-
1
-
-
0242659321
-
DNA sequence evolution with neighbor-dependent mutation
-
DOI 10.1089/10665270360688039
-
Arndt PF, Burge CB, Hwa T. 2003. DNA sequence evolution with neighbor-dependent mutation. J Comput Biol. 10:313-322. (Pubitemid 37372151)
-
(2003)
Journal of Computational Biology
, vol.10
, Issue.3-4
, pp. 313-322
-
-
Arndt, P.F.1
Burge, C.B.2
Hwa, T.3
-
2
-
-
19544383635
-
Identification and measurement of neighbor-dependent nucleotide substitution processes
-
DOI 10.1093/bioinformatics/bti376
-
Arndt PF, Hwa T. 2005. Identification and measurement of neighbordependent nucleotide substitution processes. Bioinformatics 21:2322-2328. (Pubitemid 40731586)
-
(2005)
Bioinformatics
, vol.21
, Issue.10
, pp. 2322-2328
-
-
Arndt, P.F.1
Hwa, T.2
-
3
-
-
53849128927
-
A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in non-coding sequences
-
Baele G, Van de Peer Y, Vansteelandt S. 2008. A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in non-coding sequences. Syst Biol. 57:675-692.
-
(2008)
Syst Biol
, vol.57
, pp. 675-692
-
-
Baele, G.1
Van De Peer, Y.2
Vansteelandt, S.3
-
4
-
-
77955013629
-
Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences
-
Baele G, Van de Peer Y, Vansteelandt S. 2010a. Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences. BMC Evol Biol. 10:244.
-
(2010)
BMC Evol Biol
, vol.10
, pp. 244
-
-
Baele, G.1
Van De Peer, Y.2
Vansteelandt, S.3
-
5
-
-
77955013327
-
Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences
-
Baele G, Van de Peer Y, Vansteelandt S. 2010b. Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences. J Mol Evol. 71:34-50.
-
(2010)
J Mol Evol
, vol.71
, pp. 34-50
-
-
Baele, G.1
Van De Peer, Y.2
Vansteelandt, S.3
-
6
-
-
28744439583
-
Pseudo-likelihood analysis of codon substitution models with neighbor-dependent rates
-
DOI 10.1089/cmb.2005.12.1166
-
Christensen OF, Hobolth A, Jensen JL. 2005. Pseudo-likelihood analysis of codon substitution models with neighbor-dependent rates. J Comput Biol. 12:1166-1182. (Pubitemid 41759888)
-
(2005)
Journal of Computational Biology
, vol.12
, Issue.9
, pp. 1166-1182
-
-
Christensen, O.F.1
Hobolth, A.2
Jensen, J.L.3
-
7
-
-
47149117454
-
Evolution of genes and genomes on the Drosophila phylogeny
-
DOI 10.1038/nature06341, PII NATURE06341
-
Clark AG, Eisen MB, Smith DR, et al. (150 co-authors). 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218. (Pubitemid 351972300)
-
(2007)
Nature
, vol.450
, Issue.7167
, pp. 203-218
-
-
Clark, A.G.1
Eisen, M.B.2
Smith, D.R.3
Bergman, C.M.4
Oliver, B.5
Markow, T.A.6
Kaufman, T.C.7
Kellis, M.8
Gelbart, W.9
Iyer, V.N.10
Pollard, D.A.11
Sackton, T.B.12
Larracuente, A.M.13
Singh, N.D.14
Abad, J.P.15
Abt, D.N.16
Adryan, B.17
Aguade, M.18
Akashi, H.19
Anderson, W.W.20
Aquadro, C.F.21
Ardell, D.H.22
Arguello, R.23
Artieri, C.G.24
Barbash, D.A.25
Barker, D.26
Barsanti, P.27
Batterham, P.28
Batzoglou, S.29
Begun, D.30
Bhutkar, A.31
Blanco, E.32
Bosak, S.A.33
Bradley, R.K.34
Brand, A.D.35
Brent, M.R.36
Brooks, A.N.37
Brown, R.H.38
Butlin, R.K.39
Caggese, C.40
Calvi, B.R.41
Bernardo De Carvalho, A.42
Caspi, A.43
Castrezana, S.44
Celniker, S.E.45
Chang, J.L.46
Chapple, C.47
Chatterji, S.48
Chinwalla, A.49
Civetta, A.50
Clifton, S.W.51
Comeron, J.M.52
Costello, J.C.53
Coyne, J.A.54
Daub, J.55
David, R.G.56
Delcher, A.L.57
Delehaunty, K.58
Do, C.B.59
Ebling, H.60
Edwards, K.61
Eickbush, T.62
Evans, J.D.63
Filipski, A.64
Findeiss, S.65
Freyhult, E.66
more..
