-
1
-
-
2542542256
-
Ultraconserved elements in the human genome
-
DOI 10.1126/science.1098119
-
G Bejerano M Pheasant I Makunin S Stephen WJ Kent JS Mattick D Haussler 2004 Ultraconserved elements in the human genome Science 304 1321 1325 15131266 10.1126/science.1098119 1:CAS:528:DC%2BD2cXkt1Ggu7k%3D (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
-
2
-
-
0035865202
-
Filling in the gaps
-
DOI 10.1038/35057274
-
P Bork R Copley 2001 The draft sequences. Filling in the gaps Nature 409 818 820 11236994 10.1038/35057274 (Pubitemid 32165328)
-
(2001)
Nature
, vol.409
, Issue.6822
, pp. 818-820
-
-
Bork, P.1
Copley, R.2
-
3
-
-
23744502709
-
A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts
-
DOI 10.1101/gr.4004805
-
E de la Calle-Mustienes CG Feijoo M Manzanares JJ Tena E Rodriguez-Seguel A Letizia ML Allende JL Gomez-Skarmeta 2005 A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts Genome Res 15 1061 1072 10.1101/gr.4004805 (Pubitemid 41126861)
-
(2005)
Genome Research
, vol.15
, Issue.8
, 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
-
4
-
-
33644536713
-
Tunicates and not cephalochordates are the closest living relatives of vertebrates
-
DOI 10.1038/nature04336, PII N04336
-
F Delsuc H Brinkmann D Chourrout H Philippe 2006 Tunicates and not cephalochordates are the closest living relatives of vertebrates Nature 439 965 968 16495997 10.1038/nature04336 1:CAS:528:DC%2BD28Xhs1KjsLY%3D (Pubitemid 43292413)
-
(2006)
Nature
, vol.439
, Issue.7079
, pp. 965-968
-
-
Delsuc, F.1
Brinkmann, H.2
Chourrout, D.3
Philippe, H.4
-
5
-
-
13144295005
-
Conserved non-genic sequences - An unexpected feature of mammalian genomes
-
DOI 10.1038/nrg1527
-
ET Dermitzakis A Reymond SE Antonarakis 2005 Conserved non-genic sequences-an unexpected feature of mammalian genomes Nat Rev Genet 6 151 157 15716910 10.1038/nrg1527 1:CAS:528:DC%2BD2MXhtFyjsrk%3D (Pubitemid 40179538)
-
(2005)
Nature Reviews Genetics
, vol.6
, Issue.2
, pp. 151-157
-
-
Dermitzakis, E.T.1
Reymond, A.2
Antonarakis, S.E.3
-
6
-
-
42149157760
-
Broad phylogenomic sampling improves resolution of the animal tree of life
-
18322464 10.1038/nature06614 1:CAS:528:DC%2BD1cXksFSju7k%3D
-
CW Dunn A Hejnol DQ Matus K Pang WE Browne SA Smith E Seaver GW Rouse M Obst GD Edgecombe, et al. 2008 Broad phylogenomic sampling improves resolution of the animal tree of life Nature 452 745 749 18322464 10.1038/nature06614 1:CAS:528:DC%2BD1cXksFSju7k%3D
-
(2008)
Nature
, vol.452
, pp. 745-749
-
-
Dunn, C.W.1
Hejnol, A.2
Matus, D.Q.3
Pang, K.4
Browne, W.E.5
Smith, S.A.6
Seaver, E.7
Rouse, G.W.8
Obst, M.9
Edgecombe, G.D.10
-
7
-
-
36248988972
-
Mammalian karyotype evolution
-
DOI 10.1038/nrg2199, PII NRG2199
-
MA Ferguson-Smith V Trifonov 2007 Mammalian karyotype evolution Nat Rev Genet 8 950 962 18007651 10.1038/nrg2199 1:CAS:528:DC%2BD2sXhtlajtrbM (Pubitemid 350129170)
-
(2007)
Nature Reviews Genetics
, vol.8
, Issue.12
, pp. 950-962
-
-
Ferguson-Smith, M.A.1
