-
1
-
-
85015069067
-
Controlling the double helix
-
Felsenfeld, G. and Groudine, M. (2003) Controlling the double helix. Nature, 421, 448-453.
-
(2003)
Nature
, vol.421
, pp. 448-453
-
-
Felsenfeld, G.1
Groudine, M.2
-
2
-
-
0032479079
-
Going the distance: A current view of enhancer action
-
Blackwood, E.M. and Kadonaga, J.T. (1998) Going the distance: a current view of enhancer action. Science, 281, 60-63.
-
(1998)
Science
, vol.281
, pp. 60-63
-
-
Blackwood, E.M.1
Kadonaga, J.T.2
-
3
-
-
0024811753
-
Multipartite genetic control elements: Communication by DNA loop
-
Adhya, S. (1989) Multipartite genetic control elements: communication by DNA loop. Annu. Rev. Genet., 23, 227-250.
-
(1989)
Annu. Rev. Genet.
, vol.23
, pp. 227-250
-
-
Adhya, S.1
-
4
-
-
0036898580
-
Long-range chromatin regulatory interactions in vivo
-
Carter, D., Chakalova, L., Osborne, C.S., Dai, Y.f. and Fraser, P. (2002) Long-range chromatin regulatory interactions in vivo. Nat. Genet., 32, 623-626.
-
(2002)
Nat. Genet.
, vol.32
, pp. 623-626
-
-
Carter, D.1
Chakalova, L.2
Osborne, C.S.3
Fraser, P.4
-
6
-
-
33747591451
-
The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications
-
Gheldof, N., Tabuchi, T.M. and Dekker, J. (2006) The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications. Proc. Natl Acad. Sci. USA, 103, 12463-12468.
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 12463-12468
-
-
Gheldof, N.1
Tabuchi, T.M.2
Dekker, J.3
-
7
-
-
12144289862
-
From silencing to gene expression: Real-time analysis in single cells
-
Janicki, S.M., Tsukamoto, T., Salghetti, S.E., Tansey, W.P., Sachidanandam, R., Prasanth, K.V., Ried, T., Shav-Tal, Y., Bertrand, E., Singer, R.H. et al. (2004) From silencing to gene expression: real-time analysis in single cells. Cell, 116, 683-698.
-
(2004)
Cell
, vol.116
, pp. 683-698
-
-
Janicki, S.M.1
Tsukamoto, T.2
Salghetti, S.E.3
Tansey, W.P.4
Sachidanandam, R.5
Prasanth, K.V.6
Ried, T.7
Shav-Tal, Y.8
Bertrand, E.9
Singer, R.H.10
-
8
-
-
0035833262
-
Large-scale chromatin decondensation and recondensation regulated by transcription from a natural promoter
-
Muller, W.G., Walker, D., Hager, G.L. and McNally, J.G. (2001) Large-scale chromatin decondensation and recondensation regulated by transcription from a natural promoter. J. Cell Biol., 154, 33-48.
-
(2001)
J. Cell Biol.
, vol.154
, pp. 33-48
-
-
Muller, W.G.1
Walker, D.2
Hager, G.L.3
McNally, J.G.4
-
9
-
-
0033612538
-
Large-scale chromatin unfolding and remodeling induced by VP16 acidic activation domain
-
Tumbar, T., Sudlow, G. and Belmont, A.S. (1999) Large-scale chromatin unfolding and remodeling induced by VP16 acidic activation domain. J. Cell Biol., 145, 1341-1354.
-
(1999)
J. Cell Biol.
, vol.145
, pp. 1341-1354
-
-
Tumbar, T.1
Sudlow, G.2
Belmont, A.S.3
-
10
-
-
0033546210
-
The organization of replication and transcription
-
Cook, P.R. (1999) The organization of replication and transcription. Science, 284, 1790-1795.
-
(1999)
Science
, vol.284
, pp. 1790-1795
-
-
Cook, P.R.1
-
11
-
-
0036709614
-
Chromosome positioning in the interphase nucleus
-
Parada, L.A. and Misteli, T. (2002) Chromosome positioning in the interphase nucleus. Trends Cell Biol., 12, 425-432.
