-
1
-
-
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. Evolution and functional classification of vertebrate gene deserts. Genome Res 15 (2005) 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
-
2
-
-
3142740663
-
Comparative genomics
-
Hardison R.C. Comparative genomics. PLoS Biol 1 (2003) E58
-
(2003)
PLoS Biol
, vol.1
-
-
Hardison, R.C.1
-
4
-
-
0037197967
-
Utility and distribution of conserved noncoding sequences in the grasses
-
Kaplinsky N.J., Braun D.M., Penterman J., Goff S.A., and Freeling M. Utility and distribution of conserved noncoding sequences in the grasses. Proc Natl Acad Sci U S A 99 (2002) 6147-6151
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 6147-6151
-
-
Kaplinsky, N.J.1
Braun, D.M.2
Penterman, J.3
Goff, S.A.4
Freeling, M.5
-
5
-
-
0038028675
-
Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution
-
Guo H., and Moose S.P. Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution. Plant Cell 15 (2003) 1143-1158
-
(2003)
Plant Cell
, vol.15
, pp. 1143-1158
-
-
Guo, H.1
Moose, S.P.2
-
6
-
-
38949151064
-
How to usefully compare homologous plant genes and chromosomes as DNA sequence
-
Lyons E., and Freeling M. How to usefully compare homologous plant genes and chromosomes as DNA sequence. Plant J 53 (2008) 661-673
-
(2008)
Plant J
, vol.53
, pp. 661-673
-
-
Lyons, E.1
Freeling, M.2
-
7
-
-
33847704925
-
Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics
-
Vandepoele K., Casneuf T., and Van de Peer Y. Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics. Genome Biol 7 (2006) R103
-
(2006)
Genome Biol
, vol.7
-
-
Vandepoele, K.1
Casneuf, T.2
Van de Peer, Y.3
-
8
-
-
34347389640
-
G-boxes, Bigfoot genes and environmental response: characterization of the intragenomic conserved noncoding sequences of Arabidopsis
-
Freeling M., Rapaka L., Lyons E., Pedersen B., and Thomas B.C. G-boxes, Bigfoot genes and environmental response: characterization of the intragenomic conserved noncoding sequences of Arabidopsis. Plant Cell 19 (2007) 1441-1457
-
(2007)
Plant Cell
, vol.19
, pp. 1441-1457
-
-
Freeling, M.1
Rapaka, L.2
Lyons, E.3
Pedersen, B.4
Thomas, B.C.5
-
9
-
-
42549120705
-
Synteny and collinearity in plant genomes
-
Tang H., Bowers J.E., Wang X., Ming R., Alam M., and Paterson A.H. Synteny and collinearity in plant genomes. Science 320 (2008) 486-488
-
(2008)
Science
, vol.320
, pp. 486-488
-
-
Tang, H.1
Bowers, J.E.2
Wang, X.3
Ming, R.4
Alam, M.5
Paterson, A.H.6
-
10
-
-
57749113081
-
Distribution and evolution of circular miniproteins in flowering plants
-
Gruber C.W., Elliott A.G., Ireland D.C., Delprete P.G., Dessein S., Goransson U., Trabi M., Wang C.K., Kinghorn A.B., Robbrecht E., et al. Distribution and evolution of circular miniproteins in flowering plants. Plant Cell 20 (2008) 2471-2483
-
(2008)
Plant Cell
, vol.20
, pp. 2471-2483
-
-
Gruber, C.W.1
Elliott, A.G.2
Ireland, D.C.3
Delprete, P.G.4
Dessein, S.5
Goransson, U.6
Trabi, M.7
Wang, C.K.8
Kinghorn, A.B.9
Robbrecht, E.10
-
11
-
-
19044363218
-
Arabidopsis sphingosine kinase and the effects of phytosphingosine-1-phosphate on stomatal aperture
-
Coursol S., Stunff J., Lynch D., Gilroy S., Assmann S., and Spiegel S. Arabidopsis sphingosine kinase and the effects of phytosphingosine-1-phosphate on stomatal aperture. Plant Phys 137 (2005) 724-737
-
(2005)
Plant Phys
, vol.137
, pp. 724-737
-
-
Coursol, S.1
Stunff, J.2
Lynch, D.3
Gilroy, S.4
Assmann, S.5
Spiegel, S.6
-
12
-
-
47849111627
-
Ultraconserved elements between the genomes of the plants Arabidopsis thaliana and rice
-
Zheng W.X., and Zhang C.T. Ultraconserved elements between the genomes of the plants Arabidopsis thaliana and rice. J Biomol Struct Dyn 26 (2008) 1-8
