-
1
-
-
84856088973
-
Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations
-
Kumar S, Dudley JT, Filipski A, Liu L, (2011) Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations. Trends in Genetics 27: 377-386.
-
(2011)
Trends in Genetics
, vol.27
, pp. 377-386
-
-
Kumar, S.1
Dudley, J.T.2
Filipski, A.3
Liu, L.4
-
2
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
Lichtarge O, Bourne HR, Cohen FE, (1996) An evolutionary trace method defines binding surfaces common to protein families. Journal of Molecular Biology 257: 342-358.
-
(1996)
Journal of Molecular Biology
, vol.257
, pp. 342-358
-
-
Lichtarge, O.1
Bourne, H.R.2
Cohen, F.E.3
-
4
-
-
0036300444
-
Structural clusters of evolutionary trace residues are statistically significant and common in proteins
-
Madabushi S, Yao H, Marsh M, Kristensen DM, Philippi A, et al. (2002) Structural clusters of evolutionary trace residues are statistically significant and common in proteins. Journal of Molecular Biology 316: 139-154.
-
(2002)
Journal of Molecular Biology
, vol.316
, pp. 139-154
-
-
Madabushi, S.1
Yao, H.2
Marsh, M.3
Kristensen, D.M.4
Philippi, A.5
-
5
-
-
0037022603
-
Inference of functional regions in proteins by quantification of evolutionary constraints
-
Simon AL, Stone EA, Sidow A, (2002) Inference of functional regions in proteins by quantification of evolutionary constraints. Proceedings of the National Academy of Sciences 99: 2912-2917.
-
(2002)
Proceedings of the National Academy of Sciences
, vol.99
, pp. 2912-2917
-
-
Simon, A.L.1
Stone, E.A.2
Sidow, A.3
-
6
-
-
1642325994
-
Prediction of functional sites in proteins using conserved functional group analysis
-
Innis C, Anand A, Sowdhamini R, (2004) Prediction of functional sites in proteins using conserved functional group analysis. Journal of Molecular Biology 337: 1053-1068.
-
(2004)
Journal of Molecular Biology
, vol.337
, pp. 1053-1068
-
-
Innis, C.1
Anand, A.2
Sowdhamini, R.3
-
7
-
-
4143051195
-
Comparison of site-specific rate-inference methods for protein sequences: Empirical bayesian methods are superior
-
Mayrose I, Graur D, Ben-Tal N, Pupko T, (2004) Comparison of site-specific rate-inference methods for protein sequences: Empirical bayesian methods are superior. Molecular Biology and Evolution 21: 1781-1791.
-
(2004)
Molecular Biology and Evolution
, vol.21
, pp. 1781-1791
-
-
Mayrose, I.1
Graur, D.2
Ben-Tal, N.3
Pupko, T.4
-
8
-
-
29144462537
-
In silico identification of functional regions in proteins
-
Nimrod G, Glaser F, Steinberg D, Ben-Tal N, Pupko T, (2005) In silico identification of functional regions in proteins. Bioinformatics 21: i328-i337.
-
(2005)
Bioinformatics
, vol.21
-
-
Nimrod, G.1
Glaser, F.2
Steinberg, D.3
Ben-Tal, N.4
Pupko, T.5
-
9
-
-
34548133728
-
Predicting functionally important residues from sequence conservation
-
Capra JA, Singh M, (2007) Predicting functionally important residues from sequence conservation. Bioinformatics 23: 1875-1882.
-
(2007)
Bioinformatics
, vol.23
, pp. 1875-1882
-
-
Capra, J.A.1
Singh, M.2
-
10
-
-
57049150788
-
The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures
-
Goldenberg O, Erez E, Nimrod G, Ben-Tal N, (2009) The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures. Nucleic Acids Research 37: D323-D327.
-
(2009)
Nucleic Acids Research
, vol.37
-
-
Goldenberg, O.1
Erez, E.2
Nimrod, G.3
Ben-Tal, N.4
-
11
-
-
77954257799
-
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
-
Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N, (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Research 38: W529-W533.
-
(2010)
Nucleic Acids Research
, vol.38
-
-
Ashkenazy, H.1
Erez, E.2
Martz, E.3
Pupko, T.4
Ben-Tal, N.5
-
12
-
-
8444220853
-
Three-dimensional window analysis for detecting positive selection at structural regions of proteins
-
Suzuki Y, (2004) Three-dimensional window analysis for detecting positive selection at structural regions of proteins. Molecular Biology and Evolution 21: 2352-2359.