-
8
-
-
79957577720
-
Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection
-
Cohen NM, Kenigsberg E, Tanay A. 2011. Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection. Cell 145:773-786.
-
(2011)
Cell
, vol.145
, pp. 773-786
-
-
Cohen, N.M.1
Kenigsberg, E.2
Tanay, A.3
-
9
-
-
78649420561
-
Mean field variational approximation for continuous-time Bayesian networks
-
Cohn I, El-Hay T, Friedman N, Kupferman R. 2010. Mean field variational approximation for continuous-time Bayesian networks. J Mach Learn Res. 11:2745-2783.
-
(2010)
J Mach Learn Res
, vol.11
, pp. 2745-2783
-
-
Cohn, I.1
El-Hay, T.2
Friedman, N.3
Kupferman, R.4
-
10
-
-
0038360789
-
TGF-β1-induced Smad 3 binding to the Smad 7 gene: Knockout of Smad 7 gene transcription by sense phosphorothioate oligos, autoregulation, and effect on TGF-β1 secretion: Bleomycin acts through TGF-β1
-
DOI 10.1002/jcb.10528
-
Cutroneo KR, Phan SH. 2003. TGF-beta1-induced Smad 3 binding to the Smad 7 gene:knockout of Smad 7 gene transcription by sense phosphorothioate oligos, autoregulation, and effect on TGF-beta1 secretion:bleomycin acts through TGF-beta1. J Cell Biochem. 89:474-483. (Pubitemid 36648769)
-
(2003)
Journal of Cellular Biochemistry
, vol.89
, Issue.3
, pp. 474-483
-
-
Cutroneo, K.R.1
Phan, S.H.2
-
11
-
-
3142756502
-
Open source clustering software
-
DOI 10.1093/bioinformatics/bth078
-
de Hoon MJ, Imoto S, Nolan J, Miyano S. 2004. Open source clustering software. Bioinformatics 20:1453-1454. (Pubitemid 38931415)
-
(2004)
Bioinformatics
, vol.20
, Issue.9
, pp. 1453-1454
-
-
De Hoon, M.J.L.1
Imoto, S.2
Nolan, J.3
Miyano, S.4
-
12
-
-
74549220350
-
Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories
-
de Koning AP, Gu W, Pollock DD. 2010. Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories. Mol Biol Evol. 27:249-265.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 249-265
-
-
De Koning, A.P.1
Gu, W.2
Pollock, D.D.3
-
13
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
DOI 10.1007/BF01734359
-
Felsenstein J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol. 17:368-376. (Pubitemid 11016207)
-
(1981)
Journal of Molecular Evolution
, vol.17
, Issue.6
, pp. 368-376
-
-
Felsenstein, J.1
-
14
-
-
78651320424
-
The UCSC Genome Browser database:update 2011
-
Fujita PA, Rhead B, Zweig AS, et al. (27 co-authors). 2010. The UCSC Genome Browser database:update 2011. Nucleic Acids Res. 39:D876-D882.
