-
1
-
-
0035182436
-
Nucleosome formation potential of eukaryotic DNA: Calculation and promoters analysis
-
10.1093/bioinformatics/17.11.998 11724728
-
Levitsky VG Podkolodnaya OA Kolchanov NA Podkolodny NL Nucleosome formation potential of eukaryotic DNA: Calculation and promoters analysis Bioinformatics 2001, 17:998-1010. 10.1093/bioinformatics/ 17.11.998 11724728
-
(2001)
Bioinformatics
, vol.17
, pp. 998-1010
-
-
Levitsky, V.G.1
Podkolodnaya, O.A.2
Kolchanov, N.A.3
Podkolodny, N.L.4
-
2
-
-
0035704707
-
Role of DNA sequence in nucleosome stability and dynamics
-
Widom J Role of DNA sequence in nucleosome stability and dynamics Quarterly Review of Biophysics 2001, 34:269-324.
-
(2001)
Quarterly Review of Biophysics
, vol.34
, pp. 269-324
-
-
Widom, J.1
-
3
-
-
0002524447
-
Bending of DNA in nucleoprotein complexes
-
Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press Cozzarelli NR, Wang JC 1990:57-106
-
Travers AA Klug A Bending of DNA in nucleoprotein complexes DNA Topology and its Biological Effects Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press Cozzarelli NR, Wang JC 1990 57 106
-
(1990)
DNA Topology and Its Biological Effects
, pp. 57-106
-
-
Travers, A.A.1
Klug, A.2
-
4
-
-
33747842251
-
NXSensor web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors
-
10.1093/nar/gkl158
-
Luykx P Bajic IV Khuri S NXSensor web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors Nucleic Acids Research 2006, 34:560-565. 10.1093/nar/gkl158
-
(2006)
Nucleic Acids Research
, vol.34
, pp. 560-565
-
-
Luykx, P.1
Bajic, I.V.2
Khuri, S.3
-
5
-
-
33744805985
-
Genome-wide analysis of mammalian promoter architecture and evolution
-
10.1038/ng1789 16645617
-
Carninci P Sandelin A Lenhard B Katayama S Shimokawa K Ponjavic J Semple CAM Taylor MS Engström PG Frith M Forrest ARR Alkema WB Tan SL Plessy C Kodzius R Ravasi T Kasukawa T Fukuda S Katayama MK Kitazume Y Kawaji H Kai C Nakamura M Konno H Nakano K Tabar SM Arner P Chesi A Gustincich S Persichetti F Suzuki H Grimmond SM Wells CA Orlando V Wahlestedt C Liu ET Harbers M Kawai J Bajic VB Hume DA Hayashizaki Y Genome-wide analysis of mammalian promoter architecture and evolution Nat Genet 2006, 38:626-635. 10.1038/ng1789 16645617
-
(2006)
Nat Genet
, vol.38
, pp. 626-635
-
-
Carninci, P.1
Sandelin, A.2
Lenhard, B.3
Katayama, S.4
Shimokawa, K.5
Ponjavic, J.6
Semple, C.A.M.7
Taylor, M.S.8
Engström, P.G.9
Frith, M.10
Forrest, A.R.R.11
Alkema, W.B.12
Tan, S.L.13
Plessy, C.14
Kodzius, R.15
Ravasi, T.16
Kasukawa, T.17
Fukuda, S.18
Katayama, M.K.19
Kitazume, Y.20
Kawaji, H.21
Kai, C.22
Nakamura, M.23
Konno, H.24
Nakano, K.25
Tabar, S.M.26
Arner, P.27
Chesi, A.28
Gustincich, S.29
Persichetti, F.30
Suzuki, H.31
Grimmond, S.M.32
Wells, C.A.33
Orlando, V.34
Wahlestedt, C.35
Liu, E.T.36
Harbers, M.37
Kawai, J.38
Bajic, V.B.39
Hume, D.A.40
Hayashizaki, Y.41
more..
