-
1
-
-
43349089437
-
GeneTrack—a genomic data processing and visualization framework
-
Albert I, Wachi S, Jiang C, Pugh BF. 2008. GeneTrack—a genomic data processing and visualization framework. Bioinformatics 24: 1305-1306.
-
(2008)
Bioinformatics
, vol.24
, pp. 1305-1306
-
-
Albert, I.1
Wachi, S.2
Jiang, C.3
Pugh, B.F.4
-
2
-
-
57749121616
-
A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters
-
Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, et al. 2008. A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 32: 878-887.
-
(2008)
Mol Cell
, vol.32
, pp. 878-887
-
-
Badis, G.1
Chan, E.T.2
Van Bakel, H.3
Pena-Castillo, L.4
Tillo, D.5
Tsui, K.6
Carlson, C.D.7
Gossett, A.J.8
Hasinoff, M.J.9
Warren, C.L.10
-
3
-
-
36048959205
-
Hmo1 is required for TOR-dependent regulation of ribosomal protein gene transcription
-
Berger AB, Decourty L, Badis G, Nehrbass U, Jacquier A, Gadal O. 2007. Hmo1 is required for TOR-dependent regulation of ribosomal protein gene transcription. Mol Cell Biol 27: 8015-8026.
-
(2007)
Mol Cell Biol
, vol.27
, pp. 8015-8026
-
-
Berger, A.B.1
Decourty, L.2
Badis, G.3
Nehrbass, U.4
Jacquier, A.5
Gadal, O.6
-
4
-
-
79952474518
-
Promoter architectures in the yeast ribosomal expression program
-
Bosio MC, Negri R, Dieci G. 2011. Promoter architectures in the yeast ribosomal expression program. Transcription 2: 71-77.
-
(2011)
Transcription
, vol.2
, pp. 71-77
-
-
Bosio, M.C.1
Negri, R.2
Dieci, G.3
-
5
-
-
0028966548
-
The IFH1 gene product interacts with a fork head protein in Saccharomyces cerevisiae
-
Cherel I, Thuriaux P. 1995. The IFH1 gene product interacts with a fork head protein in Saccharomyces cerevisiae. Yeast 11: 261-270.
-
(1995)
Yeast
, vol.11
, pp. 261-270
-
-
Cherel, I.1
Thuriaux, P.2
-
6
-
-
84883758231
-
Gcn5 and sirtuins regulate acetylation of the ribosomal protein transcription factor Ifh1
-
Downey M, Knight B, Vashisht AA, Seller CA, Wohlschlegel JA, Shore D, Toczyski DP. 2013. Gcn5 and sirtuins regulate acetylation of the ribosomal protein transcription factor Ifh1. Curr Biol 23: 1638-1648.
-
(2013)
Curr Biol
, vol.23
, pp. 1638-1648
-
-
Downey, M.1
Knight, B.2
Vashisht, A.A.3
Seller, C.A.4
Wohlschlegel, J.A.5
Shore, D.6
Toczyski, D.P.7
-
7
-
-
0034960967
-
Promoter-specific shifts in transcription initiation conferred by yeast TFIIB mutations are determined by the sequence in the immediate vicinity of the start sites
-
Faitar SL, Brodie SA, Ponticelli AS. 2001. Promoter-specific shifts in transcription initiation conferred by yeast TFIIB mutations are determined by the sequence in the immediate vicinity of the start sites. Mol Cell Biol 21: 4427-4440.
-
(2001)
Mol Cell Biol
, vol.21
, pp. 4427-4440
-
-
Faitar, S.L.1
Brodie, S.A.2
Ponticelli, A.S.3
-
8
-
-
0020359857
-
Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG
-
Fratini AV, Kopka ML, Drew HR, Dickerson RE. 1982. Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG. J Biol Chem 257: 14686-14707.
