-
1
-
-
34748826166
-
A high-resolution atlas of nucleosome occupancy in yeast
-
Lee W, Tillo D, Bray N, Morse RH, Davis RW, et al. (2007) A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 39: 1235-1244.
-
(2007)
Nat Genet
, vol.39
, pp. 1235-1244
-
-
Lee, W.1
Tillo, D.2
Bray, N.3
Morse, R.H.4
Davis, R.W.5
-
2
-
-
77449109503
-
Divergent human remodeling complexes remove nucleosomes from strong positioning sequences
-
Pham CD, He X, Schnitzler GR, (2010) Divergent human remodeling complexes remove nucleosomes from strong positioning sequences. Nucleic Acids Res 38: 400-413.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 400-413
-
-
Pham, C.D.1
He, X.2
Schnitzler, G.R.3
-
3
-
-
84856806926
-
Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner
-
Moshkin YM, Chalkley GE, Kan TW, Reddy BA, Ozgur Z, et al. (2012) Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner. Mol Cell Biol 32: 675-688.
-
(2012)
Mol Cell Biol
, vol.32
, pp. 675-688
-
-
Moshkin, Y.M.1
Chalkley, G.E.2
Kan, T.W.3
Reddy, B.A.4
Ozgur, Z.5
-
4
-
-
0032512794
-
New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning
-
Lowary PT, Widom J, (1998) New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J Mol Biol 276: 19-42.
-
(1998)
J Mol Biol
, vol.276
, pp. 19-42
-
-
Lowary, P.T.1
Widom, J.2
-
5
-
-
0039837085
-
Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences
-
Thastrom A, Lowary PT, Widlund HR, Cao H, Kubista M, et al. (1999) Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. J Mol Biol 288: 213-229.
-
(1999)
J Mol Biol
, vol.288
, pp. 213-229
-
-
Thastrom, A.1
Lowary, P.T.2
Widlund, H.R.3
Cao, H.4
Kubista, M.5
-
6
-
-
77955410104
-
Nucleosome sequence preferences influence in vivo nucleosome organization
-
Kaplan N, Moore I, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, et al. (2010) Nucleosome sequence preferences influence in vivo nucleosome organization. Nat Struct Mol Biol 17: 918-920 author reply 920-912.
-
(2010)
Nat Struct Mol Biol
, vol.17
, pp. 918-920
-
-
Kaplan, N.1
Moore, I.2
Fondufe-Mittendorf, Y.3
Gossett, A.J.4
Tillo, D.5
-
7
-
-
62649085538
-
The DNA-encoded nucleosome organization of a eukaryotic genome
-
Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, et al. (2009) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458: 362-366.
-
(2009)
Nature
, vol.458
, pp. 362-366
-
-
Kaplan, N.1
Moore, I.K.2
Fondufe-Mittendorf, Y.3
Gossett, A.J.4
Tillo, D.5
-
8
-
-
76949093375
-
Nucleosome positioning: how is it established, and why does it matter?
-
Radman-Livaja M, Rando OJ, (2010) Nucleosome positioning: how is it established, and why does it matter? Dev Biol 339: 258-266.
-
(2010)
Dev Biol
, vol.339
, pp. 258-266
-
-
Radman-Livaja, M.1
Rando, O.J.2
-
9
-
-
0035704707
-
Role of DNA sequence in nucleosome stability and dynamics
-
Widom J, (2001) Role of DNA sequence in nucleosome stability and dynamics. Q Rev Biophys 34: 269-324.
-
(2001)
Q Rev Biophys
, vol.34
, pp. 269-324
-
-
Widom, J.1
-
10
-
-
33747500567
-
A genomic code for nucleosome positioning
-
Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, et al. (2006) A genomic code for nucleosome positioning. Nature 442: 772-778.
-
(2006)
Nature
, vol.442
, pp. 772-778
-
-
Segal, E.1
Fondufe-Mittendorf, Y.2
Chen, L.3
Thastrom, A.4
Field, Y.5
-
11
-
-
43749099875
-
Nucleosome organization in the Drosophila genome
-
Mavrich TN, Jiang C, Ioshikhes IP, Li X, Venters BJ, et al. (2008) Nucleosome organization in the Drosophila genome. Nature 453: 358-362.