-
6
-
-
30044451918
-
Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome
-
1356123 16344566 10.1101/gr.4222606
-
Cooper SJ Trinklein ND Anton ED Nguyen L Myers RM Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome Genome Res 2006, 16:1-10. 1356123 16344566 10.1101/gr.4222606
-
(2006)
Genome Res
, vol.16
, pp. 1-10
-
-
Cooper, S.J.1
Trinklein, N.D.2
Anton, E.D.3
Nguyen, L.4
Myers, R.M.5
-
7
-
-
22744432660
-
Genome-Scale Identification of Nucleosome Positions in S. cerevisiae
-
10.1126/science.1112178 15961632
-
Yuan GC Liu YJ Dion MF Slack MD Wu LF Altschuler SJ Rando OJ Genome-Scale Identification of Nucleosome Positions in S. cerevisiae Science 2005, 309(5734):626-630. 10.1126/science.1112178 15961632
-
(2005)
Science
, vol.309
, Issue.5734
, pp. 626-630
-
-
Yuan, G.C.1
Liu, Y.J.2
Dion, M.F.3
Slack, M.D.4
Wu, L.F.5
Altschuler, S.J.6
Rando, O.J.7
-
8
-
-
33747500567
-
A genomic code for nucleosome positioning
-
10.1038/nature04979 16862119
-
Segal E Fondufe-Mittendorf Y Chen L Thastrom A Field Y Moore IK Wang JP Widom J A genomic code for nucleosome positioning Nature 2006, 442(7104):772-8. 10.1038/nature04979 16862119
-
(2006)
Nature
, vol.442
, Issue.7104
, pp. 772-778
-
-
Segal, E.1
Fondufe-Mittendorf, Y.2
Chen, L.3
Thastrom, A.4
Field, Y.5
Moore, I.K.6
Wang, J.P.7
Widom, J.8
-
9
-
-
34748826166
-
A high-resolution atlas of nucleosome occupancy in yeast
-
10.1038/ng2117 17873876
-
Lee W Tillo D Bray N Morse RH Davis RW Hughes TR Nislow C A high-resolution atlas of nucleosome occupancy in yeast Nature Genetics 2007, 39:1235-1244. 10.1038/ng2117 17873876
-
(2007)
Nature Genetics
, vol.39
, pp. 1235-1244
-
-
Lee, W.1
Tillo, D.2
Bray, N.3
Morse, R.H.4
Davis, R.W.5
Hughes, T.R.6
Nislow, C.7
-
10
-
-
0037687337
-
Permanent nucleosome exclusion from the Gal4p-inducible yeast GCY1 promoter
-
10.1074/jbc.M210932200 12536147
-
Angermayr M Bandlow W Permanent nucleosome exclusion from the Gal4p-inducible yeast GCY1 promoter The Journal of biological chemistry 2003, 278:11026-11031. 10.1074/jbc.M210932200 12536147
-
(2003)
The Journal of Biological Chemistry
, vol.278
, pp. 11026-11031
-
-
Angermayr, M.1
Bandlow, W.2
-
11
-
-
0038719686
-
Reb1p-dependent DNA Bending Effects Nucleosome Positioning and Constitutive Transcription at the Yeast Profilin Promoter
-
10.1074/jbc.M301806200 12637580
-
Angermayr M Oechsner U Bandlow W Reb1p-dependent DNA Bending Effects Nucleosome Positioning and Constitutive Transcription at the Yeast Profilin Promoter The Journal of biological chemistry 2003, 278:17918-17926. 10.1074/jbc.M301806200 12637580
-
(2003)
The Journal of Biological Chemistry
, vol.278
, pp. 17918-17926
-
-
Angermayr, M.1
Oechsner, U.2
Bandlow, W.3
-
12
-
-
34247520159
-
Nucleosome positioning in relation to nucleosome spacing and DNA sequence-specific binding of a protein
-
10.1111/j.1742-4658.2007.05775.x
-
Pusarla RH Vinayachandran V Bhargava P Nucleosome positioning in relation to nucleosome spacing and DNA sequence-specific binding of a protein FEBS 2007, 274:2396-2410. 10.1111/j.1742-4658.2007.05775.x
-
(2007)
FEBS
, vol.274
, pp. 2396-2410
-
-
Pusarla, R.H.1
Vinayachandran, V.2
Bhargava, P.3
-
13
-
-
33846862405
-
High-throughput mapping of the chromatin structure of human promoters
-
10.1038/nbt1279
-
Ozsolak F Song JS Liu XS Fisher DE High-throughput mapping of the chromatin structure of human promoters Nat Biotechnology 2007, 25(2):244-8. 10.1038/nbt1279
-
(2007)
Nat Biotechnology
, vol.25
, Issue.2
, pp. 244-248
-
-
Ozsolak, F.1
Song, J.S.2
Liu, X.S.3
Fisher, D.E.4
-
14
-
-
34250362736
-
Detection of DNA structural motifs in functional genomic elements
-
1891352 17568009 10.1101/gr.5602807
-
Greenbaum JA Parker SC Tullius TD Detection of DNA structural motifs in functional genomic elements Genome Research 2007, 17:940-946. 1891352 17568009 10.1101/gr.5602807
-
(2007)
Genome Research
, vol.17
, pp. 940-946
-
-
Greenbaum, J.A.1
Parker, S.C.2
Tullius, T.D.3
-
15
-
-
34248201771
-
Chromatin Remodeling by SWI/SNF Results in Nucleosome Mobilization to Preferential Positions in the Rat Osteocalcin Gene Promoter
-
10.1074/jbc.M609847200 17272279
-
Gutierrez J Paredes R Cruzat F Hill DA van Wijnen AJ Lian JB Stein GS Stein JL Imbalzano AN Montecino M Chromatin Remodeling by SWI/SNF Results in Nucleosome Mobilization to Preferential Positions in the Rat Osteocalcin Gene Promoter THE JOURNAL OF BIOLOGICAL CHEMISTRY 2007, 282(18):9445-9457. 10.1074/jbc.M609847200 17272279
-
(2007)
THE JOURNAL OF BIOLOGICAL CHEMISTRY
, vol.282
, Issue.18
, pp. 9445-9457
-
-
Gutierrez, J.1
Paredes, R.2
Cruzat, F.3
Hill, D.A.4
van Wijnen, A.J.5
Lian, J.B.6
Stein, G.S.7
Stein, J.L.8
Imbalzano, A.N.9
Montecino, M.10
-
17
-
-
25444499171
-
Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes
-
Ganapathi M Srivastava P Sutar SKD Kumar K Dasgupta D Singh GP Brahmacharil V Brahmachari SK Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes Crit Rev Eukaryot Gene Expr 2005, 6:126.
