-
1
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
DOI 10.1038/nature05874, PII NATURE05874
-
Birney E, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816. (Pubitemid 46920138)
-
(2007)
Nature
, vol.447
, Issue.7146
, pp. 799-816
-
-
Birney, E.1
Stamatoyannopoulos, J.A.2
Dutta, A.3
Guigo, R.4
Gingeras, T.R.5
Margulies, E.H.6
Weng, Z.7
Snyder, M.8
Dermitzakis, E.T.9
Thurman, R.E.10
Kuehn, M.S.11
Taylor, C.M.12
Neph, S.13
Koch, C.M.14
Asthana, S.15
Malhotra, A.16
Adzhubei, I.17
Greenbaum, J.A.18
Andrews, R.M.19
Flicek, P.20
Boyle, P.J.21
Cao, H.22
Carter, N.P.23
Clelland, G.K.24
Davis, S.25
Day, N.26
Dhami, P.27
Dillon, S.C.28
Dorschner, M.O.29
Fiegler, H.30
Giresi, P.G.31
Goldy, J.32
Hawrylycz, M.33
Haydock, A.34
Humbert, R.35
James, K.D.36
Johnson, B.E.37
Johnson, E.M.38
Frum, T.T.39
Rosenzweig, E.R.40
Karnani, N.41
Lee, K.42
Lefebvre, G.C.43
Navas, P.A.44
Neri, F.45
Parker, S.C.J.46
Sabo, P.J.47
Sandstrom, R.48
Shafer, A.49
Vetrie, D.50
Weaver, M.51
Wilcox, S.52
Yu, M.53
Collins, F.S.54
Dekker, J.55
Lieb, J.D.56
Tullius, T.D.57
Crawford, G.E.58
Sunyaev, S.59
Noble, W.S.60
Dunham, I.61
Denoeud, F.62
Reymond, A.63
Kapranov, P.64
Rozowsky, J.65
Zheng, D.66
Castelo, R.67
Frankish, A.68
Harrow, J.69
Ghosh, S.70
Sandelin, A.71
Hofacker, I.L.72
Baertsch, R.73
Keefe, D.74
Dike, S.75
Cheng, J.76
Hirsch, H.A.77
Sekinger, E.A.78
Lagarde, J.79
Abril, J.F.80
Shahab, A.81
Flamm, C.82
Fried, C.83
Hackermuller, J.84
Hertel, J.85
Lindemeyer, M.86
Missal, K.87
Tanzer, A.88
Washietl, S.89
Korbel, J.90
Emanuelsson, O.91
Pedersen, J.S.92
Holroyd, N.93
Taylor, R.94
Swarbreck, D.95
Matthews, N.96
Dickson, M.C.97
Thomas, D.J.98
Weirauch, M.T.99
more..
-
2
-
-
21044431735
-
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
-
DOI 10.1126/science.1108625
-
Cheng J, et al. (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308:1149-1154. (Pubitemid 40696429)
-
(2005)
Science
, vol.308
, Issue.5725
, pp. 1149-1154
-
-
Cheng, J.1
Kapranov, P.2
Drenkow, J.3
Dike, S.4
Brubaker, S.5
Patel, S.6
Long, J.7
Stern, D.8
Tammana, H.9
Helt, G.10
Sementchenko, V.11
Piccolboni, A.12
Bekiranov, S.13
Bailey, D.K.14
Ganesh, M.15
Ghosh, S.16
Bell, I.17
Gerhard, D.S.18
Gingeras, T.R.19
-
3
-
-
62449130191
-
Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions
-
Sims GE, Jun SR, Wu GA, Kim SH (2009) Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proc Natl Acad Sci USA 106:2677-2682.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 2677-2682
-
-
Sims, G.E.1
Jun, S.R.2
Wu, G.A.3
Kim, S.H.4
-
4
-
-
0242662461
-
Evolutionary discrimination of mammalian conserved nongenic sequences (CNGs)
-
Dermitzakis ET, et al. (2003) Evolutionary discrimination of mammalian conserved nongenic sequences (CNGs). Science 302:1033-1035.
-
(2003)
Science
, vol.302
, pp. 1033-1035
-
-
Dermitzakis, E.T.1
-
5
-
-
33646255212
-
Retroposed elements as archives for the evolutionary history of placental mammals
-
Kriegs JO, et al. (2006) Retroposed elements as archives for the evolutionary history of placental mammals. PLoS Biol 4:e91.