-
(2008)
Nature
, vol.453
, pp. 358-362
-
-
Mavrich, T.N.1
Jiang, C.2
Ioshikhes, I.P.3
Li, X.4
Venters, B.J.5
-
12
-
-
33749153628
-
Nucleosome positions predicted through comparative genomics
-
Ioshikhes IP, Albert I, Zanton SJ, Pugh BF, (2006) Nucleosome positions predicted through comparative genomics. Nat Genet 38: 1210-1215.
-
(2006)
Nat Genet
, vol.38
, pp. 1210-1215
-
-
Ioshikhes, I.P.1
Albert, I.2
Zanton, S.J.3
Pugh, B.F.4
-
13
-
-
84870674869
-
Controls of nucleosome positioning in the human genome
-
Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, et al. (2012) Controls of nucleosome positioning in the human genome. PLoS Genet 8: e1003036.
-
(2012)
PLoS Genet
, vol.8
-
-
Gaffney, D.J.1
McVicker, G.2
Pai, A.A.3
Fondufe-Mittendorf, Y.N.4
Lewellen, N.5
-
14
-
-
0023001414
-
Sequence periodicities in chicken nucleosome core DNA
-
Satchwell SC, Drew HR, Travers AA, (1986) Sequence periodicities in chicken nucleosome core DNA. J Mol Biol 191: 659-675.
-
(1986)
J Mol Biol
, vol.191
, pp. 659-675
-
-
Satchwell, S.C.1
Drew, H.R.2
Travers, A.A.3
-
15
-
-
0033548524
-
Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability
-
Anselmi C, Bocchinfuso G, De Santis P, Savino M, Scipioni A, (1999) Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability. J Mol Biol 286: 1293-1301.
-
(1999)
J Mol Biol
, vol.286
, pp. 1293-1301
-
-
Anselmi, C.1
Bocchinfuso, G.2
De Santis, P.3
Savino, M.4
Scipioni, A.5
-
16
-
-
0022230224
-
DNA bending and its relation to nucleosome positioning
-
Drew HR, Travers AA, (1985) DNA bending and its relation to nucleosome positioning. J Mol Biol 186: 773-790.
-
(1985)
J Mol Biol
, vol.186
, pp. 773-790
-
-
Drew, H.R.1
Travers, A.A.2
-
18
-
-
70350686719
-
The role of DNA shape in protein-DNA recognition
-
Rohs R, West SM, Sosinsky A, Liu P, Mann RS, et al. (2009) The role of DNA shape in protein-DNA recognition. Nature 461: 1248-1253.
-
(2009)
Nature
, vol.461
, pp. 1248-1253
-
-
Rohs, R.1
West, S.M.2
Sosinsky, A.3
Liu, P.4
Mann, R.S.5
-
19
-
-
77953311493
-
Electrostatic interactions between arginines and the minor groove in the nucleosome
-
West SM, Rohs R, Mann RS, Honig B, (2010) Electrostatic interactions between arginines and the minor groove in the nucleosome. J Biomol Struct Dyn 27: 861-866.
-
(2010)
J Biomol Struct Dyn
, vol.27
, pp. 861-866
-
-
West, S.M.1
Rohs, R.2
Mann, R.S.3
Honig, B.4
-
20
-
-
60349089645
-
Nucleosome positioning and gene regulation: advances through genomics
-
Jiang C, Pugh BF, (2009) Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet 10: 161-172.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 161-172
-
-
Jiang, C.1
Pugh, B.F.2
-
21
-
-
68249142923
-
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo
-
Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, et al. (2009) Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol 16: 847-852.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 847-852
-
-
Zhang, Y.1
Moqtaderi, Z.2
Rattner, B.P.3
Euskirchen, G.4
Snyder, M.5
-
22
-
-
79959557189
-
Determinants of nucleosome organization in primary human cells
-
Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, et al. (2011) Determinants of nucleosome organization in primary human cells. Nature 474: 516-520.
-
(2011)
Nature
, vol.474
, pp. 516-520
-
-
Valouev, A.1
Johnson, S.M.2
Boyd, S.D.3
Smith, C.L.4
Fire, A.Z.5
-
23
-
-
84862979650
-
A map of nucleosome positions in yeast at base-pair resolution
-
Brogaard K, Xi L, Wang JP, Widom J, (2012) A map of nucleosome positions in yeast at base-pair resolution. Nature 486: 496-501.
