-
1
-
-
78649773164
-
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition
-
Adey A, Morrison HG, Asan, Xun X, Kitzman JO, Turner EH, Stackhouse B, MacKenzie AP, Caruccio NC, Zhang X, et al. 2010. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol 11: R119.
-
(2010)
Genome Biol
, vol.11
, pp. R119
-
-
Adey, A.1
Morrison, H.G.2
Asan Xun, X.3
Kitzman, J.O.4
Turner, E.H.5
Stackhouse, B.6
MacKenzie, A.P.7
Caruccio, N.C.8
Zhang, X.9
-
2
-
-
0036786970
-
Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation
-
Anderson JD, Thåström A, Widom J. 2002. Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation. Mol Cell Biol 22: 7147-7157.
-
(2002)
Mol Cell Biol
, vol.22
, pp. 7147-7157
-
-
Anderson, J.D.1
Thåström, A.2
Widom, J.3
-
3
-
-
84862979650
-
A map of nucleosome positions in yeast at base-pair resolution
-
Brogaard K, Xi L, Wang J-P, 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
-
4
-
-
84888877924
-
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
-
Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. 2013. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10: 1213-1218.
-
(2013)
Nat Methods
, vol.10
, pp. 1213-1218
-
-
Buenrostro, J.D.1
Giresi, P.G.2
Zaba, L.C.3
Chang, H.Y.4
Greenleaf, W.J.5
-
6
-
-
84873351389
-
DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing
-
Chen K, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X, Li W. 2013. DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res 23: 341-351.
-
(2013)
Genome Res
, vol.23
, pp. 341-351
-
-
Chen, K.1
Xi, Y.2
Pan, X.3
Li, Z.4
Kaestner, K.5
Tyler, J.6
Dent, S.7
He, X.8
Li, W.9
-
7
-
-
84898022790
-
Ubiquitous nucleosome crowding in the yeast genome
-
Chereji RV, Morozov AV. 2014. Ubiquitous nucleosome crowding in the yeast genome. Proc Natl Acad Sci 111: 5236-5241.
-
(2014)
Proc Natl Acad Sci
, vol.111
, pp. 5236-5241
-
-
Chereji, R.V.1
Morozov, A.V.2
-
8
-
-
84858588614
-
Saccharomyces Genome Database: The genomics resource of budding yeast
-
Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, et al. 2012. Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res 40: D700-D705.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. D700-D705
-
-
Cherry, J.M.1
Hong, E.L.2
Amundsen, C.3
Balakrishnan, R.4
Binkley, G.5
Chan, E.T.6
Christie, K.R.7
Costanzo, M.C.8
Dwight, S.S.9
Engel, S.R.10
-
9
-
-
78650839429
-
The effect of micrococcal nuclease digestion on nucleosome positioning data
-
Chung H-R, Dunkel I, Heise F, Linke C, Krobitsch S, Ehrenhofer- Murray AE, Sperling SR, Vingron M. 2010. The effect of micrococcal nuclease digestion on nucleosome positioning data. PLoS One 5: e15754.
-
(2010)
PLoS One
, vol.5
, pp. e15754
-
-
Chung, H.-R.1
Dunkel, I.2
Heise, F.3
Linke, C.4
Krobitsch, S.5
Ehrenhofer-Murray, A.E.6
Sperling, S.R.7
Vingron, M.8
-
10
-
-
83755224395
-
Activation-induced disruption of nucleosome position clusters on the coding regions of Gcn4-dependent genes extends into neighbouring genes
-
Cole HA, Howard BH, Clark DJ. 2011. Activation-induced disruption of nucleosome position clusters on the coding regions of Gcn4-dependent genes extends into neighbouring genes. Nucleic Acids Res 39: 9521-9535.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 9521-9535
-
-
Cole, H.A.1
Howard, B.H.2
Clark, D.J.3
-
12
-
-
84883186434
-
Hog1 controls global reallocation of RNA Pol II upon osmotic shock in Saccharomyces cerevisiae
-
Cook KE, O'Shea EK. 2012. Hog1 controls global reallocation of RNA Pol II upon osmotic shock in Saccharomyces cerevisiae. G3 (Bethesda) 2: 1129-1136.
