-
1
-
-
0020041622
-
Rabl's model of the interphase chromosome arrangement tested in Chinese hamster cells by premature chromosome condensation and laser-UV-microbeam experiments
-
Cremer T, Cremer C, Baumann H, Luedtke EK, Sperling K, et al. (1982) Rabl's model of the interphase chromosome arrangement tested in Chinese hamster cells by premature chromosome condensation and laser-UV-microbeam experiments. Hum Genet 60: 46-56.
-
(1982)
Hum Genet
, vol.60
, pp. 46-56
-
-
Cremer, T.1
Cremer, C.2
Baumann, H.3
Luedtke, E.K.4
Sperling, K.5
-
2
-
-
77949919093
-
Interchromosomal association and gene regulation in trans
-
Williams A, Spilianakis CG, Flavell RA, (2010) Interchromosomal association and gene regulation in trans. Trends Genet 26: 188-197.
-
(2010)
Trends Genet
, vol.26
, pp. 188-197
-
-
Williams, A.1
Spilianakis, C.G.2
Flavell, R.A.3
-
3
-
-
0037083376
-
Capturing chromosome conformation
-
Dekker J, Rippe K, Dekker M, Kleckner N, (2002) Capturing chromosome conformation. Science 295: 1306-1311.
-
(2002)
Science
, vol.295
, pp. 1306-1311
-
-
Dekker, J.1
Rippe, K.2
Dekker, M.3
Kleckner, N.4
-
4
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
-
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, et al. (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289-293.
-
(2009)
Science
, vol.326
, pp. 289-293
-
-
Lieberman-Aiden, E.1
van Berkum, N.L.2
Williams, L.3
Imakaev, M.4
Ragoczy, T.5
-
6
-
-
33847076849
-
Chromatin modifications and their function
-
Kouzarides T, (2007) Chromatin modifications and their function. Cell 128: 693-705.
-
(2007)
Cell
, vol.128
, pp. 693-705
-
-
Kouzarides, T.1
-
7
-
-
39449088572
-
Genome-wide approaches to studying chromatin modifications
-
Schones DE, Zhao K, (2008) Genome-wide approaches to studying chromatin modifications. Nat Rev Genet 9: 179-191.
-
(2008)
Nat Rev Genet
, vol.9
, pp. 179-191
-
-
Schones, D.E.1
Zhao, K.2
-
8
-
-
37548999369
-
Computational epigenetics
-
Bock C, Lengauer T, (2008) Computational epigenetics. Bioinformatics 24: 1-10.
-
(2008)
Bioinformatics
, vol.24
, pp. 1-10
-
-
Bock, C.1
Lengauer, T.2
-
9
-
-
48949099045
-
Inferring causal relationships among different histone modifications and gene expression
-
Yu H, Zhu S, Zhou B, Xue H, Han JD, (2008) Inferring causal relationships among different histone modifications and gene expression. Genome Res 18: 1314-1324.
-
(2008)
Genome Res
, vol.18
, pp. 1314-1324
-
-
Yu, H.1
Zhu, S.2
Zhou, B.3
Xue, H.4
Han, J.D.5
-
10
-
-
78650331647
-
Identification of functional elements and regulatory circuits by Drosophila modENCODE
-
modENCODE Consortium
-
Roy S, Ernst J, Kharchenko PV, Kheradpour P, et al. modENCODE Consortium (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330: 1787-1797.
-
(2010)
Science
, vol.330
, pp. 1787-1797
-
-
Roy, S.1
Ernst, J.2
Kharchenko, P.V.3
Kheradpour, P.4
-
11
-
-
78650410139
-
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
-
Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, et al. (2010) Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330: 1775-1787.