-
(1982)
J Biol Chem
, vol.257
, pp. 14686-14707
-
-
Fratini, A.V.1
Kopka, M.L.2
Drew, H.R.3
Dickerson, R.E.4
-
9
-
-
33845783756
-
Yeast TFIID serves as a coactivator for Rap1p by direct protein-protein interaction
-
Garbett KA, Tripathi MK, Cencki B, Layer JH, Weil PA. 2007. Yeast TFIID serves as a coactivator for Rap1p by direct protein-protein interaction. Mol Cell Biol 27: 297-311.
-
(2007)
Mol Cell Biol
, vol.27
, pp. 297-311
-
-
Garbett, K.A.1
Tripathi, M.K.2
Cencki, B.3
Layer, J.H.4
Weil, P.A.5
-
10
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241-4257.
-
(2000)
Mol Biol Cell
, vol.11
, pp. 4241-4257
-
-
Gasch, A.P.1
Spellman, P.T.2
Kao, C.M.3
Carmel-Harel, O.4
Eisen, M.B.5
Storz, G.6
Botstein, D.7
Brown, P.O.8
-
11
-
-
80053140931
-
A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization
-
Gkikopoulos T, Schofield P, Singh V, Pinskaya M, Mellor J, Smolle M, Workman JL, Barton GJ, Owen-Hughes T. 2011. A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization. Science 333: 1758-1760.
-
(2011)
Science
, vol.333
, pp. 1758-1760
-
-
Gkikopoulos, T.1
Schofield, P.2
Singh, V.3
Pinskaya, M.4
Mellor, J.5
Smolle, M.6
Workman, J.L.7
Barton, G.J.8
Owen-Hughes, T.9
-
12
-
-
79953300078
-
FIMO: Scanning for occurrences of a given motif
-
Grant CE, Bailey TL, Noble WS. 2011. FIMO: scanning for occurrences of a given motif. Bioinformatics 27: 1017-1018.
-
(2011)
Bioinformatics
, vol.27
, pp. 1017-1018
-
-
Grant, C.E.1
Bailey, T.L.2
Noble, W.S.3
-
13
-
-
33646242795
-
An HMG protein, Hmo1, associates with promoters of many ribosomal protein genes and throughout the rRNA gene locus in Saccharomyces cerevisiae
-
Hall DB, Wade JT, Struhl K. 2006. An HMG protein, Hmo1, associates with promoters of many ribosomal protein genes and throughout the rRNA gene locus in Saccharomyces cerevisiae. Mol Cell Biol 26: 3672-3679.
-
(2006)
Mol Cell Biol
, vol.26
, pp. 3672-3679
-
-
Hall, D.B.1
Wade, J.T.2
Struhl, K.3
-
14
-
-
79952282412
-
Gcn4p-mediated transcriptional repression of ribosomal protein genes under amino-acid starvation
-
Joo YJ, Kim JH, Kang UB, Yu MH, Kim J. 2011. Gcn4p-mediated transcriptional repression of ribosomal protein genes under amino-acid starvation. EMBO J 30: 859-872.
-
(2011)
EMBO J
, vol.30
, pp. 859-872
-
-
Joo, Y.J.1
Kim, J.H.2
Kang, U.B.3
Yu, M.H.4
Kim, J.5
-
15
-
-
5444256434
-
A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size
-
Jorgensen P, Rupes I, Sharom JR, Schneper L, Broach JR, Tyers M. 2004. A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes Dev 18: 2491-2505.
-
(2004)
Genes Dev
, vol.18
, pp. 2491-2505
-
-
Jorgensen, P.1
Rupes, I.2
Sharom, J.R.3
Schneper, L.4
Broach, J.R.5
Tyers, M.6
-
16
-
-
11244293527
-
The Saccharomyces cerevisiae high mobility group box protein HMO1 contains two functional DNA binding domains
-
Kamau E, Bauerle KT, Grove A. 2004. The Saccharomyces cerevisiae high mobility group box protein HMO1 contains two functional DNA binding domains. J Biol Chem 279: 55234-55240.