-
(2010)
Nucleic Acids Res
, vol.39
-
-
Fujita, P.A.1
Rhead, B.2
Zweig, A.S.3
-
16
-
-
4644300141
-
Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
-
DOI 10.1073/pnas.0404142101
-
Hwang DG, Green P. 2004. Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci U S A. 101:13994-14001. (Pubitemid 39305018)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.39
, pp. 13994-14001
-
-
Hwang, D.G.1
Green, P.2
-
17
-
-
24744445362
-
Efficient approximations for learning phylogenetic HMM models from data
-
DOI 10.1093/bioinformatics/bth917
-
Jojic V, Jojic N, Meek C, Geiger D, Siepel A, Haussler D, Heckerman D. 2004. Efficient approximations for learning phylogenetic HMM models from data. Bioinformatics 20(SUPPL. 1):i161-i168. (Pubitemid 41296685)
-
(2004)
Bioinformatics
, vol.20
, Issue.SUPPL. 1
-
-
Jojic, V.1
Jojic, N.2
Meek, C.3
Geiger, D.4
Siepel, A.5
Haussler, D.6
Heckerman, D.7
-
18
-
-
0033225865
-
Introduction to variational methods for graphical models
-
DOI 10.1023/A:1007665907178
-
Jordan MI, Ghahramani Z, Jaakkola TS, Saul LK. 1999. An introduction to variational methods for graphical models. Mach Learn. 37:183-233. (Pubitemid 30544678)
-
(1999)
Machine Learning
, vol.37
, Issue.2
, pp. 183-233
-
-
Jordan, M.I.1
Ghahramani, Z.2
Jaakkola, T.S.3
Saul, L.K.4
-
19
-
-
0019296687
-
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
-
DOI 10.1007/BF01731581
-
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. (Pubitemid 11166431)
-
(1980)
Journal of Molecular Evolution
, vol.16
, Issue.2
, pp. 111-120
-
-
Kimura, M.1
-
21
-
-
13244276706
-
A nucleotide substitution model with nearest-neighbour interactions
-
DOI 10.1093/bioinformatics/bth901
-
Lunter G, Hein J. 2004. A nucleotide substitution model with nearestneighbour interactions. Bioinformatics 20(SUPPL. 1):i216-i223. (Pubitemid 41296692)
-
(2004)
Bioinformatics
, vol.20
, Issue.SUPPL. 1
-
-
Lunter, G.1
Hein, J.2
-
22
-
-
77956540776
-
Context dependent substitution biases vary within the human genome
-
Nevarez PA, DeBoever CM, Freeland BJ, Quitt MA, Bush EC. 2010. Context dependent substitution biases vary within the human genome. BMC Bioinformatics. 11:462.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 462
-
-
Nevarez, P.A.1
Deboever, C.M.2
Freeland, B.J.3
Quitt, M.A.4
Bush, E.C.5
-
23
-
-
0036804625
-
Mapping mutations on phylogenies
-
DOI 10.1080/10635150290102393
-
Nielsen R. 2002. Mapping mutations on phylogenies. Syst Biol. 51:729-739. (Pubitemid 35294805)
-
(2002)
Systematic Biology
, vol.51
, Issue.5
, pp. 729-739
-
-
Nielsen, R.1
-
26
-
-
45449111373
-
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites
-
DOI 10.1016/j.cell.2008.05.023, PII S009286740800682X
-
Noyes MB, Christensen RG, Wakabayashi A, Stormo GD, Brodsky MH, Wolfe SA. 2008. Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell 133:1277-1289. (Pubitemid 351852912)
-
(2008)
Cell
, vol.133
, Issue.7
, pp. 1277-1289
-
-
Noyes, M.B.1
Christensen, R.G.2
Wakabayashi, A.3
Stormo, G.D.4
Brodsky, M.H.5
Wolfe, S.A.6
-
27
-
-
0035035443
-
A dependent-rates model and an MCMC-based methodology for the maximum-likelihood analysis of sequences with overlapping reading frames
-
Pedersen AM, Jensen JL. 2001. A dependent-rates model and an MCMC-based methodology for the maximum-likelihood analysis of sequences with overlapping reading frames. Mol Biol Evol. 18:763-776. (Pubitemid 32372947)
