-
1
-
-
5444223488
-
Exploiting human - Fish genome comparisons for deciphering gene regulation
-
DOI 10.1093/hmg/ddh229
-
Ahituv N, Rubin EM, Nobrega MA. 2004. Exploiting human-fish genome comparisons for deciphering gene regulation. Hum Mol Genet. 13:R261-R266. (Pubitemid 39359911)
-
(2004)
Human Molecular Genetics
, vol.13
, Issue.REV. ISS. 2
-
-
Ahituv, N.1
Rubin, E.M.2
Nobrega, M.A.3
-
2
-
-
0037162885
-
Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes
-
DOI 10.1126/science.1072104
-
Aparicio S, et al. 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1301-1310. (Pubitemid 34913162)
-
(2002)
Science
, vol.297
, Issue.5585
, pp. 1301-1310
-
-
Aparicio, S.1
Chapman, J.2
Stupka, E.3
Putnam, N.4
Chia, J.-M.5
Dehal, P.6
Christoffels, A.7
Rash, S.8
Hoon, S.9
Smit, A.10
Sollewijn Gelpke, M.D.11
Roach, J.12
Oh, T.13
Ho, I.Y.14
Wong, M.15
Detter, C.16
Verhoef, F.17
Predki, P.18
Tay, A.19
Lucas, S.20
Richardson, P.21
Smith, S.F.22
Clark, M.S.23
Edwards, Y.J.K.24
Doggett, N.25
Zharkikh, A.26
Tavtigian, S.V.27
Pruss, D.28
Barnstead, M.29
Evans, C.30
Baden, H.31
Powell, J.32
Glusman, G.33
Rowen, L.34
Hood, L.35
Tan, Y.H.36
Elgar, G.37
Hawkins, T.38
Venkatesh, B.39
Rokhsar, D.40
Brenner, S.41
more..
-
3
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
DOI 10.1038/75556
-
Ashburner M, et al. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 25:25-29. (Pubitemid 30257031)
-
(2000)
Nature Genetics
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
4
-
-
3142665525
-
GOstat: Find statistically overrepresented Gene Ontologies with a group of genes
-
DOI 10.1093/bioinformatics/bth088
-
Beissbarth T, Speed TP. 2004. GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 20:1464-1465. (Pubitemid 38931420)
-
(2004)
Bioinformatics
, vol.20
, Issue.9
, pp. 1464-1465
-
-
Beissbarth, T.1
Speed, T.P.2
-
5
-
-
2542542256
-
Ultraconserved elements in the human genome
-
DOI 10.1126/science.1098119
-
Bejerano G, et al. 2004. Ultraconserved elements in the human genome. Science 304:1321-1325. (Pubitemid 38697428)
-
(2004)
Science
, vol.304
, Issue.5675
, 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
-
6
-
-
2442575665
-
Pbx marks genes for activation by MyoD indicating a role for a homeodomain protein in establishing myogenic potential
-
DOI 10.1016/S1097-2765(04)00260-6, PII S1097276504002606
-
Berkes CA, et al. 2004. Pbx marks genes for activation by MyoD indicating a role for a homeodomain protein in establishing myogenic potential. Mol Cell. 14:465-477. (Pubitemid 38648800)
-
(2004)
Molecular Cell
, vol.14
, Issue.4
, pp. 465-477
-
-
Berkes, C.A.1
Bergstrom, D.A.2
Penn, B.H.3
Seaver, K.J.4
Knoepfler, P.S.5
Tapscott, S.J.6
-
7
-
-
0033662409
-
A transgenic insertion upstream of sox9 is associated with dominant XX sex reversal in the mouse
-
Bishop CE, et al. 2000. A transgenic insertion upstream of sox9 is associated with dominant XX sex reversal in the mouse. Nat Genet. 26:490-494.
-
(2000)
Nat Genet
, vol.26
, pp. 490-494
-
-
Bishop, C.E.1
-
8
-
-
0242418246
-
Phylogenetic shadowing of primate sequences to find functional regions of the human genome
-
DOI 10.1126/science.1081331
-
Boffelli D, et al. 2003. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299:1391-1394. (Pubitemid 36254651)
-
(2003)
Science
, vol.299
, Issue.5611
, pp. 1391-1394
-
-
Boffelli, D.1
McAuliffe, J.2
Ovcharenko, D.3
Lewis, K.D.4
Ovcharenko, I.5
Pachter, L.6
Rubin, E.M.7
-
9
-
-
34547874585
-
Divergence of transcription factor binding sites across related yeast species
-
DOI 10.1126/science.1140748
-
Borneman AR, et al. 2007. Divergence of transcription factor binding sites across related yeast species. Science 317:815-819. (Pubitemid 47257921)
-
(2007)
Science
, vol.317
, Issue.5839
, pp. 815-819
-
-
Borneman, A.R.1
Gianoulis, T.A.2
Zhang, Z.D.3
Yu, H.4
Rozowsky, J.5
Seringhaus, M.R.6
Lu, Y.W.7
Gerstein, M.8
Snyder, M.9
-
10
-
-
77950566643
-
Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species
-
Bradley RK, et al. 2010. Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol. 8:e1000343.