-
(2004)
J Biol Chem
, vol.279
, pp. 55234-55240
-
-
Kamau, E.1
Bauerle, K.T.2
Grove, A.3
-
17
-
-
62649085538
-
The DNA-encoded nucleosome organization of a eukaryotic genome
-
Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, 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
Field, Y.6
Leproust, E.M.7
Hughes, T.R.8
Lieb, J.D.9
Widom, J.10
-
18
-
-
34748860813
-
Assembly of regulatory factors on rRNA and ribosomal protein genes in Saccharomyces cerevisiae
-
Kasahara K, Ohtsuki K, Ki S, Aoyama K, Takahashi H, Kobayashi T, Shirahige K, Kokubo T. 2007. Assembly of regulatory factors on rRNA and ribosomal protein genes in Saccharomyces cerevisiae. Mol Cell Biol 27: 6686-6705.
-
(2007)
Mol Cell Biol
, vol.27
, pp. 6686-6705
-
-
Kasahara, K.1
Ohtsuki, K.2
Ki, S.3
Aoyama, K.4
Takahashi, H.5
Kobayashi, T.6
Shirahige, K.7
Kokubo, T.8
-
19
-
-
40249089993
-
Saccharomyces cerevisiae HMO1 interacts with TFIID and participates in start site selection by RNA polymerase II
-
Kasahara K, Ki S, Aoyama K, Takahashi H, Kokubo T. 2008. Saccharomyces cerevisiae HMO1 interacts with TFIID and participates in start site selection by RNA polymerase II. Nucleic Acids Res 36: 1343-1357.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 1343-1357
-
-
Kasahara, K.1
Ki, S.2
Aoyama, K.3
Takahashi, H.4
Kokubo, T.5
-
20
-
-
79961179258
-
Hmo1 directs pre-initiation complex assembly to an appropriate site on its target gene promoters by masking a nucleosome-free region
-
Kasahara K, Ohyama Y, Kokubo T. 2011. Hmo1 directs pre-initiation complex assembly to an appropriate site on its target gene promoters by masking a nucleosome-free region. Nucleic Acids Res 39: 4136-4150.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 4136-4150
-
-
Kasahara, K.1
Ohyama, Y.2
Kokubo, T.3
-
21
-
-
84905260621
-
Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription
-
Knight B, Kubik S, Ghosh B, Bruzzone MJ, Geertz M, Martin V, Denervaud N, Jacquet P, Ozkan B, Rougemont J, et al. 2014. Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription. Genes Dev 28: 1695-1709.
-
(2014)
Genes Dev
, vol.28
, pp. 1695-1709
-
-
Knight, B.1
Kubik, S.2
Ghosh, B.3
Bruzzone, M.J.4
Geertz, M.5
Martin, V.6
Denervaud, N.7
Jacquet, P.8
Ozkan, B.9
Rougemont, J.10
-
22
-
-
0025809264
-
RAP1 protein activates and silences transcription of mating-type genes in yeast
-
Kurtz S, Shore D. 1991. RAP1 protein activates and silences transcription of mating-type genes in yeast. Genes Dev 5: 616-628.
-
(1991)
Genes Dev
, vol.5
, pp. 616-628
-
-
Kurtz, S.1
Shore, D.2
-
23
-
-
84881464184
-
Direct TFIIA-TFIID protein contacts drive budding yeast ribosomal protein gene transcription
-
Layer JH, Weil PA. 2013. Direct TFIIA-TFIID protein contacts drive budding yeast ribosomal protein gene transcription. J Biol Chem 288: 23273-23294.
-
(2013)
J Biol Chem
, vol.288
, pp. 23273-23294
-
-
Layer, J.H.1
Weil, P.A.2
-
24
-
-
77952087752
-
Direct transactivator-transcription factor IID (TFIID) contacts drive yeast ribosomal protein gene transcription
-
Layer JH, Miller SG, Weil PA. 2010. Direct transactivator-transcription factor IID (TFIID) contacts drive yeast ribosomal protein gene transcription. J Biol Chem 285: 15489-15499.
