-
1
-
-
34248153777
-
Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
-
Kikuta H, Laplante M, Navratilova P, et al. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res 2007;17:545-55.
-
(2007)
Genome Res
, vol.17
, pp. 545-555
-
-
Kikuta, H.1
Laplante, M.2
Navratilova, P.3
-
2
-
-
33846112470
-
VISTA Enhancer Browser - a database of tissue-specific human enhancers
-
Visel A, Minovitsky S, Dubchak I, et al. VISTA Enhancer Browser - a database of tissue-specific human enhancers. Nucleic Acids Res 2007;35:D88-92.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Visel, A.1
Minovitsky, S.2
Dubchak, I.3
-
3
-
-
33751316959
-
In vivo enhancer analysis of human conserved non-coding sequences
-
Pennacchio LA, Ahituv N, Moses AM, et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 2006; 444:499-502.
-
(2006)
Nature
, vol.444
, pp. 499-502
-
-
Pennacchio, L.A.1
Ahituv, N.2
Moses, A.M.3
-
4
-
-
23744502709
-
A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts
-
de la Calle-Mustienes E, Feijóo CG, Manzanares M, et al. A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts. Genome Res 2005;15:1061-72.
-
(2005)
Genome Res
, vol.15
, pp. 1061-1072
-
-
de la Calle-Mustienes, E.1
Feijóo, C.G.2
Manzanares, M.3
-
5
-
-
60549097668
-
Systematic human/ zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes
-
Navratilova P, Fredman D, Hawkins TA, et al. Systematic human/ zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. Dev Biol 2009;327:526-40.
-
(2009)
Dev Biol
, vol.327
, pp. 526-540
-
-
Navratilova, P.1
Fredman, D.2
Hawkins, T.A.3
-
6
-
-
20044366725
-
Highly conserved non-coding sequences are associated with vertebrate development
-
Woolfe A, Goodson M, Goode DK, et al. Highly conserved non-coding sequences are associated with vertebrate development. Plos Biol 2005;3:e7.
-
(2005)
Plos Biol
, vol.3
-
-
Woolfe, A.1
Goodson, M.2
Goode, D.K.3
-
7
-
-
25444431772
-
Large-scale enhancer detection in the zebrafish genome
-
Ellingsen S, Laplante MA, König M, et al. Large-scale enhancer detection in the zebrafish genome. Development 2005;132 3799-811.
-
(2005)
Development
, vol.132
, pp. 3799-3811
-
-
Ellingsen, S.1
Laplante, M.A.2
König, M.3
-
8
-
-
35248882434
-
The random versus fragile breakage models of chromosome evolution: A matter of resolution
-
Becker TS, Lenhard B. The random versus fragile breakage models of chromosome evolution: A matter of resolution. Mol Genet Genomics 2007;278:487-91.
-
(2007)
Mol Genet Genomics
, vol.278
, pp. 487-491
-
-
Becker, T.S.1
Lenhard, B.2
-
9
-
-
22144473057
-
Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
-
Sandelin A, Bailey PJ, Bruce S, et al. Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics 2004;5:99.
-
(2004)
BMC Genomics
, vol.5
, pp. 99
-
-
Sandelin, A.1
Bailey, P.J.2
Bruce, S.3
-
10
-
-
34447500684
-
Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans
-
Vavouri T, Walter K, Gilks WR, et al. Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans. Genome Biol 2007;8 R15.
-
(2007)
Genome Biol
, vol.8
-
-
Vavouri, T.1
Walter, K.2
Gilks, W.R.3
-
11
-
-
38849112675
-
Genomic regulatory blocks underlie extensive microsynteny conservation in insects
-
Engstrom PG, Ho Sui SJ, Drivenes O, et al. Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Res 2007;17:1898-908.
-
(2007)
Genome Res
, vol.17
, pp. 1898-1908
-
-
Engstrom, P.G.1
Ho Sui, S.J.2
Drivenes, O.3
-
12
-
-
38449118642
-
Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes
-
Kikuta H, Fredman D, Rinkwitz S, et al. Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes. Genome Biol 2007;8(Suppl 1):S4.
-
(2007)
Genome Biol
, vol.8
, Issue.SUPPL. 1
-
-
Kikuta, H.1
Fredman, D.2
Rinkwitz, S.3
-
13
-
-
58149178565
-
-
Kuhn RM, Karolchik D, Zweig AS, et al. The UCSC Genome Browser Database: Update 2009. Nucleic Acids Res 2009;37:D755-61.