-
(2010)
PLoS Biol
, vol.8
-
-
Bradley, R.K.1
-
11
-
-
0015070886
-
Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty
-
Britten RJ, Davidson EH. 1971. Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty. Q Rev Biol. 46:111-138.
-
(1971)
Q Rev Biol
, vol.46
, pp. 111-138
-
-
Britten, R.J.1
Davidson, E.H.2
-
12
-
-
0036387193
-
Forkhead transcription factors: Key players in development and metabolism
-
Carlsson P, Mahlapuu M. 2002. Forkhead transcription factors: key players in development and metabolism. Dev Biol. 250:1-23.
-
(2002)
Dev Biol
, vol.250
, pp. 1-23
-
-
Carlsson, P.1
Mahlapuu, M.2
-
13
-
-
22744439568
-
Evolution at two levels: On genes and form
-
Carroll SB. 2005. Evolution at two levels: on genes and form. PLoS Biol. 3:e245.
-
(2005)
PLoS Biol
, vol.3
-
-
Carroll, S.B.1
-
14
-
-
31144465926
-
Hearing silence: Non-neutral evolution at synonymous sites in mammals
-
DOI 10.1038/nrg1770, PII NRG1770
-
Chamary JV, Parmley JL, Hurst LD. 2006. Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet. 7:98-108. (Pubitemid 43128905)
-
(2006)
Nature Reviews Genetics
, vol.7
, Issue.2
, pp. 98-108
-
-
Chamary, J.V.1
Parmley, J.L.2
Hurst, L.D.3
-
15
-
-
19344378811
-
Functional bias and spatial organization of genes in mutational hot and cold regions in the human genome
-
Chuang JH, Li H. 2004. Functional bias and spatial organization of genes in mutational hot and cold regions in the human genome. PLoS Biol. 2:E29.
-
(2004)
PLoS Biol
, vol.2
-
-
Chuang, J.H.1
Li, H.2
-
16
-
-
0036184236
-
Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4
-
DOI 10.1016/S1097-2765(02)00459-8
-
Cirillo LA, et al. 2002. Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. Mol Cell. 9:279-289. (Pubitemid 34195554)
-
(2002)
Molecular Cell
, vol.9
, Issue.2
, pp. 279-289
-
-
Cirillo, L.A.1
Lin, F.R.2
Cuesta, I.3
Friedman, D.4
Jarnik, M.5
Zaret, K.S.6
-
17
-
-
0038724989
-
Finding functional features in Saccharomyces genomes by phylogenetic footprinting
-
DOI 10.1126/science.1084337
-
Cliften P, et al. 2003. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301:71-76. (Pubitemid 36801562)
-
(2003)
Science
, vol.301
, Issue.5629
, pp. 71-76
-
-
Cliften, P.1
Sudarsanam, P.2
Desikan, A.3
Fulton, L.4
Fulton, B.5
Majors, J.6
Waterston, R.7
Cohen, B.A.8
Johnston, M.9
-
18
-
-
22244452677
-
Distribution and intensity of constraint in mammalian genomic sequence
-
DOI 10.1101/gr.3577405
-
Cooper GM, et al. 2005. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 15:901-913. (Pubitemid 40994210)
-
(2005)
Genome Research
, vol.15
, Issue.7
, pp. 901-913
-
-
Cooper, G.M.1
Stone, E.A.2
Asimenos, G.3
Green, E.D.4
Batzoglou, S.5
Sidow, A.6
-
19
-
-
31744448843
-
Conserved noncoding sequences are selectively constrained and not mutation cold spots
-
DOI 10.1038/ng1710, PII NG1710
-
Drake JA, et al. 2006. Conserved noncoding sequences are selectively constrained and not mutation cold spots. Nat Genet. 38: 223-227. (Pubitemid 43177238)
-
(2006)
Nature Genetics
, vol.38
, Issue.2
, pp. 223-227
-
-
Drake, J.A.1
Bird, C.2
Nemesh, J.3
Thomas, D.J.4
Newton-Cheh, C.5
Reymond, A.6
Excoffier, L.7
Attar, H.8
Antonarakis, S.E.9
Dermitzakis, E.T.10
Hirschhorn, J.N.11
-
20
-
-
34948890647
-
Biased clustered substitutions in the human genome: The footprints of male-driven biased gene conversion
-
DOI 10.1101/gr.6395807
-
Dreszer TR, Wall GD, Haussler D, Pollard KS. 2007. Biased clustered substitutions in the human genome: the footprints of male driven biased gene conversion. Genome Res. 17:1420-1430. (Pubitemid 47529426)
-
(2007)
Genome Research
, vol.17
, Issue.10
, pp. 1420-1430
-
-
Dreszer, T.R.1
Wall, G.D.2
Haussler, D.3
Pollard, K.S.4
-
21
-
-
59849095985
-
Comment on human-specific gain of function in a developmental enhancer
-
Duret L, Galtier N. 2009. Comment on "human-specific gain of function in a developmental enhancer." Science 323:714c.