-
(2008)
J Biomol Struct Dyn
, vol.26
, pp. 1-8
-
-
Zheng, W.X.1
Zhang, C.T.2
-
13
-
-
2542542256
-
Ultraconserved elements in the human genome
-
Bejerano G., Pheasant M., Makunin I., Stephen S., Kent W.J., Mattick J.S., and Haussler D. Ultraconserved elements in the human genome. Science 304 (2004) 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
-
14
-
-
57149089296
-
Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar and grape: CoGe with rosids
-
Lyons E., Pedersen B., Kane J., Alam M., Ming R., Tang X.W., Bowers J., Paterson A., Lisch D., and Freeling M. Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar and grape: CoGe with rosids. Plant Phys 148 (2008) 1772-1781
-
(2008)
Plant Phys
, vol.148
, pp. 1772-1781
-
-
Lyons, E.1
Pedersen, B.2
Kane, J.3
Alam, M.4
Ming, R.5
Tang, X.W.6
Bowers, J.7
Paterson, A.8
Lisch, D.9
Freeling, M.10
-
15
-
-
47649104484
-
Horizontal gene transfer in eukaryotic evolution
-
Keeling P.J., and Palmer J.D. Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet 9 (2008) 605-618
-
(2008)
Nat Rev Genet
, vol.9
, pp. 605-618
-
-
Keeling, P.J.1
Palmer, J.D.2
-
16
-
-
42949157236
-
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
-
Ming R., Hou S., Feng Y., Yu Q., Dionne-Laporte A., Saw J.H., Senin P., Wang W., Ly B.V., Lewis K.L., et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452 (2008) 991-996
-
(2008)
Nature
, vol.452
, pp. 991-996
-
-
Ming, R.1
Hou, S.2
Feng, Y.3
Yu, Q.4
Dionne-Laporte, A.5
Saw, J.H.6
Senin, P.7
Wang, W.8
Ly, B.V.9
Lewis, K.L.10
-
17
-
-
33847643636
-
Intragenomic conserved noncoding sequences in Arabidopsis
-
Thomas B.C., Rapaka L., Lyons E., Pedersen B., and Freeling M. Intragenomic conserved noncoding sequences in Arabidopsis. Proc Natl Acad Sci U S A 104 (2007) 3348-3353
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 3348-3353
-
-
Thomas, B.C.1
Rapaka, L.2
Lyons, E.3
Pedersen, B.4
Freeling, M.5
-
18
-
-
34848886909
-
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
-
Jaillon O., Aury J.M., Noel B., Policriti A., Clepet C., Casagrande A., Choisne N., Aubourg S., Vitulo N., Jubin C., et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449 (2007) 463-467
-
(2007)
Nature
, vol.449
, pp. 463-467
-
-
Jaillon, O.1
Aury, J.M.2
Noel, B.3
Policriti, A.4
Clepet, C.5
Casagrande, A.6
Choisne, N.7
Aubourg, S.8
Vitulo, N.9
Jubin, C.10
-
19
-
-
22144473057
-
Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
-
Sandelin A., Bailey P., Bruce S., Engstrom P.G., Klos J.M., Wasserman W.W., Ericson J., and Lenhard B. Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics 5 (2004) 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
-
20
-
-
0141853991
-
Conserved noncoding sequences in the grasses
-
Inada D.C., Bashir A., Lee C., Thomas B.C., Ko C., Goff S.A., and Freeling M. Conserved noncoding sequences in the grasses. Genome Res 13 (2003) 2030-2041
-
(2003)
Genome Res
, vol.13
, pp. 2030-2041
-
-
Inada, D.C.1
Bashir, A.2
Lee, C.3
Thomas, B.C.4
Ko, C.5
Goff, S.A.6
Freeling, M.7
-
21
-
-
33750442876
-
Large-scale turnover of functional transcription factor binding sites in Drosophila
-
Moses A.M., Pollard D.A., Nix D.A., Iyer V.N., Li X.Y., Biggin M.D., and Eisen M.B. Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput Biol 2 (2006) e130
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Moses, A.M.1
Pollard, D.A.2
Nix, D.A.3
Iyer, V.N.4
Li, X.Y.5
Biggin, M.D.6
Eisen, M.B.7
-
22
-
-
34848901059
-
Adaptive evolution of conserved noncoding elements in mammals
-
Kim S., and Pritchard J. Adaptive evolution of conserved noncoding elements in mammals. PLoS Genetics 3 (2007) e147
-
(2007)
PLoS Genetics
