-
1
-
-
36349013043
-
Ethanol fermentation technologies fromsugar and starch feedstocks
-
Bai FW, Anderson WA, Moo-Young M. 2008. Ethanol fermentation technologies fromsugar and starch feedstocks. Biotechnol Adv 26: 89-105.
-
(2008)
Biotechnol Adv
, vol.26
, pp. 89-105
-
-
Bai, F.W.1
Anderson, W.A.2
Moo-Young, M.3
-
2
-
-
56049115800
-
A novel dna sequence periodicity decodes nucleosome positioning
-
Chen K, Meng Q, Ma L, Liu Q, Tang P, Chiu C, Hu S, Yu J. 2008. A novel DNA sequence periodicity decodes nucleosome positioning. Nucleic Acids Res 36: 6228-6236.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 6228-6236
-
-
Chen, K.1
Meng, Q.2
Ma, L.3
Liu, Q.4
Tang, P.5
Chiu, C.6
Hu, S.7
Yu, J.8
-
3
-
-
77953995002
-
Covalent histone modifications "miswritten, misinterpreted and mis-erased in human cancers
-
Chi P, Allis CD, Wang GG. 2010. Covalent histone modifications- miswritten, misinterpreted and mis-erased in human cancers. Nat Rev Cancer 10: 457-469.
-
(2010)
Nat Rev Cancer
, vol.10
, pp. 457-469
-
-
Chi, P.1
Allis, C.D.2
Wang, G.G.3
-
4
-
-
77950962157
-
Conserved nucleosome positioning defines replication origins
-
Eaton ML, Galani K, Kang S, Bell SP, MacAlpine DM. 2010. Conserved nucleosome positioning defines replication origins. Genes Dev 24: 748-753.
-
(2010)
Genes Dev
, vol.24
, pp. 748-753
-
-
Eaton, M.L.1
Galani, K.2
Kang, S.3
Bell, S.P.4
MacAlpine, D.M.5
-
5
-
-
79959836522
-
Chromatin structure as a mediator of aging
-
Feser J, Tyler J. 2011. Chromatin structure as a mediator of aging. FEBS Lett 585: 2041-2048.
-
(2011)
FEBS Lett
, vol.585
, pp. 2041-2048
-
-
Feser, J.1
Tyler, J.2
-
6
-
-
79960434317
-
Nucler: A package for non-parametric nucleosome positioning
-
Flores O, Orozco M. 2011. nucleR: A package for non-parametric nucleosome positioning. Bioinformatics 27: 2149-2150.
-
(2011)
Bioinformatics
, vol.27
, pp. 2149-2150
-
-
Flores, O.1
Orozco, M.2
-
7
-
-
84865117437
-
Dinup: A systematic approach to identify regions of differential nucleosome positioning
-
Fu K, Tang Q, Feng J, Liu XS, Zhang Y. 2012. DiNuP: A systematic approach to identify regions of differential nucleosome positioning. Bioinformatics 28: 1965-1971.
-
(2012)
Bioinformatics
, vol.28
, pp. 1965-1971
-
-
Fu, K.1
Tang, Q.2
Feng, J.3
Liu, X.S.4
Zhang, Y.5
-
8
-
-
82855181068
-
The role of the histone h2a ubiquitinase sce in polycomb repression
-
Gutiérrez L, Oktaba K, Scheuermann JC, Gambetta MC, Ly-Hartig N, Muller J. 2011. The role of the histone H2A ubiquitinase Sce in Polycomb repression. Development 139: 117-127.
-
(2011)
Development
, vol.139
, pp. 117-127
-
-
Gutiérrez, L.1
Oktaba, K.2
Scheuermann, J.C.3
Gambetta, M.C.4
Ly-Hartig, N.5
Muller, J.6
-
9
-
-
77950262538
-
Nucleosome dynamics define transcriptional enhancers
-
He HH, Meyer CA, Shin H, Bailey ST,Wei G,Wang Q, Zhang Y, Xu K, Ni M, Lupien M, et al. 2010. Nucleosome dynamics define transcriptional enhancers. Nat Genet 42: 343-347.
-
(2010)
Nat Genet
, vol.42
, pp. 343-347
-
-
He, H.H.1
Meyer, C.A.2
Shin, H.3
Bailey, S.T.4
Wei, G.5
Wang, Q.6
Zhang, Y.7
Xu, K.8
Ni, M.9
Lupien, M.10
-
10
-
-
80052805267
-
Histone modification: Cause or cog
-
Henikoff S, Shilatifard A. 2011. Histone modification: Cause or cog Trends Genet 27: 389-396.