-
(2012)
Nature
, vol.486
, pp. 496-501
-
-
Brogaard, K.1
Xi, L.2
Wang, J.P.3
Widom, J.4
-
24
-
-
79956316470
-
A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome
-
Zhang Z, Wippo CJ, Wal M, Ward E, Korber P, et al. (2011) A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science 332: 977-980.
-
(2011)
Science
, vol.332
, pp. 977-980
-
-
Zhang, Z.1
Wippo, C.J.2
Wal, M.3
Ward, E.4
Korber, P.5
-
25
-
-
57149119464
-
Distinct modes of regulation by chromatin encoded through nucleosome positioning signals
-
Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, et al. (2008) Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol 4: e1000216.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Field, Y.1
Kaplan, N.2
Fondufe-Mittendorf, Y.3
Moore, I.K.4
Sharon, E.5
-
26
-
-
75149135277
-
G+C content dominates intrinsic nucleosome occupancy
-
Tillo D, Hughes TR, (2009) G+C content dominates intrinsic nucleosome occupancy. BMC Bioinformatics 10: 442.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 442
-
-
Tillo, D.1
Hughes, T.R.2
-
27
-
-
20444403749
-
Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast
-
Sekinger EA, Moqtaderi Z, Struhl K, (2005) Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol Cell 18: 735-748.
-
(2005)
Mol Cell
, vol.18
, pp. 735-748
-
-
Sekinger, E.A.1
Moqtaderi, Z.2
Struhl, K.3
-
28
-
-
34047111213
-
Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome
-
Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, et al. (2007) Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446: 572-576.
-
(2007)
Nature
, vol.446
, pp. 572-576
-
-
Albert, I.1
Mavrich, T.N.2
Tomsho, L.P.3
Qi, J.4
Zanton, S.J.5
-
29
-
-
84870593313
-
Transcriptional activation of yeast genes disrupts intragenic nucleosome phasing
-
Cui F, Cole HA, Clark DJ, Zhurkin VB, (2012) Transcriptional activation of yeast genes disrupts intragenic nucleosome phasing. Nucleic Acids Res 40: 10753-10764.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 10753-10764
-
-
Cui, F.1
Cole, H.A.2
Clark, D.J.3
Zhurkin, V.B.4
-
30
-
-
77749322697
-
Mechanisms of ATP-dependent nucleosome sliding
-
Bowman GD, (2010) Mechanisms of ATP-dependent nucleosome sliding. Curr Opin Struct Biol 20: 73-81.
-
(2010)
Curr Opin Struct Biol
, vol.20
, pp. 73-81
-
-
Bowman, G.D.1
-
31
-
-
0001771498
-
Evolution in Mendelian Populations
-
Wright S, (1931) Evolution in Mendelian Populations. Genetics 16: 97-159.
-
(1931)
Genetics
, vol.16
, pp. 97-159
-
-
Wright, S.1
-
32
-
-
0025941139
-
The selection-mutation-drift theory of synonymous codon usage
-
Bulmer M, (1991) The selection-mutation-drift theory of synonymous codon usage. Genetics 129: 897-907.
-
(1991)
Genetics
, vol.129
, pp. 897-907
-
-
Bulmer, M.1
-
34
-
-
0028220048
-
Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy
-
Akashi H, (1994) Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 136: 927-935.
-
(1994)
Genetics
, vol.136
, pp. 927-935
-
-
Akashi, H.1
-
35
-
-
0029985179
-
Molecular evolution between Drosophila melanogaster and D. simulans: reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster
-
Akashi H, (1996) Molecular evolution between Drosophila melanogaster and D. simulans: reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster. Genetics 144: 1297-1307.
-
(1996)
Genetics
, vol.144
, pp. 1297-1307
-
-
Akashi, H.1
-
36
-
-
58449116917
-
Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites
-
Sasaki S, Mello CC, Shimada A, Nakatani Y, Hashimoto S-I, et al. (2009) Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. Science (New York, NY) 323: 401-404.
-
(2009)
Science (New York, NY)
, vol.323
, pp. 401-404
-
-
Sasaki, S.1
Mello, C.C.2
Shimada, A.3
Nakatani, Y.4
Hashimoto, S.-I.5
-
37
-
-
79953788666
-
Impact of chromatin structure on sequence variability in the human genome
-
Tolstorukov MY, Volfovsky N, Stephens RM, Park PJ, (2011) Impact of chromatin structure on sequence variability in the human genome. Nature Structural & Molecular Biology 18: 510-515.