-
(2012)
G3 (Bethesda)
, vol.2
, pp. 1129-1136
-
-
Cook, K.E.1
O'Shea, E.K.2
-
13
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
The ENCODE Project Consortium
-
The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
14
-
-
78149237772
-
Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation
-
Fan X, Moqtaderi Z, Jin Y, Zhang Y, Liu XS, Struhl K. 2010. Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation. Proc Natl Acad Sci 107: 17945-17950.
-
(2010)
Proc Natl Acad Sci
, vol.107
, pp. 17945-17950
-
-
Fan, X.1
Moqtaderi, Z.2
Jin, Y.3
Zhang, Y.4
Liu, X.S.5
Struhl, K.6
-
15
-
-
48249153426
-
The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome
-
Fu Y, Sinha M, Peterson CL, Weng Z. 2008. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet 4: e1000138.
-
(2008)
PLoS Genet
, vol.4
, pp. e1000138
-
-
Fu, Y.1
Sinha, M.2
Peterson, C.L.3
Weng, Z.4
-
16
-
-
84870674869
-
Controls of nucleosome positioning in the human genome
-
Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y, Pritchard JK. 2012. Controls of nucleosome positioning in the human genome. PLoS Genet 8: e1003036.
-
(2012)
PLoS Genet
, vol.8
, pp. e1003036
-
-
Gaffney, D.J.1
McVicker, G.2
Pai, A.A.3
Fondufe-Mittendorf, Y.N.4
Lewellen, N.5
Michelini, K.6
Widom, J.7
Gilad, Y.8
Pritchard, J.K.9
-
17
-
-
84864059329
-
In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae
-
Gossett AJ, Lieb JD. 2012. In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae. PLoS Genet 8: e1002771.
-
(2012)
PLoS Genet
, vol.8
, pp. e1002771
-
-
Gossett, A.J.1
Lieb, J.D.2
-
18
-
-
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
-
19
-
-
81055141350
-
Epigenome characterization at single base-pair resolution
-
Henikoff JG, Belsky JA, Krassovsky K, MacAlpine DM, Henikoff S. 2011. Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci 108: 18318-18323.
-
(2011)
Proc Natl Acad Sci
, vol.108
, pp. 18318-18323
-
-
Henikoff, J.G.1
Belsky, J.A.2
Krassovsky, K.3
MacAlpine, D.M.4
Henikoff, S.5
-
20
-
-
63849308888
-
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
-
Hesselberth J, Chen X, Zhang Z. 2009. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods 6: 283-289.
-
(2009)
Nat Methods
, vol.6
, pp. 283-289
-
-
Hesselberth, J.1
Chen, X.2
Zhang, Z.3
-
21
-
-
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
-
22
-
-
84865777820
-
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements
-
Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A. 2012. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Res 22: 1735-1747.
-
(2012)
Genome Res
, vol.22
, pp. 1735-1747
-
-
Kundaje, A.1
Kyriazopoulou-Panagiotopoulou, S.2
Libbrecht, M.3
Smith, C.L.4
Raha, D.5
Winters, E.E.6
Johnson, S.M.7
Snyder, M.8
Batzoglou, S.9
Sidow, A.10
-
23
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359.
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
24
-
-
76349103252
-
Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae
-
Lantermann AB, Straub T, Strålfors A, Yuan G-C, Ekwall K, Korber P. 2010. Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae. Nat Struct Mol Biol 17: 251-257.
-
(2010)
Nat Struct Mol Biol
, vol.17
, pp. 251-257
-
-
Lantermann, A.B.1
Straub, T.2
Strålfors, A.3
Yuan, G.-C.4
Ekwall, K.5
Korber, P.6
-
25
-
-
58149168843
-
Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species
-
Lee A, Hansen KD, Bullard J, Dudoit S, Sherlock G. 2008. Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species. PLoS Genet 4: e1000299.
