-
1
-
-
34547624303
-
Genomewide maps of chromatin state in pluripotent and lineage-committed cells
-
Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, et al. (2007) Genomewide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553-560.
-
(2007)
Nature
, vol.448
, pp. 553-560
-
-
Mikkelsen, T.S.1
Ku, M.2
Jaffe, D.B.3
Issac, B.4
Lieberman, E.5
-
2
-
-
62249133709
-
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
-
Guttman M, Amit I, Garber M, French C, Lin MF, et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458: 223-227.
-
(2009)
Nature
, vol.458
, pp. 223-227
-
-
Guttman, M.1
Amit, I.2
Garber, M.3
French, C.4
Lin, M.F.5
-
3
-
-
34249088350
-
Genome-wide transcription and the implications for genomic organization
-
Kapranov P, Willingham AT, Gingeras TR (2007) Genome-wide transcription and the implications for genomic organization. Nat Rev Genet 8: 413-423.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 413-423
-
-
Kapranov, P.1
Willingham, A.T.2
Gingeras, T.R.3
-
4
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
Birney, E.1
Stamatoyannopoulos, J.A.2
Dutta, A.3
Guigó, R.4
Gingeras, T.R.5
-
5
-
-
65549104157
-
Histone modifications at human enhancers reflect global cell-type-specific gene expression
-
Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, et al. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459: 108-112.
-
(2009)
Nature
, vol.459
, pp. 108-112
-
-
Heintzman, N.D.1
Hon, G.C.2
Hawkins, R.D.3
Kheradpour, P.4
Stark, A.5
-
6
-
-
60149091656
-
ChIP-seq accurately predicts tissue-specific activity of enhancers
-
Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, et al. (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457: 854-858.
-
(2009)
Nature
, vol.457
, pp. 854-858
-
-
Visel, A.1
Blow, M.J.2
Li, Z.3
Zhang, T.4
Akiyama, J.A.5
-
7
-
-
52449148668
-
The role of compensatory neutral mutations in molecular evolution
-
Kimura M (1985) The role of compensatory neutral mutations in molecular evolution. J Genet 64: 7-19.
-
(1985)
J Genet
, vol.64
, pp. 7-19
-
-
Kimura, M.1
-
8
-
-
0029026878
-
Maintenance of pre-mRNA secondary structure by epistatic selection
-
Kirby DA, Muse SV, Stephan W (1995) Maintenance of pre-mRNA secondary structure by epistatic selection. Proc Natl Acad Sci USA 92: 9047-9051.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 9047-9051
-
-
Kirby, D.A.1
Muse, S.V.2
Stephan, W.3
-
9
-
-
0033497101
-
RNA secondary structure and compensatory evolution
-
Chen Y, Carlini DB, Baines JF, Parsch J, Braverman JM, et al. (1999) RNA secondary structure and compensatory evolution. Genes Genet Syst 74: 271-286.
-
(1999)
Genes Genet Syst
, vol.74
, pp. 271-286
-
-
Chen, Y.1
Carlini, D.B.2
Baines, J.F.3
Parsch, J.4
Braverman, J.M.5
-
10
-
-
0027164566
-
RNA folding in Drosophila shows a distance effect for compensatory fitness interactions
-
Stephan W, Kirby Da (1993) RNA folding in Drosophila shows a distance effect for compensatory fitness interactions. Genetics 135: 97-103.
-
(1993)
Genetics
, vol.135
, pp. 97-103
-
-
Stephan, W.1
Da, K.2
-
11
-
-
33746691336
-
Extensive low-affinity transcriptional interactions in the yeast genome
-
Tanay A (2006) Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res 16: 962-972.
-
(2006)
Genome Res
, vol.16
, pp. 962-972
-
-
Tanay, A.1
-
12
-
-
77950566643
-
Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species
-
Bradley RK, Li X-Y, Trapnell C, Davidson S, Pachter L, et al. (2010) Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol 8: e1000343-e1000343.