-
(2011)
Nature Structural & Molecular Biology
, vol.18
, pp. 510-515
-
-
Tolstorukov, M.Y.1
Volfovsky, N.2
Stephens, R.M.3
Park, P.J.4
-
38
-
-
80555156662
-
Widespread signatures of recent selection linked to nucleosome positioning in the human lineage
-
Prendergast J, Semple C, (2011) Widespread signatures of recent selection linked to nucleosome positioning in the human lineage. Genome Research 21: 1777-1877.
-
(2011)
Genome Research
, vol.21
, pp. 1777-1877
-
-
Prendergast, J.1
Semple, C.2
-
39
-
-
56649089682
-
Evolutionary footprints of nucleosome positions in yeast
-
Washietl S, Machne R, Goldman N, (2008) Evolutionary footprints of nucleosome positions in yeast. Trends Genet 24: 583-587.
-
(2008)
Trends Genet
, vol.24
, pp. 583-587
-
-
Washietl, S.1
Machne, R.2
Goldman, N.3
-
40
-
-
79952255486
-
Functional conservation of nucleosome formation selectively biases presumably neutral molecular variation in yeast genomes
-
Babbitt GA, Cotter CR, (2011) Functional conservation of nucleosome formation selectively biases presumably neutral molecular variation in yeast genomes. Genome Biol Evol 3: 15-22.
-
(2011)
Genome Biol Evol
, vol.3
, pp. 15-22
-
-
Babbitt, G.A.1
Cotter, C.R.2
-
41
-
-
47649094814
-
Inferring Natural Selection on Fine-Scale Chromatin Organization in Yeast
-
Babbitt GA, Kim Y, (2008) Inferring Natural Selection on Fine-Scale Chromatin Organization in Yeast. Molecular Biology and Evolution 25: 1714-1727.
-
(2008)
Molecular Biology and Evolution
, vol.25
, pp. 1714-1727
-
-
Babbitt, G.A.1
Kim, Y.2
-
42
-
-
77953296396
-
The molecular evolution of nucleosome positioning through sequence-dependent deformation of the DNA polymer
-
Babbitt GA, Tolstorukov MY, Kim Y, (2010) The molecular evolution of nucleosome positioning through sequence-dependent deformation of the DNA polymer. J Biomol Struct Dyn 27: 765-780.
-
(2010)
J Biomol Struct Dyn
, vol.27
, pp. 765-780
-
-
Babbitt, G.A.1
Tolstorukov, M.Y.2
Kim, Y.3
-
43
-
-
57149100569
-
The impact of the nucleosome code on protein-coding sequence evolution in yeast
-
Warnecke T, Batada NN, Hurst LD, (2008) The impact of the nucleosome code on protein-coding sequence evolution in yeast. PLoS Genet 4: e1000250.
-
(2008)
PLoS Genet
, vol.4
-
-
Warnecke, T.1
Batada, N.N.2
Hurst, L.D.3
-
44
-
-
84863245662
-
Nucleosomes suppress spontaneous mutations base-specifically in eukaryotes
-
Chen X, Chen Z, Chen H, Su Z, Yang J, et al. (2012) Nucleosomes suppress spontaneous mutations base-specifically in eukaryotes. Science 335: 1235-1238.
-
(2012)
Science
, vol.335
, pp. 1235-1238
-
-
Chen, X.1
Chen, Z.2
Chen, H.3
Su, Z.4
Yang, J.5
-
45
-
-
72149111977
-
Nucleosome remodeling by hMSH2-hMSH6
-
Javaid S, Manohar M, Punja N, Mooney A, Ottesen JJ, et al. (2009) Nucleosome remodeling by hMSH2-hMSH6. Mol Cell 36: 1086-1094.
-
(2009)
Mol Cell
, vol.36
, pp. 1086-1094
-
-
Javaid, S.1
Manohar, M.2
Punja, N.3
Mooney, A.4
Ottesen, J.J.5
-
46
-
-
70450237030
-
Evidence that nucleosomes inhibit mismatch repair in eukaryotic cells
-
Li F, Tian L, Gu L, Li GM, (2009) Evidence that nucleosomes inhibit mismatch repair in eukaryotic cells. J Biol Chem 284: 33056-33061.