-
(2004)
Molecular Biology and Evolution
, vol.21
, pp. 2352-2359
-
-
Suzuki, Y.1
-
13
-
-
19944373422
-
Tertiary windowing to detect positive diversifying selection
-
Berglund AC, Wallner B, Elofsson A, Liberles DA, (2005) Tertiary windowing to detect positive diversifying selection. Journal of Molecular Evolution 60: 499-504.
-
(2005)
Journal of Molecular Evolution
, vol.60
, pp. 499-504
-
-
Berglund, A.C.1
Wallner, B.2
Elofsson, A.3
Liberles, D.A.4
-
14
-
-
33747863300
-
SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis
-
Liang H, Zhou W, Landweber LF, (2006) SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis. Nucleic Acids Research 34: W382-W384.
-
(2006)
Nucleic Acids Research
, vol.34
-
-
Liang, H.1
Zhou, W.2
Landweber, L.F.3
-
15
-
-
84864719167
-
Detecting patches of protein sites of influenza a viruses under positive selection
-
Tusche C, Steinbruck L, McHardy AC, (2012) Detecting patches of protein sites of influenza a viruses under positive selection. Molecular Biology and Evolution 29: 2063-2071.
-
(2012)
Molecular Biology and Evolution
, vol.29
, pp. 2063-2071
-
-
Tusche, C.1
Steinbruck, L.2
McHardy, A.C.3
-
16
-
-
84890371706
-
Spatial distribution of selection pressure on a protein based on the hierarchical bayesian model
-
Watabe T, Kishino H, (2013) Spatial distribution of selection pressure on a protein based on the hierarchical bayesian model. Molecular Biology and Evolution 30 (12):: 2714-22.
-
(2013)
Molecular Biology and Evolution
, vol.30
, Issue.12
, pp. 2714-2722
-
-
Watabe, T.1
Kishino, H.2
-
17
-
-
84862964759
-
Inferring sequence regions under functional divergence in duplicate genes
-
Huang YF, Golding GB, (2012) Inferring sequence regions under functional divergence in duplicate genes. Bioinformatics 28: 176-183.
-
(2012)
Bioinformatics
, vol.28
, pp. 176-183
-
-
Huang, Y.F.1
Golding, G.B.2
-
18
-
-
67650899071
-
Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences
-
Zhang Z, Townsend JP, (2009) Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences. PLoS Computational Biology 5: e1000421.
-
(2009)
PLoS Computational Biology
, vol.5
-
-
Zhang, Z.1
Townsend, J.P.2
-
19
-
-
33644826560
-
Computing Bayes factors using thermodynamic integration
-
Lartillot N, Philippe H, (2006) Computing Bayes factors using thermodynamic integration. Sys-tematic Biology 55: 195-207.
-
(2006)
Sys-Tematic Biology
, vol.55
, pp. 195-207
-
-
Lartillot, N.1
Philippe, H.2
-
22
-
-
0019797407
-
Evolutionary trees from DNA sequences: a maximum likelihood approach
-
Felsenstein J, (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17: 368-376.
-
(1981)
Journal of Molecular Evolution
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
23
-
-
5744249209
-
Equation of state calculations by fast computing machines
-
Metropolis N, Rosenbluth A, Rosenbluth M, Teller A, Teller E, (1953) Equation of state calculations by fast computing machines. The Journal of Chemical Physics 21: 1087-1092.
-
(1953)
The Journal of Chemical Physics
, vol.21
, pp. 1087-1092
-
-
Metropolis, N.1
Rosenbluth, A.2
Rosenbluth, M.3
Teller, A.4
Teller, E.5
-
24
-
-
77956890234
-
Monte Carlo sampling methods using Markov chains and their applications
-
Hastings WK, (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57: 97-109.
-
(1970)
Biometrika
, vol.57
, pp. 97-109
-
-
Hastings, W.K.1
-
25
-
-
0028064845
-
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods
-
Yang Z, (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution 39: 306-314.
-
(1994)
Journal of Molecular Evolution
, vol.39
, pp. 306-314
-
-
Yang, Z.1
-
28
-
-
33745955637
-
Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics
-
Dutheil J, Gaillard S, Bazin E, Glemin S, Ranwez V, et al. (2006) Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. BMC Bioinformatics 7: 188.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 188
-
-
Dutheil, J.1
Gaillard, S.2
Bazin, E.3
Glemin, S.4
Ranwez, V.5
-
29
-
-
84893676156
-
Bio++: Efficient extensible libraries and tools for computational molecular evolution
-
Gueguen L, Gaillard S, Boussau B, Gouy M, Groussin M, et al. (2013) Bio++: Efficient extensible libraries and tools for computational molecular evolution. Molecular Biology and Evolution 30: 1745-1750.
