-
1
-
-
33748594960
-
A global genomic transcriptional code associated with CNS-expressed genes
-
Bailey, P.J., Klos, J.M., Andersson, E., Karlen, M., Kallstrom, M., Ponjavic, J., Muhr, J., Lenhard, B., Sandelin, A., and Ericson, J. 2006. A global genomic transcriptional code associated with CNS-expressed genes. Exp. Cell Res. 312: 3108-3119.
-
(2006)
Exp. Cell Res
, vol.312
, pp. 3108-3119
-
-
Bailey, P.J.1
Klos, J.M.2
Andersson, E.3
Karlen, M.4
Kallstrom, M.5
Ponjavic, J.6
Muhr, J.7
Lenhard, B.8
Sandelin, A.9
Ericson, J.10
-
2
-
-
2542542256
-
Ultraconserved elements in the human genome
-
Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W.J., Mattick, J.S., and Haussler, D. 2004. Ultraconserved elements in the human genome. Science 304: 1321-1325.
-
(2004)
Science
, vol.304
, pp. 1321-1325
-
-
Bejerano, G.1
Pheasant, M.2
Makunin, I.3
Stephen, S.4
Kent, W.J.5
Mattick, J.S.6
Haussler, D.7
-
3
-
-
33646882068
-
Polycomb complexes repress developmental regulators in murine embryonic stem cells
-
Boyer, L.A., Plath, K., Zeitlinger, J., Brambrink, T., Medeiros, L.A., Lee, T.I., Levine, S.S., Wernig, M., Tajonar, A., Ray, M.K., et al. 2006. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441: 349-353.
-
(2006)
Nature
, vol.441
, pp. 349-353
-
-
Boyer, L.A.1
Plath, K.2
Zeitlinger, J.3
Brambrink, T.4
Medeiros, L.A.5
Lee, T.I.6
Levine, S.S.7
Wernig, M.8
Tajonar, A.9
Ray, M.K.10
-
4
-
-
4944262040
-
Glocal alignment: Finding rearrangements during alignment
-
Brudno, M., Malde, S., Poliakov, A., Do, C.B., Couronne, O., Dubchak, I., and Batzoglou, S. 2003. Glocal alignment: Finding rearrangements during alignment. Bioinformatics 19: i54-i62.
-
(2003)
Bioinformatics
, vol.19
-
-
Brudno, M.1
Malde, S.2
Poliakov, A.3
Do, C.B.4
Couronne, O.5
Dubchak, I.6
Batzoglou, S.7
-
5
-
-
0035477093
-
Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs
-
Butler, J.E. and Kadonaga, J.T. 2001. Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes & Dev. 15: 2515-2519.
-
(2001)
Genes & Dev
, vol.15
, pp. 2515-2519
-
-
Butler, J.E.1
Kadonaga, J.T.2
-
6
-
-
33744805985
-
Genome-wide analysis of mammalian promoter architecture and evolution
-
Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, K., Ponjavic, J., Semple, C.A., Taylor, M.S., Engstrom, P.G., Frith, M.C., et al. 2006. Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genet. 38: 626-635.
-
(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.7
Taylor, M.S.8
Engstrom, P.G.9
Frith, M.C.10
-
8
-
-
33846040145
-
FlyBase: Genomes by the dozen
-
doi: 10.1093/nar/gkl827
-
Crosby, M.A., Goodman, J.L., Strelets, V.B., Zhang, P., and Gelbart, W.M. 2007. FlyBase: Genomes by the dozen. Nucleic Acids Res. 35: D486-D491. doi: 10.1093/nar/gkl827.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Crosby, M.A.1
Goodman, J.L.2
Strelets, V.B.3
Zhang, P.4
Gelbart, W.M.5
-
9
-
-
23744502709
-
A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts
-
de la Calle-Mustienes, E., Feijoo, C.G., Manzanares, M., Tena, J.J., Rodriguez-Seguel, E., Letizia, A., Allende, M.L., and Gomez-Skarmeta, J.L. 2005. A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts. Genome Res. 15: 1061-1072.
-
(2005)
Genome Res
, vol.15
, pp. 1061-1072
-
-
de la Calle-Mustienes, E.1
Feijoo, C.G.2
Manzanares, M.3
Tena, J.J.4
Rodriguez-Seguel, E.5
Letizia, A.6
Allende, M.L.7
Gomez-Skarmeta, J.L.8
-
10
-
-
0036679338
-
Elbow and Noc define a family of zinc finger proteins controlling morphogenesis of specific tracheal branches
-
Dorfman, R., Glazer, L., Weihe, U., Wernet, M.F., and Shilo, B.Z. 2002. Elbow and Noc define a family of zinc finger proteins controlling morphogenesis of specific tracheal branches. Development 129: 3585-3596.