-
(2009)
Science
, vol.323
-
-
Duret, L.1
Galtier, N.2
-
22
-
-
0343183096
-
Transcriptional repression by Pax5 (BSAP) through interaction with corepressors of the Groucho family
-
Eberhard D, Jiménez G, Heavey B, Busslinger M. 2000. Transcriptional repression by Pax5 (BSAP) through interaction with corepressors of the Groucho family. EMBO J. 19:2292-2203.
-
(2000)
EMBO J
, vol.19
, pp. 2292-2203
-
-
Eberhard, D.1
Jiménez, G.2
Heavey, B.3
Busslinger, M.4
-
23
-
-
63449135035
-
Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization
-
Field Y, et al. 2009. Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization. Nat Genet. 41:438-445.
-
(2009)
Nat Genet
, vol.41
, pp. 438-445
-
-
Field, Y.1
-
24
-
-
34248641119
-
Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution
-
DOI 10.1016/j.tig.2007.03.011, PII S0168952507001138
-
Galtier N, Duret L. 2007. Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution. Trends Genet. 23:273-277. (Pubitemid 46770896)
-
(2007)
Trends in Genetics
, vol.23
, Issue.6
, pp. 273-277
-
-
Galtier, N.1
Duret, L.2
-
25
-
-
14044252090
-
Conservation and evolution of CIS-regulatory systems in ascomycete fungi
-
Gasch AP, et al. 2004. Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol. 2:e398.
-
(2004)
PLoS Biol
, vol.2
-
-
Gasch, A.P.1
-
26
-
-
1842684068
-
Genome sequence of the Brown Norway rat yields insights into mammalian evolution
-
Gibbs RA, et al. 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428:493-521.
-
(2004)
Nature
, vol.428
, pp. 493-521
-
-
Gibbs, R.A.1
-
27
-
-
79959524146
-
A haplotype map of the human genome
-
HapMapConsortium
-
HapMapConsortium. 2005. A haplotype map of the human genome. Nature 437:1299-1320.
-
(2005)
Nature
, vol.437
, pp. 1299-1320
-
-
-
28
-
-
18544404720
-
Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution
-
Hardison RC, et al. 2003. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res. 13:13-26.
-
(2003)
Genome Res
, vol.13
, pp. 13-26
-
-
Hardison, R.C.1
-
29
-
-
0037383240
-
Genomic clocks and evolutionary timescales
-
DOI 10.1016/S0168-9525(03)00053-2
-
Hedges SB, Kumar S. 2003. Genomic clocks and evolutionary timescales. Trends Genet. 19:200-206. (Pubitemid 36398422)
-
(2003)
Trends in Genetics
, vol.19
, Issue.4
, pp. 200-206
-
-
Hedges, S.B.1
Kumar, S.2
-
30
-
-
10644283823
-
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
-
Hillier LW, et al. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716.
-
(2004)
Nature
, vol.432
, pp. 695-716
-
-
Hillier, L.W.1
-
31
-
-
40649126603
-
Transcription Factor Substitution during the Evolution of Fungal Ribosome Regulation
-
DOI 10.1016/j.molcel.2008.02.006, PII S1097276508001226
-
Hogues H, et al. 2008. Transcription factor substitution during the evolution of fungal ribosome regulation. Mol Cell. 29:552-562. (Pubitemid 351374685)
-
(2008)
Molecular Cell
, vol.29
, Issue.5
, pp. 552-562
-
-
Hogues, H.1
Lavoie, H.2
Sellam, A.3
Mangos, M.4
Roemer, T.5
Purisima, E.6
Nantel, A.7
Whiteway, M.8
-
32
-
-
14644405477
-
The Ensembl genome database project
-
Hubbard T, et al. 2002. The Ensembl genome database project. Nucleic Acids Res. 32:D468-D470.
-
(2002)
Nucleic Acids Res
, vol.32
-
-
Hubbard, T.1
-
33
-
-
23244467882
-
Molecular biology: Rewiring of the yeast transcriptional network through the evolution of motif usage
-
DOI 10.1126/science.1113833
-
Ihmels J, et al. 2005. Rewiring of the yeast transcriptional network through the evolution of motif usage. Science 309:938-940. (Pubitemid 41099931)
-
(2005)
Science
, vol.309
, Issue.5736
, pp. 938-940
-
-
Ihmels, J.1
Bergmann, S.2
Gerami-Nejad, M.3
Yanai, I.4
McClellan, M.5
Berman, J.6
Barkai, N.7
-
34
-
-
7244245762
-
Finishing the euchromatic sequence of the human genome
-
International Human Genome Sequencing Consortium
-
International Human Genome Sequencing Consortium. 2004. Finishing the euchromatic sequence of the human genome. Nature 431:931-945.
