-
1
-
-
59149102602
-
Phylogenetic and functional assessment of orthologs inference projects and methods
-
Altenhoff AM, Dessimoz C. 2009. Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol. 5: e1000262.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Altenhoff, A.M.1
Dessimoz, C.2
-
2
-
-
84863639111
-
Resolving the ortholog conjecture: Orthologs tend to be weakly, but significantly,more similar in function than paralogs
-
Altenhoff AM, Studer RA, Robinson-Rechavi M, Dessimoz C. 2012. Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly,more similar in function than paralogs. PLoS Comput Biol. 8:e1002514.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Altenhoff, A.M.1
Studer, R.A.2
Robinson-Rechavi, M.3
Dessimoz, C.4
-
3
-
-
77649268965
-
Posttranslational regulation impacts the fate of duplicated genes
-
Amoutzias GD, et al. 2010. Posttranslational regulation impacts the fate of duplicated genes. Proc Natl Acad Sci U S A. 107:2967-2971.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 2967-2971
-
-
Amoutzias, G.D.1
-
4
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
Ashburner M, et al. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 25:25-29.
-
(2000)
The Gene Ontology Consortium. Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
-
5
-
-
80054976678
-
The evolution of gene expression levels in mammalian organs
-
Brawand D, et al. 2011. The evolution of gene expression levels in mammalian organs. Nature 478:343-348.
-
(2011)
Nature
, vol.478
, pp. 343-348
-
-
Brawand, D.1
-
6
-
-
84870655983
-
The ortholog conjecture is untestable by the current gene ontology but is supported by RNA sequencing data
-
Chen X, Zhang J. 2012. The ortholog conjecture is untestable by the current gene ontology but is supported by RNA sequencing data. PLoS Comput Biol. 8:e1002784.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Chen, X.1
Zhang, J.2
-
7
-
-
79551632781
-
The ecoresponsive genome of Daphnia pulex
-
Colbourne JK, et al. 2011. The ecoresponsive genome of Daphnia pulex. Science 331:555-561.
-
(2011)
Science
, vol.331
, pp. 555-561
-
-
Colbourne, J.K.1
-
8
-
-
56549119570
-
Turning a hobby into a job: How duplicated genes find new functions
-
Conant GC, Wolfe HK. 2008. Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet. 9:938-950.
-
(2008)
Nat Rev Genet
, vol.9
, pp. 938-950
-
-
Conant, G.C.1
Wolfe, H.K.2
-
9
-
-
0014800108
-
Distinguishing homologous from analogous proteins
-
Fitch WM. 1970. Distinguishing homologous from analogous proteins. Syst Zool. 19:99-106.
-
(1970)
Syst Zool
, vol.19
, pp. 99-106
-
-
Fitch, W.M.1
-
10
-
-
0034178257
-
Homology a personal view on some of the problems
-
Fitch WM. 2000. Homology a personal view on some of the problems. Trends Genet. 16:227-231.
-
(2000)
Trends Genet
, vol.16
, pp. 227-231
-
-
Fitch, W.M.1
-
11
-
-
0032893932
-
Preservation of duplicate genes by complementary, degenerative mutations
-
Force A, et al. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545.
-
(1999)
Genetics
, vol.151
, pp. 1531-1545
-
-
Force, A.1
-
12
-
-
84876665869
-
Functional and evolutionary implications of gene orthology
-
Gabaldon T, Koonin VE. 2013. Functional and evolutionary implications of gene orthology. Nat Rev Genet. 14:360-366.
-
(2013)
Nat Rev Genet
, vol.14
, pp. 360-366
-
-
Gabaldon, T.1
Koonin, V.E.2
-
13
-
-
20144374141
-
Gene complexity and gene duplicability
-
He X, Zhang J. 2005. Gene complexity and gene duplicability. Curr Biol. 15:1016-1021.
-
(2005)
Curr Biol
, vol.15
, pp. 1016-1021
-
-
He, X.1
Zhang, J.2
-
14
-
-
28944441407
-
Higher duplicability of less important genes in yeast genomes
-
He X, Zhang J. 2006. Higher duplicability of less important genes in yeast genomes. Mol Biol Evol. 23:144-151.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 144-151
-
-
He, X.1
Zhang, J.2
-
15
-
-
80053194329
-
Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication
-
Huerta-Cepas J, Dopazo J, Huynen AM, Gabaldon T. 2011. Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. Brief Bioinform. 12:442-448.
-
(2011)
Brief Bioinform
, vol.12
, pp. 442-448
-
-
Huerta-Cepas, J.1
Dopazo, J.2
Huynen, A.M.3
Gabaldon, T.4
-
16
-
-
0028342845
-
The evolution of functionally novel proteins after gene duplication
-
Hughes AL. 1994. The evolution of functionally novel proteins after gene duplication. Proc Biol Sci. 256:119-124.