Trifonov, V.2
-
8
-
-
0034001912
-
Using the past to predict the present: Confidence intervals for regression equations in phylogenetic comparative methods
-
DOI 10.1086/303327
-
TJ Garland AR Ives 2000 Using the past to predict the present: confidence intervals for regression equations in phylogenetic comparative methods Am Nat 155 346 364 10.1086/303327 (Pubitemid 30218224)
-
(2000)
American Naturalist
, vol.155
, Issue.3
, pp. 346-364
-
-
Garland Jr., T.1
Ives, A.R.2
-
9
-
-
23944504276
-
Synergy between sequence and size in large-scale genomics
-
DOI 10.1038/nrg1674
-
RT Gregory 2005 Synergy between sequence and size in the study of genomes Nat Rev Genet 6 699 708 16151375 10.1038/nrg1674 1:CAS:528:DC%2BD2MXps1erurw%3D (Pubitemid 41192321)
-
(2005)
Nature Reviews Genetics
, vol.6
, Issue.9
, pp. 699-708
-
-
Gregory, T.R.1
-
10
-
-
33748566229
-
Comparative genomics in prokaryotes
-
R.T. Gregory (eds). Elsevier San Diego, CA
-
Gregory RT, DeSalle R (2005) Comparative genomics in prokaryotes. In: Gregory RT (ed) The evolution of the genome. Elsevier, San Diego, CA, pp 585-675
-
(2005)
The Evolution of the Genome
, pp. 585-675
-
-
Gregory, R.T.1
Desalle, R.2
-
11
-
-
0242578620
-
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
-
DOI 10.1080/10635150390235520
-
S Guindon O Gascuel 2003 PhyML - A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst Biol 52 5 696 704 14530136 10.1080/10635150390235520 (Pubitemid 37365050)
-
(2003)
Systematic Biology
, vol.52
, Issue.5
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
12
-
-
27144552990
-
Identification of large ancient duplications associated with human gene deserts
-
DOI 10.1038/ng1648, PII N1648
-
T Itoh A Toyoda TD Taylor Y Sakaki M Hattori 2005 Identification of large ancient duplications associated with human gene deserts Nat Genet 37 1041 1043 16186813 10.1038/ng1648 1:CAS:528:DC%2BD2MXhtVCntLzM (Pubitemid 41486654)
-
(2005)
Nature Genetics
, vol.37
, Issue.10
, pp. 1041-1043
-
-
Itoh, T.1
Toyoda, A.2
Taylor, T.D.3
Sakaki, Y.4
Hattori, M.5
-
13
-
-
0037250168
-
The UCSC Genome Browser Database
-
DOI 10.1093/nar/gkg129
-
D Karolchik R Baertsch M Diekhans TS Furey A Hinrichs YT Lu KM Roskin M Schwartz CW Sugnet DJ Thomas, et al. 2003 The UCSC Genome Browser Database Nucleic Acids Res 31 51 54 12519945 10.1093/nar/gkg129 1:CAS:528: DC%2BD3sXhvFSgu7g%3D (Pubitemid 36150331)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, pp. 51-54
-
-
Karolchik, D.1
Baertsch, R.2
Diekhans, M.3
Furey, T.S.4
Hinrichs, A.5
Lu, Y.T.6
Roskin, K.M.7
Schwartz, M.8
Sugnet, C.W.9
Thomas, D.J.10
Weber, R.J.11
Haussler, D.12
Kent, W.J.13
-
14
-
-
33645816587
-
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
-
16563161 10.1186/1471-2148-6-29
-
TM Keane CJ Creevey MM Pentony TJ Naughton JO McInerney 2006 Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified BMC Evol Biol 6 29 16563161 10.1186/1471-2148-6-29
-
(2006)
BMC Evol Biol
, vol.6