-
Kuhn RM, Karolchik D, Zweig AS, et al. The UCSC Genome Browser Database: Update 2009. Nucleic Acids Res 2009;37:D755-61.
-
-
-
-
14
-
-
0037267806
-
Human-mouse alignments with BLASTZ
-
Schwartz S, Kent WJ, Smit A, et al. Human-mouse alignments with BLASTZ. Genome Res 2003;13:103-7.
-
(2003)
Genome Res
, vol.13
, pp. 103-107
-
-
Schwartz, S.1
Kent, W.J.2
Smit, A.3
-
15
-
-
1542748076
-
-
Blanchette M, Kent WJ, Riemer C, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 2004; 14:708-15.
-
Blanchette M, Kent WJ, Riemer C, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 2004; 14:708-15.
-
-
-
-
16
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel A, Bejerano G, Pedersen JS, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005;15:1034-50.
-
(2005)
Genome Res
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.S.3
-
18
-
-
36549090459
-
Comparative analysis and visualization of genomic sequences using VISTA browser and associated computational tools
-
Dubchak I. Comparative analysis and visualization of genomic sequences using VISTA browser and associated computational tools. Methods Mol Biol 2007;395:3-16.
-
(2007)
Methods Mol Biol
, vol.395
, pp. 3-16
-
-
Dubchak, I.1
-
19
-
-
35248843126
-
CONDOR: A database resource of developmentally associated conserved non-coding elements
-
Woolfe A, Goode DK, Cooke JE, et al. CONDOR: A database resource of developmentally associated conserved non-coding elements. BMC Dev Biol 2007;7:100.
-
(2007)
BMC Dev Biol
, vol.7
, pp. 100
-
-
Woolfe, A.1
Goode, D.K.2
Cooke, J.E.3
-
20
-
-
34548527597
-
Comparative genomics using Fugu reveals insights into regulatory subfunctionalization
-
Woolfe A, Elgar G. Comparative genomics using Fugu reveals insights into regulatory subfunctionalization. Genome Biol 2007;8:R53.
-
(2007)
Genome Biol
, vol.8
-
-
Woolfe, A.1
Elgar, G.2
-
21
-
-
4944260940
-
The regulatory content of intergenic DNA shapes genome architecture
-
Nelson CE, Hersh BM, Carroll SB. The regulatory content of intergenic DNA shapes genome architecture. Genome Biol 2004;5:R25.
-
(2004)
Genome Biol
, vol.5
-
-
Nelson, C.E.1
Hersh, B.M.2
Carroll, S.B.3
-
22
-
-
37349042272
-
TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements
-
Lee AP, Yang Y, Brenner S, et al. TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements. BMC Genomics 2007;8:441.
-
(2007)
BMC Genomics
, vol.8
, pp. 441
-
-
Lee, A.P.1
Yang, Y.2
Brenner, S.3
-
23
-
-
18644378331
-
The generic genome browser: A building block for a model organism system database
-
Stein LD, Mungall C, Shu S, et al. The generic genome browser: A building block for a model organism system database. Genome Res 2002;12:1599-610.
-
(2002)
Genome Res
, vol.12
, pp. 1599-1610
-
-
Stein, L.D.1
Mungall, C.2
Shu, S.3
-
24
-
-
53749098979
-
cneViewer: A database of conserved non-coding elements for studies of tissue-specific gene regulation
-
Persampieri J, Ritter DI, Lees D, et al. cneViewer: A database of conserved non-coding elements for studies of tissue-specific gene regulation. Bioinformatics 2008;24:2418-9.
-
(2008)
Bioinformatics
, vol.24
, pp. 2418-2419
-
-
Persampieri, J.1
Ritter, D.I.2
Lees, D.3
-
25
-
-
43549106605
-
Ancora: A web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes
-
Engstrom PG, Fredman D, Lenhard B. Ancora: A web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes. Genome Biol 2008;9:R34.
