741894
-
Nucleoid occlusion factor SlmA is a DNA-activated FtsZ polymerization antagonist
-
10.1073/pnas.1018674108 0027-8424
-
Cho H, McManus H R, Dove S L and Bernhardt T G 2011 Nucleoid occlusion factor SlmA is a DNA-activated FtsZ polymerization antagonist Proc. Natl Acad. Sci. USA 108 37738
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, Issue.9
, pp. 3773-3778
-
-
Cho, H.1
McManus, H.R.2
Dove, S.L.3
Bernhardt, T.G.4
-
16
-
-
44449086377
-
Probing microscopic origins of confined subdiffusion by first-passage observables
-
DOI 10.1073/pnas.0712158105
-
Condamin S, Tejedor V, Voituriez R, Bnichou O and Klafter J 2008 Probing microscopic origins of confined subdiffusion by first-passage observables Proc. Natl Acad. Sci. USA 105 567580 (Pubitemid 351758430)
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.15
, pp. 5675-5680
-
-
Condamin, S.1
Tejedor, V.2
Voituriez, R.3
Benichou, O.4
Klafter, J.5
-
17
-
-
0027159512
-
Reverse gyrase: A helicase-like domain and a type I topoisomerase in the same polypeptide
-
Confalonieri F, Elie C, Nadal M, de La Tour C, Forterre P and Duguet M 1993 Reverse gyrase: a helicase-like domain and a type I topoisomerase in the same polypeptide Proc. Natl Acad. Sci. USA 90 47537 (Pubitemid 23148984)
-
(1993)
Proceedings of the National Academy of Sciences of the United States of America
, vol.90
, Issue.10
, pp. 4753-4757
-
-
Confalonieri, F.1
Elie, C.2
Nadal, M.3
De La Tour, C.B.4
Forterre, P.5
Duguet, M.6
-
18
-
-
77956155529
-
Dimerization and DNA-dependent aggregation of the Escherichia coli nucleoid protein and chaperone CbpA
-
10.1111/j.1365-2958.2010.07292.x 0950-382X
-
Cosgriff S, Chintakayala K, Chim Y T A, Chen X, Allen S, Lovering A L and Grainger D C 2010 Dimerization and DNA-dependent aggregation of the Escherichia coli nucleoid protein and chaperone CbpA Mol. Microbiol. 77 1289300
-
(2010)
Mol. Microbiol.
, vol.77
, Issue.5
, pp. 1289-1300
-
-
Cosgriff, S.1
Chintakayala, K.2
Chim, Y.T.A.3
Chen, X.4
Allen, S.5
Lovering, A.L.6
Grainger, D.C.7
-
19
-
-
0035084721
-
Isolation of the Escherichia coli nucleoid
-
DOI 10.1016/S0300-9084(01)01245-7
-
Cunha S, Odijk T, Suleymanoglu E and Woldringh C L 2001 Isolation of the Escherichia coli nucleoid Biochimie 83 14954 (Pubitemid 32243558)
-
(2001)
Biochimie
, vol.83
, Issue.2
, pp. 149-154
-
-
Cunha, S.1
Odijk, T.2
Suleymanoglu, E.3
Woldringh, C.L.4
-
20
-
-
18144393456
-
Restricted diffusion of DNA segments within the isolated Escherichia coli nucleoid
-
DOI 10.1016/j.jsb.2005.02.004
-
Cunha S, Woldringh C L and Odijk T 2005 Restricted diffusion of DNA segments within the isolated Escherichia coli nucleoid J. Struct. Biol. 150 22632 (Pubitemid 40615747)
-
(2005)
Journal of Structural Biology
, vol.150
, Issue.2
, pp. 226-232
-
-
Cunha, S.1
Woldringh, C.L.2
Odijk, T.3
-
21
-
-
33751098486
-
Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation
-
DOI 10.1038/nature05283, PII NATURE05283
-
Dame R T, Noom M C and Wuite G J L 2006 Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation Nature 444 38790 (Pubitemid 44764116)
-
(2006)
Nature
, vol.444
, Issue.7117
, pp. 387-390
-
-
Dame, R.T.1
Noom, M.C.2
Wuite, G.J.L.3
-
22
-
-
79959843457
-
Chromosomal macrodomains and associated proteins: Implications for DNA organization and replication in gram negative bacteria
-
10.1371/journal.pgen.1002123 1553-7404 e1002123
-
Dame R T, Kalmykowa O J and Grainger D C 2011 Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in gram negative bacteria PLoS Genet. 7 e1002123
-
(2011)
PLoS Genet.
, vol.7
, Issue.6
-
-
Dame, R.T.1
Kalmykowa, O.J.2
Grainger, D.C.3
-
24
-
-
19944406574
-
Dynamics of entangled polymer solutions: I. The Rouse model
-
10.1021/ma60052a011 0024-9297
-
DeGennes P G 1976 Dynamics of entangled polymer solutions: I. The Rouse model Macromolecules 9 587
-
(1976)
Macromolecules
, vol.9
, Issue.4
, pp. 587
-
-
Degennes, P.G.1
-
26
-
-
38849141628
-
Intracellular mobility of plasmid DNA is limited by the para family of partitioning systems
-
DOI 10.1111/j.1365-2958.2007.06066.x
-
Derman A I, Lim-Fong G and Pogliano J 2008 Intracellular mobility of plasmid DNA is limited by the parA family of partitioning systems Mol. Microbiol. 67 93546 (Pubitemid 351207325)
-
(2008)
Molecular Microbiology
, vol.67
, Issue.5
, pp. 935-946
-
-
Derman, A.I.1
Lim-Fong, G.2
Pogliano, J.3
-
27
-
-
78649882848
-
DNA condensation in bacteria: Interplay between macromolecular crowding and nucleoid proteins
-
10.1016/j.biochi.2010.06.024 0300-9084
-
de Vries R 2010 DNA condensation in bacteria: Interplay between macromolecular crowding and nucleoid proteins Biochimie 92 171521
-
(2010)
Biochimie
, vol.92
, Issue.12
, pp. 1715-1721
-
-
De Vries, R.1
-
28
-
-
0034195169
-
Binding of molecules to DNA and other semiflexible polymers
-
10.1103/PhysRevE.61.6740 1063-651X E
-
Diamant H and Andelman D 2000 Binding of molecules to DNA and other semiflexible polymers Phys. Rev. E 61 67409
-
(2000)
Phys. Rev.
, vol.61
, Issue.6
, pp. 6740-6749
-
-
Diamant, H.1
Andelman, D.2
-
29
-
-
76949089832
-
Bacterial nucleoid-associated proteins, nucleoid structure and gene expression
-
10.1038/nrmicro2261 1740-1526
-
Dillon S C and Dorman C J 2010 Bacterial nucleoid-associated proteins, nucleoid structure and gene expression Nature Rev. Microbiol. 8 18595
-
(2010)
Nature Rev. Microbiol.