, pp. 29
-
-
Keane, T.M.1
Creevey, C.J.2
Pentony, M.M.3
Naughton, T.J.4
McInerney, J.O.5
-
15
-
-
0036021699
-
Transposable elements and the evolution of genome size in eukaryotes
-
DOI 10.1023/A:1016072014259
-
MG Kidwell 2002 Transposable elements and the evolution of genome size in eukaryotes Genetica 115 49 63 12188048 10.1023/A:1016072014259 1:CAS:528:DC%2BD38XkvVaisLY%3D (Pubitemid 34842170)
-
(2002)
Genetica
, vol.115
, Issue.1
, pp. 49-63
-
-
Kidwell, M.G.1
-
16
-
-
0037015621
-
The Plasmodium genome database
-
12368860 10.1038/419490a 1:CAS:528:DC%2BD38XnsFaisr0%3D
-
JC Kissinger BP Brunk J Crabtree MJ Fraunholz B Gajria AJ Milgram DS Pearson J Schug A Bahl SJ Diskin, et al. 2002 The Plasmodium genome database Nature 419 490 492 12368860 10.1038/419490a 1:CAS:528:DC%2BD38XnsFaisr0%3D
-
(2002)
Nature
, vol.419
, pp. 490-492
-
-
Kissinger, J.C.1
Brunk, B.P.2
Crabtree, J.3
Fraunholz, M.J.4
Gajria, B.5
Milgram, A.J.6
Pearson, D.S.7
Schug, J.8
Bahl, A.9
Diskin, S.J.10
-
17
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
DOI 10.1038/35057062
-
ES Lander LM Linton B Birren C Nusbaum MC Zody J Baldwin K Devon K Dewar M Doyle W FitzHugh, et al. 2001 Initial sequencing and analysis of the human genome Nature 409 860 921 11237011 10.1038/35057062 1:CAS:528: DC%2BD3MXhsFCjtLc%3D (Pubitemid 32165345)
-
(2001)
Nature
, vol.409
, Issue.6822
, pp. 860-921
-
-
Lander, E.S.1
Linton, L.M.2
Birren, B.3
Nusbaum, C.4
Zody, M.C.5
Baldwin, J.6
Devon, K.7
Dewar, K.8
Doyle, M.9
Fitzhugh, W.10
-
18
-
-
34248159030
-
Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
-
DOI 10.1186/1471-2148-7-S1-S4
-
N Lartillot H Brinkmann H Philippe 2007 Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model BMC Evol Biol 7 Suppl. 1 S4 17288577 10.1186/1471-2148-7-S1-S4 (Pubitemid 351826841)
-
(2007)
BMC Evolutionary Biology
, vol.7
, Issue.SUPPL. 1
-
-
Lartillot, N.1
Brinkmann, H.2
Philippe, H.3
-
19
-
-
28644447707
-
Genome sequence, comparative analysis and haplotype structure of the domestic dog
-
DOI 10.1038/nature04338
-
K Lindblad-Toh CM Wade TS Mikkelsen EK Karlsson DB Jaffe M Kamal M Clamp JL Chang EJ Kulbokas 3rd MC Zody, et al. 2005 Genome sequence, comparative analysis and haplotype structure of the domestic dog Nature 438 803 819 16341006 10.1038/nature04338 1:CAS:528:DC%2BD2MXht1yns7%2FF (Pubitemid 41753059)
-
(2005)
Nature
, vol.438
, Issue.7069
, 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
Mauceli, E.11
Xie, X.12
Breen, M.13
Wayne, R.K.14
Ostrander, E.A.15
Ponting, C.P.16
Galibert, F.17
Smith, D.R.18
DeJong, P.J.19
Kirkness, E.20
Alvarez, P.21
Biagi, T.22
Brockman, W.23
Butler, J.24
Chin, C.-W.25
Cook, A.26
Cuff, J.27
Daly, M.J.28
DeCaprio, D.29
Gnerre, S.30
Grabherr, M.31
Kellis, M.32
Kleber, M.33
Bardeleben, C.34
Goodstadt, L.35
Heger, A.36
Hitte, C.37
Kim, L.38
Koepfli, K.-P.39
Parker, H.G.40
Pollinger, J.P.41
Searle, S.M.J.42
Sutter, N.B.43
Thomas, R.44
Webber, C.45
Lander, E.S.46
more..