-
(2008)
Genome Biol
, vol.9
-
-
Engstrom, P.G.1
Fredman, D.2
Lenhard, B.3
-
26
-
-
3242878193
-
ECR Browser: A tool for visualizing and accessing data from comparisons of multiple vertebrate genomes
-
Ovcharenko I, Nobrega MA, Loots GG, et al. ECR Browser: A tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. Nucleic Acids Res 2004;32:W280-6.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Ovcharenko, I.1
Nobrega, M.A.2
Loots, G.G.3
-
27
-
-
3242888285
-
rVISTA 2.0: Evolutionary analysis of transcription factor binding sites
-
Loots GG, Ovcharenko I. rVISTA 2.0: Evolutionary analysis of transcription factor binding sites. Nucleic Acids Res 2004; 32 W217-21.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Loots, G.G.1
Ovcharenko, I.2
-
28
-
-
0037246723
-
The Zebrafish Information Network (ZFIN): The zebrafish model organism database
-
Sprague J, Clements D, Conlin T, et al. The Zebrafish Information Network (ZFIN): The zebrafish model organism database. Nucleic Acids Res 2003;31:241-3.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 241-243
-
-
Sprague, J.1
Clements, D.2
Conlin, T.3
-
29
-
-
48249136122
-
Integrating biological data - the Distributed Annotation System
-
Jenkinson AM, Albrecht M, Birney E, et al. Integrating biological data - the Distributed Annotation System. BMC Bioinformatics 2008;9(Suppl 8):S3.
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.SUPPL. 8
-
-
Jenkinson, A.M.1
Albrecht, M.2
Birney, E.3
-
30
-
-
29444452159
-
Defining a genomic radius for long-range enhancer action: Duplicated conserved non-coding elements hold the key
-
Vavouri T, McEwen GK, Woolfe A, et al. Defining a genomic radius for long-range enhancer action: Duplicated conserved non-coding elements hold the key. Trends Genet 2006;22:5-10.
-
(2006)
Trends Genet
, vol.22
, pp. 5-10
-
-
Vavouri, T.1
McEwen, G.K.2
Woolfe, A.3
-
31
-
-
33645519275
-
Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis
-
McEwen GK, Woolfe A, Goode DK, et al. Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis. Genome Res 2006;16:451-65.
-
(2006)
Genome Res
, vol.16
, pp. 451-465
-
-
McEwen, G.K.1
Woolfe, A.2
Goode, D.K.3
-
32
-
-
38949097100
-
Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock
-
Stephen S, Pheasant M, Makunin IV, et al. Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock. Mol Biol Evol 2008; 25:402-8.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 402-408
-
-
Stephen, S.1
Pheasant, M.2
Makunin, I.V.3
-
33
-
-
2542542256
-
Ultraconserved elements in the human genome
-
Bejerano G, Pheasant M, Makunin I, et al. Ultraconserved elements in the human genome. Science 2004;304:1321-5.
-
(2004)
Science
, vol.304
, pp. 1321-1325
-
-
Bejerano, G.1
Pheasant, M.2
Makunin, I.3
-
34
-
-
58149204055
-
ArrayExpress update - from an archive of functional genomics experiments to the atlas of gene expression
-
Parkinson H, Kapushesky M, Kolesnikov N, et al. ArrayExpress update - from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res 2009;37:D868-72.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Parkinson, H.1
Kapushesky, M.2
Kolesnikov, N.3
-
35
-
-
33744805985
-
Genome-wide analysis of mammalian promoter architecture and evolution
-
Carninci P, Sandelin A, Lenhard B, et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 2006; 38:626-35.
-
(2006)
Nat Genet
, vol.38
, pp. 626-635
-
-
Carninci, P.1
Sandelin, A.2
Lenhard, B.3
-
36
-
-
0036144048
-
DNA methylation patterns and epigenetic memory
-
Bird A. DNA methylation patterns and epigenetic memory. Genes Dev 2002;16:6-21.
-
(2002)
Genes Dev
, vol.16
, pp. 6-21
-
-
Bird, A.1
-
37
-
-
65149092197
-
Transcriptional features of genomic regulatory blocks
-
Akalin A, Fredman D, Arner E, etal. Transcriptional features of genomic regulatory blocks. Genome Biol 2009;10:R38.
-
(2009)
Genome Biol
, vol.10
-
-
Akalin, A.1
Fredman, D.2
Arner, E.3
-
38
-
-
34248358308
-
Hyperconserved CpG domains underlie Polycomb-binding sites
-
Tanay A, O'Donnell AH, Damelin M, et al. Hyperconserved CpG domains underlie Polycomb-binding sites. Proc Natl Acad Sci USA 2007;104:5521-6.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 5521-5526
-
-
Tanay, A.1
O'Donnell, A.H.2
Damelin, M.3
-
39
-
-
33646070846
-
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
-
Bernstein BE, Mikkelsen TS, Xie X, et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 2006;125:315-26.