-
(2010)
J Biol Chem
, vol.285
, pp. 15489-15499
-
-
Layer, J.H.1
Miller, S.G.2
Weil, P.A.3
-
25
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
26
-
-
0032788547
-
Transcriptional elements involved in the repression of ribosomal protein synthesis
-
Li B, Nierras CR, Warner JR. 1999. Transcriptional elements involved in the repression of ribosomal protein synthesis. Mol Cell Biol 19: 5393-5404.
-
(1999)
Mol Cell Biol
, vol.19
, pp. 5393-5404
-
-
Li, B.1
Nierras, C.R.2
Warner, J.R.3
-
27
-
-
0034934774
-
Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association
-
Lieb JD, Liu X, Botstein D, Brown PO. 2001. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 28: 327-334.
-
(2001)
Nat Genet
, vol.28
, pp. 327-334
-
-
Lieb, J.D.1
Liu, X.2
Botstein, D.3
Brown, P.O.4
-
28
-
-
58249107143
-
Emerging functions of ribosomal proteins in gene-specific transcription and translation
-
Lindstrom MS. 2009. Emerging functions of ribosomal proteins in gene-specific transcription and translation. Biochem Biophys Res Commun 379: 167-170.
-
(2009)
Biochem Biophys Res Commun
, vol.379
, pp. 167-170
-
-
Lindstrom, M.S.1
-
29
-
-
84879048698
-
The evolutionary rewiring of the ribosomal protein transcription pathway modifies the interaction of transcription factor heteromer Ifh1-Fhl1 (Interacts with forkhead 1-forkhead-like 1) with the DNA-binding specificity element
-
Mallick J, Whiteway M. 2013. The evolutionary rewiring of the ribosomal protein transcription pathway modifies the interaction of transcription factor heteromer Ifh1-Fhl1 (interacts with forkhead 1-forkhead-like 1) with the DNA-binding specificity element. J Biol Chem 288: 17508-17519.
-
(2013)
J Biol Chem
, vol.288
, pp. 17508-17519
-
-
Mallick, J.1
Whiteway, M.2
-
30
-
-
5144229125
-
Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression
-
Marion RM, Regev A, Segal E, Barash Y, Koller D, Friedman N, O’Shea EK. 2004. Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression. Proc Natl Acad Sci 101: 14315-14322.
-
(2004)
Proc Natl Acad Sci
, vol.101
, pp. 14315-14322
-
-
Marion, R.M.1
Regev, A.2
Segal, E.3
Barash, Y.4
Koller, D.5
Friedman, N.6
O’shea, E.K.7
-
31
-
-
11144273952
-
TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1
-
Martin DE, Soulard A, Hall MN. 2004. TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1. Cell 119: 969-979.
-
(2004)
Cell
, vol.119
, pp. 969-979
-
-
Martin, D.E.1
Soulard, A.2
Hall, M.N.3
-
32
-
-
3042801306
-
Precise nucleosome positioning and the TATA box dictate requirements for the histone H4 tail and the bromodomain factor Bdf1
-
Martinez-Campa C, Politis P, Moreau JL, Kent N, Goodall J, Mellor J, Goding CR. 2004. Precise nucleosome positioning and the TATA box dictate requirements for the histone H4 tail and the bromodomain factor Bdf1. Mol Cell 15: 69-81.
-
(2004)
Mol Cell
, vol.15
, pp. 69-81
-
-
Martinez-Campa, C.1
Politis, P.2
Moreau, J.L.3
Kent, N.4
Goodall, J.5
Mellor, J.6
Goding, C.R.7
-
33
-
-
0036239962
-
Activator-specific recruitment of TFIID and regulation of ribosomal protein genes in yeast
-
Mencia M, Moqtaderi Z, Geisberg JV, Kuras L, Struhl K. 2002. Activator-specific recruitment of TFIID and regulation of ribosomal protein genes in yeast. Mol Cell 9: 823-833.