-
21
-
-
0345306751
-
The Origins of Genome Complexity
-
DOI 10.1126/science.1089370
-
M Lynch JS Conery 2003 The origins of genome complexity Science 302 1401 1404 14631042 10.1126/science.1089370 1:CAS:528:DC%2BD3sXptVGjsrs%3D (Pubitemid 37452183)
-
(2003)
Science
, vol.302
, Issue.5649
, pp. 1401-1404
-
-
Lynch, M.1
Conery, J.S.2
-
23
-
-
5144226813
-
Sequence composition and genome organization of maize
-
DOI 10.1073/pnas.0406163101
-
J Messing AK Bharti WM Karlowski H Gundlach HR Kim Y Yu F Wei G Fuks CA Soderlund KF Mayer, et al. 2004 Sequence composition and genome organization of maize Proc Natl Acad Sci U S A 101 14349 14354 15388850 10.1073/pnas.0406163101 1:CAS:528:DC%2BD2cXovVertL0%3D (Pubitemid 39346752)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.40
, pp. 14349-14354
-
-
Messing, J.1
Bharti, A.K.2
Karlowski, W.M.3
Gundlach, H.4
Hye, R.K.5
Yu, Y.6
Wei, F.7
Fuks, G.8
Soderlund, C.A.9
Mayer, K.F.X.10
Wing, R.A.11
-
24
-
-
34248576291
-
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
-
DOI 10.1038/nature05805, PII NATURE05805
-
TS Mikkelsen MJ Wakefield B Aken CT Amemiya JL Chang S Duke M Garber AJ Gentles L Goodstadt A Heger, et al. 2007 Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences Nature 447 167 177 17495919 10.1038/nature05805 1:CAS:528:DC%2BD2sXltVGrsLw%3D (Pubitemid 46763085)
-
(2007)
Nature
, vol.447
, Issue.7141
, pp. 167-177
-
-
Mikkelsen, T.S.1
Wakefield, M.J.2
Aken, B.3
Amemiya, C.T.4
Chang, J.L.5
Duke, S.6
Garber, M.7
Gentles, A.J.8
Goodstadt, L.9
Heger, A.10
-
25
-
-
4944260940
-
The regulatory content of intergenic DNA shapes genome architecture
-
15059258 10.1186/gb-2004-5-4-r25
-
CE Nelson BM Hersh SB Carroll 2004 The regulatory content of intergenic DNA shapes genome architecture Genome Biol 5 R25 15059258 10.1186/gb-2004-5-4- r25
-
(2004)
Genome Biol
, vol.5
, pp. 25
-
-
Nelson, C.E.1
Hersh, B.M.2
Carroll, S.B.3
-
26
-
-
0142084743
-
Scanning Human Gene Deserts for Long-Range Enhancers
-
DOI 10.1126/science.1088328
-
MA Nobrega I Ovcharenko V Afzal EM Rubin 2003 Scanning human gene deserts for long-range enhancers Science 302 413 14563999 10.1126/science.1088328 1:CAS:528:DC%2BD3sXotlSns74%3D (Pubitemid 37296259)
-
(2003)
Science
, vol.302
, Issue.5644
, pp. 413
-
-
Nobrega, M.A.1
Ovcharenko, I.2
Afzal, V.3
Rubin, E.M.4
-
27
-
-
7244259100
-
Megabase deletions of gene deserts result in viable mice
-
DOI 10.1038/nature03022
-
MA Nobrega Y Zhu I Plajzer-Frick V Afzal EM Rubin 2004 Megabase deletions of gene deserts result in viable mice Nature 431 988 993 15496924 10.1038/nature03022 1:CAS:528:DC%2BD2cXoslSlt7k%3D (Pubitemid 39434420)
-
(2004)
Nature
, vol.431
, Issue.7011
, pp. 988-993
-
-
Nobrega, M.A.1
Zhu, Y.2
Plajer-Frick, I.3
Afzal, Y.4
Rubin, E.M.5
-
28
-
-
0002335754
-
Dispensable genes
-
10.1016/0168-9525(85)90070-8 1:CAS:528:DyaL2MXlslensrw%3D
-
S Ohno 1985 Dispensable genes Trends Genet 1 160 164 10.1016/0168- 9525(85)90070-8 1:CAS:528:DyaL2MXlslensrw%3D
-
(1985)
Trends Genet
, vol.1
, pp. 160-164
-
-
Ohno, S.1
-
29
-
-
12744261452
-
Evolution and functional classification of vertebrate gene deserts
-
15590943 10.1101/gr.3015505 1:CAS:528:DC%2BD2MXlsVSrtQ%3D%3D
-
I Ovcharenko GG Loots MA Nobrega RC Hardison W Miller L Stubbs 2005 Evolution and functional classification of vertebrate gene deserts Genome Res 15 137 145 15590943 10.1101/gr.3015505 1:CAS:528:DC%2BD2MXlsVSrtQ%3D%3D
-