-
(2009)
J Biol Chem
, vol.284
, pp. 33056-33061
-
-
Li, F.1
Tian, L.2
Gu, L.3
Li, G.M.4
-
47
-
-
77949528928
-
Rotational dynamics of DNA on the nucleosome surface markedly impact accessibility to a DNA repair enzyme
-
Hinz JM, Rodriguez Y, Smerdon MJ, (2010) Rotational dynamics of DNA on the nucleosome surface markedly impact accessibility to a DNA repair enzyme. Proc Natl Acad Sci U S A 107: 4646-4651.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 4646-4651
-
-
Hinz, J.M.1
Rodriguez, Y.2
Smerdon, M.J.3
-
48
-
-
84877696971
-
The structural location of DNA lesions in nucleosome core particles determines accessibility by base excision repair enzymes
-
Rodriguez Y, Smerdon MJ, (2013) The structural location of DNA lesions in nucleosome core particles determines accessibility by base excision repair enzymes. J Biol Chem 288: 13863-13875.
-
(2013)
J Biol Chem
, vol.288
, pp. 13863-13875
-
-
Rodriguez, Y.1
Smerdon, M.J.2
-
49
-
-
84865852567
-
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
-
Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, et al. (2012) Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res 22: 1798-1812.
-
(2012)
Genome Res
, vol.22
, pp. 1798-1812
-
-
Wang, J.1
Zhuang, J.2
Iyer, S.3
Lin, X.4
Whitfield, T.W.5
-
50
-
-
34547643563
-
Nucleosome positioning signals in genomic DNA
-
Peckham HE, Thurman RE, Fu Y, Stamatoyannopoulos JA, Noble WS, et al. (2007) Nucleosome positioning signals in genomic DNA. Genome Res 17: 1170-1177.
-
(2007)
Genome Res
, vol.17
, pp. 1170-1177
-
-
Peckham, H.E.1
Thurman, R.E.2
Fu, Y.3
Stamatoyannopoulos, J.A.4
Noble, W.S.5
-
51
-
-
84857653293
-
Micrococcal nuclease does not substantially bias nucleosome mapping
-
Allan J, Fraser RM, Owen-Hughes T, Keszenman-Pereyra D, (2012) Micrococcal nuclease does not substantially bias nucleosome mapping. J Mol Biol 417: 152-164.
-
(2012)
J Mol Biol
, vol.417
, pp. 152-164
-
-
Allan, J.1
Fraser, R.M.2
Owen-Hughes, T.3
Keszenman-Pereyra, D.4
-
52
-
-
84876540763
-
Population Genomic Analysis of Base Composition Evolution in Drosophila melanogaster
-
Poh YP, Ting CT, Fu HW, Langley CH, Begun DJ, (2012) Population Genomic Analysis of Base Composition Evolution in Drosophila melanogaster. Genome Biol Evol 4: 1245-1255.
-
(2012)
Genome Biol Evol
, vol.4
, pp. 1245-1255
-
-
Poh, Y.P.1
Ting, C.T.2
Fu, H.W.3
Langley, C.H.4
Begun, D.J.5
-
53
-
-
0030034357
-
Intraspecific nuclear DNA variation in Drosophila
-
Moriyama EN, Powell JR, (1996) Intraspecific nuclear DNA variation in Drosophila. Mol Biol Evol 13: 261-277.
-
(1996)
Mol Biol Evol
, vol.13
, pp. 261-277
-
-
Moriyama, E.N.1
Powell, J.R.2
-
54
-
-
67650064592
-
Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines
-
Keightley PD, Trivedi U, Thomson M, Oliver F, Kumar S, et al. (2009) Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines. Genome Res 19: 1195-1201.
-
(2009)
Genome Res
, vol.19
, pp. 1195-1201
-
-
Keightley, P.D.1
Trivedi, U.2
Thomson, M.3
Oliver, F.4
Kumar, S.5
-
55
-
-
0036307707
-
Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9 a Resolution
-
Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ, (2002) Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9 a Resolution. Journal of Molecular Biology 319: 1097-1113.