-
(2002)
Development
, vol.129
, pp. 3585-3596
-
-
Dorfman, R.1
Glazer, L.2
Weihe, U.3
Wernet, M.F.4
Shilo, B.Z.5
-
11
-
-
25444431772
-
Large-scale enhancer detection in the zebrafish genome
-
Ellingsen, S., Laplante, M.A., Konig, M., Kikuta, H., Furmanek, T., Hoivik, E.A., and Becker, T.S. 2005. Large-scale enhancer detection in the zebrafish genome. Development 132: 3799-3811.
-
(2005)
Development
, vol.132
, pp. 3799-3811
-
-
Ellingsen, S.1
Laplante, M.A.2
Konig, M.3
Kikuta, H.4
Furmanek, T.5
Hoivik, E.A.6
Becker, T.S.7
-
12
-
-
0030754620
-
The vrille gene of Drosophila is a maternal enhancer of decapentaplegic and encodes a new member of the bZIP family of transcription factors
-
George, H. and Terracol, R. 1997. The vrille gene of Drosophila is a maternal enhancer of decapentaplegic and encodes a new member of the bZIP family of transcription factors. Genetics 146: 1345-1363.
-
(1997)
Genetics
, vol.146
, pp. 1345-1363
-
-
George, H.1
Terracol, R.2
-
13
-
-
22344454794
-
Ultraconserved elements in insect genomes: A highly conserved intronic sequence implicated in the control of homothorax mRNA splicing
-
Glazov, E.A., Pheasant, M., McGraw, E.A., Bejerano, G., and Mattick, J.S. 2005. Ultraconserved elements in insect genomes: A highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. Genome Res. 15: 800-808.
-
(2005)
Genome Res
, vol.15
, pp. 800-808
-
-
Glazov, E.A.1
Pheasant, M.2
McGraw, E.A.3
Bejerano, G.4
Mattick, J.S.5
-
14
-
-
0033972132
-
Analysis of vertebrate SCL loci identifies conserved enhancers
-
Gottgens, B., Barton, L.M., Gilbert, J.G., Bench, A.J., Sanchez, M.J., Bahn, S., Mistry, S., Grafham, D., McMurray, A., Vaudin, M., et al. 2000. Analysis of vertebrate SCL loci identifies conserved enhancers. Nat. Biotechnol. 18: 181-186.
-
(2000)
Nat. Biotechnol
, vol.18
, pp. 181-186
-
-
Gottgens, B.1
Barton, L.M.2
Gilbert, J.G.3
Bench, A.J.4
Sanchez, M.J.5
Bahn, S.6
Mistry, S.7
Grafham, D.8
McMurray, A.9
Vaudin, M.10
-
15
-
-
18644380652
-
GETDB, a database compiling expression patterns and molecular locations of a collection of Gal4 enhancer traps
-
Hayashi, S., Ito, K., Sado, Y., Taniguchi, M., Akimoto, A., Takeuchi, H., Aigaki, T., Matsuzaki, F., Nakagoshi, H., Tanimura, T., et al. 2002. GETDB, a database compiling expression patterns and molecular locations of a collection of Gal4 enhancer traps. Genesis 34: 58-61.
-
(2002)
Genesis
, vol.34
, pp. 58-61
-
-
Hayashi, S.1
Ito, K.2
Sado, Y.3
Taniguchi, M.4
Akimoto, A.5
Takeuchi, H.6
Aigaki, T.7
Matsuzaki, F.8
Nakagoshi, H.9
Tanimura, T.10
-
16
-
-
33846039019
-
-
Ensembl, doi: 10.1093/nar/gkl996
-
Hubbard, T.J., Aken, B.L., Beal, K., Ballester, B., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cunningham, F., Cutts, T., et al. 2007. Ensembl 2007. Nucleic Acids Res. 35: D610-D617. doi: 10.1093/nar/gkl996.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Hubbard, T.J.1
Aken, B.L.2
Beal, K.3
Ballester, B.4
Caccamo, M.5
Chen, Y.6
Clarke, L.7
Coates, G.8
Cunningham, F.9
Cutts, T.10
-
17
-
-
34247249709
-
Tombola, a tesmin/TSO1-family protein, regulates transcriptional activation in the Drosophila male germline and physically interacts with Always early
-
Jiang, J., Benson, E., Bausek, N., Doggett, K., and White-Cooper, H. 2007. Tombola, a tesmin/TSO1-family protein, regulates transcriptional activation in the Drosophila male germline and physically interacts with Always early. Development 134: 1549-1559.