-
(2010)
Science
, vol.330
, pp. 1775-1787
-
-
Gerstein, M.B.1
Lu, Z.J.2
Van Nostrand, E.L.3
Cheng, C.4
Arshinoff, B.I.5
-
12
-
-
78650747491
-
Discovery and characterization of chromatin states for systematic annotation of the human genome
-
Ernst J, Kellis M, (2010) Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28: 817-825.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 817-825
-
-
Ernst, J.1
Kellis, M.2
-
13
-
-
68149176840
-
Chimeric transcript discovery by paired-end transcriptome sequencing
-
Maher CA, Palanisamy N, Brenner JC, Cao X, Kalyana-Sundaram S, et al. (2009) Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A 106: 12353-12358.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 12353-12358
-
-
Maher, C.A.1
Palanisamy, N.2
Brenner, J.C.3
Cao, X.4
Kalyana-Sundaram, S.5
-
14
-
-
70249129382
-
Implications of chimaeric non-co-linear transcripts
-
Gingeras TR, (2009) Implications of chimaeric non-co-linear transcripts. Nature 461: 206-211.
-
(2009)
Nature
, vol.461
, pp. 206-211
-
-
Gingeras, T.R.1
-
15
-
-
77955622547
-
Global analysis of trans-splicing in Drosophila
-
McManus CJ, Duff MO, Eipper-Mains J, Graveley BR, (2010) Global analysis of trans-splicing in Drosophila. Proc Natl Acad Sci U S A 107: 12975-12979.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 12975-12979
-
-
McManus, C.J.1
Duff, M.O.2
Eipper-Mains, J.3
Graveley, B.R.4
-
16
-
-
33746683274
-
Reverse transcriptase template switching and false alternative transcripts
-
Cocquet J, Chong A, Zhang G, Veitia RA, (2006) Reverse transcriptase template switching and false alternative transcripts. Genomics 88: 127-131.
-
(2006)
Genomics
, vol.88
, pp. 127-131
-
-
Cocquet, J.1
Chong, A.2
Zhang, G.3
Veitia, R.A.4
-
17
-
-
74049108922
-
BLAST+: architecture and applications
-
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10: 421-421.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 421
-
-
Camacho, C.1
Coulouris, G.2
Avagyan, V.3
Ma, N.4
Papadopoulos, J.5
-
18
-
-
0037250168
-
The UCSC genome browser database
-
Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, et al. (2003) The UCSC genome browser database. Nucleic Acids Res 31: 51-54.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 51-54
-
-
Karolchik, D.1
Baertsch, R.2
Diekhans, M.3
Furey, T.S.4
Hinrichs, A.5
-
19
-
-
34249937354
-
Thousands of human mobile element fragments undergo strong purifying selection near developmental genes
-
Lowe CB, Bejerano G, Haussler D, (2007) Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci U S A 104: 8005-8010.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 8005-8010
-
-
Lowe, C.B.1
Bejerano, G.2
Haussler, D.3
-
20
-
-
80054984337
-
Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture
-
Yaffe E, Tanay A, (2011) Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet 43: 1059-1065.
-
(2011)
Nat Genet
, vol.43
, pp. 1059-1065
-
-
Yaffe, E.1
Tanay, A.2
-
21
-
-
77951942707
-
GOSemSim: an R package for measuring semantic similarity among GO terms and gene products
-
Yu G, Li F, Qin Y, Bo X, Wu Y, et al. (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics 26: 976-978.
-
(2010)
Bioinformatics
, vol.26
, pp. 976-978
-
-
Yu, G.1
Li, F.2
Qin, Y.3
Bo, X.4
Wu, Y.5
-
22
-
-
34447294237
-
A new method to measure the semantic similarity of GO terms
-
Wang JZ, Du Z, Payattakool R, Yu PS, Chen CF, (2007) A new method to measure the semantic similarity of GO terms. Bioinformatics 23: 1274-1281.
-
(2007)
Bioinformatics
, vol.23
, pp. 1274-1281
-
-
Wang, J.Z.1
Du, Z.2
Payattakool, R.3
Yu, P.S.4
Chen, C.F.5
-
23
-
-
78651280402
-
COXPRESdb: a database to compare gene coexpression in seven model animals
-
Obayashi T, Kinoshita K, (2011) COXPRESdb: a database to compare gene coexpression in seven model animals. Nucleic Acids Res 39: 1016-1022.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 1016-1022
-
-
Obayashi, T.1
Kinoshita, K.2
-
24
-
-
84944178665
-
Hierarchical grouping to optimize an objective function
-
Ward J, (1963) Hierarchical grouping to optimize an objective function. Journal of the American Statistical Association 58: 236-244.