-
(2002)
Journal of Molecular Biology
, vol.319
, pp. 1097-1113
-
-
Davey, C.A.1
Sargent, D.F.2
Luger, K.3
Maeder, A.W.4
Richmond, T.J.5
-
56
-
-
84864487717
-
The mechanics behind DNA sequence-dependent properties of the nucleosome
-
Chua EY, Vasudevan D, Davey GE, Wu B, Davey CA, (2012) The mechanics behind DNA sequence-dependent properties of the nucleosome. Nucleic Acids Res 40: 6338-6352.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 6338-6352
-
-
Chua, E.Y.1
Vasudevan, D.2
Davey, G.E.3
Wu, B.4
Davey, C.A.5
-
57
-
-
0019949369
-
Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs
-
Ikemura T, (1982) Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. J Mol Biol 158: 573-597.
-
(1982)
J Mol Biol
, vol.158
, pp. 573-597
-
-
Ikemura, T.1
-
58
-
-
0036889468
-
Evolution of synonymous codon usage in metazoans
-
Duret L, (2002) Evolution of synonymous codon usage in metazoans. Curr Opin Genet Dev 12: 640-649.
-
(2002)
Curr Opin Genet Dev
, vol.12
, pp. 640-649
-
-
Duret, L.1
-
59
-
-
0024313579
-
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism
-
Tajima F, (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
-
(1989)
Genetics
, vol.123
, pp. 585-595
-
-
Tajima, F.1
-
60
-
-
0000699546
-
The Sampling Theory of Selectively Neutral Alleles
-
Waterson GA, (1974) The Sampling Theory of Selectively Neutral Alleles. Advances in Applied Probability 6: 463-488.
-
(1974)
Advances in Applied Probability
, vol.6
, pp. 463-488
-
-
Waterson, G.A.1
-
61
-
-
0032749124
-
A Population Genetic Model for the Evolution of Synonymous Codon Usage: Patterns and Predictions
-
McVean GAT, Charlesworth B, (1999) A Population Genetic Model for the Evolution of Synonymous Codon Usage: Patterns and Predictions. Genetics Research 74: 145-158.
-
(1999)
Genetics Research
, vol.74
, pp. 145-158
-
-
McVean, G.A.T.1
Charlesworth, B.2
-
62
-
-
0026460082
-
Population genetics of polymorphism and divergence
-
Sawyer SA, Hartl DL, (1992) Population genetics of polymorphism and divergence. Genetics 132: 1161-1176.
-
(1992)
Genetics
, vol.132
, pp. 1161-1176
-
-
Sawyer, S.A.1
Hartl, D.L.2
-
63
-
-
0001111819
-
The Distribution of Gene Frequencies Under Irreversible Mutation
-
Wright S, (1938) The Distribution of Gene Frequencies Under Irreversible Mutation. Proc Natl Acad Sci U S A 24: 253-259.
-
(1938)
Proc Natl Acad Sci U S A
, vol.24
, pp. 253-259
-
-
Wright, S.1
-
64
-
-
0033870688
-
When did the human population size start increasing?
-
Wall JD, Przeworski M, (2000) When did the human population size start increasing? Genetics 155: 1865-1874.
-
(2000)
Genetics
, vol.155
, pp. 1865-1874
-
-
Wall, J.D.1
Przeworski, M.2
-
65
-
-
84866081815
-
Genomic Variation in Natural Populations of Drosophila melanogaster
-
Langley CH, Stevens K, Cardeno C, Lee YC, Schrider DR, et al. (2012) Genomic Variation in Natural Populations of Drosophila melanogaster. Genetics 192: 533-598.
-
(2012)
Genetics
, vol.192
, pp. 533-598
-
-
Langley, C.H.1
Stevens, K.2
Cardeno, C.3
Lee, Y.C.4
Schrider, D.R.5
-
66
-
-
34547808850
-
Context dependence, ancestral misidentification, and spurious signatures of natural selection
-
Hernandez RD, Williamson SH, Bustamante CD, (2007) Context dependence, ancestral misidentification, and spurious signatures of natural selection. Mol Biol Evol 24: 1792-1800.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1792-1800
-
-
Hernandez, R.D.1
Williamson, S.H.2
Bustamante, C.D.3
-
67
-
-
33745612972
-
Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison
-
Halligan DL, Keightley PD, (2006) Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison. Genome Res 16: 875-884.