-
(2007)
Development
, vol.134
, pp. 1549-1559
-
-
Jiang, J.1
Benson, E.2
Bausek, N.3
Doggett, K.4
White-Cooper, H.5
-
18
-
-
0036079158
-
The human genome browser at UCSC
-
Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M., and Haussler, D. 2002. The human genome browser at UCSC. Genome Res. 12: 996-1006.
-
(2002)
Genome Res
, vol.12
, pp. 996-1006
-
-
Kent, W.J.1
Sugnet, C.W.2
Furey, T.S.3
Roskin, K.M.4
Pringle, T.H.5
Zahler, A.M.6
Haussler, D.7
-
19
-
-
0141815478
-
Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
-
Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. 2003. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl. Acad. Sci. 100: 11484-11489.
-
(2003)
Proc. Natl. Acad. Sci
, vol.100
, pp. 11484-11489
-
-
Kent, W.J.1
Baertsch, R.2
Hinrichs, A.3
Miller, W.4
Haussler, D.5
-
20
-
-
34248153777
-
Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
-
Kikuta, H., Laplante, M., Navratilova, P., Komisarczuk, A.Z., Engstrom, P.G., Fredman, D., Akalin, A., Caccamo, M., Sealy, I., Howe, K., et al. 2007. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res. 17: 545-555.
-
(2007)
Genome Res
, vol.17
, pp. 545-555
-
-
Kikuta, H.1
Laplante, M.2
Navratilova, P.3
Komisarczuk, A.Z.4
Engstrom, P.G.5
Fredman, D.6
Akalin, A.7
Caccamo, M.8
Sealy, I.9
Howe, K.10
-
21
-
-
33947201809
-
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome
-
Kim, T.H., Abdullaev, Z.K., Smith, A.D., Ching, K.A., Loukinov, D.I., Green, R.D., Zhang, M.Q., Lobanenkov, V.V., and Ren, B. 2007. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128: 1231-1245.
-
(2007)
Cell
, vol.128
, pp. 1231-1245
-
-
Kim, T.H.1
Abdullaev, Z.K.2
Smith, A.D.3
Ching, K.A.4
Loukinov, D.I.5
Green, R.D.6
Zhang, M.Q.7
Lobanenkov, V.V.8
Ren, B.9
-
22
-
-
9144268889
-
Characterization of the pufferfish Otx2 cis-regulators reveals evolutionarily conserved genetic mechanisms for vertebrate head specification
-
Kimura-Yoshida, C., Kitajima, K., Oda-Ishii, I., Tian, E., Suzuki, M., Yamamoto, M., Suzuki, T., Kobayashi, M., Aizawa, S., and Matsuo, I. 2004. Characterization of the pufferfish Otx2 cis-regulators reveals evolutionarily conserved genetic mechanisms for vertebrate head specification. Development 131: 57-71.
-
(2004)
Development
, vol.131
, pp. 57-71
-
-
Kimura-Yoshida, C.1
Kitajima, K.2
Oda-Ishii, I.3
Tian, E.4
Suzuki, M.5
Yamamoto, M.6
Suzuki, T.7
Kobayashi, M.8
Aizawa, S.9
Matsuo, I.10
-
23
-
-
33846078622
-
The UCSC genome browser database: Update 2007
-
doi: 10.1093/nar/gkl928
-
Kuhn, R.M., Karolchik, D., Zweig, A.S., Trumbower, H., Thomas, D.J., Thakkapallayil, A., Sugnet, C.W., Stanke, M., Smith, K.E., Siepel, A., et al. 2007. The UCSC genome browser database: Update 2007. Nucleic Acids Res. 35: D668-D673. doi: 10.1093/nar/gkl928.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Kuhn, R.M.1
Karolchik, D.2
Zweig, A.S.3
Trumbower, H.4
Thomas, D.J.5
Thakkapallayil, A.6
Sugnet, C.W.7
Stanke, M.8
Smith, K.E.9
Siepel, A.10
-
24
-
-
33646865180
-
Control of developmental regulators by Polycomb in human embryonic stem cells
-
Lee, T.I., Jenner, R.G., Boyer, L.A., Guenther, M.G., Levine, S.S., Kumar, R.M., Chevalier, B., Johnstone, S.E., Cole, M.F., Isono, K., et al. 2006. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125: 301-313.