-
(2002)
Trends Cell Biol.
, vol.12
, pp. 425-432
-
-
Parada, L.A.1
Misteli, T.2
-
12
-
-
78650994865
-
The three-dimensional folding of the a-globin gene domain reveals formation of chromatin globules
-
Bau, D., Sanyal, A., Lajoie, B.R., Capriotti, E., Byron, M., Lawrence, J.B., Dekker, J. and Marti-Renom, MA. (2011) The three-dimensional folding of the a-globin gene domain reveals formation of chromatin globules. Nat. Struct. Mol. Biol., 18, 107-114.
-
(2011)
Nat. Struct. Mol. Biol.
, vol.18
, pp. 107-114
-
-
Bau, D.1
Sanyal, A.2
Lajoie, B.R.3
Capriotti, E.4
Byron, M.5
Lawrence, J.B.6
Dekker, J.7
Marti-Renom, M.A.8
-
13
-
-
79957855283
-
Transcription and recombination factories: Common features?
-
Lucas, J.S., Bossen, C. and Murre, C. (2011) Transcription and recombination factories: common features? Curr. Opin. Cell Biol., 23, 318-324.
-
(2011)
Curr. Opin. Cell Biol.
, vol.23
, pp. 318-324
-
-
Lucas, J.S.1
Bossen, C.2
Murre, C.3
-
14
-
-
0035316574
-
Chromosome territories, nuclear architecture and gene regulation in mammalian cells
-
Cremer, T. and Cremer, C. (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat. Rev. Genet., 2, 292-301.
-
(2001)
Nat. Rev. Genet.
, vol.2
, pp. 292-301
-
-
Cremer, T.1
Cremer, C.2
-
15
-
-
0042671348
-
Fluorescence in situ hybridization: Past, present and future
-
Levsky, J.M. and Singer, R.H. (2003) Fluorescence in situ hybridization: past, present and future. J. Cell Sci., 116, 2833-2838.
-
(2003)
J. Cell Sci.
, vol.116
, pp. 2833-2838
-
-
Levsky, J.M.1
Singer, R.H.2
-
16
-
-
78650512639
-
Breaking the diffraction barrier: Super-resolution imaging of cells
-
Huang, B., Babcock, H. and Zhuang, X. (2010) Breaking the diffraction barrier: super-resolution imaging of cells. Cell, 143, 1047-1058.
-
(2010)
Cell
, vol.143
, pp. 1047-1058
-
-
Huang, B.1
Babcock, H.2
Zhuang, X.3
-
17
-
-
33750203582
-
Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra-and interchromosomal interactions
-
Zhao, Z., Tavoosidana, G., Sjolinder, M., Gondor, A., Mariano, P., Wang, S., Kanduri, C, Lezcano, M., Singh Sandhu, K., Singh, U. et al. (2006) Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra-and interchromosomal interactions. Nat. Genet., 38, 1341-1347.
-
(2006)
Nat. Genet.
, vol.38
, pp. 1341-1347
-
-
Zhao, Z.1
Tavoosidana, G.2
Sjolinder, M.3
Gondor, A.4
Mariano, P.5
Wang, S.6
Kanduri, C.7
Lezcano, M.8
Singh Sandhu, K.9
Singh, U.10
-
18
-
-
33750212321
-
Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C)
-
Simonis, M., Klous, P., Splinter, E., Moshkin, Y., Willemsen, R., de Wit, E., van Steensel, B. and de Laat, W. (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat. Genet., 38, 1348-1354.
-
(2006)
Nat. Genet.
, vol.38
, pp. 1348-1354
-
-
Simonis, M.1
Klous, P.2
Splinter, E.3
Moshkin, Y.4
Willemsen, R.5
De Wit, E.6
Van Steensel, B.7
De Laat, W.8
-
19
-
-
33749400168
-
Chromosome conformation capture carbon copy (5C): A massively parallel solution for mapping interactions between genomic elements
-
Dostie, J., Richmond, TA., Arnaout, RA., Selzer, R.R., Lee, W.L., Honan, TA., Rubio, E.D., Krumm, A., Lamb, J., Nusbaum, C. et al. (2006) Chromosome conformation capture carbon copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res., 16, 1299-1309.