-
(2006)
Genome Res
, vol.16
, pp. 875-884
-
-
Halligan, D.L.1
Keightley, P.D.2
-
68
-
-
35348873167
-
Purifying selection maintains highly conserved noncoding sequences in Drosophila
-
Casillas S, Barbadilla A, Bergman CM, (2007) Purifying selection maintains highly conserved noncoding sequences in Drosophila. Mol Biol Evol 24: 2222-2234.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 2222-2234
-
-
Casillas, S.1
Barbadilla, A.2
Bergman, C.M.3
-
69
-
-
84855428748
-
The effects of deleterious mutations on evolution at linked sites
-
Charlesworth B, (2012) The effects of deleterious mutations on evolution at linked sites. Genetics 190: 5-22.
-
(2012)
Genetics
, vol.190
, pp. 5-22
-
-
Charlesworth, B.1
-
70
-
-
0029036829
-
The hitchhiking effect on the site frequency spectrum of DNA polymorphisms
-
Braverman JM, Hudson RR, Kaplan NL, Langley CH, Stephan W, (1995) The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics 140: 783-796.
-
(1995)
Genetics
, vol.140
, pp. 783-796
-
-
Braverman, J.M.1
Hudson, R.R.2
Kaplan, N.L.3
Langley, C.H.4
Stephan, W.5
-
71
-
-
84872014607
-
Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture
-
Pool JE, Corbett-Detig RB, Sugino RP, Stevens KA, Cardeno CM, et al. (2012) Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture. PLoS Genet 8: e1003080.
-
(2012)
PLoS Genet
, vol.8
-
-
Pool, J.E.1
Corbett-Detig, R.B.2
Sugino, R.P.3
Stevens, K.A.4
Cardeno, C.M.5
-
72
-
-
0036964070
-
Molecular population genetics of Xdh and the evolution of base composition in Drosophila
-
Begun DJ, Whitley P, (2002) Molecular population genetics of Xdh and the evolution of base composition in Drosophila. Genetics 162: 1725-1735.
-
(2002)
Genetics
, vol.162
, pp. 1725-1735
-
-
Begun, D.J.1
Whitley, P.2
-
73
-
-
84857131972
-
Interplay between mismatch repair and chromatin assembly
-
Schopf B, Bregenhorn S, Quivy JP, Kadyrov FA, Almouzni G, et al. (2012) Interplay between mismatch repair and chromatin assembly. Proc Natl Acad Sci U S A 109: 1895-1900.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 1895-1900
-
-
Schopf, B.1
Bregenhorn, S.2
Quivy, J.P.3
Kadyrov, F.A.4
Almouzni, G.5
-
74
-
-
0038381469
-
Chromatin remodeling activities act on UV-damaged nucleosomes and modulate DNA damage accessibility to photolyase
-
Gaillard H, Fitzgerald DJ, Smith CL, Peterson CL, Richmond TJ, et al. (2003) Chromatin remodeling activities act on UV-damaged nucleosomes and modulate DNA damage accessibility to photolyase. J Biol Chem 278: 17655-17663.
-
(2003)
J Biol Chem
, vol.278
, pp. 17655-17663
-
-
Gaillard, H.1
Fitzgerald, D.J.2
Smith, C.L.3
Peterson, C.L.4
Richmond, T.J.5
-
75
-
-
79955978866
-
Activity of FEN1 endonuclease on nucleosome substrates is dependent upon DNA sequence but not flap orientation
-
Jagannathan I, Pepenella S, Hayes JJ, (2011) Activity of FEN1 endonuclease on nucleosome substrates is dependent upon DNA sequence but not flap orientation. J Biol Chem 286: 17521-17529.
-
(2011)
J Biol Chem
, vol.286
, pp. 17521-17529
-
-
Jagannathan, I.1
Pepenella, S.2
Hayes, J.J.3
-
76
-
-
84864447350
-
Enzymatic excision of uracil residues in nucleosomes depends on the local DNA structure and dynamics
-
Ye Y, Stahley MR, Xu J, Friedman JI, Sun Y, et al. (2012) Enzymatic excision of uracil residues in nucleosomes depends on the local DNA structure and dynamics. Biochemistry 51: 6028-6038.