-
(2006)
PLoS Biol
, vol.4
-
-
Kriegs, J.O.1
-
6
-
-
33846552919
-
Early history of mammals is elucidated with the ENCODE multiple species sequencing data
-
DOI 10.1371/journal.pgen.0030002
-
Nikolaev S, et al. (2007) Early history of mammals is elucidated with the encode multiple species sequencing data. PloS Genetics 5:e2. (Pubitemid 46168828)
-
(2007)
PLoS Genetics
, vol.3
, Issue.1
, pp. 3-8
-
-
Nikolaev, S.1
Montoya-Burgos, J.I.2
Margulies, E.H.3
Bouffard, G.G.4
Idol, J.R.5
Maduro, V.V.B.6
Blakesley, R.W.7
Guan, X.8
Hansen, N.F.9
Maskeri, B.10
McDowell, J.C.11
Park, M.12
Thomas, P.J.13
Young, A.C.14
Rougemont, J.15
Nyffeler, B.16
Antonarakis, S.E.17
-
7
-
-
0034826388
-
Maximum likelihood analysis of the complete mitochondrial genomes eutherians and a reevaluation of the phylogeny of bats and insectivores
-
DOI 10.1007/s002390010241
-
Nikaido M, et al. (2001) Maximum likelihood analysis of the complete mitochondrial genomes of eutherians and a reevalution of the phylogeny of bats and insectivores. J Mol Evol 53:508-516. (Pubitemid 32889559)
-
(2001)
Journal of Molecular Evolution
, vol.53
, Issue.4-5
, pp. 508-516
-
-
Nikaido, M.1
Kawai, K.2
Cao, Y.3
Harada, M.4
Tomita, S.5
Okada, N.6
Hasegawa, M.7
-
8
-
-
0035252080
-
Molecular phylogenetics and the origins of placental mammals
-
DOI 10.1038/35054550
-
Murphy WJ, et al. (2001) Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618. (Pubitemid 32154812)
-
(2001)
Nature
, vol.409
, Issue.6820
, pp. 614-618
-
-
Murphy, W.J.1
Eizirik, E.2
Johnson, W.E.3
Zhang, Y.P.4
Ryder, O.A.5
O'Brien, S.J.6
-
10
-
-
38549137819
-
PhylomeDB: A database for genome-wide collections of gene phylogenies
-
DOI 10.1093/nar/gkm899
-
Huerta-Cepas J, Bueno A, Dopazo J, Gabaldon T (2008) PhylomeDB: A database for genome-wide collections of gene phylogenies. Nucleic Acids Res 36:D491-D496. (Pubitemid 351149772)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Huerta-Cepas, J.1
Bueno, A.2
Dopazo, J.3
Gabaldon, T.4
-
11
-
-
49749129961
-
Confirming the phylogeny ofmammalsby the use of large comparative sequence data sets
-
Prasad AB, AllardMW(2008) Confirming the phylogeny ofmammalsby the use of large comparative sequence data sets. Mol Biol Evol 25:1795-1808.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 1795-1808
-
-
Prasad, A.B.1
Allard, M.W.2
-
12
-
-
58149178565
-
The UCSC genome browser database: 2008 update
-
Kuhn RM, et al. (2008) The UCSC genome browser database: 2008 update. Nucleic Acids Res 37:D755-D761.
-
(2008)
Nucleic Acids Res
, vol.37
-
-
Kuhn, R.M.1
-
13
-
-
0026458222
-
Freeing phylogenies from artifacts of alignment
-
Thorne JL, Kishino H (1992) Freeing phylogenies from artifacts of alignment. Mol Biol Evol 9:1148-1162.
-
(1992)
Mol Biol Evol
, vol.9
, pp. 1148-1162
-
-
Thorne, J.L.1
Kishino, H.2
-
14
-
-
34147184456
-
Using genomic data to unravel the root of the placental mammal phylogeny
-
Murphy WJ, Pringle TH, Crider TA, Springer MS,MillerW(2007) Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res 17:413-421.