-
(1994)
Proc Biol Sci
, vol.256
, pp. 119-124
-
-
Hughes, A.L.1
-
17
-
-
75549087305
-
The evolution of gene duplications: Classifying and distinguishing between models
-
Innan H, Kondrashov F. 2010. The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet. 11:97-108.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 97-108
-
-
Innan, H.1
Kondrashov, F.2
-
19
-
-
27644472372
-
Orthologs, paralogs, and evolutionary genomics
-
Koonin EV. 2005. Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet. 39:309-338.
-
(2005)
Annu Rev Genet
, vol.39
, pp. 309-338
-
-
Koonin, E.V.1
-
21
-
-
0036066765
-
The role of lineagespecific gene family expansion in the evolution of eukaryotes
-
Lespinet O, Wolf YI, Koonin VE, Aravind L. 2002. The role of lineagespecific gene family expansion in the evolution of eukaryotes. Genome Res. 12:1048-1059.
-
(2002)
Genome Res
, vol.12
, pp. 1048-1059
-
-
Lespinet, O.1
Wolf, Y.I.2
Koonin, V.E.3
Aravind, L.4
-
22
-
-
84859128110
-
Organ and cell type-specific complementary expression patterns and regulatory neofunctionalization between duplicated genes in Arabidopsis thaliana
-
Liu SL, Baute JG, Adams KL. 2011. Organ and cell type-specific complementary expression patterns and regulatory neofunctionalization between duplicated genes in Arabidopsis thaliana. Genome Biol Evol. 3: 1419-1436.
-
(2011)
Genome Biol Evol
, vol.3
, pp. 1419-1436
-
-
Liu, S.L.1
Baute, J.G.2
Adams, K.L.3
-
23
-
-
0037047587
-
Genomics. Gene duplication and evolution
-
Lynch M. 2002. Genomics. Gene duplication and evolution. Science 297: 945-947.
-
(2002)
Science
, vol.297
, pp. 945-947
-
-
Lynch, M.1
-
24
-
-
34548724489
-
The evolution of genetic networks by non-adaptive processes
-
Lynch M. 2007. The evolution of genetic networks by non-adaptive processes. Nat Rev Genet. 8:803-813.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 803-813
-
-
Lynch, M.1
-
25
-
-
4744343021
-
The altered evolutionary trajectories of gene duplicates
-
Lynch M, Katju V. 2004. The altered evolutionary trajectories of gene duplicates. Trends Genet. 20:544-549.
-
(2004)
Trends Genet
, vol.20
, pp. 544-549
-
-
Lynch, M.1
Katju, V.2
-
26
-
-
0038486898
-
Divergence in the spatial pattern of gene expression between human duplicate genes
-
Makova KD, Li HW. 2003. Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Res. 13: 1638-1645.
-
(2003)
Genome Res
, vol.13
, pp. 1638-1645
-
-
Makova, K.D.1
Li, H.W.2
-
27
-
-
11944260171
-
Higher gene duplicabilities for metabolic proteins than for nonmetabolic proteins in yeast and E. Coli
-
Marland E, Prachumwat A, Maltsev N, Gu Z, Li HW. 2004. Higher gene duplicabilities for metabolic proteins than for nonmetabolic proteins in yeast and E. coli. J Mol Evol. 59:806-814.
-
(2004)
J Mol Evol
, vol.59
, pp. 806-814
-
-
Marland, E.1
Prachumwat, A.2
Maltsev, N.3
Gu, Z.4
Li, H.W.5
-
28
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi A,Williams BA, McCue K, Schaeffer L,Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 5:621-628.
-
(2008)
Nat Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
29
-
-
79959828326
-
Testing the ortholog conjecture with comparative functional genomic data frommammals
-
Nehrt NL, Clark WT, Radivojac P, Hahn WM. 2011. Testing the ortholog conjecture with comparative functional genomic data frommammals. PLoS Comput Biol. 7:e1002073.
-
(2011)
PLoS Comput Biol.
, vol.7
-
-
Nehrt, N.L.1
Clark, W.T.2
Radivojac, P.3
Hahn, W.M.4
-
30
-
-
1842466312
-
Parameters behind "nonparametric" statistics: Kendall's tau, Somers' D and median differences
-
Newson R. 2002. Parameters behind "nonparametric" statistics: Kendall's tau, Somers' D and median differences. Stata J. 2:45-63.
-
(2002)
Stata J
, vol.2
, pp. 45-63
-
-
Newson, R.1
-
32
-
-
0037472928
-
Genomic function: Rate of evolution and gene dispensability
-
discussion 497-498
-
Pal C, Papp B, Hurst DL. 2003. Genomic function: rate of evolution and gene dispensability. Nature 421:496-497; discussion 497-498.