-
(2012)
Biochemistry
, vol.51
, pp. 6028-6038
-
-
Ye, Y.1
Stahley, M.R.2
Xu, J.3
Friedman, J.I.4
Sun, Y.5
-
77
-
-
0034735780
-
DNA methylation in Drosophila melanogaster
-
Lyko F, Ramsahoye BH, Jaenisch R, (2000) DNA methylation in Drosophila melanogaster. Nature 408: 538-540.
-
(2000)
Nature
, vol.408
, pp. 538-540
-
-
Lyko, F.1
Ramsahoye, B.H.2
Jaenisch, R.3
-
78
-
-
4644300141
-
Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
-
Hwang DG, Green P, (2004) Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci U S A 101: 13994-14001.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 13994-14001
-
-
Hwang, D.G.1
Green, P.2
-
79
-
-
0021022685
-
Evolution of a large population under gene conversion
-
Nagylaki T, (1983) Evolution of a large population under gene conversion. Proc Natl Acad Sci U S A 80: 5941-5945.
-
(1983)
Proc Natl Acad Sci U S A
, vol.80
, pp. 5941-5945
-
-
Nagylaki, T.1
-
80
-
-
0035986891
-
Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution
-
Birdsell JA, (2002) Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution. Mol Biol Evol 19: 1181-1197.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 1181-1197
-
-
Birdsell, J.A.1
-
81
-
-
33644780844
-
GC-biased segregation of noncoding polymorphisms in Drosophila
-
Galtier N, Bazin E, Bierne N, (2006) GC-biased segregation of noncoding polymorphisms in Drosophila. Genetics 172: 221-228.
-
(2006)
Genetics
, vol.172
, pp. 221-228
-
-
Galtier, N.1
Bazin, E.2
Bierne, N.3
-
82
-
-
0029034063
-
Accessibility of a glucocorticoid response element in a nucleosome depends on its rotational positioning
-
Li Q, Wrange O, (1995) Accessibility of a glucocorticoid response element in a nucleosome depends on its rotational positioning. Mol Cell Biol 15: 4375-4384.
-
(1995)
Mol Cell Biol
, vol.15
, pp. 4375-4384
-
-
Li, Q.1
Wrange, O.2
-
83
-
-
69949124307
-
Nucleosome positioning as a determinant of exon recognition
-
Tilgner H, Nikolaou C, Althammer S, Sammeth M, Beato M, et al. (2009) Nucleosome positioning as a determinant of exon recognition. Nat Struct Mol Biol 16: 996-1001.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 996-1001
-
-
Tilgner, H.1
Nikolaou, C.2
Althammer, S.3
Sammeth, M.4
Beato, M.5
-
84
-
-
84874175008
-
Precise maps of RNA polymerase reveal how promoters direct initiation and pausing
-
Kwak H, Fuda NJ, Core LJ, Lis JT, (2013) Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 339: 950-953.
-
(2013)
Science
, vol.339
, pp. 950-953
-
-
Kwak, H.1
Fuda, N.J.2
Core, L.J.3
Lis, J.T.4
-
85
-
-
40149095913
-
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm
-
Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, et al. (2008) Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 6: e27.
-
(2008)
PLoS Biol
, vol.6
-
-
Li, X.Y.1
MacArthur, S.2
Bourgon, R.3
Nix, D.4
Pollard, D.A.5
-
86
-
-
0012340085
-
Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence
-
Celniker SE, Wheeler DA, Kronmiller B, Carlson JW, Halpern A, et al. (2002) Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biol 3: RESEARCH0079.
-
(2002)
Genome Biol
, vol.3
-
-
Celniker, S.E.1
Wheeler, D.A.2
Kronmiller, B.3
Carlson, J.W.4
Halpern, A.5
-
87
-
-
79551575925
-
Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin
-
Riddle NC, Minoda A, Kharchenko PV, Alekseyenko AA, Schwartz YB, et al. (2011) Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Research 21: 147-163.
-
(2011)
Genome Research
, vol.21
, pp. 147-163
-
-
Riddle, N.C.1
Minoda, A.2
Kharchenko, P.V.3
Alekseyenko, A.A.4
Schwartz, Y.B.5
-
88
-
-
84907095419
-
R: A language and environment for statistical computing
-
R Development Core Team
-
R Development Core Team (2012) R: A language and environment for statistical computing. R Foundation for Statistical Computing.
-
(2012)
R Foundation for Statistical Computing
-
-
|