-
(2007)
Genome Res
, vol.17
, pp. 413-421
-
-
Murphy, W.J.1
Pringle, T.H.2
Crider, T.A.3
Springer, M.S.4
Miller, W.5
-
16
-
-
33847644967
-
Indel evolution of mammalian introns and the utility of noncoding nuclear markers in eutherian phylogenetics
-
Matthee CA, et al. (2007) Indel evolution of mammalian introns and the utility of noncoding nuclear markers in eutherian phylogenetics. Mol Phylogenet Evol 42:827-837.
-
(2007)
Mol Phylogenet Evol
, vol.42
, pp. 827-837
-
-
Matthee, C.A.1
-
17
-
-
0036853613
-
Sequence gaps join mice and men: Phylogenetic evidence from deletions in two proteins
-
Poux C, van Rheede T,MadsenO, de JongWW(2002) Sequence gaps join mice and men: Phylogenetic evidence from deletions in two proteins. Mol Biol Evol 19:2035-2037.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 2035-2037
-
-
Poux, C.1
Van Rheede, T.2
Madsen, O.3
De Jong, W.W.4
-
18
-
-
34547609849
-
Evolutionary history of mammalian transposons determined by genome-wide defragmentation
-
DOI 10.1371/journal.pcbi.0030137
-
Giordano J, et al. (2007) Evolutionary history of mammalian transposons determined by genome-wide defragmentations. PLoS Comp Biol 3:e137. (Pubitemid 47196173)
-
(2007)
PLoS Computational Biology
, vol.3
, Issue.7
, pp. 1321-1334
-
-
Giordano, J.1
Ge, Y.2
Gelfand, Y.3
Abrusan, G.4
Benson, G.5
Warburton, P.E.6
-
19
-
-
0041465867
-
Comparative analyses of multi-species sequences from targeted genomic regions
-
DOI 10.1038/nature01858
-
Thomas JW, et al. (2003) Comparative analyses of multi-species sequence from targeted genomic regions. Nature 424:788-793. (Pubitemid 37021709)
-
(2003)
Nature
, vol.424
, Issue.6950
, pp. 788-793
-
-
Thomas, J.W.1
Touchman, J.W.2
Blakesley, R.W.3
Bouffard, G.G.4
Beckstrom-Sternberg, S.M.5
Margulies, E.H.6
Blanchette, M.7
Siepel, A.C.8
Thomas, P.J.9
McDowell, J.C.10
Maskeri, B.11
Hansen, N.F.12
Schwartz, M.S.13
Weber, R.J.14
Kent, W.J.15
Karolchik, D.16
Bruen, T.C.17
Bevan, R.18
Cutler, D.J.19
Schwartz, S.20
Elnitski, L.21
Idol, J.R.22
Prasad, A.B.23
Lee-Lin, S.-Q.24
Maduro, V.V.B.25
Summers, T.J.26
Portnoy, M.E.27
Dietrich, N.L.28
Akhter, N.29
Ayele, K.30
Benjamin, B.31
Cariaga, K.32
Brinkley, C.P.33
Brooks, S.Y.34
Granite, S.35
Guan, X.36
Gupta, J.37
Haghighi, P.38
Ho, S.-L.39
Huang, M.C.40
Karlins, E.41
Laric, P.L.42
Legaspi, R.43
Lim, M.J.44
Maduro, Q.L.45
Masiello, C.A.46
Mastrian, S.D.47
McCloskey, J.C.48
Pearson, R.49
Stantripop, S.50
Tiongson, E.E.51
Tran, J.T.52
Tsurgeon, C.53
Vogt, J.L.54
Walker, M.A.55
Wetherby, K.D.56
Wiggins, L.S.57
Young, A.C.58
Zhang, L.-H.59
Osoegawa, K.60
Zhu, B.61
Zhao, B.62
Shu, C.L.63
De Jong, P.J.64
Lawrence, C.E.65
Smit, A.F.66
Chakravarti, A.67
Haussler, D.68
Green, P.69
Miller, W.70
Green, E.D.71
more..
-
20
-
-
23944505784
-
Aretroposon analysis of Afrotherian phylogeny
-
Nishihara H, et al. (2005)Aretroposon analysis of Afrotherian phylogeny. Mol Biol Evol 22:1823-1833.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1823-1833
-
-
Nishihara, H.1
-
21
-
-
0033964296
-
SINE insertions: Powerful tools for molecular systematics
-
DOI 10.1002/(SICI)1521-1878(200002)22:2<148::AID-BIES6>3.0.CO;2-Z
-
ShedlockAM,OkadaN(2000) SINE insertions: Powerful tools for molecular systematics. Bioessays 22:148-160. (Pubitemid 30092081)
-
(2000)
BioEssays
, vol.22
, Issue.2
, pp. 148-160
-
-
Shedlock, A.M.1
Okada, N.2
-
22
-
-
0033793019
-
Rare genomic changes as a tool for phylogenetics
-
Rokas A, HollandPWH(2000) Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol 11:454-459.