-
(2011)
Trends Genet
, vol.27
, pp. 389-396
-
-
Henikoff, S.1
Shilatifard, A.2
-
11
-
-
80053501181
-
Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by brg1
-
Hu G, Schones DE, Cui K, Ybarra R, Northrup D, Tang Q, Gattinoni L, Restifo NP, Huang S, Zhao K. 2011. Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1. Genome Res 21: 1650-1658.
-
(2011)
Genome Res
, vol.21
, pp. 1650-1658
-
-
Hu, G.1
Schones, D.E.2
Cui, K.3
Ybarra, R.4
Northrup, D.5
Tang, Q.6
Gattinoni, L.7
Restifo, N.P.8
Huang, S.9
Zhao, K.10
-
12
-
-
58549112996
-
Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
-
Huang da W, Sherman BT, Lempicki RA. 2009. Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37: 1-13.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 1-13
-
-
Huang Da, W.1
Sherman, B.T.2
Lempicki, R.A.3
-
13
-
-
75349098018
-
A compiled and systematic reference map of nucleosome positions across the saccharomyces cerevisiae genome
-
Jiang C, Pugh BF. 2009. A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome. Genome Biol 10: R109.
-
(2009)
Genome Biol
, vol.10
-
-
Jiang, C.1
Pugh, B.F.2
-
14
-
-
77953287072
-
Synergistic action of rna polymerases in overcoming the nucleosomal barrier
-
Jin J, Bai L, Johnson DS, Fulbright RM, Kireeva ML, Kashlev M, Wang MD. 2010. Synergistic action of RNA polymerases in overcoming the nucleosomal barrier. Nat Struct Mol Biol 17: 745-752.
-
(2010)
Nat Struct Mol Biol
, vol.17
, pp. 745-752
-
-
Jin, J.1
Bai, L.2
Johnson, D.S.3
Fulbright, R.M.4
Kireeva, M.L.5
Kashlev, M.6
Wang, M.D.7
-
15
-
-
62649085538
-
The dnaencoded 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 DNAencoded 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
-
16
-
-
78650576256
-
Contribution of histone sequence preferences to nucleosome organization: Proposed definitions and methodology
-
Kaplan N, Hughes TR, Lieb JD, Widom J, Segal E. 2010. Contribution of histone sequence preferences to nucleosome organization: Proposed definitions and methodology. Genome Biol 11: 140.
-
(2010)
Genome Biol
, vol.11
, pp. 140
-
-
Kaplan, N.1
Hughes, T.R.2
Lieb, J.D.3
Widom, J.4
Segal, E.5
-
17
-
-
57449100870
-
Design and analysis of chipseq experiments for dna-binding proteins
-
Kharchenko PV, TolstorukovMY, Park PJ. 2008. Design and analysis of ChIPseq experiments for DNA-binding proteins. Nat Biotechnol 26: 1351-1359.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1351-1359
-
-
Kharchenko, P.V.1
Tolstorukov, M.Y.2
Park, P.J.3
-
18
-
-
84871539869
-
Foxa2 and h2a.z mediate nucleosome depletion during embryonic stem cell differentiation
-
(in press)
-
Li Z, Gadue P, Chen K, Jiao Y, Tuteja G, Schug J, Li W, Kaestner YH. 2012. Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation. Cell (in press).
-
(2012)
Cell
-
-
Li, Z.1
Gadue, P.2
Chen, K.3
Jiao, Y.4
Tuteja, G.5
Schug, J.6
Li, W.7
Kaestner, Y.H.8
-
19
-
-
1842411320
-
Crystal structure of the nucleosome core particle at 2.8 a ́resolution
-
Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. 1997. Crystal structure of the nucleosome core particle at 2.8 A ́resolution. Nature 389: 251-260.
-
(1997)
Nature
, vol.389
, pp. 251-260
-
-
Luger, K.1
Mader, A.W.2
Richmond, R.K.3
Sargent, D.F.4
Richmond, T.J.5
-
20
-
-
77952214662
-
Great improves functional interpretation of cisregulatory regions
-
Mclean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB,Wenger AM, Bejerano G. 2010. GREAT improves functional interpretation of cisregulatory regions. Nat Biotechnol 28: 495-501.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 495-501
-
-
Mclean, C.Y.1
Bristor, D.2
Hiller, M.3
Clarke, S.L.4
Schaar, B.T.5
Lowe, C.B.6
Wenger, A.M.7
Bejerano, G.8
-
21
-
-
77955388311
-
A preoccupied position on nucleosomes
-
Pugh BF. 2010. A preoccupied position on nucleosomes. Nat Struct Mol Biol 17: 923.