-
(2004)
Nature
, vol.431
, pp. 931-945
-
-
-
35
-
-
0038577171
-
Disruption of the neuronal PAS3 gene in a family affected with schizophrenia
-
Kamnasaran D, Muir WJ, Ferguson-Smith MA, Cox DW. 2003. Disruption of the neuronal PAS3 gene in a family affected with schizophrenia. Med Genet. 40:325-332. (Pubitemid 36613468)
-
(2003)
Journal of Medical Genetics
, vol.40
, Issue.5
, pp. 325-332
-
-
Kamnasaran, D.1
Muir, W.J.2
Ferguson-Smith, M.A.3
Cox, D.W.4
-
36
-
-
34548131708
-
Human genome ultraconserved elements are ultraselected
-
DOI 10.1126/science.1142430
-
Katzman S, et al. 2007. Human genome ultraconserved elements are ultraselected. Science 317:915. (Pubitemid 47301312)
-
(2007)
Science
, vol.317
, Issue.5840
, pp. 915
-
-
Katzman, S.1
Kern, A.D.2
Bejerano, G.3
Fewell, G.4
Fulton, L.5
Wilson, R.K.6
Salama, S.R.7
Haussler, D.8
-
37
-
-
17344379513
-
Five years on the wings of fork head
-
DOI 10.1016/0925-4773(96)00539-4
-
Kaufmann E, Knochel W. 1996. Five years on the wings of fork head. Mech Dev. 57:3-20. (Pubitemid 26197454)
-
(1996)
Mechanisms of Development
, vol.57
, Issue.1
, pp. 3-20
-
-
Kaufmann, E.1
Knochel, W.2
-
38
-
-
15744388330
-
Evidence for widespread degradation of gene control regions in hominid genomes
-
Keightley PD, Lercher MJ, Eyre-Walker A. 2005. Evidence for widespread degradation of gene control regions in hominid genomes. PLoS Biol. 3:e42.
-
(2005)
PLoS Biol
, vol.3
-
-
Keightley, P.D.1
Lercher, M.J.2
Eyre-Walker, A.3
-
39
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
DOI 10.1038/nature01644
-
Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241-254. (Pubitemid 40852689)
-
(2003)
Nature
, vol.423
, Issue.6937
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
40
-
-
77952367798
-
Widespread transcription at neuronal activityregulated enhancers
-
Kim TK, et al. 2010. Widespread transcription at neuronal activityregulated enhancers. Nature 465:182-187.
-
(2010)
Nature
, vol.465
, pp. 182-187
-
-
Kim, T.K.1
-
42
-
-
0016669094
-
Evolution at two levels in humans and chimpanzees
-
King MC, Wilson AC. 1975. Evolution at two levels in humans and chimpanzees. Science 188:107-116.
-
(1975)
Science
, vol.188
, pp. 107-116
-
-
King, M.C.1
Wilson, A.C.2
-
43
-
-
26444606420
-
Small fitness effect of mutations in highly conserved non-coding regions
-
DOI 10.1093/hmg/ddi226
-
Kryukov GV, Schmidt S, Sunyaev S. 2005. Small fitness effect of mutations in highly conserved non-coding regions. Hum Mol Genet. 14:2221-2229. (Pubitemid 41418021)
-
(2005)
Human Molecular Genetics
, vol.14
, Issue.15
, pp. 2221-2229
-
-
Kryukov, G.V.1
Schmidt, S.2
Sunyaev, S.3
-
44
-
-
34247330971
-
Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements
-
DOI 10.1038/nature05676, PII NATURE05676
-
Lareau LF, Inada M, Green RE, Wengrod JC, Brenner SE. 2007. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature 446:926-929. (Pubitemid 46633161)
-
(2007)
Nature
, vol.446
, Issue.7138
, pp. 926-929
-
-
Lareau, L.F.1
Inada, M.2
Green, R.E.3
Wengrod, J.C.4
Brenner, S.E.5
-
45
-
-
77950553742
-
Evolutionary tinkering with conserved components of a transcriptional regulatory network
-
Lavoie H, et al. 2010. Evolutionary tinkering with conserved components of a transcriptional regulatory network. PLoS Biol. 8:e1000329.
-
(2010)
PLoS Biol
, vol.8
-
-
Lavoie, H.1
-
46
-
-
0042810698
-
A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly
-
DOI 10.1093/hmg/ddg180
-
Lettice LA, et al. 2003. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum Mol Genet. 12:1725-1735. (Pubitemid 36896664)
-
(2003)
Human Molecular Genetics
, vol.12
, Issue.14
, pp. 1725-1735
-
-
Lettice, L.A.1
Heaney, S.J.H.2
Purdie, L.A.3
Li, L.4
De Beer, P.5
Oostra, B.A.6
Goode, D.7
Elgar, G.8
Hill, R.E.9
De Graaff, E.10
-
47
-
-
79952163548
-
Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes
-
Lee AP, Kerk SY, Tan YY, Brenner S, Venkatesh B. 2008. Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes. Mol Biol Evol. 28:1205-1215.