-
(2002)
Mol Cell
, vol.9
, pp. 823-833
-
-
Mencia, M.1
Moqtaderi, Z.2
Geisberg, J.V.3
Kuras, L.4
Struhl, K.5
-
34
-
-
77951219542
-
Genomewide localization analysis of a complete set of Tafs reveals a specific effect of the taf1 mutation on Taf2 occupancy and provides indirect evidence for different TFIID conformations at different promoters
-
Ohtsuki K, Kasahara K, Shirahige K, Kokubo T. 2010. Genomewide localization analysis of a complete set of Tafs reveals a specific effect of the taf1 mutation on Taf2 occupancy and provides indirect evidence for different TFIID conformations at different promoters. Nucleic Acids Res 38: 1805-1820.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 1805-1820
-
-
Ohtsuki, K.1
Kasahara, K.2
Shirahige, K.3
Kokubo, T.4
-
35
-
-
77953711351
-
TFIIA and the transactivator Rap1 cooperate to commit TFIID for transcription initiation
-
Papai G, Tripathi MK, Ruhlmann C, Layer JH, Weil PA, Schultz P. 2010. TFIIA and the transactivator Rap1 cooperate to commit TFIID for transcription initiation. Nature 465: 956-960.
-
(2010)
Nature
, vol.465
, pp. 956-960
-
-
Papai, G.1
Tripathi, M.K.2
Ruhlmann, C.3
Layer, J.H.4
Weil, P.A.5
Schultz, P.6
-
36
-
-
0034515772
-
Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase
-
Reid JL, Iyer VR, Brown PO, Struhl K. 2000. Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase. Mol Cell 6: 1297-1307.
-
(2000)
Mol Cell
, vol.6
, pp. 1297-1307
-
-
Reid, J.L.1
Iyer, V.R.2
Brown, P.O.3
Struhl, K.4
-
37
-
-
83255164884
-
Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution
-
Rhee HS, Pugh BF. 2011. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147: 1408-1419.
-
(2011)
Cell
, vol.147
, pp. 1408-1419
-
-
Rhee, H.S.1
Pugh, B.F.2
-
38
-
-
84858165145
-
Genome-wide structure and organization of eukaryotic pre-initiation complexes
-
Rhee HS, Pugh BF. 2012. Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature 483: 295-301.
-
(2012)
Nature
, vol.483
, pp. 295-301
-
-
Rhee, H.S.1
Pugh, B.F.2
-
39
-
-
14844282303
-
Central role of Ifh1p-Fhl1p interaction in the synthesis of yeast ribosomal proteins
-
Rudra D, Zhao Y, Warner JR. 2005. Central role of Ifh1p-Fhl1p interaction in the synthesis of yeast ribosomal proteins. EMBO J 24: 533-542.
-
(2005)
EMBO J
, vol.24
, pp. 533-542
-
-
Rudra, D.1
Zhao, Y.2
Warner, J.R.3
-
40
-
-
11144244771
-
Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1
-
Schawalder SB, Kabani M, Howald I, Choudhury U, Werner M, Shore D. 2004. Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1. Nature 432: 1058-1061.
-
(2004)
Nature
, vol.432
, pp. 1058-1061
-
-
Schawalder, S.B.1
Kabani, M.2
Howald, I.3
Choudhury, U.4
Werner, M.5
Shore, D.6
-
41
-
-
41749091787
-
Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation
-
Shivaswamy S, Bhinge A, Zhao Y, Jones S, Hirst M, Iyer VR. 2008. Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol 6: e65.
-
(2008)
Plos Biol
, vol.6
-
-
Shivaswamy, S.1
Bhinge, A.2
Zhao, Y.3
Jones, S.4
Hirst, M.5
Iyer, V.R.6
-
42
-
-
0028130685
-
RAP1: A protean regulator in yeast
-
Shore D. 1994. RAP1: a protean regulator in yeast. Trends Genet 10: 408-412.