, vol.8
, Issue.3
, pp. 185-195
-
-
Dillon, S.C.1
Dorman, C.J.2
-
30
-
-
68249087576
-
Dynamics of semiflexible treelike polymeric networks
-
10.1063/1.3184797 0021-9606 044905
-
Dolgushev M and Blumen A 2009 Dynamics of semiflexible treelike polymeric networks J. Chem. Phys. 131 044905
-
(2009)
J. Chem. Phys.
, vol.131
, Issue.4
-
-
Dolgushev, M.1
Blumen, A.2
-
31
-
-
0344851112
-
The entropy of a confined polymer: I
-
10.1088/0305-4470/2/2/001 0022-3689
-
Edwards S F and Freed K F 1969 The entropy of a confined polymer: I. J. Phys. A: Gen. Phys. 2 145
-
(1969)
J. Phys. A: Gen. Phys.
, vol.2
, Issue.2
, pp. 145
-
-
Edwards, S.F.1
Freed, K.F.2
-
33
-
-
33750495828
-
Organization of the Escherichia coli chromosome into macrodomains and its possible functional implications
-
DOI 10.1016/j.jsb.2006.07.010, PII S104784770600219X
-
Espéli O and Boccard F 2006 Organization of the Escherichia coli chromosome into macrodomains and its possible functional implications J. Struct. Biol. 156 30410 (Pubitemid 44666450)
-
(2006)
Journal of Structural Biology
, vol.156
, Issue.2
, pp. 304-310
-
-
Espeli, O.1
Boccard, F.2
-
34
-
-
44249103292
-
DNA dynamics vary according to macrodomain topography in the E. coli chromosome
-
DOI 10.1111/j.1365-2958.2008.06239.x
-
Espéli O, Mercier R and Boccard F 2008 DNA dynamics vary according to macrodomain topography in the E. coli chromosome Mol. Microbiol. 68 141827 (Pubitemid 351725253)
-
(2008)
Molecular Microbiology
, vol.68
, Issue.6
, pp. 1418-1427
-
-
Espeli, O.1
Mercier, R.2
Boccard, F.3
-
35
-
-
79960808394
-
DNA compaction: Fundamentals and applications
-
10.1039/c1sm05373f 1744-683X
-
Estevez-Torres A and Baigl D 2011 DNA compaction: fundamentals and applications Soft Matter 7 674656
-
(2011)
Soft Matter
, vol.7
, Issue.15
, pp. 6746-6756
-
-
Estevez-Torres, A.1
Baigl, D.2
-
37
-
-
84863117103
-
A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation
-
10.1093/nar/gkr779 0305-1048
-
Fritsche M, Li S, Heermann D W and Wiggins P A 2011 A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation Nucl. Acids Res. 40 97280
-
(2011)
Nucl. Acids Res.
, vol.40
, Issue.3
, pp. 972-980
-
-
Fritsche, M.1
Li, S.2
Heermann, D.W.3
Wiggins, P.A.4
-
38
-
-
0001966018
-
Linear viscoelasticity in Gaussian networks
-
10.1021/ma60074a032 0024-9297
-
Graessley W W 1980 Linear viscoelasticity in Gaussian networks Macromolecules 13 3726
-
(1980)
Macromolecules
, vol.13
, Issue.2
, pp. 372-376
-
-
Graessley, W.W.1
-
39
-
-
29144431508
-
Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome
-
DOI 10.1073/pnas.0506687102
-
Grainger D C, Hurd D, Harrison M, Holdstock J and Busby S J 2005 Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along theE. coli chromosome Proc. Natl Acad. Sci. USA 102 176938 (Pubitemid 41803559)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.49
, pp. 17693-17698
-
-
Grainger, D.C.1
Hurd, D.2
Harrison, M.3
Holdstock, J.4
Busby, S.J.W.5
-
40
-
-
33750000118
-
Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome
-
DOI 10.1093/nar/gkl542
-
Grainger D C, Hurd D, Goldberg M D and Busby S J W 2006 Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome Nucl. Acids Res. 34 464252 (Pubitemid 44567058)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.16
, pp. 4642-4652
-
-
Grainger, D.C.1
Hurd, D.2
Goldberg, M.D.3
Busby, S.J.W.4
-
41
-
-
33846659467
-
Transcription factor distribution in Escherichia coli: Studies with FNR protein
-
DOI 10.1093/nar/gkl1023
-
Grainger D C, Aiba H, Hurd D, Browning D F and Busby S J 2007 Transcription factor distribution in Escherichia coli: studies with FNR protein Nucl. Acids Res. 35 26978 (Pubitemid 46189851)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.1
, pp. 269-278
-
-
Grainger, D.C.1
Aiba, H.2
Hurd, D.3
Browning, D.F.4
Busby, S.J.W.5
-
42
-
-
44249126516
-
Selective repression by Fis and H-NS at the Escherichia coli dps promoter
-
DOI 10.1111/j.1365-2958.2008.06253.x
-
Grainger D C, Goldberg M D, Lee D J and Busby S J 2008 Selective repression by Fis and H-NS at the Escherichia coli dps promoter Mol. Microbiol. 68 136677 (Pubitemid 351725264)
-
(2008)
Molecular Microbiology
, vol.68
, Issue.6
, pp. 1366-1377
-
-
Grainger, D.C.1
Goldberg, M.D.2
Lee, D.J.3
Busby, S.J.W.4
-
44
-
-
84956136196
-
Crumpled globule model of the three-dimensional structure of DNA
-
10.1209/0295-5075/23/5/012 0295-5075 012
-
Grosberg A, Rabin Y, Havlin S and Neer A 1993 Crumpled globule model of the three-dimensional structure of DNA Europhys. Lett. 23 3738
-
(1993)
Europhys. Lett.
, vol.23
, Issue.5
, pp. 373-378
-
-
Grosberg, A.1
Rabin, Y.2
Havlin, S.3
Neer, A.4
-
45
-
-
0031751368
-
Fused nucleoids resegregate faster than cell elongation in Escherichia coli pbpB(Ts) filaments after release from chloramphenicol inhibition
-
Helvoort J M V, Huls P G, Vischer N O and Woldringh C L 1998 Fused nucleoids resegregate faster than cell elongation in Escherichia coli pbpB(Ts) filaments after release from chloramphenicol inhibition Microbiology 144 130917 (Pubitemid 28233835)
-
(1998)
Microbiology
, vol.144
, Issue.5
, pp. 1309-1317
-
-
Helvoort, J.M.V.1
Huls, P.G.2
Vischer, N.O.E.3
Woldringh, C.L.4
-
46
-
-
48849092363
-
Random time-scale invariant diffusion and transport coefficients
-
10.1103/PhysRevLett.101.058101 0031-9007 058101
-
He Y, Burov S, Metzler R and Barkai E 2008 Random time-scale invariant diffusion and transport coefficients Phys. Rev. Lett. 101 058101
-
(2008)
Phys. Rev. Lett.
, vol.101
, Issue.5
-
-
He, Y.1
Burov, S.2
Metzler, R.3
Barkai, E.4
-
47
-
-
35349030892
-
Dynamic conformational behavior and molecular interaction discrimination of DNA/binder complexes by single-chain stretching in a microdevice
-
DOI 10.1002/cbic.200700229
-
Huang W-H, Zinchenko A A, Pawlak C, Chen Y and Baigl D 2007 Dynamic conformational behavior and molecular interaction discrimination of DNA/binder complexes by single-chain stretching in a microdevice Chembiochem 8 17714 (Pubitemid 47612863)
-
(2007)
ChemBioChem
, vol.8
, Issue.15
, pp. 1771-1774
-
-
Huang, W.-H.1
Zinchenko, A.A.2
Pawlak, C.3
Chen, Y.4
Baigl, D.5
-
48
-
-
79961062430
-
Collapse transition of randomly branched polymers: Renormalized field theory
-
10.1103/PhysRevE.83.051126 1539-3755 E 051126
-
Janssen H-K and Stenull O 2011 Collapse transition of randomly branched polymers: renormalized field theory Phys. Rev. E 83 051126
-
(2011)
Phys. Rev.
, vol.83
, Issue.5
-
-
Janssen, H.-K.1
Stenull, O.2
-
49
-
-
0942300123
-
Dynamics of randomly branched polymers: Configuration averages and solvable models
-
10.1103/PhysRevE.68.051106 1063-651X E 051106
-
Jasch F, von Ferber Ch and Blumen A 2003 Dynamics of randomly branched polymers: configuration averages and solvable models Phys. Rev. E 68 051106
-
(2003)
Phys. Rev.