-
(1963)
Journal of the American Statistical Association
, vol.58
, pp. 236-244
-
-
Ward, J.1
-
25
-
-
79951480123
-
R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria
-
R Development Core Team, URL. ISBN 3-900051-07-0
-
R Development Core Team (2010) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org. ISBN 3-900051-07-0.
-
(2010)
-
-
-
26
-
-
77957929225
-
Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq
-
Xu AG, He L, Li Z, Xu Y, Li M, et al. (2010) Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq. PLoS Comput Biol 6.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Xu, A.G.1
He, L.2
Li, Z.3
Xu, Y.4
Li, M.5
-
27
-
-
7444260846
-
The ENCODE (ENCyclopedia Of DNA Elements) project
-
ENCODE Project Consortium
-
ENCODE Project Consortium (2004) The ENCODE (ENCyclopedia Of DNA Elements) project. Science 306: 636-640.
-
(2004)
Science
, vol.306
, pp. 636-640
-
-
-
28
-
-
77950633122
-
Integrative analysis of the melanoma transcriptome
-
Berger MF, Levin JZ, Vijayendran K, Sivachenko A, Adiconis X, et al. (2010) Integrative analysis of the melanoma transcriptome. Genome Res 20: 413-427.
-
(2010)
Genome Res
, vol.20
, pp. 413-427
-
-
Berger, M.F.1
Levin, J.Z.2
Vijayendran, K.3
Sivachenko, A.4
Adiconis, X.5
-
29
-
-
43049143055
-
Mapping and sequencing of structural variation from eight human genomes
-
Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature 453: 56-64.
-
(2008)
Nature
, vol.453
, pp. 56-64
-
-
Kidd, J.M.1
Cooper, G.M.2
Donahue, W.F.3
Hayden, H.S.4
Sampas, N.5
-
30
-
-
75549092352
-
ChimerDB 2.0-a knowledgebase for fusion genes updated
-
Kim P, Yoon S, Kim N, Lee S, Ko M, et al. (2010) ChimerDB 2.0-a knowledgebase for fusion genes updated. Nucleic Acids Res 38: 81-85.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 81-85
-
-
Kim, P.1
Yoon, S.2
Kim, N.3
Lee, S.4
Ko, M.5
-
32
-
-
48749102722
-
A chromatin-wide transition to H4K20 monomethylation impairs genome integrity and programmed DNA rearrangements in the mouse
-
Schotta G, Sengupta R, Kubicek S, Malin S, Kauer M, et al. (2008) A chromatin-wide transition to H4K20 monomethylation impairs genome integrity and programmed DNA rearrangements in the mouse. Genes Dev 22: 2048-2061.
-
(2008)
Genes Dev
, vol.22
, pp. 2048-2061
-
-
Schotta, G.1
Sengupta, R.2
Kubicek, S.3
Malin, S.4
Kauer, M.5
-
33
-
-
0037436410
-
Chromatin fiber folding: requirement for the histone H4 N-terminal tail
-
Dorigo B, Schalch T, Bystricky K, Richmond TJ, (2003) Chromatin fiber folding: requirement for the histone H4 N-terminal tail. J Mol Biol 327: 85-96.
-
(2003)
J Mol Biol
, vol.327
, pp. 85-96
-
-
Dorigo, B.1
Schalch, T.2
Bystricky, K.3
Richmond, T.J.4
-
34
-
-
79952762476
-
Histone H4 Lys 20 monomethylation by histone methylase SET8 mediates Wnt target gene activation
-
Li Z, Nie F, Wang S, Li L, (2011) Histone H4 Lys 20 monomethylation by histone methylase SET8 mediates Wnt target gene activation. Proc Natl Acad Sci U S A 108: 3116-3123.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 3116-3123
-
-
Li, Z.1
Nie, F.2
Wang, S.3
Li, L.4
-
35
-
-
33644701666
-
Histone H4-lysine 20 monomethylation is increased in promoter and coding regions of active genes and correlates with hyperacetylation
-
Talasz H, Lindner HH, Sarg B, Helliger W, (2005) Histone H4-lysine 20 monomethylation is increased in promoter and coding regions of active genes and correlates with hyperacetylation. J Biol Chem 280: 38814-38822.