-
(1994)
Trends Genet
, vol.10
, pp. 408-412
-
-
Shore, D.1
-
43
-
-
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 102: 7203-7208.
-
(2005)
Proc Natl Acad Sci
, vol.102
, pp. 7203-7208
-
-
Tanay, A.1
Regev, A.2
Shamir, R.3
-
44
-
-
11144231369
-
The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes
-
Wade JT, Hall DB, Struhl K. 2004. The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes. Nature 432: 1054-1058.
-
(2004)
Nature
, vol.432
, pp. 1054-1058
-
-
Wade, J.T.1
Hall, D.B.2
Struhl, K.3
-
45
-
-
77950395160
-
Gene duplication and the evolution of ribosomal protein gene regulation in yeast
-
Wapinski I, Pfiffner J, French C, Socha A, Thompson DA, Regev A. 2010. Gene duplication and the evolution of ribosomal protein gene regulation in yeast. Proc Natl Acad Sci 107: 5505-5510.
-
(2010)
Proc Natl Acad Sci
, vol.107
, pp. 5505-5510
-
-
Wapinski, I.1
Pfiffner, J.2
French, C.3
Socha, A.4
Thompson, D.A.5
Regev, A.6
-
46
-
-
0033229970
-
The economics of ribosome biosynthesis in yeast
-
Warner JR. 1999. The economics of ribosome biosynthesis in yeast. Trends Biochem Sci 24: 437-440.
-
(1999)
Trends Biochem Sci
, vol.24
, pp. 437-440
-
-
Warner, J.R.1
-
47
-
-
33745847547
-
Antagonistic forces that position nucleosomes in vivo
-
Whitehouse I, Tsukiyama T. 2006. Antagonistic forces that position nucleosomes in vivo. Nat Struct Mol Biol 13: 633-640.
-
(2006)
Nat Struct Mol Biol
, vol.13
, pp. 633-640
-
-
Whitehouse, I.1
Tsukiyama, T.2
-
48
-
-
0030947344
-
Molecular evidence for an ancient duplication of the entire yeast genome
-
Wolfe KH, Shields DC. 1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.
-
(1997)
Nature
, vol.387
, pp. 708-713
-
-
Wolfe, K.H.1
Shields, D.C.2
-
49
-
-
80053998078
-
Expression of yeast high mobility group protein HMO1 is regulated by TOR signaling
-
Xiao L, Kamau E, Donze D, Grove A. 2011. Expression of yeast high mobility group protein HMO1 is regulated by TOR signaling. Gene 489: 55-62.
-
(2011)
Gene
, vol.489
, pp. 55-62
-
-
Xiao, L.1
Kamau, E.2
Donze, D.3
Grove, A.4
-
50
-
-
60549108380
-
Bidirectional promoters generate pervasive transcription in yeast
-
Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Munster S, Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz LM. 2009. Bidirectional promoters generate pervasive transcription in yeast. Nature 457: 1033-1037.
-
(2009)
Nature
, vol.457
, pp. 1033-1037
-
-
Xu, Z.1
Wei, W.2
Gagneur, J.3
Perocchi, F.4
Clauder-Munster, S.5
Camblong, J.6
Guffanti, E.7
Stutz, F.8
Huber, W.9
Steinmetz, L.M.10
-
51
-
-
84862643713
-
Genome-wide nucleosome specificity and directionality of chromatin remodelers
-
Yen K, Vinayachandran V, Batta K, Koerber RT, Pugh BF. 2012. Genome-wide nucleosome specificity and directionality of chromatin remodelers. Cell 149: 1461-1473.
-
(2012)
Cell
, vol.149
, pp. 1461-1473
-
-
Yen, K.1
Vinayachandran, V.2
Batta, K.3
Koerber, R.T.4
Pugh, B.F.5
-
52
-
-
0032793066
-
Chromatin opening and transactivator potentiation by RAP1 in Saccharomyces cerevisiae
-
Yu L, Morse RH. 1999. Chromatin opening and transactivator potentiation by RAP1 in Saccharomyces cerevisiae. Mol Cell Biol 19: 5279-5288.