-
(2005)
Crit Rev Eukaryot Gene Expr
, vol.6
, pp. 126
-
-
Ganapathi, M.1
Srivastava, P.2
Sutar, S.K.D.3
Kumar, K.4
Dasgupta, D.5
Singh, G.P.6
Brahmacharil, V.7
Brahmachari, S.K.8
-
18
-
-
32044442759
-
Promoter features related to tissue specificity as measured by Shannon entropy
-
1088961 15833120 10.1186/gb-2005-6-4-r33
-
Schug J Schuller WP Kappen C Salbaum JM Bucan M CJS Jr Promoter features related to tissue specificity as measured by Shannon entropy Genome Biol 2005, 6:R33. 1088961 15833120 10.1186/gb-2005-6-4-r33
-
(2005)
Genome Biol
, vol.6
-
-
Schug, J.1
Schuller, W.P.2
Kappen, C.3
Salbaum, J.M.4
Bucan Jr., M.C.J.S.5
-
22
-
-
7444260846
-
The ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project
-
10.1126/science.1105136 15499007
-
The ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project Science 2004, 306:636-640. 10.1126/science.1105136 15499007
-
(2004)
Science
, vol.306
, pp. 636-640
-
-
-
23
-
-
84946031884
-
Procedures for detecting outlying observations in samples
-
10.2307/1266761
-
Grubbs FE Procedures for detecting outlying observations in samples Technometrics 1969, 11:1-21. 10.2307/1266761
-
(1969)
Technometrics
, vol.11
, pp. 1-21
-
-
Grubbs, F.E.1
-
24
-
-
84856043672
-
A Mathematical Theory of Communication
-
623-656
-
Shannon CE A Mathematical Theory of Communication Bell System Technical Journal 1948, 27:379-423. 623-656.
-
(1948)
Bell System Technical Journal
, vol.27
, pp. 379-423
-
-
Shannon, C.E.1
-
25
-
-
34250305146
-
The ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
2212820 17571346 10.1038/nature05874
-
The ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature 2007, 447:799-816. 2212820 17571346 10.1038/nature05874
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
-
27
-
-
11144358198
-
A gene atlas of the mouse and human protein-encoding transcriptomes
-
395923 15075390 10.1073/pnas.0400782101
-
Su AI Wiltshire T Batalov S Lapp H Ching KA Block D Zhang J Soden R Hayakawa M Kreiman G Cooke MP Walker JR Hogenesch JB A gene atlas of the mouse and human protein-encoding transcriptomes Proceedings of the National Academy of Sciences of the United States of America 2004, 101:6062-6067. 395923 15075390 10.1073/pnas.0400782101
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, pp. 6062-6067
-
-
Su, A.I.1
Wiltshire, T.2
Batalov, S.3
Lapp, H.4
Ching, K.A.5
Block, D.6
Zhang, J.7
Soden, R.8
Hayakawa, M.9
Kreiman, G.10
Cooke, M.P.11
Walker, J.R.12
Hogenesch, J.B.13
-
28
-
-
34447643262
-
Nucleosome positioning determinants
-
10.1016/j.jmb.2007.05.090 17586522
-
Fernandeza AG Anderson JN Nucleosome positioning determinants J Mol Biol 2007, 371(3):649-668. 10.1016/j.jmb.2007.05.090 17586522
-
(2007)
J Mol Biol
, vol.371
, Issue.3
, pp. 649-668
-
-
Fernandeza, A.G.1
Anderson, J.N.2
-
29
-
-
34548441932
-
Identification and Characterization of Cell Type-Specific and Ubiquitous Chromatin Regulatory Strcutures in the Human Genome
-
Xi H Shulha HP Lin JM Vales TR Fu Y Bodine DM McKay RDG Chenoweth JG Tesar PJ Furey TS Ren B Weng Z Crawford GE Identification and Characterization of Cell Type-Specific and Ubiquitous Chromatin Regulatory Strcutures in the Human Genome PLoS Genestics 2007, 3(8):1377-1388.