-
(2008)
PLoS Genet
, vol.4
, pp. e1000299
-
-
Lee, A.1
Hansen, K.D.2
Bullard, J.3
Dudoit, S.4
Sherlock, G.5
-
26
-
-
84889256682
-
Functional roles of pulsing in genetic circuits
-
Levine J, Lin Y, Elowitz M. 2013. Functional roles of pulsing in genetic circuits. Science 342: 1193-1201.
-
(2013)
Science
, vol.342
, pp. 1193-1201
-
-
Levine, J.1
Lin, Y.2
Elowitz, M.3
-
27
-
-
84859582058
-
Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function
-
Lickwar CR, Mueller F, Hanlon SE, McNally JG, Lieb JD. 2012. Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. Nature 484: 251-257.
-
(2012)
Nature
, vol.484
, pp. 251-257
-
-
Lickwar, C.R.1
Mueller, F.2
Hanlon, S.E.3
McNally, J.G.4
Lieb, J.D.5
-
28
-
-
84885633646
-
Inferring nucleosome positions with their histone mark annotation from ChIP data
-
Mammana A, Vingron M, Chung H-R. 2013. Inferring nucleosome positions with their histone mark annotation from ChIP data. Bioinformatics 29: 2547-2554.
-
(2013)
Bioinformatics
, vol.29
, pp. 2547-2554
-
-
Mammana, A.1
Vingron, M.2
Chung, H.-R.3
-
29
-
-
60549106999
-
Recruitment of a chromatin remodelling complex by the Hog1 MAP kinase to stress genes
-
Mas G, de Nadal E, Dechant R, Rodríguez de la Concepción ML, Logie C, Jimeno-González S, Chávez S, Ammerer G, Posas F. 2009. Recruitment of a chromatin remodelling complex by the Hog1 MAP kinase to stress genes. EMBO J 28: 326-336.
-
(2009)
EMBO J
, vol.28
, pp. 326-336
-
-
Mas, G.1
De Nadal, E.2
Dechant, R.3
Rodríguezdela Concepción, M.L.4
Logie, C.5
Jimeno-González, S.6
Chávez, S.7
Ammerer, G.8
Posas, F.9
-
30
-
-
84890280929
-
Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning
-
Moyle-Heyrman G, Zaichuk T, Xi L, Zhang Q, Uhlenbeck OC, Holmgren R, Widom J, Wang J-P. 2013. Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning. Proc Natl Acad Sci 110: 20158-20163.
-
(2013)
Proc Natl Acad Sci
, vol.110
, pp. 20158-20163
-
-
Moyle-Heyrman, G.1
Zaichuk, T.2
Xi, L.3
Zhang, Q.4
Uhlenbeck, O.C.5
Holmgren, R.6
Widom, J.7
Wang, J.-P.8
-
31
-
-
84869014491
-
Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling
-
Nadal-Ribelles M, Conde N, Flores O, González-Vallinas J, Eyras E, Orozco M, de Nadal E, Posas F. 2012. Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling. Genome Biol 13: R106.
-
(2012)
Genome Biol
, vol.13
, pp. R106
-
-
Nadal-Ribelles, M.1
Conde, N.2
Flores, O.3
González-Vallinas, J.4
Eyras, E.5
Orozco, M.6
De Nadal, E.7
Posas, F.8
-
32
-
-
66149163332
-
Dynamic and complex transcription factor binding during an inducible response in yeast
-
Ni L, Bruce C, Hart C, Leigh-Bell J, Gelperin D, Umansky L, Gerstein MB, Snyder M. 2009. Dynamic and complex transcription factor binding during an inducible response in yeast. Genes Dev 23: 1351-1363.