-
(2006)
Cell
, vol.125
, pp. 301-313
-
-
Lee, T.I.1
Jenner, R.G.2
Boyer, L.A.3
Guenther, M.G.4
Levine, S.S.5
Kumar, R.M.6
Chevalier, B.7
Johnstone, S.E.8
Cole, M.F.9
Isono, K.10
-
25
-
-
0028123693
-
Compatibility between enhancers and promoters determines the transcriptional specificity of gooseberry and gooseberry neuro in the Drosophila embryo
-
Li, X. and Noll, M. 1994. Compatibility between enhancers and promoters determines the transcriptional specificity of gooseberry and gooseberry neuro in the Drosophila embryo. EMBO J. 13: 400-406.
-
(1994)
EMBO J
, vol.13
, pp. 400-406
-
-
Li, X.1
Noll, M.2
-
26
-
-
28644447707
-
Genome sequence, comparative analysis and haplotype structure of the domestic dog
-
Lindblad-Toh, K., Wade, C.M., Mikkelsen, T.S., Karlsson, E.K., Jaffe, D.B., Kamal, M., Clamp, M., Chang, J.L., Kulbokas III, E.J., Zody, M.C., et al. 2005. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438: 803-819.
-
(2005)
Nature
, vol.438
, pp. 803-819
-
-
Lindblad-Toh, K.1
Wade, C.M.2
Mikkelsen, T.S.3
Karlsson, E.K.4
Jaffe, D.B.5
Kamal, M.6
Clamp, M.7
Chang, J.L.8
Kulbokas III, E.J.9
Zody, M.C.10
-
27
-
-
14544303674
-
Bursicon, the insect cuticle-hardening hormone, is a heterodimeric cystine knot protein that activates G protein-coupled receptor LGR2
-
Luo, C.W., Dewey, E.M., Sudo, S., Ewer, J., Hsu, S.Y., Honegger, H.W., and Hsueh, A.J. 2005. Bursicon, the insect cuticle-hardening hormone, is a heterodimeric cystine knot protein that activates G protein-coupled receptor LGR2. Proc. Natl. Acad. Sci. 102: 2820-2825.
-
(2005)
Proc. Natl. Acad. Sci
, vol.102
, pp. 2820-2825
-
-
Luo, C.W.1
Dewey, E.M.2
Sudo, S.3
Ewer, J.4
Hsu, S.Y.5
Honegger, H.W.6
Hsueh, A.J.7
-
28
-
-
33749153857
-
Biological function of unannotated transcription during the early development of Drosophila melanogaster
-
Manak, J.R., Dike, S., Sementchenko, V., Kapranov, P., Biemar, F., Long, J., Cheng, J., Bell, I., Ghosh, S., Piccolboni, A., et al. 2006. Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nat. Genet. 38: 1151-1158.
-
(2006)
Nat. Genet
, vol.38
, pp. 1151-1158
-
-
Manak, J.R.1
Dike, S.2
Sementchenko, V.3
Kapranov, P.4
Biemar, F.5
Long, J.6
Cheng, J.7
Bell, I.8
Ghosh, S.9
Piccolboni, A.10
-
29
-
-
0142026139
-
A targeted gain of function screen in the embryonic CNS of Drosophila
-
McGovern, V.L., Pacak, C.A., Sewell, S.T., Turski, M.L., and Seeger, M.A. 2003. A targeted gain of function screen in the embryonic CNS of Drosophila. Mech. Dev. 120: 1193-1207.
-
(2003)
Mech. Dev
, vol.120
, pp. 1193-1207
-
-
McGovern, V.L.1
Pacak, C.A.2
Sewell, S.T.3
Turski, M.L.4
Seeger, M.A.5
-
30
-
-
0029973108
-
Promoter specificity mediates the independent regulation of neighboring genes
-
Merli, C., Bergstrom, D.E., Cygan, J.A., and Blackman, R.K. 1996. Promoter specificity mediates the independent regulation of neighboring genes. Genes & Dev. 10: 1260-1270.
-
(1996)
Genes & Dev
, vol.10
, pp. 1260-1270
-
-
Merli, C.1
Bergstrom, D.E.2
Cygan, J.A.3
Blackman, R.K.4
-
31
-
-
1342327349
-
Identification of minimal enhancer elements sufficient for Pax3 expression in neural crest and implication of Tead2 as a regulator of Pax3
-
Milewski, R.C., Chi, N.C., Li, J., Brown, C., Lu, M.M., and Epstein, J.A. 2004. Identification of minimal enhancer elements sufficient for Pax3 expression in neural crest and implication of Tead2 as a regulator of Pax3. Development 131: 829-837.