, vol.68
, Issue.5
-
-
Jasch, F.1
Von Ferber, Ch.2
Blumen, A.3
-
50
-
-
0035801637
-
A moving DNA replication factory in Caulobacter crescentus
-
DOI 10.1093/emboj/20.17.4952
-
Jensen R B, Wang S C and Shapiro L 2001 A moving DNA replication factory in Caulobacter crescentus EMBO J. 20 495263 (Pubitemid 32848647)
-
(2001)
EMBO Journal
, vol.20
, Issue.17
, pp. 4952-4963
-
-
Jensen, R.B.1
Wang, S.C.2
Shapiro, L.3
-
51
-
-
33750529760
-
Coupling the distribution of RNA polymerase to global gene regulation and the dynamic structure of the bacterial nucleoid in Escherichia coli
-
DOI 10.1016/j.jsb.2006.07.005, PII S1047847706002139
-
Jin D J and Cabrera J E 2006 Coupling the distribution of RNA polymerase to global gene regulation and the dynamic structure of the bacterial nucleoid in Escherichia coli J. Struct. Biol. 156 28491 (Pubitemid 44666448)
-
(2006)
Journal of Structural Biology
, vol.156
, Issue.2
, pp. 284-291
-
-
Jin, D.J.1
Cabrera, J.E.2
-
52
-
-
79952591477
-
Escherichia coli sister chromosome separation includes an abrupt global transition with concomitant release of late-splitting intersister snaps
-
10.1073/pnas.1019593108 0027-8424
-
Joshi M C, Bourniquel A, Fisher J, Ho B T, Magnan D, Kleckner N and Bates D 2011 Escherichia coli sister chromosome separation includes an abrupt global transition with concomitant release of late-splitting intersister snaps Proc. Natl Acad. Sci. USA 108 276570
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, Issue.7
, pp. 2765-2770
-
-
Joshi, M.C.1
Bourniquel, A.2
Fisher, J.3
Ho, B.T.4
Magnan, D.5
Kleckner, N.6
Bates, D.7
-
53
-
-
78651347562
-
Overlapping two self-avoiding polymers in a closed cylindrical pore: Implications for chromosome segregation in a bacterial cell
-
10.1103/PhysRevE.82.051926 1539-3755 E
-
Jung Y and Ha B-Y 2010 Overlapping two self-avoiding polymers in a closed cylindrical pore: Implications for chromosome segregation in a bacterial cell Phys. Rev. E 82 5192631
-
(2010)
Phys. Rev.
, vol.82
, Issue.5
, pp. 51926-51931
-
-
Jung, Y.1
Ha, B.-Y.2
-
54
-
-
77649198707
-
Spatial and topological organization of DNA chains induced by gene co-localization
-
10.1371/journal.pcbi.1000678 1553-7358 e1000678
-
Junier I, Martin O and Képès F 2010 Spatial and topological organization of DNA chains induced by gene co-localization PLoS Comput. Biol. 6 e1000678
-
(2010)
PLoS Comput. Biol.
, vol.6
, Issue.2
-
-
Junier, I.1
Martin, O.2
Képès, F.3
-
55
-
-
77954719357
-
Entropy as the driver of chromosome segregation
-
10.1038/nrmicro2391 1740-1526
-
Jun S and Wright A 2010 Entropy as the driver of chromosome segregation Nature Rev. Micro. 8 6007
-
(2010)
Nature Rev. Micro.
, vol.8
, Issue.8
, pp. 600-607
-
-
Jun, S.1
Wright, A.2
-
57
-
-
79953676877
-
Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli
-
10.1093/nar/gkq934 0305-1048
-
Kahramanoglou C, Seshasayee A S N, Prieto A I, Ibberson D, Schmidt S, Zimmermann J, Benes V, Fraser G M and Luscombe N M 2011 Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli Nucl. Acids Res. 39 207391
-
(2011)
Nucl. Acids Res.
, vol.39
, Issue.6
, pp. 2073-2091
-
-
Kahramanoglou, C.1
Seshasayee, A.S.N.2
Prieto, A.I.3
Ibberson, D.4
Schmidt, S.5
Zimmermann, J.6
Benes, V.7
Fraser, G.M.8
Luscombe, N.M.9
-
59
-
-
0017045430
-
Electron microscopy of membrane free folded chromosomes from Escherichia coli
-
DOI 10.1007/BF00328479
-
Kavenoff R and Bowen B C 1976 Electron microscopy of membrane-free folded chromosomes from Escherichia coli Chromosoma 59 89101 (Pubitemid 8002265)
-
(1976)
Chromosoma
, vol.59
, Issue.2
, pp. 89-101
-
-
Kavenoff, R.1
Bowen, B.C.2
-
60
-
-
17444389603
-
Transcription-based solenoidal model of chromosome
-
10.1159/000082184 1424-8492
-
Képès F and Valliant C 2003 Transcription-based solenoidal model of chromosome ComPlexUs 1 17180
-
(2003)
ComPlexUs
, vol.1
, Issue.4
, pp. 171-180
-
-
Képès, F.1
Valliant, C.2
-
61
-
-
3042660143
-
Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy
-
DOI 10.1093/nar/gkh512
-
Kim J, Yoshimura S H, Hizume K, Ohniwa R L, Ishihama A and Takeyasu K 2004 Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy Nucl. Acids Res. 32 198292 (Pubitemid 38842538)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.6
, pp. 1982-1992
-
-
Kim, J.1
Yoshimura, S.H.2
Hizume, K.3
Ohniwa, R.L.4
Ishihama, A.5
Takeyasu, K.6
-
62
-
-
53449099613
-
Bacterial partitioning proteins affect the subcellular location of broad-host-range plasmid RK2
-
10.1099/mic.0.2008/018762-0 1350-0872
-
Kolatka K, Witosinska M, Pierechod M and Konieczny I 2008 Bacterial partitioning proteins affect the subcellular location of broad-host-range plasmid RK2 Microbiology 154 284756
-
(2008)
Microbiology
, vol.154
, Issue.9
, pp. 2847-2856
-
-
Kolatka, K.1
Witosinska, M.2
Pierechod, M.3
Konieczny, I.4
-
63
-
-
33749018832
-
Crowding and confinement effects on protein diffusion in vivo
-
DOI 10.1128/JB.01982-05
-
Konopka M C, Shkel I A, Cayley S, Record M T and Weisshaar J C 2006 Crowding and confinement effects on protein diffusion in vivo J. Bacteriol. 188 611523 (Pubitemid 44448553)
-
(2006)
Journal of Bacteriology
, vol.188
, Issue.17
, pp. 6115-6123
-
-
Konopka, M.C.1
Shkel, I.A.2
Cayley, S.3
Record, M.T.4
Weisshaar, J.C.5
-
64
-
-
33645717867
-
Mass fractal dimension of the ribosome and implication of its dynamic characteristics
-
10.1103/PhysRevE.73.042901 1539-3755 E 042901
-
Lee C-Y 2006 Mass fractal dimension of the ribosome and implication of its dynamic characteristics Phys. Rev. E 73 042901
-
(2006)
Phys. Rev.
, vol.73
, Issue.4
-
-
Lee, C.-Y.1
-
65
-
-
22144463194
-
Roles for replichores and macrodomains in segregation of the Escherichia coli chromosome
-
DOI 10.1038/sj.embor.7400428
-
Lesterlin C, Mercier R, Boccard F, Barre F X and Cornet F 2005 Roles for replichores and macrodomains in segregation of the Escherichia coli chromosome EMBO Rep. 6 55762 (Pubitemid 40973965)
-
(2005)
EMBO Reports
, vol.6
, Issue.6
, pp. 557-562
-
-
Lesterlin, C.1
Mercier, R.2
Boccard, F.3
Barre, F.-X.4
Cornet, F.5
-
66
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
-
10.1126/science.1181369 0036-8075
-
Lieberman-Aiden E et al 2009 Comprehensive mapping of long-range interactions reveals folding principles of the human genome Science 326 28993
-
(2009)
Science
, vol.326
, Issue.5950
, pp. 289-293
-
-
Lieberman-Aiden, E.1
-
67
-
-
84860359300
-
Gene silencing H-NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility
-
10.1093/nar/gkr1247 0305-1048
-
Lim C J, Whang Y R, Kenney L J and Yan J 2011 Gene silencing H-NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility Nucl. Acids Res. 40 331628
-
(2011)
Nucl. Acids Res.