-
(2010)
PLoS Biol
, vol.8
-
-
Bradley, R.K.1
Li, X.-Y.2
Trapnell, C.3
Davidson, S.4
Pachter, L.5
-
13
-
-
34249723155
-
Frequent gain and loss of functional transcription factor binding sites
-
Doniger SW, Fay JC (2007) Frequent gain and loss of functional transcription factor binding sites. PLoS Comp Biol 3: e99-e99.
-
(2007)
PLoS Comp Biol
, vol.3
-
-
Doniger, S.W.1
Fay, J.C.2
-
14
-
-
76749088015
-
Evolutionary mirages: Selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers
-
Lusk RW, Eisen MB (2010) Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers. PLoS Genet 6: e1000829-e1000829.
-
(2010)
PLoS Genet
, vol.6
-
-
Lusk, R.W.1
Eisen, M.B.2
-
15
-
-
78651235562
-
Functional analysis of eve stripe 2 enhancer evolution in Drosophila: Rules governing conservation and change
-
Ludwig MZ, Patel NH, Kreitman M (1998) Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. BioSyst 958: 949-958.
-
(1998)
BioSyst
, vol.958
, pp. 949-958
-
-
Ludwig, M.Z.1
Patel, N.H.2
Kreitman, M.3
-
16
-
-
33749173831
-
Evolution of alternative transcriptional circuits with identical logic
-
Tsong AE, Tuch BB, Li H, Johnson AD (2006) Evolution of alternative transcriptional circuits with identical logic. Nature 443: 415-420.
-
(2006)
Nature
, vol.443
, pp. 415-420
-
-
Tsong, A.E.1
Tuch, B.B.2
Li, H.3
Johnson, A.D.4
-
17
-
-
18844374522
-
Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast
-
Tanay A, Regev A, Shamir R (2005) Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. Proc Natl Acad Sci USA 102: 7203-7208.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 7203-7208
-
-
Tanay, A.1
Regev, A.2
Shamir, R.3
-
18
-
-
0023001414
-
Sequence periodicities in chicken nucleosome core DNAN 1
-
Satchwell SC, Drew HR, Travers AA (1986) Sequence periodicities in chicken nucleosome core DNAN 1. 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
-
19
-
-
33747500567
-
A genomic code for nucleosome positioning
-
Segal E, Fondufe-Mittendorf Y, Chen L, Thaström 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
Thaström, A.4
Field, Y.5
-
20
-
-
22744432660
-
Genome-scale identification of nucleosome positions in S. cerevisiae
-
Yuan G-C, Liu Y-J, Dion MF, Slack MD, Wu LF, et al. (2005) Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309: 626-630.
-
(2005)
Science
, vol.309
, pp. 626-630
-
-
Yuan, G.-C.1
Liu, Y.-J.2
Dion, M.F.3
Slack, M.D.4
Wu, L.F.5
-
21
-
-
62649085538
-
The DNA-encoded nucleosome organization of a eukaryotic genome
-
Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, et al. (2008) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458: 362-366.
-
(2008)
Nature
, vol.458
, pp. 362-366
-
-
Kaplan, N.1
Moore, I.K.2
Fondufe-Mittendorf, Y.3
Gossett, A.J.4
Tillo, D.5
-
22
-
-
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
-
23
-
-
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
-
24
-
-
39749145198
-
Dynamic regulation of nucleosome positioning in the human genome
-
Schones DE, Cui K, Cuddapah S, Roh T-Y, Barski A, et al. (2008) Dynamic regulation of nucleosome positioning in the human genome. Cell 132: 887-898.
-
(2008)
Cell
, vol.132
, pp. 887-898
-
-
Schones, D.E.1
Cui, K.2
Cuddapah, S.3
Roh, T.-Y.4
Barski, A.5
-
25
-
-
60349115060
-
Poly (dA: DT) tracts: Major determinants of nucleosome organization
-
Segal E, Widom J (2009) Poly (dA: dT) tracts: major determinants of nucleosome organization. Curr Opin Struct Biol 19: 65-71.