, vol.3
-
-
Kim, S.1
Pritchard, J.2
-
23
-
-
31744448843
-
Conserved noncoding sequences are selectively constrained and not mutation cold spots
-
Drake J., Bird C., Nemesh J., Thomas D., Newton-Cheh C., Raymond A., Excoffler L., Attar H., Antonarakis S., Dermitzakis E., et al. Conserved noncoding sequences are selectively constrained and not mutation cold spots. Nature Genetics 38 (2006) 223-227
-
(2006)
Nature Genetics
, vol.38
, pp. 223-227
-
-
Drake, J.1
Bird, C.2
Nemesh, J.3
Thomas, D.4
Newton-Cheh, C.5
Raymond, A.6
Excoffler, L.7
Attar, H.8
Antonarakis, S.9
Dermitzakis, E.10
-
24
-
-
57649220038
-
Isolation and characterization of conserved noncoding sequences among rice (Oryza sativa L.) paralogous regions
-
Li X., Tan L., Wang L., Hu S., and Sun C. Isolation and characterization of conserved noncoding sequences among rice (Oryza sativa L.) paralogous regions. Mol Genet Genomics 281 (2009) 11-18
-
(2009)
Mol Genet Genomics
, vol.281
, pp. 11-18
-
-
Li, X.1
Tan, L.2
Wang, L.3
Hu, S.4
Sun, C.5
-
25
-
-
37249045857
-
Extensive concerted evolution of rice paralogs and the road to regaining independence
-
Wang X., Tang H., Bowers J.E., Feltus F.A., and Paterson A.H. Extensive concerted evolution of rice paralogs and the road to regaining independence. Genetics 177 (2007) 1753-1763
-
(2007)
Genetics
, vol.177
, pp. 1753-1763
-
-
Wang, X.1
Tang, H.2
Bowers, J.E.3
Feltus, F.A.4
Paterson, A.H.5
-
26
-
-
41549137777
-
Gene conversion in the rice genome
-
Xu S., Clark T., Zheng H., Vang S., Li R., Wong G.K.-S., Wang J., and Zheng X. Gene conversion in the rice genome. BMC Genomics 9 (2008) 1-8
-
(2008)
BMC Genomics
, vol.9
, pp. 1-8
-
-
Xu, S.1
Clark, T.2
Zheng, H.3
Vang, S.4
Li, R.5
Wong, G.K.-S.6
Wang, J.7
Zheng, X.8
-
27
-
-
58549101102
-
Proteogenomic discovery, correction and confirmation of Arabidopsis gene models
-
Castellana N., Payne S., Shen Z., Stanke M., Bafna V., and Briggs S. Proteogenomic discovery, correction and confirmation of Arabidopsis gene models. Proc Natl Acad Sci U S A 105 (2008) 21034-21038
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 21034-21038
-
-
Castellana, N.1
Payne, S.2
Shen, Z.3
Stanke, M.4
Bafna, V.5
Briggs, S.6
-
28
-
-
33749357831
-
Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice
-
Rizzon C., Ponger L., and Gaut B.S. Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comput Biol (2006) 2
-
(2006)
PLoS Comput Biol
, pp. 2
-
-
Rizzon, C.1
Ponger, L.2
Gaut, B.S.3
-
29
-
-
57149120510
-
Many or most genes in Arabidopsis transposed after the origin of the order Brasicales
-
Freeling M., Lyons E., Pedersen B., Alam M., Ming R., and Lisch D. Many or most genes in Arabidopsis transposed after the origin of the order Brasicales. Genome Res 18 (2008) 1924-1937
-
(2008)
Genome Res
, vol.18
, pp. 1924-1937
-
-
Freeling, M.1
Lyons, E.2
Pedersen, B.3
Alam, M.4
Ming, R.5
Lisch, D.6
-
30
-
-
0032004775
-
Matrix attachment regions and structural colinearity in the genomes of two grass species
-
Avramova Z., Tikhonov A., Chen M., and Bennetzen J.L. Matrix attachment regions and structural colinearity in the genomes of two grass species. Nucleic Acids Res 26 (1998) 761-767
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 761-767
-
-
Avramova, Z.1
Tikhonov, A.2
Chen, M.3
Bennetzen, J.L.4
-
31
-
-
50549100596
-
Conserved upstream open reading frames in higher plants
-
Tran M., Schultz C., and Baumann U. Conserved upstream open reading frames in higher plants. BMC Genomics 9 (2008) 361
-
(2008)
BMC Genomics
, vol.9
, pp. 361
-
-
Tran, M.1
Schultz, C.2
Baumann, U.3
-
32
-
-
35649024269
-
Regulation of SHOOT MERISTEMLESS genes via an upstream-conserved noncoding sequence coordinates leaf development