, vol.40
, Issue.8
, pp. 3316-3328
-
-
Lim, C.J.1
Whang, Y.R.2
Kenney, L.J.3
Yan, J.4
-
68
-
-
77349104369
-
Replication-directed sister chromosome alignment in Escherichia coli
-
10.1111/j.1365-2958.2009.06791.x 0950-382X
-
Liu X, Wang X, Reyes-Lamothe R and Sherratt D 2010 Replication-directed sister chromosome alignment in Escherichia coli Mol. Microbiol. 75 10907
-
(2010)
Mol. Microbiol.
, vol.75
, Issue.5
, pp. 1090-1097
-
-
Liu, X.1
Wang, X.2
Reyes-Lamothe, R.3
Sherratt, D.4
-
69
-
-
33750527566
-
The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: A molecular perspective
-
DOI 10.1016/j.jsb.2006.05.006, PII S1047847706001614
-
Luijsterburg M S, Noom M C, Wuite G J and Dame R T 2006 The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective J. Struct. Biol. 156 26272 (Pubitemid 44666444)
-
(2006)
Journal of Structural Biology
, vol.156
, Issue.2
, pp. 262-272
-
-
Luijsterburg, M.S.1
Noom, M.C.2
Wuite, G.J.L.3
Dame, R.Th.4
-
70
-
-
33845295824
-
The depletion attraction: An underappreciated force driving cellular organization
-
DOI 10.1083/jcb.200609066
-
Marenduzzo D, Finan K and Cook P R 2006a The depletion attraction: an underappreciated force driving cellular organization J. Cell. Biol. 175 6816 (Pubitemid 44878499)
-
(2006)
Journal of Cell Biology
, vol.175
, Issue.5
, pp. 681-686
-
-
Marenduzzo, D.1
Finan, K.2
Cook, P.R.3
-
71
-
-
33646195227
-
Entropy-driven genome organization
-
10.1529/biophysj.105.077685 0006-3495
-
Marenduzzo D, Micheletti C and Cook P R 2006b Entropy-driven genome organization Biophys. J. 90 371221
-
(2006)
Biophys. J.
, vol.90
, Issue.10
, pp. 3712-3721
-
-
Marenduzzo, D.1
Micheletti, C.2
Cook, P.R.3
-
73
-
-
66749191436
-
Linking topology of tethered polymer rings with applications to chromosome segregation and estimation of the knotting length
-
10.1103/PhysRevE.79.051905 1539-3755 E 051905
-
Marko J F 2009 Linking topology of tethered polymer rings with applications to chromosome segregation and estimation of the knotting length Phys. Rev. E 79 051905
-
(2009)
Phys. Rev.
, vol.79
, Issue.5
-
-
Marko, J.F.1
-
74
-
-
0037336483
-
The micromechanics of DNA
-
0953-8585
-
Marko J F and Cocco S 2003 The micromechanics of DNA Phys. World 3741 http://www.phys.ens.fr/cocco/Art/24physworld.pdf
-
(2003)
Phys. World
, pp. 37-41
-
-
Marko, J.F.1
Cocco, S.2
-
75
-
-
40649089205
-
Dissecting the logical types of network control in gene expression profiles
-
DOI 10.1186/1752-0509-2-18
-
Marr C, Geertz M, Hütt M T and Muskhelishvili G 2008 Dissecting the logical types of network control in gene expression profiles BMC Syst. Biol. 2 18 (Pubitemid 351372426)
-
(2008)
BMC Systems Biology
, vol.2
, pp. 18
-
-
Marr, C.1
Geertz, M.2
Hutt, M.-T.3
Muskhelishvili, G.4
-
76
-
-
62649137535
-
Spatially confined folding of chromatin in the interphase nucleus
-
10.1073/pnas.0809501106 0027-8424
-
Mateos-Langerak J et al 2009 Spatially confined folding of chromatin in the interphase nucleus Proc. Natl Acad. Sci. USA 106 38127
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, Issue.10
, pp. 3812-3817
-
-
Mateos-Langerak, J.1
-
77
-
-
77952268971
-
Chromosomal periodicity and positional networks of genes in Escherichia coli
-
10.1038/msb.2010.21 1744-4292
-
Mathelier A and Carbone A 2010 Chromosomal periodicity and positional networks of genes in Escherichia coli Mol. Syst. Biol. 6 366
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 366
-
-
Mathelier, A.1
Carbone, A.2
-
78
-
-
63449089710
-
A systematic in vitro study of nucleoprotein complexes formed by bacterial nucleoid-associated proteins revealing novel types of DNA organization
-
10.1016/j.jmb.2009.02.050 0022-2836
-
Maurer S, Fritz J and Muskhelishvili G 2009 A systematic in vitro study of nucleoprotein complexes formed by bacterial nucleoid-associated proteins revealing novel types of DNA organization J. Mol. Biol. 387 126176
-
(2009)
J. Mol. Biol.
, vol.387
, Issue.5
, pp. 1261-1276
-
-
Maurer, S.1
Fritz, J.2
Muskhelishvili, G.3
-
79
-
-
79251604784
-
The terminal region of theE. coli chromosome localises at the periphery of the nucleoid
-
10.1186/1471-2180-11-28 1471-2180
-
Meile J-C, Mercier R, Stouf M, Pages C, Bouet J-Y and Cornet F 2011 The terminal region of theE. coli chromosome localises at the periphery of the nucleoid BMC Microbiol. 11 28
-
(2011)
BMC Microbiol.
, vol.11
, Issue.1
, pp. 28
-
-
Meile, J.-C.1
Mercier, R.2
Stouf, M.3
Pages, C.4
Bouet, J.-Y.5
Cornet, F.6
-
80
-
-
54949146519
-
The MatP/matS site-specific system organizes the terminus region of theE. coli chromosome into a macrodomain
-
10.1016/j.cell.2008.08.031 0092-8674
-
Mercier R, Petit M-A, Schbath S, Robin S, Karoui M El, Boccard F and Espéli O 2008 The MatP/matS site-specific system organizes the terminus region of theE. coli chromosome into a macrodomain Cell 135 47585
-
(2008)
Cell
, vol.135
, Issue.3
, pp. 475-485
-
-
Mercier, R.1
Petit, M.-A.2
Schbath, S.3
Robin, S.4
El, K.M.5
Boccard, F.6
Espéli, O.7
-
81
-
-
79952279926
-
The fractal globule as a model of chromatin architecture in the cell
-
10.1007/s10577-010-9177-0 0967-3849
-
Mirny L A 2011 The fractal globule as a model of chromatin architecture in the cell Chromosome Res. 19 3751
-
(2011)
Chromosome Res.
, vol.19
, Issue.1
, pp. 37-51
-
-
Mirny, L.A.1
-
82
-
-
13144257718
-
Topological insulators inhibit diffusion of transcription-induced positive supercoils in the chromosome of Escherichia coli
-
DOI 10.1111/j.1365-2958.2004.04411.x
-
Moulin L, Rahmouni A R and Boccard F 2005 Topological insulators inhibit diffusion of transcription-induced positive supercoils in the chromosome of Escherichia coli Mol. Microbiol. 55 60110 (Pubitemid 40179390)
-
(2005)
Molecular Microbiology
, vol.55
, Issue.2
, pp. 601-610
-
-
Moulin, L.1
Rahmouni, A.R.2
Boccard, F.3
-
83
-
-
77949706153
-
General organisational principles of the transcriptional regulation system: A tree or a circle?
-
10.1039/b909192k 1742-206X
-
Muskhelishvili G, Sobetzko P, Geertz M and Berger M 2010 General organisational principles of the transcriptional regulation system: a tree or a circle? Mol. Biosyst. 6 66276
-
(2010)
Mol. Biosyst.