-
(2006)
Genome Res.
, vol.16
, pp. 1299-1309
-
-
Dostie, J.1
Richmond, T.A.2
Arnaout, R.A.3
Selzer, R.R.4
Lee, W.L.5
Honan, T.A.6
Rubio, E.D.7
Krumm, A.8
Lamb, J.9
Nusbaum, C.10
-
20
-
-
70149094741
-
Global identification of yeast chromosome interactions using genome conformation capture
-
Rodley, C.D.M., Bertels, F., Jones, B. and O'Sullivan, J.M. (2009) Global identification of yeast chromosome interactions using genome conformation capture. Fungal Genet. Biol., 46, 879-886.
-
(2009)
Fungal Genet. Biol.
, vol.46
, pp. 879-886
-
-
Rodley, C.D.M.1
Bertels, F.2
Jones, B.3
O'Sullivan, J.M.4
-
21
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
-
Lieberman-Aiden, E., van Berkum, N.L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B.R., Sabo, P.J., Dorschner, M.O. et al. (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 326, 289-293.
-
(2009)
Science
, vol.326
, pp. 289-293
-
-
Lieberman-Aiden, E.1
Van Berkum, N.L.2
Williams, L.3
Imakaev, M.4
Ragoczy, T.5
Telling, A.6
Amit, I.7
Lajoie, B.R.8
Sabo, P.J.9
Dorschner, M.O.10
-
22
-
-
0037083376
-
Capturing chromosome conformation
-
Dekker, J., Rippe, K., Dekker, M. and Kleckner, N. (2002) Capturing chromosome conformation. Science, 295, 1306-1311.
-
(2002)
Science
, vol.295
, pp. 1306-1311
-
-
Dekker, J.1
Rippe, K.2
Dekker, M.3
Kleckner, N.4
-
23
-
-
84855297335
-
A decade of 3C technologies: Insights into nuclear organization
-
de Wit, E. and de Laat, W. (2012) A decade of 3C technologies: insights into nuclear organization. Genes Dev., 26, 11-24.
-
(2012)
Genes Dev.
, vol.26
, pp. 11-24
-
-
De Wit, E.1
De Laat, W.2
-
24
-
-
80052904110
-
Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations
-
Iyer, B., Kenward, M. and Arya, G (2011) Hierarchies in eukaryotic genome organization: insights from polymer theory and simulations. BMC Biophys., 4, 8.
-
(2011)
BMC Biophys.
, vol.4
, pp. 8
-
-
Iyer, B.1
Kenward, M.2
Arya, G.3
-
25
-
-
79960948298
-
Bridging the resolution gap in structural modeling of 3D genome organization
-
Marti-Renom, MA. and Mirny, LA. (2011) Bridging the resolution gap in structural modeling of 3D genome organization. PLoS Comput. Biol., 7, e1002125.
-
(2011)
PLoS Comput. Biol.
, vol.7
-
-
Marti-Renom, M.A.1
Mirny, L.A.2
-
26
-
-
0035668536
-
Making contacts on a nucleic acid polymer
-
Rippe, K. (2001) Making contacts on a nucleic acid polymer. Trends Biochem. Sci., 26, 733-740.
-
(2001)
Trends Biochem. Sci.
, vol.26
, pp. 733-740
-
-
Rippe, K.1
-
27
-
-
65149100263
-
Chromatin conformation signatures of cellular differentiation
-
Fraser, J., Rousseau, M., Shenker, S., Ferraiuolo, M., Hayashizaki, Y., Blanchette, M. and Dostie, J. (2009) Chromatin conformation signatures of cellular differentiation. Genome Biol., 10, R37.
-
(2009)
Genome Biol.
, vol.10
-
-
Fraser, J.1
Rousseau, M.2
Shenker, S.3
Ferraiuolo, M.4
Hayashizaki, Y.5
Blanchette, M.6
Dostie, J.7
-
28
-
-
77952744854
-
A three-dimensional model of the yeast genome
-
Duan, Z., Andronescu, M., Schutz, K., McIlwain, S., Kim, Y.J., Lee, C, Shendure, J., Fields, S., Blau, CA. and Noble, W.S. (2010) A three-dimensional model of the yeast genome. Nature, 465, 363-367.