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 65-71
-
-
Segal, E.1
Widom, J.2
-
26
-
-
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 Comp Biol 4: e1000216-e1000216.
-
(2008)
PLoS Comp Biol
, vol.4
-
-
Field, Y.1
Kaplan, N.2
Fondufe-Mittendorf, Y.3
Moore, I.K.4
Sharon, E.5
-
27
-
-
68349125112
-
What controls nucleosome positions?
-
Segal E, Widom J (2009) What controls nucleosome positions? Trends Genet 25: 335-343.
-
(2009)
Trends Genet
, vol.25
, pp. 335-343
-
-
Segal, E.1
Widom, J.2
-
28
-
-
56649089682
-
Evolutionary footprints of nucleosome positions in yeast
-
Washietl S, Machné 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
Machné, R.2
Goldman, N.3
-
29
-
-
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- e1000250.
-
(2008)
PLoS Genet
, vol.4
-
-
Warnecke, T.1
Batada, N.N.2
Hurst, L.D.3
-
30
-
-
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. Mol Biol Evol 25: 1714-1727.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 1714-1727
-
-
Babbitt, G.A.1
Kim, Y.2
-
31
-
-
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 323: 401-404.
-
(2009)
Science
, vol.323
, pp. 401-404
-
-
Sasaki, S.1
Mello, C.C.2
Shimada, A.3
Nakatani, Y.4
Hashimoto, S.-I.5
-
32
-
-
75149135277
-
G+C content dominates intrinsic nucleosome occupancy
-
Tillo D, Hughes T (2009) G+C content dominates intrinsic nucleosome occupancy. BMC Bioinformatics 10: 442-442.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 442
-
-
Tillo, D.1
Hughes, T.2
-
33
-
-
0038724989
-
Finding functional features in Saccharomyces genomes by phylogenetic footprinting
-
Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71-76.
-
(2003)
Science
, vol.301
, pp. 71-76
-
-
Cliften, P.1
Sudarsanam, P.2
Desikan, A.3
Fulton, L.4
Fulton, B.5
-
34
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
-
(2003)
Nature
, vol.423
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
35
-
-
1542510106
-
Phylogenetic estimation of context-dependent substitution rates by maximum likelihood
-
Siepel A, Haussler D (2004) Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol 21: 468-488.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 468-488
-
-
Siepel, A.1
Haussler, D.2
-
36
-
-
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 USA 101: 13994-14001.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 13994-14001
-
-
Hwang, D.G.1
Green, P.2
-
37
-
-
77955045449
-
The Role of Nucleosome Positioning in the Evolution of Gene Regulation
-
Tsankov AM, Thompson DA, Socha A, Regev A, Rando OJ (2010) The Role of Nucleosome Positioning in the Evolution of Gene Regulation. PLoS Biol 8: e1000414-e1000414.
-
(2010)
PLoS Biol
, vol.8
-
-
Tsankov, A.M.1
Thompson, D.A.2
Socha, A.3
Regev, A.4
Rando, O.J.5
-
38
-
-
77952245290
-
Divergence of nucleosome positioning between two closely related yeast species: Genetic basis and functional consequences
-
Tirosh I, Sigal N, Barkai N (2010) Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences. Mol Syst Biol 6: 365-365.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 365
-
-
Tirosh, I.1
Sigal, N.2
Barkai, N.3
-
39
-
-
62649089109
-
Population genomics of domestic and wild yeasts
-
Liti G, Carter DM, Moses AM, Warringer J, Parts L, et al. (2009) Population genomics of domestic and wild yeasts. Nature 458: 337-341.