, vol.6
, Issue.4
, pp. 662-676
-
-
Muskhelishvili, G.1
Sobetzko, P.2
Geertz, M.3
Berger, M.4
-
84
-
-
66149104488
-
Thermodynamic pathways to genome spatial organization in the cell nucleus
-
10.1016/j.bpj.2008.12.3919 0006-3495
-
Nicodemi M and Prisco A 2009 Thermodynamic pathways to genome spatial organization in the cell nucleus Biophys. J. 96 216877
-
(2009)
Biophys. J.
, vol.96
, Issue.6
, pp. 2168-2177
-
-
Nicodemi, M.1
Prisco, A.2
-
85
-
-
33749177128
-
The Escherichia coli chromosome is organized with the left and right chromosome arms in separate cell halves
-
DOI 10.1111/j.1365-2958.2006.05346.x
-
Nielsen H J, Ottesen J R, Youngren B, Austin S J and Hansen F G 2006 The Escherichia coli chromosome is organized with the left and right chromosome arms in separate cell halves Mol. Microbiol. 62 3318 (Pubitemid 44477225)
-
(2006)
Molecular Microbiology
, vol.62
, Issue.2
, pp. 331-338
-
-
Nielsen, H.J.1
Ottesen, J.R.2
Youngren, B.3
Austin, S.J.4
Hansen, F.G.5
-
86
-
-
36749101359
-
Dynamics of Escherichia coli chromosome segregation during multifork replication
-
DOI 10.1128/JB.01212-07
-
Nielsen H J, Youngren B, Hansen F G and Austin S 2007 Dynamics of Escherichia coli chromosome segregation during multifork replication J. Bacteriol. 189 86606 (Pubitemid 350210036)
-
(2007)
Journal of Bacteriology
, vol.189
, Issue.23
, pp. 8660-8666
-
-
Nielsen, H.J.1
Youngren, B.2
Hansen, F.G.3
Austin, S.4
-
87
-
-
0034650256
-
Dynamic organization of chromosomal DNA in Escherichia coli
-
0890-9369
-
Niki H, Yamaichi Y and Hiraga S 2000 Dynamic organization of chromosomal DNA in Escherichia coli Genes Dev. 14 21223
-
(2000)
Genes Dev.
-
-
Niki, H.1
Yamaichi, Y.2
Hiraga, S.3
-
88
-
-
0029165965
-
Hypothesis: Chromosome separation in Escherichia coli involves autocatalytic gene expression, transertion and membrane-domain formation
-
10.1111/j.1365-2958.1995.tb02330.x 0950-382X
-
Norris V 1995 Hypothesis: chromosome separation in Escherichia coli involves autocatalytic gene expression, transertion and membrane-domain formation Mol. Microbiol. 16 10517
-
(1995)
Mol. Microbiol.
, vol.16
, Issue.6
, pp. 1051-1057
-
-
Norris, V.1
-
89
-
-
0028697888
-
The origin evolution of species differences in Escherichia coli and salmonella typhimurium
-
1023-294X
-
Ochman H and Groisman E A 1994 The origin evolution of species differences in Escherichia coli and salmonella typhimurium EXS 69 47993
-
(1994)
EXS
-
-
Ochman, H.1
Groisman, E.A.2
-
90
-
-
0032050083
-
Dimensions of a plectonemic DNA supercoil under fairly general perturbations
-
PII S0378437197005888
-
Odijk T and Ubbink J 1998 Dimensions of a plectonemic DNA supercoil under fairly general perturbations Physica A 252 616 (Pubitemid 128417612)
-
(1998)
Physica A: Statistical Mechanics and its Applications
, vol.252
, Issue.1-2
, pp. 61-66
-
-
Odijk, T.1
Ubbink, J.2
-
91
-
-
0032514107
-
Osmotic compaction of supercoiled DNA into a bacterial nucleoid
-
DOI 10.1016/S0301-4622(98)00115-X, PII S030146229800115X
-
Odijk T 1998 Osmotic compaction of supercoiled DNA into a bacterial nucleoid Biophys. Chem. 73 239 (Pubitemid 28325691)
-
(1998)
Biophysical Chemistry
, vol.73
, Issue.1-2
, pp. 23-29
-
-
Odijk, T.1
-
92
-
-
79955588726
-
Proteomic analyses of nucleoid-associated proteins in Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, and Staphylococcus aureus
-
10.1371/journal.pone.0019172 1932-6203
-
Ohniwa R L, Ushijima Y, Saito S and Morikawa K 2011 Proteomic analyses of nucleoid-associated proteins in Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, and Staphylococcus aureus PLoS One 6 e19172
-
(2011)
PLoS One
, vol.6
, Issue.4
, pp. 19172
-
-
Ohniwa, R.L.1
Ushijima, Y.2
Saito, S.3
Morikawa, K.4
-
93
-
-
33751580332
-
Dynamic state of DNA topology is essential for genome condensation in bacteria
-
DOI 10.1038/sj.emboj.7601414, PII 7601414
-
Ohniwa R L, Morikawa K, Kim J, Ohta T, Ishihama A, Wada C and Takeyasu K 2006 Dynamic state of DNA topology is essential for genome condensation in bacteria EMBO J. 25 5591602 (Pubitemid 44847199)
-
(2006)
EMBO Journal
, vol.25
, Issue.23
, pp. 5591-5602
-
-
Ohniwa, R.L.1
Morikawa, K.2
Kim, J.3
Ohta, T.4
Ishihama, A.5
Wada, C.6
Takeyasu, K.7
-
94
-
-
33750898424
-
Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase
-
DOI 10.1093/dnares/dsl009
-
Oshima T, Ishikawa S, Kurokawa K, Aiba H and Ogasawara N 2006 Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase DNA Res. 13 14153 (Pubitemid 44726365)
-
(2006)
DNA Research
, vol.13
, Issue.4
, pp. 141-153
-
-
Oshima, T.1
Ishikawa, S.2
Kurokawa, K.3
Aiba, H.4
Ogasawara, N.5
-
95
-
-
0032519183
-
Dynamics of the swelling or collapse of a homopolymer
-
10.1209/epl/i1998-00175-8 0295-5075 467
-
Pitard E and Orland H 1998 Dynamics of the swelling or collapse of a homopolymer Europhys. Lett. 41 46772
-
(1998)
Europhys. Lett.
, vol.41
, Issue.4
, pp. 467-472
-
-
Pitard, E.1
Orland, H.2
-
96
-
-
3142774839
-
Topological domain structure of the Escherichia coli chromosome
-
DOI 10.1101/gad.1207504
-
Postow L, Hardy C D, Arsuaga J and Cozzarelli N R 2004 Topological domain structure of the Escherichia coli chromosome Genes Dev. 18 176679 (Pubitemid 38938191)
-
(2004)
Genes and Development
, vol.18
, Issue.14
, pp. 1766-1779
-
-
Postow, L.1
Hardy, C.D.2
Arsuaga, J.3
Cozzarelli, N.R.4
-
97
-
-
77956363480
-
Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure
-
10.1073/pnas.1002018107 0027-8424
-
Reuveni S, Granek R and Klafter J 2010 Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure Proc. Natl Acad. Sci. USA 107 13696700
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, Issue.31
, pp. 13696-13700
-
-
Reuveni, S.1
Granek, R.2
Klafter, J.3
-
98
-
-
41149121779
-
Independent Positioning and Action of Escherichia coli Replisomes in Live Cells
-
DOI 10.1016/j.cell.2008.01.044, PII S0092867408002092
-
Reyes-Lamothe R, Possoz C, Danilova O and Sherratt D J 2008 Independent positioning and action of Escherichia coli replisomes in live cells Cell 133 90102 (Pubitemid 351442987)
-
(2008)
Cell
, vol.133
, Issue.1
, pp. 90-102
-
-
Reyes-Lamothe, R.1
Possoz, C.2
Danilova, O.3
Sherratt, D.J.4
-
100
-
-
58449118337
-
The organization of the bacterial genome
-
10.1146/annurev.genet.42.110807.091653 0066-4197
-
Rocha E P C 2008 The organization of the bacterial genome Annu. Rev. Genet. 42 21133
-
(2008)
Annu. Rev. Genet.