-
(2010)
Nature
, vol.465
, pp. 363-367
-
-
Duan, Z.1
Andronescu, M.2
Schutz, K.3
McIlwain, S.4
Kim, Y.J.5
Lee, C.6
Shendure, J.7
Fields, S.8
Blau, C.A.9
Noble, W.S.10
-
29
-
-
78650458168
-
Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation
-
Tanizawa, H., Iwasaki, O., Tanaka, A., Capizzi, J.R., Wickramasinghe, P., Lee, M., Fu, Z. and Noma, K. (2010) Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation. Nucleic Acids Res., 38, 8164-8177.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 8164-8177
-
-
Tanizawa, H.1
Iwasaki, O.2
Tanaka, A.3
Capizzi, J.R.4
Wickramasinghe, P.5
Lee, M.6
Fu, Z.7
Noma, K.8
-
30
-
-
80054875965
-
Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling
-
Rousseau, M., Fraser, J., Ferraiuolo, M., Dostie, J. and Blanchette, M. (2011) Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling. BMC Bioinformatics, 12, 414.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 414
-
-
Rousseau, M.1
Fraser, J.2
Ferraiuolo, M.3
Dostie, J.4
Blanchette, M.5
-
31
-
-
85052275006
-
Chromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions
-
Gehlen, L.R., Gruenert, G., Jones, M.B., Rodley, C.D., Langowski, J. and O'Sullivan, J.M. (2012) Chromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions. Nucleus, 3, 370-383.
-
(2012)
Nucleus
, vol.3
, pp. 370-383
-
-
Gehlen, L.R.1
Gruenert, G.2
Jones, M.B.3
Rodley, C.D.4
Langowski, J.5
O'Sullivan, J.M.6
-
33
-
-
0000545475
-
Ring-closure probabilities for twisted wormlike chains
-
Shimada, J. and Yamakawa, H. (1984) Ring-closure probabilities for twisted wormlike chains. Application to DNA. Macromolecules, 17, 689-698.
-
(1984)
Application to DNA. Macromolecules
, vol.17
, pp. 689-698
-
-
Shimada, J.1
Yamakawa, H.2
-
34
-
-
33646242052
-
EM measurements define the dimensions of the "30-nm" chromatin fiber: Evidence for a compact, interdigitated structure
-
Robinson, P.J.J., Fairall, L., Huynh, V.A.T. and Rhodes, D. (2006) EM measurements define the dimensions of the "30-nm" chromatin fiber: evidence for a compact, interdigitated structure. Proc. Natl Acad. Sci. USA, 103, 6506-6511.
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 6506-6511
-
-
Robinson, P.J.J.1
Fairall, L.2
Huynh, V.A.T.3
Rhodes, D.4
-
35
-
-
77953012431
-
Looping probabilities in model interphase chromosomes
-
Rosa, A., Becker, N.B. and Everaers, R. (2010) Looping probabilities in model interphase chromosomes. Biophys. J., 98, 2410-2419.
-
(2010)
Biophys. J.
, vol.98
, pp. 2410-2419
-
-
Rosa, A.1
Becker, N.B.2
Everaers, R.3
-
36
-
-
84856002587
-
Dynamical modeling of three-dimensional genome organization in interphase budding yeast
-
Tokuda, N., Terada, T.P. and Sasai, M. (2012) Dynamical modeling of three-dimensional genome organization in interphase budding yeast. Biophys. J., 102, 296-304.
-
(2012)
Biophys. J.
, vol.102
, pp. 296-304
-
-
Tokuda, N.1
Terada, T.P.2
Sasai, M.3
-
38
-
-
35649021219
-
Computational modeling of the chromatin fiber
-
Langowski, J. and Heermann, D.W. (2007) Computational modeling of the chromatin fiber. Semin. Cell Dev. Biol., 18, 659-667.
-
(2007)
Semin. Cell Dev. Biol.