-
(2004)
Development
, vol.131
, pp. 829-837
-
-
Milewski, R.C.1
Chi, N.C.2
Li, J.3
Brown, C.4
Lu, M.M.5
Epstein, J.A.6
-
32
-
-
12944309290
-
The Drosophila melanogaster T-box genes midline and H15 are conserved regulators of heart development
-
Miskolczi-McCallum, C.M., Scavetta, R.J., Svendsen, P.C., Soanes, K.H., and Brook, W.J. 2005. The Drosophila melanogaster T-box genes midline and H15 are conserved regulators of heart development. Dev. Biol. 278: 459-472.
-
(2005)
Dev. Biol
, vol.278
, pp. 459-472
-
-
Miskolczi-McCallum, C.M.1
Scavetta, R.J.2
Svendsen, P.C.3
Soanes, K.H.4
Brook, W.J.5
-
33
-
-
20044379936
-
-
Moon, H., Filippova, G., Loukinov, D., Pugacheva, E., Chen, Q., Smith, S.T., Munhall, A., Grewe, B., Bartkuhn, M., Arnold, R., et al. 2005. CTCF is conserved from Drosophila to humans and confers enhancer blocking of the Fab-8 insulator. EMBO Rep. 6: 165-170.
-
Moon, H., Filippova, G., Loukinov, D., Pugacheva, E., Chen, Q., Smith, S.T., Munhall, A., Grewe, B., Bartkuhn, M., Arnold, R., et al. 2005. CTCF is conserved from Drosophila to humans and confers enhancer blocking of the Fab-8 insulator. EMBO Rep. 6: 165-170.
-
-
-
-
34
-
-
26644466996
-
Generating and interpreting the Brinker gradient in the Drosophila wing
-
Moser, M. and Campbell, G. 2005. Generating and interpreting the Brinker gradient in the Drosophila wing. Dev. Biol. 286: 647-658.
-
(2005)
Dev. Biol
, vol.286
, pp. 647-658
-
-
Moser, M.1
Campbell, G.2
-
35
-
-
22744440499
-
Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps
-
Murphy, W.J., Larkin, D.M., Everts-van der Wind, A., Bourque, G., Tesler, G., Auvil, L., Beever, J.E., Chowdhary, B.P., Galibert, F., Gatzke, L., et al. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309: 613-617.
-
(2005)
Science
, vol.309
, pp. 613-617
-
-
Murphy, W.J.1
Larkin, D.M.2
Everts-van der Wind, A.3
Bourque, G.4
Tesler, G.5
Auvil, L.6
Beever, J.E.7
Chowdhary, B.P.8
Galibert, F.9
Gatzke, L.10
-
36
-
-
0035972762
-
Role of the multifunctional CDP/Cut/Cux homeodomain transcription factor in regulating differentiation, cell growth and development
-
Nepveu, A. 2001. Role of the multifunctional CDP/Cut/Cux homeodomain transcription factor in regulating differentiation, cell growth and development. Gene 270: 1-15.
-
(2001)
Gene
, vol.270
, pp. 1-15
-
-
Nepveu, A.1
-
37
-
-
0142084743
-
Scanning human gene deserts for long-range enhancers
-
Nobrega, M.A., Ovcharenko, I., Afzal, V., and Rubin, E.M. 2003. Scanning human gene deserts for long-range enhancers. Science 302: 413.
-
(2003)
Science
, vol.302
, pp. 413
-
-
Nobrega, M.A.1
Ovcharenko, I.2
Afzal, V.3
Rubin, E.M.4
-
38
-
-
33845622415
-
Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction
-
doi: 10.1093/nar/gkl608
-
Ohler, U. 2006. Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction. Nucleic Acids Res. 34: 5943-5950. doi: 10.1093/nar/gkl608.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 5943-5950
-
-
Ohler, U.1
-
39
-
-
0032519586
-
Different core promoters possess distinct regulatory activities in the Drosophila embryo
-
Ohtsuki, S., Levine, M., and Cai, H.N. 1998. Different core promoters possess distinct regulatory activities in the Drosophila embryo. Genes & Dev. 12: 547-556.
-
(1998)
Genes & Dev
, vol.12
, pp. 547-556
-
-
Ohtsuki, S.1
Levine, M.2
Cai, H.N.3
-
40
-
-
12744261452
-
Evolution and functional classification of vertebrate gene deserts
-
Ovcharenko, I., Loots, G.G., Nobrega, M.A., Hardison, R.C., Miller, W., and Stubbs, L. 2005. Evolution and functional classification of vertebrate gene deserts. Genome Res. 15: 137-145.