-
(2000)
Trends Ecol Evol
, vol.11
, pp. 454-459
-
-
Rokas, A.1
Holland, P.W.H.2
-
25
-
-
0019951634
-
Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences
-
DOI 10.1038/297197a0
-
Penny D, Foulds LR, Hendy MD (1982) Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences. Nature 297:197-200. (Pubitemid 12066444)
-
(1982)
Nature
, vol.297
, Issue.5863
, pp. 197-200
-
-
Penny, D.1
Foulds, L.R.2
Hendy, M.D.3
-
28
-
-
13144295005
-
Conserved non-genic sequences - An unexpected feature of mammalian genomes
-
DOI 10.1038/nrg1527
-
Dermitzakis ET, Reymond A, Antonarakis SE (2005) Conserved nongenic sequences: An unexpected feature of mammalian genomes. Nat Rev Genet 6:151-157. (Pubitemid 40179538)
-
(2005)
Nature Reviews Genetics
, vol.6
, Issue.2
, pp. 151-157
-
-
Dermitzakis, E.T.1
Reymond, A.2
Antonarakis, S.E.3
-
29
-
-
33748068074
-
Housekeeping genes for phylogenetic analysis of eutherian relationships
-
DOI 10.1093/molbev/msl027
-
Kullberg M, Nilsson MA, Arnason U, Harley EH, Janke A (2006) Houskeeping genes for phylogenetic analysis of eutherian relationships. Mol Biol Evol 23:1493-1503. (Pubitemid 44297408)
-
(2006)
Molecular Biology and Evolution
, vol.23
, Issue.8
, pp. 1493-1503
-
-
Kullberg, M.1
Nilsson, M.A.2
Arnason, U.3
Harley, E.H.4
Janke, A.5
-
30
-
-
0141832717
-
Revisiting the Glires concept - Phylogenetic analysis of nuclear sequences
-
DOI 10.1016/S1055-7903(03)00079-4
-
Misawa K, Janke A (2003) Revisting the Glires concept - phylogenetic analysis of nuclear sequences. Mol Phylogenet Evol 28:320-327. (Pubitemid 37435997)
-
(2003)
Molecular Phylogenetics and Evolution
, vol.28
, Issue.2
, pp. 320-327
-
-
Misawa, K.1
Janke, A.2
-
31
-
-
66049158304
-
Breakpoint graphs and ancestral genome reconstructions
-
Max A. Alekseyev and Pavel A. Pevzner (2009) Breakpoint graphs and ancestral genome reconstructions. Genome Res 19: 943-957.
-
(2009)
Genome Res
, vol.19
, pp. 943-957
-
-
Alekseyev, M.A.1
Pevzner, P.A.2
-
32
-
-
84959798530
-
Cases in which parsimony or compatibility methods will be positively misleading
-
Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27:401-410.
-
(1978)
Syst Zool
, vol.27
, pp. 401-410
-
-
Felsenstein, J.1
-
33
-
-
0033921902
-
Rates of conservation and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes
-
Zhang J (2000) Rates of conservation and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes. J Mol Evol 50:56-68.
-
(2000)
J Mol Evol
, vol.50
, pp. 56-68
-
-
Zhang, J.1
-
36
-
-
0004327233
-
-
Johns Hopkins Univ Press, Baltimore, 5th Ed
-
Nowak, RM (1990) Walker's Mammals of the World (Johns Hopkins Univ Press, Baltimore), 5th Ed, Vol 1.