-
(2003)
Nature
, vol.421
, pp. 496-497
-
-
Pal, C.1
Papp, B.2
Hurst, D.L.3
-
33
-
-
84885432704
-
Accelerated evolution after gene duplication: A time-dependent process affecting just one copy
-
Pegueroles C, Laurie S, Alba MM. 2013. Accelerated evolution after gene duplication: a time-dependent process affecting just one copy. Mol Biol Evol. 30:1830-1842.
-
(2013)
Mol Biol Evol
, vol.30
, pp. 1830-1842
-
-
Pegueroles, C.1
Laurie, S.2
Alba, M.M.3
-
34
-
-
71549114836
-
A problem with the correlation coefficient as a measure of gene expression divergence
-
Pereira V, Waxman D, Eyre-Walker A. 2009. A problem with the correlation coefficient as a measure of gene expression divergence. Genetics 183:1597-1600.
-
(2009)
Genetics
, vol.183
, pp. 1597-1600
-
-
Pereira, V.1
Waxman, D.2
Eyre-Walker, A.3
-
35
-
-
84864142569
-
Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human
-
Piasecka B, Robinson-Rechavi M, Bergmann S. 2012. Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human. Bioinformatics 28:1865-1872.
-
(2012)
Bioinformatics
, vol.28
, pp. 1865-1872
-
-
Piasecka, B.1
Robinson-Rechavi, M.2
Bergmann, S.3
-
36
-
-
28944434076
-
Protein function, connectivity, and duplicability in yeast
-
Prachumwat A, Li HW. 2006. Protein function, connectivity, and duplicability in yeast. Mol Biol Evol. 23:30-39.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 30-39
-
-
Prachumwat, A.1
Li, H.W.2
-
37
-
-
77956781437
-
Maintenance of duplicate genes and their functional redundancy by reduced expression
-
Qian W, Liao BY, Chang YA, Zhang J. 2010. Maintenance of duplicate genes and their functional redundancy by reduced expression. Trends Genet. 26:425-430.
-
(2010)
Trends Genet.
, vol.26
, pp. 425-430
-
-
Qian, W.1
Liao, B.Y.2
Chang, Y.A.3
Zhang, J.4
-
38
-
-
65449142156
-
How confident can we be that orthologs are similar, but paralogs differ?
-
Studer RA, Robinson-Rechavi M. 2009. How confident can we be that orthologs are similar, but paralogs differ? Trends Genet. 25: 210-216.
-
(2009)
Trends Genet
, vol.25
, pp. 210-216
-
-
Studer, R.A.1
Robinson-Rechavi, M.2
-
39
-
-
11144358198
-
A gene atlas of themouse and human protein-encoding transcriptomes
-
Su AI, et al. 2004. A gene atlas of themouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A. 101:6062-6067.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 6062-6067
-
-
Su, A.I.1
-
40
-
-
84861123821
-
On the use of gene ontology annotations to assess functional similarity among orthologs and paralogs: A short report
-
Thomas PD, Wood V, Mungall CJ, Lewis ES, Blake AJ. 2012. On the use of gene ontology annotations to assess functional similarity among orthologs and paralogs: a short report. PLoS Comput Biol. 8: e1002386.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Thomas, P.D.1
Wood, V.2
Mungall, C.J.3
Lewis, E.S.4
Blake, A.J.5
-
41
-
-
84859885816
-
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
-
Trapnell C, et al. 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 7: 562-578.
-
(2012)
Nat Protoc
, vol.7
, pp. 562-578
-
-
Trapnell, C.1
-
42
-
-
84881249508
-
Density peaks of paralog pairs in human and mouse genomes
-
Vinogradov AE. 2013. Density peaks of paralog pairs in human and mouse genomes. Gene 527:55-61.
-
(2013)
Gene
, vol.527
, pp. 55-61
-
-
Vinogradov, A.E.1
-
43
-
-
57749195712
-
RNA-Seq: A revolutionary tool for transcriptomics
-
Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 10:57-63.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
44
-
-
78649458548
-
RNA sequencing shows no dosage compensation of the active X-chromosome
-
Xiong Y, et al. 2010. RNA sequencing shows no dosage compensation of the active X-chromosome. Nat Genet. 42:1043-1047.
-
(2010)
Nat Genet
, vol.42
, pp. 1043-1047
-
-
Xiong, Y.1
-
45
-
-
0346734130
-
Organismal complexity, protein complexity, and gene duplicability
-
Yang J, Lusk R, Li HW. 2003. Organismal complexity, protein complexity, and gene duplicability. Proc Natl Acad Sci U S A. 100: 15661-15665.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 15661-15665
-
-
Yang, J.1
Lusk, R.2
Li, H.W.3
-
46
-
-
85193400856
-
Gene duplication
-
Losos J, editor.Princeton (NJ): Princeton University Press
-
Zhang J. 2013. Gene duplication. In: Losos J, editor.Princeton guide to evolution. Princeton (NJ): Princeton University Press. p. 397-405.
-
(2013)
Princeton Guide to Evolution
, pp. 397-405
-
-
Zhang, J.1
|