-
(2005)
Genome Res
, vol.15
, pp. 137-145
-
-
Ovcharenko, I.1
Loots, G.G.2
Nobrega, M.A.3
Hardison, R.C.4
Miller, W.5
Stubbs, L.6
-
41
-
-
33748705337
-
Conservation patterns in different functional sequence categories of divergent Drosophila species
-
Papatsenko, D., Kislyuk, A., Levine, M., and Dubchak, I. 2006. Conservation patterns in different functional sequence categories of divergent Drosophila species. Genomics 88: 431-442.
-
(2006)
Genomics
, vol.88
, pp. 431-442
-
-
Papatsenko, D.1
Kislyuk, A.2
Levine, M.3
Dubchak, I.4
-
42
-
-
33751316959
-
In vivo enhancer analysis of human conserved non-coding sequences
-
Pennacchio, L.A., Ahituv, N., Moses, A.M., Prabhakar, S., Nobrega, M.A., Shoukry, M., Minovitsky, S., Dubchak, I., Holt, A., Lewis, K.D., et al. 2006. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444: 499-502.
-
(2006)
Nature
, vol.444
, pp. 499-502
-
-
Pennacchio, L.A.1
Ahituv, N.2
Moses, A.M.3
Prabhakar, S.4
Nobrega, M.A.5
Shoukry, M.6
Minovitsky, S.7
Dubchak, I.8
Holt, A.9
Lewis, K.D.10
-
43
-
-
33846876333
-
Predicting tissue-specific enhancers in the human genome
-
Pennacchio, L.A., Loots, G.G., Nobrega, M.A., and Ovcharenko, I. 2007. Predicting tissue-specific enhancers in the human genome. Genome Res. 17: 201-211.
-
(2007)
Genome Res
, vol.17
, pp. 201-211
-
-
Pennacchio, L.A.1
Loots, G.G.2
Nobrega, M.A.3
Ovcharenko, I.4
-
44
-
-
0037264074
-
Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes
-
Pevzner, P. and Tesler, G. 2003. Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes. Genome Res. 13: 37-45.
-
(2003)
Genome Res
, vol.13
, pp. 37-45
-
-
Pevzner, P.1
Tesler, G.2
-
45
-
-
23144464213
-
Tbx20-related genes, mid and H15, are required for tinman expression, proper patterning, and normal differentiation of cardioblasts in Drosophila
-
Reim, I., Mohler, J.P., and Frasch, M. 2005. Tbx20-related genes, mid and H15, are required for tinman expression, proper patterning, and normal differentiation of cardioblasts in Drosophila. Mech. Dev. 122: 1056-1069.
-
(2005)
Mech. Dev
, vol.122
, pp. 1056-1069
-
-
Reim, I.1
Mohler, J.P.2
Frasch, M.3
-
46
-
-
22144473057
-
Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
-
doi: 10.1186/1471-2164-5-99
-
Sandelin, A., Bailey, P., Bruce, S., Engstrom, P.G., Klos, J.M., Wasserman, W.W., Ericson, J., and Lenhard, B. 2004. Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics 5: 99. doi: 10.1186/1471-2164-5-99.
-
(2004)
BMC Genomics
, vol.5
, pp. 99
-
-
Sandelin, A.1
Bailey, P.2
Bruce, S.3
Engstrom, P.G.4
Klos, J.M.5
Wasserman, W.W.6
Ericson, J.7
Lenhard, B.8
-
47
-
-
33745225872
-
Genome-wide analysis of Polycomb targets in Drosophila melanogaster
-
Schwartz, Y.B., Kahn, T.G., Nix, D.A., Li, X.Y., Bourgon, R., Biggin, M., and Pirrotta, V. 2006. Genome-wide analysis of Polycomb targets in Drosophila melanogaster. Nat. Genet. 38: 700-705.
-
(2006)
Nat. Genet
, vol.38
, pp. 700-705
-
-
Schwartz, Y.B.1
Kahn, T.G.2
Nix, D.A.3
Li, X.Y.4
Bourgon, R.5
Biggin, M.6
Pirrotta, V.7
-
48
-
-
27144526227
-
Human-zebrafish non-coding conserved elements act in vivo to regulate transcription
-
doi: 10.1093/nar/gki853
-
Shin, J.T., Priest, J.R., Ovcharenko, I., Ronco, A., Moore, R.K., Burns, C.G., and MacRae, C.A. 2005. Human-zebrafish non-coding conserved elements act in vivo to regulate transcription. Nucleic Acids Res. 33: 5437-5445. doi: 10.1093/nar/gki853.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 5437-5445
-
-
Shin, J.T.1
Priest, J.R.2
Ovcharenko, I.3
Ronco, A.4
Moore, R.K.5
Burns, C.G.6
MacRae, C.A.7
-
49
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A.S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S., et al. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15: 1034-1050.