-
(2009)
Nature
, vol.458
, pp. 337-341
-
-
Liti, G.1
Carter, D.M.2
Moses, A.M.3
Warringer, J.4
Parts, L.5
-
40
-
-
33645769260
-
An improved map of conserved regulatory sites for Saccharomyces cerevisiae
-
MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, et al. (2006) An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics 7: 113-113.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 113
-
-
Macisaac, K.D.1
Wang, T.2
Gordon, D.B.3
Gifford, D.K.4
Stormo, G.D.5
-
41
-
-
33846551980
-
Empirical fitness landscapes reveal accessible evolutionary paths
-
Poelwijk FJ, Kiviet DJ, Weinreich DM, Tans SJ (2007) Empirical fitness landscapes reveal accessible evolutionary paths. Nature 445: 383-386.
-
(2007)
Nature
, vol.445
, pp. 383-386
-
-
Poelwijk, F.J.1
Kiviet, D.J.2
Weinreich, D.M.3
Tans, S.J.4
-
42
-
-
77949423534
-
Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness
-
Meer MV, Kondrashov AS, Artzy-Randrup Y, Kondrashov FA (2010) Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. Nature 464: 279-282.
-
(2010)
Nature
, vol.464
, pp. 279-282
-
-
Meer, M.V.1
Kondrashov, A.S.2
Artzy-Randrup, Y.3
Kondrashov, F.A.4
-
43
-
-
0028797897
-
Inferring Weak Selection From Patterns of Polymorphism and Divergence at ''Silent'' Sites in Drosophila DNA
-
Akashi H (1995) Inferring Weak Selection From Patterns of Polymorphism and Divergence at ''Silent'' Sites in Drosophila DNA. Genetics 139: 1067-1076.
-
(1995)
Genetics
, vol.139
, pp. 1067-1076
-
-
Akashi, H.1
-
44
-
-
0023064998
-
Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons
-
Li W-H (1987) Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons. J Mol Evol 24: 337-345.
-
(1987)
J Mol Evol
, vol.24
, pp. 337-345
-
-
Li, W.-H.1
-
45
-
-
0034696762
-
A population genetics model for multiple quantitative traits exhibiting pleiotropy and epistasis
-
Taylor CF, Higgs PG (2000) A population genetics model for multiple quantitative traits exhibiting pleiotropy and epistasis. J Theor Biol 203: 419-437.
-
(2000)
J Theor Biol
, vol.203
, pp. 419-437
-
-
Taylor, C.F.1
Higgs, P.G.2
-
46
-
-
33845672511
-
Compensatory vs. pseudocompensatory evolution in molecular and developmental interactions
-
Haag ES (2007) Compensatory vs. pseudocompensatory evolution in molecular and developmental interactions. Genetica 129: 45-55.
-
(2007)
Genetica
, vol.129
, pp. 45-55
-
-
Haag, E.S.1
-
47
-
-
7344226239
-
Mathematical properties of mutation-selection models
-
Bürger R (1998) Mathematical properties of mutation-selection models. Genetica 102-103: 279-298.
-
(1998)
Genetica
, vol.102-103
, pp. 279-298
-
-
Bürger, R.1
-
48
-
-
75549089967
-
The UCSC Genome Browser database: Update 2010
-
Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, et al. (2010) The UCSC Genome Browser database: update 2010. Nucleic Acids Res 38: D613-D619.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Rhead, B.1
Karolchik, D.2
Kuhn, R.M.3
Hinrichs, A.S.4
Zweig, A.S.5
-
49
-
-
0031858914
-
SGD: Saccharomyces Genome Database
-
Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, et al. (1998) SGD: Saccharomyces Genome Database. Nucleic Acids Res 26: 73-79.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 73-79
-
-
Cherry, J.M.1
Adler, C.2
Ball, C.3
Chervitz, S.A.4
Dwight, S.S.5
-
50
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104.
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
Rinaldi, N.J.4
Macisaac, K.D.5
-
52
-
-
0000800333
-
On the probability of fixation of mutant genes in a population
-
Kimura M (1962) On the probability of fixation of mutant genes in a population. Genetics 47: 713-719.
-
(1962)
Genetics
, vol.47
, pp. 713-719
-
-
Kimura, M.1
|