-
(2008)
Mol Biol Evol
, vol.28
, pp. 1205-1215
-
-
Lee, A.P.1
Kerk, S.Y.2
Tan, Y.Y.3
Brenner, S.4
Venkatesh, B.5
-
48
-
-
0037061501
-
Strong male-driven evolution of DNA sequences in humans and apes
-
DOI 10.1038/416624a
-
Makova KD, Li WH. 2002. Strong male-driven evolution of DNA sequences in humans and apes. Nature 416:624-626. (Pubitemid 34406760)
-
(2002)
Nature
, vol.416
, Issue.6881
, pp. 624-626
-
-
Makova, K.D.1
Li, W.-H.2
-
49
-
-
0029379593
-
The specificity of homeotic gene function
-
Mann RS. 1995. The specificity of homeotic gene function. BioEssays 17:855-863.
-
(1995)
BioEssays
, vol.17
, pp. 855-863
-
-
Mann, R.S.1
-
51
-
-
0029898760
-
Extra specificity from extradenticle: The partnership between HOX and PBX/EXD homeodomain proteins
-
Mann RS, Chan SK. 1996. Extra specificity from extradenticle: the partnership between HOX and PBX/EXD homeodomain proteins. Trends Genet. 12:258-262.
-
(1996)
Trends Genet
, vol.12
, pp. 258-262
-
-
Mann, R.S.1
Chan, S.K.2
-
52
-
-
0038543069
-
Biased gene conversion: Implications for genome and sex evolution
-
DOI 10.1016/S0168-9525(03)00116-1
-
Marais G. 2003. Biased gene conversion: implications for genome and sex evolution. Trends Genet. 19:330-338. (Pubitemid 36694616)
-
(2003)
Trends in Genetics
, vol.19
, Issue.6
, pp. 330-338
-
-
Marais, G.1
-
53
-
-
39049147650
-
Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b
-
DOI 10.1101/gr.6929408
-
McGaughey DM, et al. 2008. Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b. Genome Res. 18:252-260. (Pubitemid 351240735)
-
(2008)
Genome Research
, vol.18
, Issue.2
, pp. 252-260
-
-
McGaughey, D.M.1
Vinton, R.M.2
Huynh, J.3
Al-Saif, A.4
Beer, M.A.5
McCallion, A.S.6
-
54
-
-
55549128249
-
Dispensability of mammalian DNA
-
McLean C, Bejerano G. 2008. Dispensability of mammalian DNA. Genome Res. 18:1743-1751.
-
(2008)
Genome Res
, vol.18
, pp. 1743-1751
-
-
McLean, C.1
Bejerano, G.2
-
55
-
-
0023508919
-
Male-driven molecular evolution: A model and nucleotide sequence analysis
-
Miyata T, Hayashida H, Kuma K, Mitsuyasu K, Yasunaga T. 1987. Maledriven molecular evolution: a model and nucleotide sequence analysis. Cold Spring Harb Symp Quant Biol. 52:863-867. (Pubitemid 18262395)
-
(1987)
Cold Spring Harbor Symposia on Quantitative Biology
, vol.52
, pp. 863-867
-
-
Miyata, T.1
Hayashida, H.2
Kuma, K.3
Mitsuyasu, K.4
Yasunaga, T.5
-
56
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
Mouse Genome Sequencing Consortium
-
Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
-
58
-
-
33947305594
-
Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay
-
DOI 10.1101/gad.1525507
-
Ni JZ, et al. 2007. Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev. 21:708-718. (Pubitemid 46440292)
-
(2007)
Genes and Development
, vol.21
, Issue.6
, pp. 708-718
-
-
Ni, J.Z.1
Grate, L.2
Donohue, J.P.3
Preston, C.4
Nobida, N.5
O'Brien, G.6
Shiue, L.7
Clark, T.A.8
Blume, J.E.9
Ares Jr., M.10
-
59
-
-
47649125626
-
Widespread ultraconservation divergence in primates
-
DOI 10.1093/molbev/msn116
-
Ovcharenko I. 2008. Widespread ultraconservation divergence in primates. Mol Biol Evol. 25:1668-1676. (Pubitemid 352019851)
-
(2008)
Molecular Biology and Evolution
, vol.25
, Issue.8
, pp. 1668-1676
-
-
Ovcharenko, I.1
-
60
-
-
33751316959
-
In vivo enhancer analysis of human conserved non-coding sequences
-
DOI 10.1038/nature05295, PII NATURE05295
-
Pennacchio LA, et al. 2006. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444:499-502. (Pubitemid 44809068)
-
(2006)
Nature
, vol.444
, Issue.7118
, 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
Plajzer-Frick, I.11
Akiyama, J.12
De Val, S.13
Afzal, V.14
Black, B.L.15
Couronne, O.16
Eisen, M.B.17
Visel, A.18
Rubin, E.M.19
-
61
-
-
33748675254
-
An RNA gene expressed during cortical development evolved rapidly in humans
-
DOI 10.1038/nature05113, PII NATURE05113
-
Pollard KS, et al. 2006. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 433:167-172. (Pubitemid 44387600)
-
(2006)
Nature
, vol.443
, Issue.7108
, pp. 167-172
-
-
Pollard, K.S.1
Salama, S.R.2
Lambert, N.3
Lambot, M.-A.4
Coppens, S.5
Pedersen, J.S.6
Katzman, S.7
King, B.8
Onodera, C.9
Siepel, A.10
Kern, A.D.11
Dehay, C.12
Igel, H.13
Ares Jr., M.14
Vanderhaeghen, P.15
Haussler, D.16
-
62
-
-
38049147787
-
MEF2: A central regulator of diverse developmental programs
-
Potthoff MJ, Olson EN. 2007. MEF2: a central regulator of diverse developmental programs. Development 134:4131-4140.