-
Uchida N., Townsley B., Chung K.H., and Sinha N. Regulation of SHOOT MERISTEMLESS genes via an upstream-conserved noncoding sequence coordinates leaf development. Proc Natl Acad Sci U S A 104 (2007) 15953-15958
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 15953-15958
-
-
Uchida, N.1
Townsley, B.2
Chung, K.H.3
Sinha, N.4
-
33
-
-
34547398400
-
Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize
-
Salvi S., Sponza G., Morgante M., Tomes D., Niu X., Fengler K.A., Meeley R., Ananiev E.V., Svitashev S., Bruggemann E., et al. Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proc Natl Acad Sci U S A 104 (2007) 11376-11381
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 11376-11381
-
-
Salvi, S.1
Sponza, G.2
Morgante, M.3
Tomes, D.4
Niu, X.5
Fengler, K.A.6
Meeley, R.7
Ananiev, E.V.8
Svitashev, S.9
Bruggemann, E.10
-
34
-
-
0000399441
-
Cytoplasmic inheritance of the organization of the cell cortex of Paramecium aurelia
-
Beissen J., and Sonneborn T. Cytoplasmic inheritance of the organization of the cell cortex of Paramecium aurelia. Proc Natl Acad Sci U S A 53 (1965) 275-282
-
(1965)
Proc Natl Acad Sci U S A
, vol.53
, pp. 275-282
-
-
Beissen, J.1
Sonneborn, T.2
-
35
-
-
2142765527
-
Nuclear architecture and genome functioning in plants and animals: what can we learn from both?
-
van Driel R., and Fransz P. Nuclear architecture and genome functioning in plants and animals: what can we learn from both?. Exp Cell Res 296 (2004) 86-90
-
(2004)
Exp Cell Res
, vol.296
, pp. 86-90
-
-
van Driel, R.1
Fransz, P.2
-
36
-
-
1242316978
-
Dynamic association of mammalian insulator protein CTCF with centrosomes and the midbody
-
Zhang R., Burke L., Rasko J., Lobanenkov V., and Renkawitz R. Dynamic association of mammalian insulator protein CTCF with centrosomes and the midbody. Exp Cell Res 294 (2004) 86-93
-
(2004)
Exp Cell Res
, vol.294
, pp. 86-93
-
-
Zhang, R.1
Burke, L.2
Rasko, J.3
Lobanenkov, V.4
Renkawitz, R.5
-
37
-
-
53149107845
-
Chromatin insulators: regulatory mechanisms and epigenetic inheritance
-
Bushey A.M., Dorman E.R., and Corces V.G. Chromatin insulators: regulatory mechanisms and epigenetic inheritance. Mol Cell 32 (2008) 1-9
-
(2008)
Mol Cell
, vol.32
, pp. 1-9
-
-
Bushey, A.M.1
Dorman, E.R.2
Corces, V.G.3
-
38
-
-
0028090085
-
Mutator insertions in an intron of the maize knotted1 gene result in dominant suppressible mutations
-
Greene B., Walko R., and Hake S. Mutator insertions in an intron of the maize knotted1 gene result in dominant suppressible mutations. Genetics 138 (1994) 1275-1285
-
(1994)
Genetics
, vol.138
, pp. 1275-1285
-
-
Greene, B.1
Walko, R.2
Hake, S.3
-
39
-
-
10844267448
-
Phylogenetic analysis of 5′-noncoding regions from the ABA-responsive rab16/17 gene family of sorghum, maize and rice provides insight into the composition, organization and function of cis-regulatory modules
-
Buchanan C., Klein P., and Mullet J. Phylogenetic analysis of 5′-noncoding regions from the ABA-responsive rab16/17 gene family of sorghum, maize and rice provides insight into the composition, organization and function of cis-regulatory modules. Genetics 168 (2004) 1639-1654
-
(2004)
Genetics
, vol.168
, pp. 1639-1654
-
-
Buchanan, C.1
Klein, P.2
Mullet, J.3
-
40
-
-
34247141438
-
Evolutionary hierarchies of conserved blocks in 5′-noncoding sequences of dicot rbcS genes
-
Weeks K.E., Chuzhanova N.A., Donnison I.S., and Scott I.M. Evolutionary hierarchies of conserved blocks in 5′-noncoding sequences of dicot rbcS genes. BMC Evol Biol 7 (2007) 51
-
(2007)
BMC Evol Biol
, vol.7
, pp. 51
-
-
Weeks, K.E.1
Chuzhanova, N.A.2
Donnison, I.S.3
Scott, I.M.4
|