-
(2013)
Molecular Biology and Evolution
, vol.30
, pp. 1745-1750
-
-
Gueguen, L.1
Gaillard, S.2
Boussau, B.3
Gouy, M.4
Groussin, M.5
-
30
-
-
27544491192
-
ROCR: visualizing classifier performance in R
-
Sing T, Sander O, Beerenwinkel N, Lengauer T, (2005) ROCR: visualizing classifier performance in R. Bioinformatics 21: 3940-3941.
-
(2005)
Bioinformatics
, vol.21
, pp. 3940-3941
-
-
Sing, T.1
Sander, O.2
Beerenwinkel, N.3
Lengauer, T.4
-
31
-
-
2542445427
-
ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information
-
Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, et al. (2003) ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19: 163-164.
-
(2003)
Bioinformatics
, vol.19
, pp. 163-164
-
-
Glaser, F.1
Pupko, T.2
Paz, I.3
Bell, R.E.4
Bechor-Shental, D.5
-
32
-
-
5244224827
-
X-ray and NMR structure of human Bcl-xL, an inhibitor of programmed cell death
-
Muchmore SW, Sattler M, Liang H, Meadows RP, Harlan JE, et al. (1996) X-ray and NMR structure of human Bcl-xL, an inhibitor of programmed cell death. Nature 381: 335-341.
-
(1996)
Nature
, vol.381
, pp. 335-341
-
-
Muchmore, S.W.1
Sattler, M.2
Liang, H.3
Meadows, R.P.4
Harlan, J.E.5
-
34
-
-
0033971597
-
Structure and dimerization of a soluble form of B7-1
-
Ikemizu S, Gilbert RJ, Fennelly JA, Collins AV, Harlos K, et al. (2000) Structure and dimerization of a soluble form of B7-1. Immunity 12: 51-60.
-
(2000)
Immunity
, vol.12
, pp. 51-60
-
-
Ikemizu, S.1
Gilbert, R.J.2
Fennelly, J.A.3
Collins, A.V.4
Harlos, K.5
-
35
-
-
0035967146
-
Crystal structure of the B7-1/CTLA-4 complex that inhibits human immune responses
-
Stamper CC, Zhang Y, Tobin JF, Erbe DV, Ikemizu S, et al. (2001) Crystal structure of the B7-1/CTLA-4 complex that inhibits human immune responses. Nature 410: 608-611.
-
(2001)
Nature
, vol.410
, pp. 608-611
-
-
Stamper, C.C.1
Zhang, Y.2
Tobin, J.F.3
Erbe, D.V.4
Ikemizu, S.5
-
36
-
-
84857745267
-
Database resources of the National Center for Biotechnology Information
-
Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, et al. (2012) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 40: D13-D25.
-
(2012)
Nucleic Acids Research
, vol.40
-
-
Sayers, E.W.1
Barrett, T.2
Benson, D.A.3
Bolton, E.4
Bryant, S.H.5
-
37
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52: 696-704.
-
(2003)
Systematic Biology
, vol.52
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
38
-
-
0029133256
-
Both extracellular immunoglobin-like domains of cd80 contain residues critical for binding t cell surface receptors CTLA-4 and CD28
-
Peach RJ, Bajorath J, Naemura J, Leytze G, Greene J, et al. (1995) Both extracellular immunoglobin-like domains of cd80 contain residues critical for binding t cell surface receptors CTLA-4 and CD28. Journal of Biological Chemistry 270: 21181-21187.
-
(1995)
Journal of Biological Chemistry
, vol.270
, pp. 21181-21187
-
-
Peach, R.J.1
Bajorath, J.2
Naemura, J.3
Leytze, G.4
Greene, J.5
-
39
-
-
51649122492
-
Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates
-
Yokoyama S, Tada T, Zhang H, Britt L, (2008) Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates. Proceedings of the National Academy of Sciences 105: 13480-13485.
-
(2008)
Proceedings of the National Academy of Sciences
, vol.105
, pp. 13480-13485
-
-
Yokoyama, S.1
Tada, T.2
Zhang, H.3
Britt, L.4
-
41
-
-
1542642309
-
Protein evolution with depen- dence among codons due to tertiary structure
-
Robinson DM, Jones DT, Kishino H, Goldman N, Thorne JL, (2003) Protein evolution with depen- dence among codons due to tertiary structure. Molecular Biology and Evolution 20: 1692-1704.