-
(2007)
Development
, vol.134
, pp. 4131-4140
-
-
Potthoff, M.J.1
Olson, E.N.2
-
63
-
-
18844376318
-
In vivo characterization of a vertebrate ultraconserved enhancer
-
DOI 10.1016/j.ygeno.2005.03.003, PII S0888754305000649
-
Poulin F, et al. 2005. In vivo characterization of a vertebrate ultraconserved enhancer. Genomics 85:774-781. (Pubitemid 40693364)
-
(2005)
Genomics
, vol.85
, Issue.6
, pp. 774-781
-
-
Poulin, F.1
Nobrega, M.A.2
Plajzer-Frick, I.3
Holt, A.4
Afzal, V.5
Rubin, E.M.6
Pennacchio, L.A.7
-
64
-
-
33750737061
-
Accelerated evolution of conserved noncoding sequences in humans
-
DOI 10.1126/science.1130738
-
Prabhakar A, Noonan JP, Pä äbo S, Rubin EM. 2006. Accelerated evolution of conserved noncoding sequences in humans. Science 314:786. (Pubitemid 44706638)
-
(2006)
Science
, vol.314
, Issue.5800
, pp. 786
-
-
Prabhakar, S.1
Noonan, J.P.2
Paabo, S.3
Rubin, E.M.4
-
65
-
-
51149097366
-
Human-specific gain of function in a developmental enhancer
-
Prabhakar S, et al. 2008. Human-specific gain of function in a developmental enhancer. Science 321:1346-1350.
-
(2008)
Science
, vol.321
, pp. 1346-1350
-
-
Prabhakar, S.1
-
66
-
-
34249006235
-
Chromatin structure and evolution in the human genome
-
Prendergast JG, et al. 2007. Chromatin structure and evolution in the human genome. BMC Evol Biol. 7:72.
-
(2007)
BMC Evol Biol
, vol.7
, pp. 72
-
-
Prendergast, J.G.1
-
67
-
-
67650064594
-
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
-
Pruitt KD, et al. 2009. The consensus coding sequence (CCDS) project: identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 19:1316-1323.
-
(2009)
Genome Res
, vol.19
, pp. 1316-1323
-
-
Pruitt, K.D.1
-
68
-
-
0027934301
-
Coordinate regulation of downstream genes by extradenticle and the homeotic selector proteins
-
Rauskolb C, Wieschaus E. 1994. Coordinate regulation of downstream genes by extradenticle and the homeotic selector proteins. EMBO J. 13:3561-3569. (Pubitemid 24246193)
-
(1994)
EMBO Journal
, vol.13
, Issue.15
, pp. 3561-3569
-
-
Rauskolb, C.1
Wieschaus, E.2
-
69
-
-
0032497485
-
The Xenopus Wnt effector XTcf-3 interacts with Groucho-related transcriptional repressors
-
DOI 10.1038/26989
-
Roose J, et al. 1998. The Xenopus Wnt effector XTcf-3 interacts with Groucho-related transcriptional repressors. Nature 395: 608-612. (Pubitemid 28475715)
-
(1998)
Nature
, vol.395
, Issue.6702
, pp. 608-612
-
-
Roose, J.1
Molenaar, M.2
Peterson, J.3
Hurenkamp, J.4
Brantjes, H.5
Moerer, P.6
Van De Wetering, M.7
Destree, O.8
Clevers, H.9
-
70
-
-
33846617772
-
Long-range conserved non-coding SHOX sequences regulate expression in developing chicken limb and are associated with short stature phenotypes in human patients
-
DOI 10.1093/hmg/ddl470
-
Sabherwal N, et al. 2007. Long-range conserved non-coding SHOX sequences regulate expression in developing chicken limb and are associated with short stature phenotypes in human patients. Hum Mol Genet. 16:210-222. (Pubitemid 46179003)
-
(2007)
Human Molecular Genetics
, vol.16
, Issue.2
, pp. 210-222
-
-
Sabherwal, N.1
Bangs, F.2
Roth, R.3
Weiss, B.4
Jantz, K.5
Tiecke, E.6
Hinkel, G.K.7
Spaich, C.8
Hauffa, B.P.9
Van Der Kamp, H.10
Kapeller, J.11
Tickle, C.12
Rappold, G.13
-
71
-
-
14844341770
-
Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb
-
DOI 10.1242/dev.01613
-
Sagai T, Hosoya M, Mizushina Y, Tamura M, Shiroishi T. 2005. Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb. Development 132:797-803. (Pubitemid 40352838)
-
(2005)
Development
, vol.132
, Issue.4
, pp. 797-803
-
-
Sagai, T.1
Hosoya, M.2
Mizushina, Y.3
Tamura, M.4
Shiroishi, T.5
-
72
-
-
77953062527
-
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
-
Schmidt D, et al. 2010. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328:1036-1040.