-
(2007)
PLoS Genestics
, vol.3
, Issue.8
, pp. 1377-1388
-
-
Xi, H.1
Shulha, H.P.2
Lin, J.M.3
Vales, T.R.4
Fu, Y.5
Bodine, D.M.6
McKay, R.D.G.7
Chenoweth, J.G.8
Tesar, P.J.9
Furey, T.S.10
Ren, B.11
Weng, Z.12
Crawford, G.E.13
-
32
-
-
0023001414
-
Sequence periodicities in chicken nucleosome core DNA
-
10.1016/0022-2836(86)90452-3 3806678
-
Satchwell SC Drew HR Travers AA Sequence periodicities in chicken nucleosome core DNA J Mol Biol 1986, 191:659-675. 10.1016/ 0022-2836(86)90452-3 3806678
-
(1986)
J Mol Biol
, vol.191
, pp. 659-675
-
-
Satchwell, S.C.1
Drew, H.R.2
Travers, A.A.3
-
33
-
-
0029664913
-
The [(G/C)3NN]n motif: A common DNA repeat that excludes nucleosomes
-
Wang YH Griffith JD The [(G/C)3NN]n motif: A common DNA repeat that excludes nucleosomes J Mol Biol 1996, 93:8863-8867.
-
(1996)
J Mol Biol
, vol.93
, pp. 8863-8867
-
-
Wang, Y.H.1
Griffith, J.D.2
-
34
-
-
0034310723
-
Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo
-
113125 11058103 10.1093/nar/28.21.4083
-
Suter B Schnappauf G Thoma F Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo Nucleic Acids Res 2000, 28:4083-4089. 113125 11058103 10.1093/nar/28.21.4083
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 4083-4089
-
-
Suter, B.1
Schnappauf, G.2
Thoma, F.3
-
35
-
-
0032516764
-
TGGA Repeats Impair Nucleosome Formation
-
10.1006/jmbi.1998.1925 9698546
-
Cao H Widlund HR Simonsson T Kubista M TGGA Repeats Impair Nucleosome Formation J Mol Biol 1998, 281:253-120. 10.1006/jmbi.1998.1925 9698546
-
(1998)
J Mol Biol
, vol.281
, pp. 120-253
-
-
Cao, H.1
Widlund, H.R.2
Simonsson, T.3
Kubista, M.4
-
36
-
-
33745951206
-
ROKU: A novel method for identification of tissue-specific genes
-
1501047 16764735 10.1186/1471-2105-7-294
-
Kadota K Ye J Nakai Y Terada T Shimizu K ROKU: A novel method for identification of tissue-specific genes BMC Bioinformatics 2006, 7:294. 1501047 16764735 10.1186/1471-2105-7-294
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 294
-
-
Kadota, K.1
Ye, J.2
Nakai, Y.3
Terada, T.4
Shimizu, K.5
-
37
-
-
0037421634
-
Detection of genes with tissue-specific expression patterns using Akaike's information criterion procedure
-
12499447
-
Kadota K Nishimura SI Bono H Nakamura S Hayashizaki Y Okazaki Y Takahashi K Detection of genes with tissue-specific expression patterns using Akaike's information criterion procedure Physiol Genomics 2003, 12:251-259. 12499447
-
(2003)
Physiol Genomics
, vol.12
, pp. 251-259
-
-
Kadota, K.1
Nishimura, S.I.2
Bono, H.3
Nakamura, S.4
Hayashizaki, Y.5
Okazaki, Y.6
Takahashi, K.7
-
38
-
-
43749113386
-
-
SymAtlas http://symatlas.gnf.org/SymAtlas/
-
SymAtlas
-
-
-
39
-
-
0036079158
-
The Human Genome Browser at UCSC
-
186604 12045153 10.1101/gr.229102. Article published online before print in May 2002
-
Kent W Sugnet C Furey T Roskin K Pringle T Zahler A Haussler D The Human Genome Browser at UCSC Genome Research 2002, 12(6):996-1006. 186604 12045153 10.1101/gr.229102. Article published online before print in May 2002
-
(2002)
Genome Research
, vol.12
, Issue.6
, pp. 996-1006
-
-
Kent, W.1
Sugnet, C.2
Furey, T.3
Roskin, K.4
Pringle, T.5
Zahler, A.6
Haussler, D.7
-
40
-
-
43749095203
-
-
BioJava http://biojava.org/
-
BioJava
-
-
|