-
(2003)
Molecular Biology and Evolution
, vol.20
, pp. 1692-1704
-
-
Robinson, D.M.1
Jones, D.T.2
Kishino, H.3
Goldman, N.4
Thorne, J.L.5
-
42
-
-
15544374861
-
Site interdependence attributed to tertiary structure in amino acid sequence evolution
-
Rodrigue N, Lartillot N, Bryant D, Philippe H, (2005) Site interdependence attributed to tertiary structure in amino acid sequence evolution. Gene 347: 207-217.
-
(2005)
Gene
, vol.347
, pp. 207-217
-
-
Rodrigue, N.1
Lartillot, N.2
Bryant, D.3
Philippe, H.4
-
44
-
-
65349140199
-
Solvent exposure imparts similar selective pressures across a range of yeast proteins
-
Conant GC, Stadler PF, (2009) Solvent exposure imparts similar selective pressures across a range of yeast proteins. Molecular Biology and Evolution 26: 1155-1161.
-
(2009)
Molecular Biology and Evolution
, vol.26
, pp. 1155-1161
-
-
Conant, G.C.1
Stadler, P.F.2
-
45
-
-
84871840207
-
Integrating sequence variation and protein structure to identify sites under selection
-
Meyer AG, Wilke CO, (2013) Integrating sequence variation and protein structure to identify sites under selection. Molecular Biology and Evolution 30: 36-44.
-
(2013)
Molecular Biology and Evolution
, vol.30
, pp. 36-44
-
-
Meyer, A.G.1
Wilke, C.O.2
-
47
-
-
1542537849
-
Combining phylogenetic and hidden markov models in biosequence analysis
-
Siepel A, Haussler D, (2004) Combining phylogenetic and hidden markov models in biosequence analysis. Journal of Computational Biology 11: 413-428.
-
(2004)
Journal of Computational Biology
, vol.11
, pp. 413-428
-
-
Siepel, A.1
Haussler, D.2
-
48
-
-
0028813337
-
A space-time process model for the evolution of DNA sequences
-
Yang Z, (1995) A space-time process model for the evolution of DNA sequences. Genetics 139: 993-1005.
-
(1995)
Genetics
, vol.139
, pp. 993-1005
-
-
Yang, Z.1
-
49
-
-
0030034795
-
A hidden Markov model approach to variation among sites in rate of evolution
-
Felsenstein J, Churchill GA, (1996) A hidden Markov model approach to variation among sites in rate of evolution. Molecular Biology and Evolution 13: 93-104.
-
(1996)
Molecular Biology and Evolution
, vol.13
, pp. 93-104
-
-
Felsenstein, J.1
Churchill, G.A.2
-
50
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Research 15: 1034-1050.
-
(2005)
Genome Research
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.S.3
Hinrichs, A.S.4
Hou, M.5
-
52
-
-
34547844134
-
Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates
-
Mayrose I, Doron-Faigenboim A, Bacharach E, Pupko T, (2007) Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates. Bioinformatics 23: i319-i327.
-
(2007)
Bioinformatics
, vol.23
-
-
Mayrose, I.1
Doron-Faigenboim, A.2
Bacharach, E.3
Pupko, T.4
-
53
-
-
84873573348
-
Estimating empirical codon hidden markov models
-
De Maio N, Holmes I, Schltterer C, Kosiol C, (2013) Estimating empirical codon hidden markov models. Molecular Biology and Evolution 30: 725-736.
-
(2013)
Molecular Biology and Evolution
, vol.30
, pp. 725-736
-
-
De Maio, N.1
Holmes, I.2
Schltterer, C.3
Kosiol, C.4
-
54
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
Yang Z, (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24: 1586-1591.
-
(2007)
Molecular Biology and Evolution
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
55
-
-
39549117235
-
A nonparametric method for accommodating and testing across-site rate variation
-
Huelsenbeck JP, Suchard MA, (2007) A nonparametric method for accommodating and testing across-site rate variation. Systematic Biology 56: 975-987.
-
(2007)
Systematic Biology
, vol.56
, pp. 975-987
-
-
Huelsenbeck, J.P.1
Suchard, M.A.2
-
58
-
-
0002628667
-
Regression and classification using Gaussian process priors
-
Neal R, (1999) Regression and classification using Gaussian process priors. Bayesian Statistics 6: 475-501.
-
(1999)
Bayesian Statistics
, vol.6
, pp. 475-501
-
-
Neal, R.1
|