-
(1990)
Walker's Mammals of the World
, vol.1
-
-
Nowak, R.M.1
-
37
-
-
3042550872
-
Genome-scale phylogeny and the detection of systematic biases
-
DOI 10.1093/molbev/msh137
-
Phillips MJ, Delsuc F, Penny D (2004) Genome-scale phylogeny and the detection of systematic biases. Mol Biol Evol 21:1455-1458. (Pubitemid 38823748)
-
(2004)
Molecular Biology and Evolution
, vol.21
, Issue.7
, pp. 1455-1458
-
-
Phillips, M.J.1
Delsuc, F.2
Penny, D.3
-
38
-
-
0025952777
-
Archael phylogeny: Reexamination of the phylogenetic position of archaeoglobus fulgidus in light of certain composition-induced artifacts
-
Woese CR Achenbach L, Rouviere P, Madelco L (1991) Archael phylogeny: Reexamination of the phylogenetic position of archaeoglobus fulgidus in light of certain composition-induced artifacts. Syst Appl Microbiol 14:364-371.
-
(1991)
Syst Appl Microbiol
, vol.14
, pp. 364-371
-
-
Woese, C.R.1
Achenbach, L.2
Rouviere, P.3
Madelco, L.4
-
39
-
-
0030829126
-
Effect of nucleotides excision repair on hprt gene mutations in rodent cells exposed to DNA ethylating agents
-
Op het Veld CW, Van Hees-Stuivenberg S, van Zeeland AA, Jansen JG (1997) Effect of nucleotides excision repair on hprt gene mutations in rodent cells exposed to DNA ethylating agents. Mutagenesis 12:417-424.
-
(1997)
Mutagenesis
, vol.12
, pp. 417-424
-
-
Op Het Veld, C.W.1
Van Hees-Stuivenberg, S.2
Van Zeeland, A.A.3
Jansen, J.G.4
-
40
-
-
0028343610
-
Rate of transition and transversion in coding sequences since the human-rodent divergence
-
Collins DW, Jukes TH (1994) Rate of transition and transversion in coding sequences since the human-rodent divergence. Genomics 20:386-396.
-
(1994)
Genomics
, vol.20
, pp. 386-396
-
-
Collins, D.W.1
Jukes, T.H.2
-
41
-
-
0027500136
-
Ribosomal RNA secondary structure: Compensatory mutations and implications for phylogenetic analysis
-
Dixon MT, Hillis DM (1993) Ribosomal RNA secondary structure: Compensatory mutations and implications for phylogenetic analysis. Mol Biol Evol 10:256-267. (Pubitemid 23040235)
-
(1993)
Molecular Biology and Evolution
, vol.10
, Issue.1
, pp. 256-267
-
-
Dixon, M.T.1
Hillis, D.M.2
-
43
-
-
54149110091
-
Distance conservation of transcription regulatory motifs in human promoters
-
Lu J, Luo L, Zhang Y (2008) Distance conservation of transcription regulatory motifs in human promoters. Comp Biol Chem 23:433-437.
-
(2008)
Comp Biol Chem
, vol.23
, pp. 433-437
-
-
Lu, J.1
Luo, L.2
Zhang, Y.3
-
44
-
-
0035252569
-
Parallel adaptive radiations in two major clades of placental mammals
-
DOI 10.1038/35054544
-
Madsen O, et al. (2001) Parallel adaptive radiations in two major clades of placental mammals. Nature 409:610-614. (Pubitemid 32154811)
-
(2001)
Nature
, vol.409
, Issue.6820
, pp. 610-614
-
-
Madsen, O.1
Scally, M.2
Douady, C.J.3
Kao, D.J.4
Debry, R.W.5
Adkins, R.6
Amrine, H.M.7
Stanhope, M.J.8
De Jong, W.W.9
Springer, M.S.10
-
45
-
-
0000122573
-
PHYLIP - Phylogeny inference package
-
Version 3.2
-
Felsenstein J (1989) PHYLIP - Phylogeny inference package (Version 3.2). Cladistics 5:164-166.
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
46
-
-
0019296687
-
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
-
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120.
-
(1980)
J Mol Evol
, vol.16
, pp. 111-120
-
-
Kimura, M.1
-
47
-
-
0023375195
-
The neighbor-joining method:Anewmethod for reconstructing phylogenetic trees
-
Saitou N, NeiM(1987) The neighbor-joining method:Anewmethod for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425.
-
(1987)
Mol Biol Evol
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
48
-
-
0019424782
-
Comparison of phylogenetic trees
-
Robinson DR, Foulds LR (1981) Comparison of phylogenetic trees. Math Biosci 53:131-147.
-
(1981)
Math Biosci
, vol.53
, pp. 131-147
-
-
Robinson, D.R.1
Foulds, L.R.2
|