, vol.42
, Issue.1
, pp. 211-233
-
-
Rocha, E.P.C.1
-
101
-
-
34147130136
-
Internal structure and dynamics of isolated Escherichia coli nucleoids assessed by fluorescence correlation spectroscopy
-
DOI 10.1529/biophysj.106.095729
-
Romantsov T, Fishov I and Krichevsky O 2007 Internal structure and dynamics of isolated Escherichia coli nucleoids assessed by fluorescence correlation spectroscopy Biophys. J. 92 287584 (Pubitemid 46557861)
-
(2007)
Biophysical Journal
, vol.92
, Issue.8
, pp. 2875-2884
-
-
Romantsov, T.1
Fishov, I.2
Krichevsky, O.3
-
102
-
-
78649639015
-
Dynamic distribution of SeqA protein across the chromosome of Escherichia coli K-12
-
10.1128/mBio.00012-10 2150-7511
-
Sánchez-Romero M A, Busby S J W, Dyer N P, Ott S, Millard A D and Grainger D C 2010 Dynamic distribution of SeqA protein across the chromosome of Escherichia coli K-12 MBio 1 e0012-1
-
(2010)
MBio
, vol.1
, Issue.1
-
-
Sánchez-Romero, M.A.1
Busby, S.J.W.2
Dyer, N.P.3
Ott, S.4
Millard, A.D.5
Grainger, D.C.6
-
103
-
-
0035945265
-
An architectural role of the Escherichia coli chromatin protein FIS in organising DNA
-
Schneider R, Lurz R, Lder G, Tolksdorf C, Travers A and Muskhelishvili G 2001 An architectural role of the Escherichia coli chromatin protein FIS in organising DNA Nucl. Acids Res. 29 510714 (Pubitemid 34065428)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.24
, pp. 5107-5114
-
-
Schneider, R.1
Lurz, R.2
Luder, G.3
Tolksdorf, C.4
Travers, A.5
Muskhelishvili, G.6
-
104
-
-
79951661202
-
Gene clusters reflecting macrodomain structure respond to nucleoid perturbations
-
10.1039/c0mb00213e 1742-206X
-
Scolari V F, Bassetti B, Sclavi B and Lagomarsino M C 2011 Gene clusters reflecting macrodomain structure respond to nucleoid perturbations Mol. Biosyst. 7 87888
-
(2011)
Mol. Biosyst.
, vol.7
, Issue.3
, pp. 878-888
-
-
Scolari, V.F.1
Bassetti, B.2
Sclavi, B.3
Lagomarsino, M.C.4
-
105
-
-
79960943853
-
Bacterial growth laws and their applications
-
10.1016/j.copbio.2011.04.014 0958-1669
-
Scott M and Hwa T 2011 Bacterial growth laws and their applications Curr. Opin. Biotechnol. 22 55965
-
(2011)
Curr. Opin. Biotechnol.
, vol.22
, Issue.4
, pp. 559-565
-
-
Scott, M.1
Hwa, T.2
-
106
-
-
78449268845
-
Interdependence of cell growth and gene expression: Origins and consequences
-
10.1126/science.1192588 0036-8075
-
Scott M, Gunderson C W, Mateescu E M, Zhang Z and Hwa T 2010 Interdependence of cell growth and gene expression: origins and consequences Science 330 1099102
-
(2010)
Science
, vol.330
, Issue.6007
, pp. 1099-1102
-
-
Scott, M.1
Gunderson, C.W.2
Mateescu, E.M.3
Zhang, Z.4
Hwa, T.5
-
107
-
-
0041853574
-
Bacterial chromosome dynamics
-
DOI 10.1126/science.1084780
-
Sherratt D J 2003 Bacterial chromosome dynamics Science 301 7805 (Pubitemid 36962608)
-
(2003)
Science
, vol.301
, Issue.5634
, pp. 780-785
-
-
Sherratt, D.J.1
-
108
-
-
33745593972
-
Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence
-
DOI 10.1083/jcb.200603083
-
Shopland L S et al 2006 Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence J. Cell. Biol. 174 2738 (Pubitemid 43992894)
-
(2006)
Journal of Cell Biology
, vol.174
, Issue.1
, pp. 27-38
-
-
Shopland, L.S.1
Lynch, C.R.2
Peterson, K.A.3
Thornton, K.4
Kepper, N.5
Von Hase, J.6
Stein, S.7
Vincent, S.8
Molloy, K.R.9
Kreth, G.10
Cremer, C.11
Bult, C.J.12
O'Brien, T.P.13
-
109
-
-
33750954891
-
Mechanism of Chromosome Compaction and Looping by the Escherichia coli Nucleoid Protein Fis
-
DOI 10.1016/j.jmb.2006.09.043, PII S0022283606012496
-
Skoko D, Yoo D, Bai H, Schnurr B, Yan J, McLeod S M, Marko J F and Johnson R C 2006 Mechanism of chromosome compaction and looping by the Escherichia coli nucleoid protein fis J. Mol. Biol. 364 77798 (Pubitemid 44737831)
-
(2006)
Journal of Molecular Biology
, vol.364
, Issue.4
, pp. 777-798
-
-
Skoko, D.1
Yoo, D.2
Bai, H.3
Schnurr, B.4
Yan, J.5
McLeod, S.M.6
Marko, J.F.7
Johnson, R.C.8
-
110
-
-
0000873404
-
On the statistics of generalized Gaussian structures: Collapse and random external fields
-
10.1088/0305-4470/28/23/018 0305-4470
-
Sommer J U and Blumen A 1995 On the statistics of generalized Gaussian structures: collapse and random external fields J. Phys. A: Math. Gen. 28 6669
-
(1995)
J. Phys. A: Math. Gen.
, vol.28
, Issue.23
, pp. 6669
-
-
Sommer, J.U.1
Blumen, A.2
-
111
-
-
34247517469
-
DNA-protein interactions and bacterial chromosome architecture
-
1478-3975 R01
-
Stavans J and Oppenheim A 2006 DNA-protein interactions and bacterial chromosome architecture Phys. Biol. 3 R110
-
(2006)
Phys. Biol.
, vol.3
, Issue.4
, pp. 1-10
-
-
Stavans, J.1
Oppenheim, A.2
-
112
-
-
0036038278
-
DNA supercoiling by gyrase is linked to nucleoid compaction
-
DOI 10.1023/A:1020318705894
-
Stuger R, Woldringh C L, van der Weijden C C, Vischer N O E, Bakker B M, van Spanning R J M, Snoep J L and Weterhoff H V 2002 DNA supercoiling by gyrase is linked to nucleoid compaction Mol. Biol. Rep. 29 7982 (Pubitemid 35021864)
-
(2002)
Molecular Biology Reports
, vol.29
, Issue.1-2
, pp. 79-82
-
-
Stuger, R.1
Woldringh, C.L.2
Van Der Weijden, C.C.3
Vischer, N.O.E.4
Bakker, B.M.5
Van Spanning, R.J.M.6
Snoep, J.L.7
Weterhoff, H.V.8
-
113
-
-
65549143001
-
A thermodynamic model for the agglomeration of DNA-looping proteins
-
1742-5468 P11005
-
Sumedha and Weigt M 2008 A thermodynamic model for the agglomeration of DNA-looping proteins J. Stat. Mech. Theory Exp. 2008 P11005
-
(2008)