-
(2005)
Genome Res
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.S.3
Hinrichs, A.S.4
Hou, M.5
Rosenbloom, K.6
Clawson, H.7
Spieth, J.8
Hillier, L.W.9
Richards, S.10
-
50
-
-
0035477896
-
Core promoters: Active contributors to combinatorial gene regulation
-
Smale, S.T. 2001. Core promoters: Active contributors to combinatorial gene regulation. Genes & Dev. 15: 2503-2508.
-
(2001)
Genes & Dev
, vol.15
, pp. 2503-2508
-
-
Smale, S.T.1
-
51
-
-
0025291545
-
Molecular organization of the decapentaplegic gene in Drosophila melanogaster
-
St. Johnston, R.D., Hoffmann, F.M., Blackman, R.K., Segal, D., Grimaila, R., Padgett, R.W., Irick, H.A., and Gelbart, W.M. 1990. Molecular organization of the decapentaplegic gene in Drosophila melanogaster. Genes & Dev. 4: 1114-1127.
-
(1990)
Genes & Dev
, vol.4
, pp. 1114-1127
-
-
St. Johnston, R.D.1
Hoffmann, F.M.2
Blackman, R.K.3
Segal, D.4
Grimaila, R.5
Padgett, R.W.6
Irick, H.A.7
Gelbart, W.M.8
-
52
-
-
7444233156
-
A gene expression map for the euchromatic genome of Drosophila melanogaster
-
Stolc, V., Gauhar, Z., Mason, C., Halasz, G., van Batenburg, M.F., Rifkin, S.A., Hua, S., Herreman, T., Tongprasit, W., Barbano, P.E., et al. 2004. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 306: 655-660.
-
(2004)
Science
, vol.306
, pp. 655-660
-
-
Stolc, V.1
Gauhar, Z.2
Mason, C.3
Halasz, G.4
van Batenburg, M.F.5
Rifkin, S.A.6
Hua, S.7
Herreman, T.8
Tongprasit, W.9
Barbano, P.E.10
-
53
-
-
0037388173
-
Regulation of Dlx3 gene expression in visceral arches by evolutionarily conserved enhancer elements
-
Sumiyama, K. and Ruddle, F.H. 2003. Regulation of Dlx3 gene expression in visceral arches by evolutionarily conserved enhancer elements. Proc. Natl. Acad. Sci. 100: 4030-4034.
-
(2003)
Proc. Natl. Acad. Sci
, vol.100
, pp. 4030-4034
-
-
Sumiyama, K.1
Ruddle, F.H.2
-
54
-
-
34248358308
-
Hyperconserved CpG domains underlie Polycomb-binding sites
-
Tanay, A., O'Donnell, A.H., Damelin, M., and Bestor, T.H. 2007. Hyperconserved CpG domains underlie Polycomb-binding sites. Proc. Natl. Acad. Sci. 104: 5521-5526.
-
(2007)
Proc. Natl. Acad. Sci
, vol.104
, pp. 5521-5526
-
-
Tanay, A.1
O'Donnell, A.H.2
Damelin, M.3
Bestor, T.H.4
-
55
-
-
0030939130
-
The Drosophila islet gene governs axon pathfinding and neurotransmitter identity
-
Thor, S. and Thomas, J.B. 1997. The Drosophila islet gene governs axon pathfinding and neurotransmitter identity. Neuron 18: 397-409.
-
(1997)
Neuron
, vol.18
, pp. 397-409
-
-
Thor, S.1
Thomas, J.B.2
-
56
-
-
33745258986
-
Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster
-
Tolhuis, B., de Wit, E., Muijrers, I., Teunissen, H., Talhout, W., van Steensel, B., and van Lohuizen, M. 2006. Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster. Nat. Genet. 38: 694-699.
-
(2006)
Nat. Genet
, vol.38
, pp. 694-699
-
-
Tolhuis, B.1
de Wit, E.2
Muijrers, I.3
Teunissen, H.4
Talhout, W.5
van Steensel, B.6
van Lohuizen, M.7
-
58
-
-
34447500684
-
Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans
-
doi: 10.1186/gb-2007-8-2-r15
-
Vavouri, T., Walter, K., Gilks, W.R., Lehner, B., and Elgar, G. 2007. Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans. Genome Biol. 8: R15. doi: 10.1186/gb-2007-8-2-r15.