-
(2005)
J Biol Chem
, vol.280
, pp. 38814-38822
-
-
Talasz, H.1
Lindner, H.H.2
Sarg, B.3
Helliger, W.4
-
36
-
-
33845451555
-
Profile of histone lysine methylation across transcribed mammalian chromatin
-
Vakoc CR, Sachdeva MM, Wang H, Blobel GA, (2006) Profile of histone lysine methylation across transcribed mammalian chromatin. Mol Cell Biol 26: 9185-9195.
-
(2006)
Mol Cell Biol
, vol.26
, pp. 9185-9195
-
-
Vakoc, C.R.1
Sachdeva, M.M.2
Wang, H.3
Blobel, G.A.4
-
37
-
-
50349085791
-
Catalytic function of the PR-Set7 histone H4 lysine 20 monomethyltransferase is essential for mitotic entry and genomic stability
-
Houston SI, McManus KJ, Adams MM, Sims JK, Carpenter PB, et al. (2008) Catalytic function of the PR-Set7 histone H4 lysine 20 monomethyltransferase is essential for mitotic entry and genomic stability. J Biol Chem 283: 19478-19488.
-
(2008)
J Biol Chem
, vol.283
, pp. 19478-19488
-
-
Houston, S.I.1
McManus, K.J.2
Adams, M.M.3
Sims, J.K.4
Carpenter, P.B.5
-
38
-
-
77954954200
-
PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression
-
Liu W, Tanasa B, Tyurina OV, Zhou TY, Gassmann R, et al. (2010) PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression. Nature 466: 508-512.
-
(2010)
Nature
, vol.466
, pp. 508-512
-
-
Liu, W.1
Tanasa, B.2
Tyurina, O.V.3
Zhou, T.Y.4
Gassmann, R.5
-
39
-
-
62049085786
-
Transcriptome sequencing to detect gene fusions in cancer
-
Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, et al. (2009) Transcriptome sequencing to detect gene fusions in cancer. Nature 458: 97-101.
-
(2009)
Nature
, vol.458
, pp. 97-101
-
-
Maher, C.A.1
Kumar-Sinha, C.2
Cao, X.3
Kalyana-Sundaram, S.4
Han, B.5
-
40
-
-
34250369629
-
Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions
-
Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, et al. (2007) Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res 17: 746-759.
-
(2007)
Genome Res
, vol.17
, pp. 746-759
-
-
Denoeud, F.1
Kapranov, P.2
Ucla, C.3
Frankish, A.4
Castelo, R.5
-
41
-
-
59849091728
-
Short homologous sequences are strongly associated with the generation of chimeric RNAs in eukaryotes
-
Li X, Zhao L, Jiang H, Wang W, (2009) Short homologous sequences are strongly associated with the generation of chimeric RNAs in eukaryotes. J Mol Evol 68: 56-65.
-
(2009)
J Mol Evol
, vol.68
, pp. 56-65
-
-
Li, X.1
Zhao, L.2
Jiang, H.3
Wang, W.4
-
42
-
-
40049104732
-
SOAP: short oligonucleotide alignment program
-
Li R, Li Y, Kristiansen K, Wang J, (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24: 713-714.
-
(2008)
Bioinformatics
, vol.24
, pp. 713-714
-
-
Li, R.1
Li, Y.2
Kristiansen, K.3
Wang, J.4
-
43
-
-
0000418073
-
On the stability of inverse problems
-
Tychonoff AN, (1943) On the stability of inverse problems. Doklady Akademii Nauk SSSR 39: 195-198.
-
(1943)
Doklady Akademii Nauk SSSR
, vol.39
, pp. 195-198
-
-
Tychonoff, A.N.1
|