-
(2006)
Cell
, vol.125
, pp. 315-326
-
-
Bernstein, B.E.1
Mikkelsen, T.S.2
Xie, X.3
-
40
-
-
55449105221
-
-
Ku M, Koche RP, Rheinbay E, et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet 2008;4:e1000242.
-
Ku M, Koche RP, Rheinbay E, et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet 2008;4:e1000242.
-
-
-
-
41
-
-
65549104157
-
Histone modifications at human enhancers reflect global cell-type -specific gene expression
-
Heintzman ND, Hon GC, Hawkins RD, et al. Histone modifications at human enhancers reflect global cell-type -specific gene expression. Nature 2009;459:108-12.
-
(2009)
Nature
, vol.459
, pp. 108-112
-
-
Heintzman, N.D.1
Hon, G.C.2
Hawkins, R.D.3
-
42
-
-
34548441932
-
Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome
-
Xi H, Shulha HP, Lin JM, et al. Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet 2007;3 e136.
-
(2007)
PLoS Genet
, vol.3
-
-
Xi, H.1
Shulha, H.P.2
Lin, J.M.3
-
43
-
-
60149091656
-
ChIP-seq accurately predicts tissue-specific activity of enhancers
-
Visel A, Blow MJ, Li Z, et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 2009;457:854-8.
-
(2009)
Nature
, vol.457
, pp. 854-858
-
-
Visel, A.1
Blow, M.J.2
Li, Z.3
-
45
-
-
38549105493
-
REDfly 2.0: An integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila
-
Halfon MS, Gallo SM, Bergman CM. REDfly 2.0: An integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. Nucleic Acids Res 2008;36: D594-8.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Halfon, M.S.1
Gallo, S.M.2
Bergman, C.M.3
-
46
-
-
33644861212
-
ORegAnno: An open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation
-
Montgomery SB, Griffith OL, Sleumer MC, et al. ORegAnno: An open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics 2006;22:637-40.
-
(2006)
Bioinformatics
, vol.22
, pp. 637-640
-
-
Montgomery, S.B.1
Griffith, O.L.2
Sleumer, M.C.3
-
47
-
-
60749125717
-
An anatomic gene expression atlas of the adult mouse brain
-
Ng L, Bernard A, Lau C, etal. An anatomic gene expression atlas of the adult mouse brain. Nat Neurosci 2009;12:356-62.
-
(2009)
Nat Neurosci
, vol.12
, pp. 356-362
-
-
Ng, L.1
Bernard, A.2
Lau, C.3
-
48
-
-
38349127974
-
Global analysis of patterns of gene expression during Drosophila embryogenesis
-
Tomancak P, Berman BP, Beaton A, et al. Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol 2007;8:R145.
-
(2007)
Genome Biol
, vol.8
-
-
Tomancak, P.1
Berman, B.P.2
Beaton, A.3
-
49
-
-
49649116149
-
-
Drysdale R, Consortium F. FlyBase: A database for the Drosophila research community. Methods Mol Biol 2008; 420:45-59.
-
Drysdale R, Consortium F. FlyBase: A database for the Drosophila research community. Methods Mol Biol 2008; 420:45-59.
-
-
-
-
53
-
-
25844449770
-
Galaxy: A plat-form for interactive large-scale genome analysis
-
Giardine B, Riemer C, Hardison RC, et al. Galaxy: A plat-form for interactive large-scale genome analysis. Genome Res 2005;15 1451-5.
-
(2005)
Genome Res
, vol.15
, pp. 1451-1455
-
-
Giardine, B.1
Riemer, C.2
Hardison, R.C.3
-
54
-
-
33846475402
-
Automated querying of genome databases
-
Schattner P. Automated querying of genome databases. PLoS Comput Biol 2007;3:e1.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Schattner, P.1
-
55
-
-
59849127664
-
Genomics made easier: An introductory tutorial to genome datamining
-
Schattner P. Genomics made easier: An introductory tutorial to genome datamining. Genomics 2009;93: 187-95.
-
(2009)
Genomics
, vol.93
, pp. 187-195
-
-
Schattner, P.1
|