J. Stat. Mech. Theory Exp.
, vol.2008
, Issue.11
-
-
Sumedha1
Weigt, M.2
-
114
-
-
33750531252
-
Chromosome organization and segregation in bacteria
-
DOI 10.1016/j.jsb.2006.05.007, PII S1047847706001869
-
Thanbichler M and Shapiro L 2006 Chromosome organization and segregation in bacteria J. Struct. Biol. 156 292303 (Pubitemid 44666446)
-
(2006)
Journal of Structural Biology
, vol.156
, Issue.2
, pp. 292-303
-
-
Thanbichler, M.1
Shapiro, L.2
-
115
-
-
27144448812
-
The bacterial nucleoid: A highly organized and dynamic structure
-
DOI 10.1002/jcb.20519
-
Thanbichler M, Wang S C and Shapiro L 2005 The bacterial nucleoid: a highly organized and dynamic structure J. Cell. Biochem. 96 50621 (Pubitemid 41504649)
-
(2005)
Journal of Cellular Biochemistry
, vol.96
, Issue.3
, pp. 506-521
-
-
Thanbichler, M.1
Wang, S.C.2
Shapiro, L.3
-
116
-
-
78650910561
-
Molecular mechanism by which the nucleoid occlusion factor, SlmA, keeps cytokinesis in check
-
10.1038/emboj.2010.288 0261-4189
-
Tonthat N Ky, Arold S T, Pickering B F, Dyke M W V, Liang S, Lu Y, Beuria T K, Margolin W and Schumacher M A 2011 Molecular mechanism by which the nucleoid occlusion factor, SlmA, keeps cytokinesis in check EMBO J. 30 15464
-
(2011)
EMBO J.
, vol.30
, Issue.1
, pp. 154-164
-
-
Ky, T.N.1
Arold, S.T.2
Pickering, B.F.3
Dyke, M.W.V.4
Liang, S.5
Lu, Y.6
Beuria, T.K.7
Margolin, W.8
Schumacher, M.A.9
-
117
-
-
77957262402
-
Bacterial chromosome organization and segregation
-
10.1101/cshperspect.a000349 1943-0264 a000349
-
Toro E and Shapiro L 2010 Bacterial chromosome organization and segregation Cold Spring Harb Perspect Biol. 2 a000349
-
(2010)
Cold Spring Harb Perspect Biol.
, vol.2
, Issue.2
-
-
Toro, E.1
Shapiro, L.2
-
118
-
-
0000457477
-
Architecture of a bacterial chromosome (review)
-
Trun N J and Marko J F 1998 Architecture of a bacterial chromosome (review) Am. Soc. Microbiol. News 64 276
-
(1998)
Am. Soc. Microbiol. News
, vol.64
, pp. 276
-
-
Trun, N.J.1
Marko, J.F.2
-
119
-
-
0033062960
-
Electrostatic-undulatory theory of plectonemically supercoiled DNA
-
Ubbink J and Odijk T 1999 Electrostatic-undulatory theory of plectonemically supercoiled DNA Biophys. J. 76 250219 (Pubitemid 29264612)
-
(1999)
Biophysical Journal
, vol.76
, Issue.5
, pp. 2502-2519
-
-
Ubbink, J.1
Odijk, T.2
-
120
-
-
81255146230
-
The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation
-
10.1016/j.molcel.2011.09.010 1097-2765
-
Umbarger M A et al 2011 The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation Mol. Cell. 44 25264
-
(2011)
Mol. Cell.
, vol.44
, Issue.2
, pp. 252-264
-
-
Umbarger, M.A.1
-
121
-
-
9144264275
-
Macrodomain organization of the Escherichia coli chromosome
-
DOI 10.1038/sj.emboj.7600434
-
Valens M, Penaud S, Rossignol M, Cornet F and Boccard F 2004 Macrodomain organization of the Escherichia coli chromosome EMBO J. 23 433041 (Pubitemid 39546170)
-
(2004)
EMBO Journal
, vol.23
, Issue.21
, pp. 4330-4341
-
-
Valens, M.1
Penaud, S.2
Rossignol, M.3
Cornet, F.4
Boccard, F.5
-
122
-
-
0029978680
-
Chloramphenicol causes fusion of separated nucleoids in Escherichia coli K-12 cells and filaments
-
van Helvoort J M, Kool J and Woldringh C L 1996 Chloramphenicol causes fusion of separated nucleoids in Escherichia coli K-12 cells and filaments J. Bacteriol. 178 428993
-
(1996)
J. Bacteriol.
-
-
Van Helvoort, J.M.1
Kool, J.2
Woldringh, C.L.3
-
123
-
-
2342454974
-
Dual architectural roles of HU: Formation of flexible hinges and rigid filaments
-
DOI 10.1073/pnas.0308230101
-
van Noort J, Verbrugge S, Goosen N, Dekker C and Dame R T 2004 Dual architectural roles of HU: formation of flexible hinges and rigid filaments Proc. Natl Acad. Sci. USA 101 696974 (Pubitemid 38596427)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.18
, pp. 6969-6974
-
-
Van Noort, J.1
Verbrugge, S.2
Goosen, N.3
Dekker, C.4
Dame, R.T.5
-
124
-
-
68349150613
-
Statistics of polymer rings in the melt: A numerical simulation study
-
1478-3975 025013
-
Vettorel T, Grosberg A Y and Kremer K 2009 Statistics of polymer rings in the melt: a numerical simulation study Phys. Biol. 6 025013
-
(2009)
Phys. Biol.
, vol.6
, Issue.2
-
-
Vettorel, T.1
Grosberg, A.Y.2
Kremer, K.3
-
125
-
-
3042548402
-
Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication
-
DOI 10.1073/pnas.0402606101
-
Viollier P H, Thanbichler M, McGrath P T, West L, Meewan M, McAdams H H and Shapiro L 2004 Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication Proc. Natl Acad. Sci. USA 101 925762 (Pubitemid 38812862)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.25
, pp. 9257-9262
-
-
Viollier, P.H.1
Thanbichler, M.2
McGrath, P.T.3
West, L.4
Meewan, M.5
McAdams, H.H.6
Shapiro, L.7
-
126
-
-
67651102745
-
Protein occupancy landscape of a bacterial genome
-
10.1016/j.molcel.2009.06.035 1097-2765
-
Vora T, Hottes A K and Tavazoie S 2009 Protein occupancy landscape of a bacterial genome Molecular Cell 35 24753
-
(2009)
Molecular Cell
, vol.35
, Issue.2
, pp. 247-253
-
-
Vora, T.1
Hottes, A.K.2
Tavazoie, S.3
-
127
-
-
34250619055
-
Genomic analysis of protein-DNA interactions in bacteria: Insights into transcription and chromosome organization
-
DOI 10.1111/j.1365-2958.2007.05781.x
-
Wade J T, Struhl K, Busby S J and Grainger D C 2007 Genomic analysis of protein-DNA interactions in bacteria: insights into transcription and chromosome organization Mol. Microbiol. 65 216 (Pubitemid 46934493)
-
(2007)
Molecular Microbiology
, vol.65
, Issue.1
, pp. 21-26
-
-
Wade, J.T.1
Struhl, K.2
Busby, S.J.W.3
Grainger, D.C.4
-
128
-
-
80052643394
-
Chromosome organization by a nucleoid-associated protein in live bacteria
-
10.1126/science.1204697 0036-8075
-
Wang W, Li G-W, Chen C, Xie X S and Zhuang X 2011a Chromosome organization by a nucleoid-associated protein in live bacteria Science 333 14459
-
(2011)
Science
, vol.333
, Issue.6048
, pp. 1445-1449
-
-
Wang, W.1
Li, G.-W.2
Chen, C.3
Xie, X.S.4
Zhuang, X.5
-
129
-
-
79960584723
-
Replication and segregation of an Escherichia coli chromosome with two replication origins
-
10.1073/pnas.1100874108 0027-8424
-
Wang X, Lesterlin C, Reyes-Lamothe R, Ball G and Sherratt D J 2011b Replication and segregation of an Escherichia coli chromosome with two replication origins Proc. Natl Acad. Sci. USA 108 E24350
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, Issue.26
-
-
Wang, X.1
Lesterlin, C.2
Reyes-Lamothe, R.3
Ball, G.4
Sherratt, D.J.5
-
130
-
-
33745603713
-
The two Escherichia coli chromosome arms locate to separate cell halves
-
DOI 10.1101/gad.388406
-
Wang X, Liu X, Possoz C and Sherratt D J 2006 The two Escherichia coli chromosome arms locate to separate cell halves Genes Dev. 20 172731 (Pubitemid 43992881)
-
(2006)
Genes and Development
, vol.20
, Issue.13
, pp. 1727-1731
-
-
Wang, X.1
Liu, X.2
Possoz, C.3
Sherratt, D.J.4
-
131
-
-
4444340534
-
Statistical analysis of the spatial distribution of operons in the transcriptional regulation network of Escherichia coli
-
DOI 10.1016/j.jmb.2004.07.074, PII S0022283604009155
-
Warren P B and ten Wolde P R 2004 Statistical analysis of the spatial distribution of operons in the transcriptional regulation network of Escherichia coli J. Mol. Biol. 342 137990 (Pubitemid 39208666)
-
(2004)
Journal of Molecular Biology
, vol.342
, Issue.5
, pp. 1379-1390
-
-
Warren, P.B.1
Ten Wolde, P.R.2
-
132
-
-
77953494844
-
Bacterial chromosomal loci move subdiffusively through a viscoelastic cytoplasm
-
10.1103/PhysRevLett.104.238102 0031-9007 238102
-
Weber S C, Spakowitz A J and Theriot J A 2010a Bacterial chromosomal loci move subdiffusively through a viscoelastic cytoplasm Phys. Rev. Lett. 104 238102
-
(2010)
Phys. Rev. Lett.