, vol.18
, pp. 659-667
-
-
Langowski, J.1
Heermann, D.W.2
-
39
-
-
0003474751
-
-
2nd edn. Cambridge University Press, Cambridge, UK
-
Press, W.H., Teukolsky, S.A., Vetterling, W.T. and Flannery, B.P. (1992) Numerical Recipes in C, 2nd edn. Cambridge University Press, Cambridge, UK.
-
(1992)
Numerical Recipes in C
-
-
Press, W.H.1
Teukolsky, S.A.2
Vetterling, W.T.3
Flannery, B.P.4
-
40
-
-
36549098189
-
A second-order algorithm for the simulation of the Brownian dynamics of macromolecular models
-
Iniesta, A. and de la Torre, J.G. (1990) A second-order algorithm for the simulation of the Brownian dynamics of macromolecular models. J. Chem. Phys., 92, 2015-2018.
-
(1990)
J. Chem. Phys.
, vol.92
, pp. 2015-2018
-
-
Iniesta, A.1
De La Torre, J.G.2
-
41
-
-
0031880233
-
A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes
-
Klenin, K., Merlitz, H. and Langowski, J. (1998) A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes. Biophys. J., 74, 780-788.
-
(1998)
Biophys. J.
, vol.74
, pp. 780-788
-
-
Klenin, K.1
Merlitz, H.2
Langowski, J.3
-
42
-
-
0842289673
-
Physical properties of a genomic condensed chromatin fragment
-
Ghirlando, R., Litt, M.D., Prioleau, M.N., Recillas-Targa, F. and Felsenfeld, G. (2004) Physical properties of a genomic condensed chromatin fragment. J. Mol. Biol., 336, 597-605.
-
(2004)
J. Mol. Biol.
, vol.336
, pp. 597-605
-
-
Ghirlando, R.1
Litt, M.D.2
Prioleau, M.N.3
Recillas-Targa, F.4
Felsenfeld, G.5
-
43
-
-
65249169329
-
Forces and torques in the nucleus: Chromatin under mechanical constraints
-
Lavelle, C. (2009) Forces and torques in the nucleus: chromatin under mechanical constraints. Biochem. Cell Biol., 87, 307-322.
-
(2009)
Biochem. Cell Biol.
, vol.87
, pp. 307-322
-
-
Lavelle, C.1
-
44
-
-
33846842713
-
-
92nd edn. CRC Press, Boca Raton, FL, USA
-
Haynes, W.M. (ed.), (2011) CRC Handbook of Chemistry and Physics, 92nd edn. CRC Press, Boca Raton, FL, USA.
-
(2011)
CRC Handbook of Chemistry and Physics
-
-
Haynes, W.M.1
-
45
-
-
0016643045
-
Adaptive noise cancelling: Principles and applications
-
Widrow, B., Glover, J.R.J., McCool, J., Kaunitz, J., Williams, C., Hearn, R., Zeidler, J., Eugene Dong, J. and Goodlin, R. (1975) Adaptive noise cancelling: principles and applications. Proceedings of the IEEE, Vol 63, pp. 1692-1716.
-
(1975)
Proceedings of the IEEE
, vol.63
, pp. 1692-1716
-
-
Widrow, B.1
Glover, J.R.J.2
McCool, J.3
Kaunitz, J.4
Williams, C.5
Hearn, R.6
Zeidler, J.7
Eugene Dong, J.8
Goodlin, R.9
-
46
-
-
0001792571
-
Adaptive filters
-
Kalman, R.E. and De Claris, N. (eds) Holt, Rinehart and Winston, New York
-
Widrow, B. (1970) Adaptive filters. In: Kalman, R.E. and De Claris, N. (eds), Aspects of Network and System Theory. Holt, Rinehart and Winston, New York, pp. 503-587.
-
(1970)
Aspects of Network and System Theory
, pp. 503-587
-
-
Widrow, B.1
-
48
-
-
4444221565
-
UCSF chimera-a visualization system for exploratory research and analysis
-
Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C. and Ferrin, T.E. (2004) UCSF chimera-a visualization system for exploratory research and analysis. J. Comput. Chem., 25, 1605-1612.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
|