-
(2010)
Science
, vol.328
, pp. 1036-1040
-
-
Schmidt, D.1
-
73
-
-
33745175531
-
A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications
-
She X, et al. 2006. A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications. Genome Res. 16:576-583.
-
(2006)
Genome Res
, vol.16
, pp. 576-583
-
-
She, X.1
-
74
-
-
0035173378
-
DbSNP: The NCBI database of genetic variation
-
Sherry ST, et al. 2001. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29:308-311. (Pubitemid 32054478)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.1
, pp. 308-311
-
-
Sherry, S.T.1
Ward, M.-H.2
Kholodov, M.3
Baker, J.4
Phan, L.5
Smigielski, E.M.6
Sirotkin, K.7
-
75
-
-
0028934434
-
The MADS-box family of transcription factors
-
Shore P, Sharrocks AD. 1995. The MADS-box family of transcription factors. Eur J Biochem. 229:1-13.
-
(1995)
Eur J Biochem
, vol.229
, pp. 1-13
-
-
Shore, P.1
Sharrocks, A.D.2
-
76
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
DOI 10.1101/gr.3715005
-
Siepel A, et al. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15:1034-1050. (Pubitemid 41126859)
-
(2005)
Genome Research
, vol.15
, Issue.8
, 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
Weinstock, G.M.11
Wilson, R.K.12
Gibbs, R.A.13
Kent, W.J.14
Miller, W.15
Haussler, D.16
-
77
-
-
36049018312
-
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
-
DOI 10.1038/nature06340, PII NATURE06340
-
Stark A, et al. 2007. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450:219-232. (Pubitemid 350100553)
-
(2007)
Nature
, vol.450
, Issue.7167
, pp. 219-232
-
-
Stark, A.1
Lin, M.F.2
Kheradpour, P.3
Pedersen, J.S.4
Parts, L.5
Carlson, J.W.6
Crosby, M.A.7
Rasmussen, M.D.8
Roy, S.9
Deoras, A.N.10
Ruby, J.G.11
Brennecke, J.12
Hodges, E.13
Hinrichs, A.S.14
Caspi, A.15
Paten, B.16
Park, S.-W.17
Han, M.V.18
Maeder, M.L.19
Polansky, B.J.20
Robson, B.E.21
Aerts, S.22
Van Helden, J.23
Hassan, B.24
Gilbert, D.G.25
Eastman, D.A.26
Rice, M.27
Weir, M.28
Hahn, M.W.29
Park, Y.30
Dewey, C.N.31
Pachter, L.32
Kent, W.J.33
Haussler, D.34
Lai, E.C.35
Bartel, D.P.36
Hannon, G.J.37
Kaufman, T.C.38
Eisen, M.B.39
Clark, A.G.40
Smith, D.41
Celniker, S.E.42
Gelbart, W.M.43
Kellis, M.44
Matthews, B.B.45
Schroeder, A.J.46
Gramates, L.S.47
St Pierre, S.E.48
Roark, M.49
Wiley Jr., K.L.50
Kulathinal, R.J.51
Zhang, P.52
Myrick, K.V.53
Antone, J.V.54
Yu, C.55
Park, S.56
Wan, K.H.57
more..
-
78
-
-
38949097100
-
Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock
-
DOI 10.1093/molbev/msm268
-
Stephen S, Pheasant M, Makunin IV, Mattick JS. 2008. Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock. Mol Biol Evol. 25: 402-408. (Pubitemid 351231613)
-
(2008)
Molecular Biology and Evolution
, vol.25
, Issue.2
, pp. 402-408
-
-
Stephen, S.1
Pheasant, M.2
Makunin, I.V.3
Mattick, J.S.4
-
79
-
-
80155192425
-
Loss-of-function mutation in a repressor module of human-specifically activated enhancer HACNS1
-
Sumiyama K, Saitou N. 2011. Loss-of-function mutation in a repressor module of human-specifically activated enhancer HACNS1. Mol Biol Evol. 28:3005-3007.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 3005-3007
-
-
Sumiyama, K.1
Saitou, N.2
-
80
-
-
0029415835
-
Divergence time and population size in the lineage leading to modern humans
-
DOI 10.1006/tpbi.1995.1026
-
Takahata N, Satta Y, Klein J. 1995. Divergence time and population size in the lineage leading to modern humans. Theor Popul Biol. 48:198-221. (Pubitemid 26460272)
-
(1995)
Theoretical Population Biology
, vol.48
, Issue.2
, pp. 198-221
-
-
Takahata, N.1
Satta, Y.2
Klein, J.3
-
82
-
-
40149098862
-
The evolution of combinatorial gene regulation in fungi
-
Tuch BB, Galgoczy DJ, Hernday AD, Li H, Johnson AD. 2008. The evolution of combinatorial gene regulation in fungi. PLoS Biol. 6:e38.