, vol.104
, Issue.23
-
-
Weber, S.C.1
Spakowitz, A.J.2
Theriot, J.A.3
-
133
-
-
77954819972
-
Subdiffusive motion of a polymer composed of subdiffusive monomers
-
10.1103/PhysRevE.82.011913 1539-3755 E 011913
-
Weber S C, Theriot J A and Spakowitz A J 2010b Subdiffusive motion of a polymer composed of subdiffusive monomers Phys. Rev. E 82 011913
-
(2010)
Phys. Rev.
, vol.82
, Issue.1
-
-
Weber, S.C.1
Theriot, J.A.2
Spakowitz, A.J.3
-
134
-
-
0031633272
-
Dynamics of selfavoiding tethered membranes. I. Model A dynamics (Rouse model)
-
Wiese K J 1998 Dynamics of selfavoiding tethered membranes I Model A Dynamics (Rouse Model) Eur. Phys. J. B1 26972 (Pubitemid 128437435)
-
(1998)
European Physical Journal B
, vol.1
, Issue.3
, pp. 269-272
-
-
Wiese, K.J.1
-
135
-
-
77950455981
-
Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament
-
10.1073/pnas.0912062107 0027-8424
-
Wiggins P A, Cheveralls K C, Martin J S, Lintner R and Kondev J 2010 Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament Proc. Natl Acad. Sci. 107 49915
-
(2010)
Proc. Natl Acad. Sci.
, vol.107
, Issue.11
, pp. 4991-4995
-
-
Wiggins, P.A.1
Cheveralls, K.C.2
Martin, J.S.3
Lintner, R.4
Kondev, J.5
-
136
-
-
70349957921
-
Protein-mediated molecular bridging: A key mechanism in biopolymer organization
-
10.1016/j.bpj.2009.06.051 0006-3495
-
Wiggins P A, Dame R Th, Noom M C and Wuite G J L 2009 Protein-mediated molecular bridging: a key mechanism in biopolymer organization Biophys. J. 97 19972003
-
(2009)
Biophys. J.
, vol.97
, Issue.7
, pp. 1997-2003
-
-
Wiggins, P.A.1
Th, D.R.2
Noom, M.C.3
Wuite, G.J.L.4
-
137
-
-
33750504444
-
Structural and physical aspects of bacterial chromosome segregation
-
DOI 10.1016/j.jsb.2006.04.013, PII S1047847706001560
-
Woldringh C L and Nanninga N 2006 Structural and physical aspects of bacterial chromosome segregation J. Struct. Biol. 156 27383 (Pubitemid 44666441)
-
(2006)
Journal of Structural Biology
, vol.156
, Issue.2
, pp. 273-283
-
-
Woldringh, C.L.1
Nanninga, N.2
-
138
-
-
84863406341
-
Polymer-monovalent salt-induced DNA compaction studied via single-molecule microfluidic trapping
-
10.1039/c2lc20880f 1473-0197
-
Xu W and Muller S J 2012 Polymer-monovalent salt-induced DNA compaction studied via single-molecule microfluidic trapping Lab Chip 12 64751
-
(2012)
Lab Chip
, vol.12
, Issue.3
, pp. 647-651
-
-
Xu, W.1
Muller, S.J.2
-
139
-
-
73449149110
-
Invariant distribution of promoter activities in Escherichia coli
-
10.1371/journal.pcbi.1000545 1553-7358 e1000545
-
Zaslaver A, Kaplan S, Bren A, Jinich A, Mayo A, Dekel E, Alon U and Itzkovitz S 2009 Invariant distribution of promoter activities in Escherichia coli PLoS Comput. Biol. 5 e1000545
-
(2009)
PLoS Comput. Biol.
, vol.5
, Issue.10
-
-
Zaslaver, A.1
Kaplan, S.2
Bren, A.3
Jinich, A.4
Mayo, A.5
Dekel, E.6
Alon, U.7
Itzkovitz, S.8
-
140
-
-
70349728576
-
Macromolecular crowding induced elongation and compaction of single DNA molecules confined in a nanochannel
-
10.1073/pnas.0904741106 0027-8424
-
Zhang C, Shao P G, van Kan J A and van der Maarel J R C 2009 Macromolecular crowding induced elongation and compaction of single DNA molecules confined in a nanochannel Proc. Natl Acad. Sci. USA 106 166516
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, Issue.39
, pp. 16651-16656
-
-
Zhang, C.1
Shao, P.G.2
Van Kan, J.A.3
Van Der Maarel, J.R.C.4
-
141
-
-
2942515131
-
Studies on the compaction of isolated nucleoids from Escherichia coli
-
DOI 10.1016/j.jsb.2004.02.003, PII S1047847704000401
-
Zimmerman S B 2004 Studies on the compaction of isolated nucleoids from Escherichia coli J. Struct. Biol. 147 14658 (Pubitemid 38757510)
-
(2004)
Journal of Structural Biology
, vol.147
, Issue.2
, pp. 146-158
-
-
Zimmerman, S.B.1
-
142
-
-
31344453142
-
Cooperative transitions of isolated Escherichia coli nucleoids: Implications for the nucleoid as a cellular phase
-
DOI 10.1016/j.jsb.2005.10.011, PII S1047847705002327
-
Zimmerman S B 2006a Cooperative transitions of isolated Escherichia coli nucleoids: implications for the nucleoid as a cellular phase J. Struct. Biol. 153 16075 (Pubitemid 43139695)
-
(2006)
Journal of Structural Biology
, vol.153
, Issue.2
, pp. 160-175
-
-
Zimmerman, S.B.1
-
143
-
-
33750510057
-
Shape and compaction of Escherichia coli nucleoids
-
DOI 10.1016/j.jsb.2006.03.022, PII S1047847706001274
-
Zimmerman S B 2006b Shape and compaction of Escherichia coli nucleoids J. Struct. Biol. 156 25561 (Pubitemid 44666440)
-
(2006)
Journal of Structural Biology
, vol.156
, Issue.2
, pp. 255-261
-
-
Zimmerman, S.B.1
-
144
-
-
33646941247
-
The dimensions of chain molecules containing branches and rings
-
10.1063/1.1747157 0021-9606
-
Zimm B H and Stockmayer W H 1949 The dimensions of chain molecules containing branches and rings J. Chem. Phys. 17 1301
-
(1949)
J. Chem. Phys.
, vol.17
, Issue.12
, pp. 1301
-
-
Zimm, B.H.1
Stockmayer, W.H.2
|