-
(2007)
Genome Biol
, vol.8
-
-
Vavouri, T.1
Walter, K.2
Gilks, W.R.3
Lehner, B.4
Elgar, G.5
-
59
-
-
32844459336
-
The Polycomb group protein EZH2 directly controls DNA methylation
-
Vire, E., Brenner, C., Deplus, R., Blanchon, L., Fraga, M., Didelot, C., Morey, L., Van Eynde, A., Bernard, D., Vanderwinden, J.M., et al. 2006. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 439: 871-874.
-
(2006)
Nature
, vol.439
, pp. 871-874
-
-
Vire, E.1
Brenner, C.2
Deplus, R.3
Blanchon, L.4
Fraga, M.5
Didelot, C.6
Morey, L.7
Van Eynde, A.8
Bernard, D.9
Vanderwinden, J.M.10
-
60
-
-
0034739843
-
Skeletor, a novel chromosomal protein that redistributes during mitosis provides evidence for the formation of a spindle matrix
-
Walker, D.L., Wang, D., Jin, Y., Rath, U., Wang, Y., Johansen, J., and Johansen, K.M. 2000. Skeletor, a novel chromosomal protein that redistributes during mitosis provides evidence for the formation of a spindle matrix. J. Cell Biol. 151: 1401-1412.
-
(2000)
J. Cell Biol
, vol.151
, pp. 1401-1412
-
-
Walker, D.L.1
Wang, D.2
Jin, Y.3
Rath, U.4
Wang, Y.5
Johansen, J.6
Johansen, K.M.7
-
61
-
-
1342284828
-
Proximodistal subdivision of Drosophila legs and wings: The elbow-no ocelli gene complex
-
Weihe, U., Dorfman, R., Wernet, M.F., Cohen, S.M., and Milan, M. 2004. Proximodistal subdivision of Drosophila legs and wings: The elbow-no ocelli gene complex. Development 131: 767-774.
-
(2004)
Development
, vol.131
, pp. 767-774
-
-
Weihe, U.1
Dorfman, R.2
Wernet, M.F.3
Cohen, S.M.4
Milan, M.5
-
62
-
-
20044366725
-
Highly conserved non-coding sequences are associated with vertebrate development
-
doi: 10.1371/journal.pbio.0030007
-
Woolfe, A., Goodson, M., Goode, D.K., Snell, P., McEwen, G.K., Vavouri, T., Smith, S.F., North, P., Callaway, H., Kelly, K., et al. 2005. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3: e7. doi: 10.1371/journal.pbio.0030007.
-
(2005)
PLoS Biol
, vol.3
-
-
Woolfe, A.1
Goodson, M.2
Goode, D.K.3
Snell, P.4
McEwen, G.K.5
Vavouri, T.6
Smith, S.F.7
North, P.8
Callaway, H.9
Kelly, K.10
-
63
-
-
34249848791
-
Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites
-
Xie, X., Mikkelsen, T.S., Gnirke, A., Lindblad-Toh, K., Kellis, M., and Lander, E.S. 2007. Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites. Proc. Natl. Acad. Sci. 104: 7145-7150.
-
(2007)
Proc. Natl. Acad. Sci
, vol.104
, pp. 7145-7150
-
-
Xie, X.1
Mikkelsen, T.S.2
Gnirke, A.3
Lindblad-Toh, K.4
Kellis, M.5
Lander, E.S.6
-
64
-
-
33845670418
-
Quantification of insect genome divergence
-
Zdobnov, E.M. and Bork, P. 2007. Quantification of insect genome divergence. Trends Genet. 23: 16-20.
-
(2007)
Trends Genet
, vol.23
, pp. 16-20
-
-
Zdobnov, E.M.1
Bork, P.2
-
65
-
-
0037020194
-
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster
-
Zdobnov, E.M., von Mering, C., Letunic, I., Torrents, D., Suyama, M., Copley, R.R., Christophides, G.K., Thomasova, D., Holt, R.A., Subramanian, G.M., et al. 2002. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science 298: 149-159. 1909-1918
-
(2002)
Science
, vol.298
-
-
Zdobnov, E.M.1
von Mering, C.2
Letunic, I.3
Torrents, D.4
Suyama, M.5
Copley, R.R.6
Christophides, G.K.7
Thomasova, D.8
Holt, R.A.9
Subramanian, G.M.10
|