-
(1999)
Mol Cell Biol
, vol.19
, pp. 5279-5288
-
-
Yu, L.1
Morse, R.H.2
-
53
-
-
82255185461
-
Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters
-
Zeevi D, Sharon E, Lotan-Pompan M, Lubling Y, Shipony Z, Raveh-Sadka T, Keren L, Levo M, Weinberger A, Segal E. 2011. Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters. Genome Res 21: 2114-2128.
-
(2011)
Genome Res
, vol.21
, pp. 2114-2128
-
-
Zeevi, D.1
Sharon, E.2
Lotan-Pompan, M.3
Lubling, Y.4
Shipony, Z.5
Raveh-Sadka, T.6
Keren, L.7
Levo, M.8
Weinberger, A.9
Segal, E.10
-
54
-
-
53849146020
-
Model-based analysis of ChIP-seq (MACS)
-
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, et al. 2008. Model-based analysis of ChIP-seq (MACS). Genome Biol 9: R137.
-
(2008)
Genome Biol
, vol.9
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
Bernstein, B.E.6
Nusbaum, C.7
Myers, R.M.8
Brown, M.9
Li, W.10
-
55
-
-
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, Kadonaga JT, Liu XS, Struhl K. 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
Kadonaga, J.T.6
Liu, X.S.7
Struhl, K.8
-
56
-
-
79957929301
-
Stable and dynamic nucleosome states during a meiotic developmental process
-
Zhang L, Ma H, Pugh BF. 2011a. Stable and dynamic nucleosome states during a meiotic developmental process. Genome Res 21: 875-884.
-
(2011)
Genome Res
, vol.21
, pp. 875-884
-
-
Zhang, L.1
Ma, H.2
Pugh, B.F.3
-
57
-
-
79956316470
-
A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome
-
Zhang Z, Wippo CJ, Wal M, Ward E, Korber P, Pugh BF. 2011b. 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
Pugh, B.F.6
-
58
-
-
33745433124
-
Fine-structure analysis of ribosomal protein gene transcription
-
Zhao Y, McIntosh KB, Rudra D, Schawalder S, Shore D, Warner JR. 2006. Fine-structure analysis of ribosomal protein gene transcription. Mol Cell Biol 26: 4853-4862.
-
(2006)
Mol Cell Biol
, vol.26
, pp. 4853-4862
-
-
Zhao, Y.1
McIntosh, K.B.2
Rudra, D.3
Schawalder, S.4
Shore, D.5
Warner, J.R.6
-
59
-
-
84883590358
-
DNAshape: A method for the highthroughput prediction of DNA structural features on a genomic scale
-
Zhou T, Yang L, Lu Y, Dror I, Dantas Machado AC, Ghane T, Di Felice R, Rohs R. 2013. DNAshape: a method for the highthroughput prediction of DNA structural features on a genomic scale. Nucleic Acids Res 41: W56-W62.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Zhou, T.1
Yang, L.2
Lu, Y.3
Dror, I.4
Dantas Machado, A.C.5
Ghane, T.6
Di Felice, R.7
Rohs, R.8
-
60
-
-
63849315606
-
High-resolution DNA-binding specificity analysis of yeast transcription factors
-
Zhu C, Byers KJ, McCord RP, Shi Z, Berger MF, Newburger DE, Saulrieta K, Smith Z, Shah MV, Radhakrishnan M, et al. 2009. High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19: 556-566.
-
(2009)
Genome Res
, vol.19
, pp. 556-566
-
-
Zhu, C.1
Byers, K.J.2
McCord, R.P.3
Shi, Z.4
Berger, M.F.5
Newburger, D.E.6
Saulrieta, K.7
Smith, Z.8
Shah, M.V.9
Radhakrishnan, M.10
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