(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
-
30
-
-
22144473057
-
Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
-
DOI 10.1186/1471-2164-5-99
-
A Sandelin P Bailey S Bruce PG Engstrom JM Klos WW Wasserman J Ericson B Lenhard 2004 Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes BMC Genomics 5 99 15613238 10.1186/1471-2164-5-99 (Pubitemid 41357634)
-
(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
-
31
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
DOI 10.1101/gr.3715005
-
A Siepel G Bejerano JS Pedersen AS Hinrichs M Hou K Rosenbloom H Clawson J Spieth LW Hillier S Richards, et al. 2005 Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes Genome Res 15 1034 1050 16024819 10.1101/gr.3715005 1:CAS:528:DC%2BD2MXotFaht7o%3D (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
-
32
-
-
19444364990
-
Clues to function in gene deserts
-
DOI 10.1016/j.tibtech.2005.04.003, PII S0167779905000879
-
J Taylor 2005 Clues to function in gene deserts Trends Biotechnol 23 269 271 15922077 10.1016/j.tibtech.2005.04.003 1:CAS:528:DC%2BD2MXks1Cnu7o%3D (Pubitemid 40726266)
-
(2005)
Trends in Biotechnology
, vol.23
, Issue.6
, pp. 269-271
-
-
Taylor, J.1
-
33
-
-
0035895505
-
The sequence of the human genome
-
DOI 10.1126/science.1058040
-
JC Venter MD Adams EW Myers PW Li RJ Mural GG Sutton HO Smith M Yandell CA Evans RA Holt, et al. 2001 The sequence of the human genome Science 291 1304 1351 11181995 10.1126/science.1058040 1:CAS:528:DC%2BD3MXhtlSgsbo%3D (Pubitemid 32173090)
-
(2001)
Science
, vol.291
, Issue.5507
, pp. 1304-1351
-
-
Craig Venter, J.1
Adams, M.D.2
Myers, E.W.3
Li, P.W.4
Mural, R.J.5
Sutton, G.G.6
Smith, H.O.7
Yandell, M.8
Evans, C.A.9
Holt, R.A.10
Gocayne, J.D.11
Amanatides, P.12
Ballew, R.M.13
Huson, D.H.14
Wortman, J.R.15
Zhang, Q.16
Kodira, C.D.17
Zheng, X.H.18
Chen, L.19
Skupski, M.20
Subramanian, G.21
Thomas, P.D.22
Zhang, J.23
Gabor Miklos, G.L.24
Nelson, C.25
Broder, S.26
Clark, A.G.27
Nadeau, J.28
McKusick, V.A.29
Zinder, N.30
Levine, A.J.31
Roberts, R.J.32
Simon, M.33
Slayman, C.34
Hunkapiller, M.35
Bolanos, R.36
Delcher, A.37
Dew, I.38
Fasulo, D.39
Flanigan, M.40
Florea, L.41
Halpern, A.42
Hannenhalli, S.43
Kravitz, S.44
Levy, S.45
Mobarry, C.46
Reinert, K.47
Remington, K.48
Abu-Threideh, J.49
Beasley, E.50
Biddick, K.51
Bonazzi, V.52
Brandon, R.53
Cargill, M.54
Chandramouliswaran, I.55
Charlab, R.56
Chaturvedi, K.57
Deng, Z.58
Di Francesco, V.59
Dunn, P.60
Eilbeck, K.61
Evangelista, C.62
Gabrielian, A.E.63
Gan, W.64
Ge, W.65
Gong, F.66
Gu, Z.67
Guan, P.68
Heiman, T.J.69
Higgins, M.E.70
Ji, R.-R.71
Ke, Z.72
Ketchum, K.A.73
Lai, Z.74
Lei, Y.75
Li, Z.76
Li, J.77
Liang, Y.78
Lin, X.79
Lu, F.80
Merkulov, G.V.81
Milshina, N.82
Moore, H.M.83
Naik, A.K.84
Narayan, V.A.85
Neelam, B.86
Nusskern, D.87
Rusch, D.B.88
Salzberg, S.89
Shao, W.90
Shue, B.91
Sun, J.92
Zhen Yuan Wang93
Wang, A.94
Wang, X.95
Wang, J.96
Wei, M.-H.97
Wides, R.98
Xiao, C.99
more..
-
34
-
-
33646876182
-
Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between the two kingdoms
-
DOI 10.1093/molbev/msk019
-
L Xu H Chen X Hu R Zhang Z Zhang ZW Luo 2006 Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between the two kingdoms Mol Biol Evol 23 1107 1108 16611645 10.1093/molbev/msk019 1:CAS:528:DC%2BD28XlsVGqtbo%3D (Pubitemid 43781585)
-
(2006)
Molecular Biology and Evolution
, vol.23
, Issue.6
, pp. 1107-1108
-
-
Xu, L.1
Chen, H.2
Hu, X.3
Zhang, R.4
Zhang, Z.5
Luo, Z.W.6
|