-
(2010)
Nat Struct Mol Biol
, vol.17
, pp. 923
-
-
Pugh, B.F.1
-
22
-
-
76949093375
-
Nucleosome positioning: How is it established, and why does it matter
-
Radman-Livaja M, Rando OJ. 2009. Nucleosome positioning: How is it established, and why does it matter Dev Biol 339: 258-266.
-
(2009)
Dev Biol
, vol.339
, pp. 258-266
-
-
Radman-Livaja, M.1
Rando, O.J.2
-
23
-
-
54049094030
-
Differential sage analysis in arabidopsis uncovers increased transcriptome complexity in response to low temperature
-
Robinson SJ, Parkin IA. 2008. Differential SAGE analysis in Arabidopsis uncovers increased transcriptome complexity in response to low temperature. BMC Genomics 9: 434.
-
(2008)
BMC Genomics
, vol.9
, pp. 434
-
-
Robinson, S.J.1
Parkin, I.A.2
-
24
-
-
75249087100
-
Edger: A bioconductor package for differential expression analysis of digital gene expression data
-
Robinson MD, McCarthy DJ, Smyth GK. 2009. edgeR: A bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
-
(2009)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
25
-
-
39749145198
-
Dynamic regulation of nucleosome positioning in the human genome
-
Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. 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
Wang, Z.6
Wei, G.7
Zhao, K.8
-
26
-
-
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
-
27
-
-
80555154347
-
The epigenetic modifier prdm5 functions as a tumor suppressor through modulating wnt/b-catenin signaling and is frequently silenced in multiple tumors
-
Shu XS, Geng H, Li L, Ying J, Ma C,Wang Y, Poon FF,Wang X, Ying Y, YeoW, et al. 2011. The epigenetic modifier PRDM5 functions as a tumor suppressor through modulating WNT/b-catenin signaling and is frequently silenced in multiple tumors. PLoS ONE 6: e27346.
-
(2011)
PLoS ONE
, vol.6
-
-
Shu, X.S.1
Geng, H.2
Li, L.3
Ying, J.4
Ma, C.5
Wang, Y.6
Poon, F.F.7
Wang, X.8
Ying, Y.9
Yeo, W.10
-
28
-
-
69949124307
-
Nucleosome positioning as a determinant of exon recognition
-
Tilgner H, Nikolaou C, Althammer S, Sammeth M, Beato M, Valcarcel J, Guigo R. 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
Valcarcel, J.6
Guigo, R.7
-
29
-
-
46249112085
-
Combinatorial patterns of histone acetylations and methylations in the human genome
-
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, et al. 2008. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40: 897-903.
-
(2008)
Nat Genet
, vol.40
, pp. 897-903
-
-
Wang, Z.1
Zang, C.2
Rosenfeld, J.A.3
Schones, D.E.4
Barski, A.5
Cuddapah, S.6
Cui, K.7
Roh, T.Y.8
Peng, W.9
Zhang, M.Q.10
-
30
-
-
79955559703
-
Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation
-
Xi Y, Yao J, Chen R, Li W, He X. 2011. Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation. Genome Res 21: 718-724.
-
(2011)
Genome Res
, vol.21
, pp. 718-724
-
-
Xi, Y.1
Yao, J.2
Chen, R.3
Li, W.4
He, X.5
-
31
-
-
77249125310
-
Evidence that localized variation in primate sequence divergence arises from an influence of nucleosome placement on dna repair
-
Ying H, Epps J, Williams R, Huttley G. 2010. Evidence that localized variation in primate sequence divergence arises from an influence of nucleosome placement on DNA repair. Mol Biol Evol 27: 637-649.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 637-649
-
-
Ying, H.1
Epps, J.2
Williams, R.3
Huttley, G.4
-
32
-
-
78651477233
-
High-resolution genome-wide mapping of the primary structure of chromatin
-
Zhang Z, Pugh BF. 2011. High-resolution genome-wide mapping of the primary structure of chromatin. Cell 144: 175-186.
-
(2011)
Cell
, vol.144
, pp. 175-186
-
-
Zhang, Z.1
Pugh, B.F.2
-
33
-
-
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. 2008a. Model-based analysis of ChIPSeq (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
-
34
-
-
57449095143
-
Identifying positioned nucleosomes with epigenetic marks in human from chip-seq
-
Zhang Y, Shin H, Song JS, Lei Y, Liu XS. 2008b. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics 9: 537.
-
(2008)
BMC Genomics
, vol.9
, pp. 537
-
-
Zhang, Y.1
Shin, H.2
Song, J.S.3
Lei, Y.4
Liu, X.S.5
-
35
-
-
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
|