-
(2008)
PLoS Biol
, vol.6
-
-
Tuch, B.B.1
Galgoczy, D.J.2
Hernday, A.D.3
Li, H.4
Johnson, A.D.5
-
83
-
-
59949096873
-
EnsemblCompara GeneTrees: Analysis of complete, duplication aware phylogenetic trees in vertebrates
-
Vilella AJ, et al. 2008. EnsemblCompara GeneTrees: analysis of complete, duplication aware phylogenetic trees in vertebrates. Genome Res. 19:327-335.
-
(2008)
Genome Res
, vol.19
, pp. 327-335
-
-
Vilella, A.J.1
-
84
-
-
77950395160
-
Gene duplication and the evolution of ribosomal protein gene regulation in yeast
-
Wapinski I, et al. 2010. Gene duplication and the evolution of ribosomal protein gene regulation in yeast. Proc Natl Acad Sci U S A. 107:5505-5510.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 5505-5510
-
-
Wapinski, I.1
-
85
-
-
0033559518
-
From head to toes: The multiple facets of Sox proteins
-
DOI 10.1093/nar/27.6.1409
-
Wegner M. 1999. From head to toes: the multiple facets of Sox proteins. Nucleic Acids Res. 27:1409-1420. (Pubitemid 29206280)
-
(1999)
Nucleic Acids Research
, vol.27
, Issue.6
, pp. 1409-1420
-
-
Wegner, M.1
-
86
-
-
26944436250
-
From stem cells to neurons and glia: A Soxist's view of neural development
-
Wegner M, Stolt CC. 1995. From stem cells to neurons and glia: a Soxist's view of neural development. Trends Neurosci. 28: 583-588.
-
(1995)
Trends Neurosci
, vol.28
, pp. 583-588
-
-
Wegner, M.1
Stolt, C.C.2
-
87
-
-
20044366725
-
Highly conserved non-coding sequences are associated with vertebrate development
-
Woolfe A, et al. 2005. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3:e7.
-
(2005)
PLoS Biol
, vol.3
-
-
Woolfe, A.1
-
88
-
-
35248843126
-
CONDOR: A database resource of developmentallyassociated conserved non-coding elements
-
Woolfe A, et al. 2007. CONDOR: a database resource of developmentallyassociated conserved non-coding elements. BMC Dev Biol. 7:100.
-
(2007)
BMC Dev Biol
, vol.7
, pp. 100
-
-
Woolfe, A.1
-
89
-
-
34047249770
-
FoxD3 and Grg4 physically interact to repress transcription and induce mesoderm in Xenopus
-
DOI 10.1074/jbc.M607412200
-
Yaklichkin S, Steiner AB, Lu Q, Kessler DS. 2007. FoxD3 and Grg4 physically interact to repress transcription and induce mesoderm in Xenopus. J Biol Chem. 282:2548-2557. (Pubitemid 47076798)
-
(2007)
Journal of Biological Chemistry
, vol.282
, Issue.4
, pp. 2548-2557
-
-
Yaklichkin, S.1
Steiner, A.B.2
Lu, Q.3
Kessler, D.S.4
-
90
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood
-
Yang Z. 1997. "PAML: a program package for phylogenetic analysis by maximum likelihood." Comput Appl Biosci. 13:555-556. (Pubitemid 27480216)
-
(1997)
Computer Applications in the Biosciences
, vol.13
, Issue.5
, pp. 555-556
-
-
Yang, Z.1
-
91
-
-
0034053725
-
A greedy algorithm for aligning DNA sequences
-
DOI 10.1089/10665270050081478
-
Zhang Z, Schwartz S, Wagner L, Miller W. 2000. A greedy algorithm for aligning DNA sequences. J Comput Biol. 7:203-214. (Pubitemid 30412170)
-
(2000)
Journal of Computational Biology
, vol.7
, Issue.1-2
, pp. 203-214
-
-
Zhang, Z.1
Schwartz, S.2
Wagner, L.3
Miller, W.4
-
92
-
-
0001895697
-
Evolutionary divergence and convergence in proteins
-
Bryson V, Vogel HJ, editors. New York: Academic Press
-
Zuckerkandl E, Pauling L. 1965. Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ, editors. Evolving genes and proteins. New York: Academic Press. p. 97-166.
-
(1965)
Evolving Genes and Proteins
, pp. 97-166
-
-
Zuckerkandl, E.1
Pauling, L.2
|