-
(2009)
Genes Dev
, vol.23
, pp. 1351-1363
-
-
Ni, L.1
Bruce, C.2
Hart, C.3
Leigh-Bell, J.4
Gelperin, D.5
Umansky, L.6
Gerstein, M.B.7
Snyder, M.8
-
33
-
-
84877574893
-
Extensive transcriptional heterogeneity revealed by isoform profiling
-
Pelechano V, WeiW, Steinmetz LM. 2013. Extensive transcriptional heterogeneity revealed by isoform profiling. Nature 497: 127-131.
-
(2013)
Nature
, vol.497
, pp. 127-131
-
-
Pelechano, V.1
Weiw Steinmetz, L.M.2
-
34
-
-
84921759025
-
PuFFIN - A parameterfree method to build nucleosome maps from paired-end reads
-
Polishko A, Bunnik EM, Le Roch KG, Lonardi S. 2014. PuFFIN - a parameterfree method to build nucleosome maps from paired-end reads. BMC Bioinformatics 15: S11.
-
(2014)
BMC Bioinformatics
, vol.15
, pp. S11
-
-
Polishko, A.1
Bunnik, E.M.2
Le Roch, K.G.3
Lonardi, S.4
-
35
-
-
79956319465
-
Comparative functional genomics of the fission yeasts
-
Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, et al. 2011. Comparative functional genomics of the fission yeasts. Science 332: 930-936.
-
(2011)
Science
, vol.332
, pp. 930-936
-
-
Rhind, N.1
Chen, Z.2
Yassour, M.3
Thompson, D.A.4
Haas, B.J.5
Habib, N.6
Wapinski, I.7
Roy, S.8
Lin, M.F.9
Heiman, D.I.10
-
36
-
-
75249087100
-
EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
37
-
-
0347125328
-
JASPAR: An open-access database for eukaryotic transcription factor binding profiles
-
Sandelin A. 2004. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res 32: D91-D94.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. D91-D94
-
-
Sandelin, A.1
-
38
-
-
77954541844
-
Singlecell NF-κB dynamics reveal digital activation and analogue information processing
-
Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW. 2010. Singlecell NF-κB dynamics reveal digital activation and analogue information processing. Nature 466: 267-271.
-
(2010)
Nature
, vol.466
, pp. 267-271
-
-
Tay, S.1
Hughey, J.J.2
Lee, T.K.3
Lipniacki, T.4
Quake, S.R.5
Covert, M.W.6
-
39
-
-
80555156654
-
Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization
-
Tsankov A, Yanagisawa Y, Rhind N, Regev A, Rando OJ. 2011. Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. Genome Res 21: 1851-1862.
-
(2011)
Genome Res
, vol.21
, pp. 1851-1862
-
-
Tsankov, A.1
Yanagisawa, Y.2
Rhind, N.3
Regev, A.4
Rando, O.J.5
-
40
-
-
79959557189
-
Determinants of nucleosome organization in primary human cells
-
Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A. 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
Sidow, A.6
-
41
-
-
53849146020
-
Model-based analysis of ChIPSeq (MACS)
-
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, LiW, et al. 2008. Model-based analysis of ChIPSeq (MACS). Genome Biol 9: R137.
-
(2008)
Genome Biol
, vol.9
, pp. R137
-
-
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
-
42
-
-
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
-
43
-
-
84922515063
-
The NF-κB genomic landscape in lymphoblastoid B cells
-
Zhao B, Barrera LA, Ersing I, Willox B, Schmidt SCS, Greenfeld H, Zhou H, Mollo SB, Shi TT, Takasaki K, et al. 2014. The NF-κB genomic landscape in lymphoblastoid B cells. Cell Rep 8: 1595-1606.
-
(2014)
Cell Rep
, vol.8
, pp. 1595-1606
-
-
Zhao, B.1
Barrera, L.A.2
Ersing, I.3
Willox, B.4
Schmidt, S.C.S.5
Greenfeld, H.6
Zhou, H.7
Mollo, S.B.8
Shi, T.T.9
Takasaki, K.10
|