-
(2001)
Molecular Biology and Evolution
, vol.18
, Issue.5
, pp. 763-776
-
-
Pedersen, A.-M.K.1
Jensen, J.L.2
-
29
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
DOI 10.1093/bioinformatics/btg180
-
Ronquist F, Huelsenbeck JP. 2003. MrBayes 3:Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574. (Pubitemid 37038874)
-
(2003)
Bioinformatics
, vol.19
, Issue.12
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
30
-
-
0034050446
-
The mouse Nkx-1.2 homeobox gene: Alternative RNA splicing at canonical and noncanonical splice sites
-
DOI 10.1073/pnas.030539397
-
Rovescalli AC, Cinquanta M, Ferrante J, Kozak CA, Nirenberg M. 2000. The mouse Nkx-1.2 homeobox gene: Alternative RNA splicing at canonical and noncanonical splice sites. Proc Natl Acad Sci U S A. 97:1982-1987. (Pubitemid 30134008)
-
(2000)
Proceedings of the National Academy of Sciences of the United States of America
, vol.97
, Issue.5
, pp. 1982-1987
-
-
Rovescalli, A.C.1
Cinquanta, M.2
Ferrante, J.3
Kozak, C.A.4
Nirenberg, M.5
-
31
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
DOI 10.1101/gr.3715005
-
Siepel A, Bejerano G, Pedersen JS, et al. (16 co-authors). 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
-
32
-
-
1542510106
-
Phylogenetic estimation of context-dependent substitution rates by maximum likelihood
-
DOI 10.1093/molbev/msh039
-
Siepel A, Haussler D. 2004. Phylogenetic estimation of contextdependent substitution rates by maximum likelihood. Mol Biol Evol. 21:468-488. (Pubitemid 38339664)
-
(2004)
Molecular Biology and Evolution
, vol.21
, Issue.3
, pp. 468-488
-
-
Siepel, A.1
Haussler, D.2
-
33
-
-
67649376350
-
Strong evidence for lineage and sequence specificity of substitution rates and patterns in Drosophila
-
Singh ND, Arndt PF, Clark AG, Aquadro CF. 2009. Strong evidence for lineage and sequence specificity of substitution rates and patterns in Drosophila. Mol Biol Evol. 26:1591-1605.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 1591-1605
-
-
Singh, N.D.1
Arndt, P.F.2
Clark, A.G.3
Aquadro, C.F.4
-
35
-
-
34248358308
-
Hyperconserved CpG domains underlie Polycomb-binding sites
-
DOI 10.1073/pnas.0609746104
-
Tanay A, O'Donnell AH, Damelin M, Bestor TH. 2007. Hyperconserved CpG domains underlie Polycomb-binding sites. Proc Natl Acad Sci U S A. 104:5521-5526. (Pubitemid 47175713)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.13
, pp. 5521-5526
-
-
Tanay, A.1
O'Donnell, A.H.2
Damelin, M.3
Bestor, T.H.4
-
36
-
-
43549095247
-
Sequence context affects the rate of short insertions and deletions in flies and primates
-
Tanay A, Siggia ED. 2008. Sequence context affects the rate of short insertions and deletions in flies and primates. Genome Biol. 9:R37.
-
(2008)
Genome Biol
, vol.9
-
-
Tanay, A.1
Siggia, E.D.2
-
37
-
-
0032014216
-
Human Smad3 and Smad4 are sequence-specific transcription activators
-
Zawel L, Dai JL, Buckhaults P, Zhou S, Kinzler KW, Vogelstein B, Kern SE. 1998. Human Smad3 and Smad4 are sequence-specific transcription activators. Mol CE.L.L. 1:611-617. (Pubitemid 128374697)
-
(1998)
Molecular Cell
, vol.1
, Issue.4
, pp. 611-617
-
-
Zawel, L.1
Le Dai, J.2
Buckhaults, P.3
Zhou, S.4
Kinzler, K.W.5
Vogelstein, B.6
Kern, S.E.7
|