-
1
-
-
84872503128
-
Y-chromosome evolution: Emerging insights into processes of Y-chromosome degeneration
-
Bachtrog D. 2013. Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration. Nat Rev Genet. 14:113–124.
-
(2013)
Nat Rev Genet
, vol.14
, pp. 113-124
-
-
Bachtrog, D.1
-
3
-
-
85016183703
-
The X to autosome expression ratio in haploid and diploid human embryonic stem cells
-
Chen X, Zhang J. 2016. The X to autosome expression ratio in haploid and diploid human embryonic stem cells. Mol Biol Evol. 33:3104–3107.
-
(2016)
Mol Biol Evol
, vol.33
, pp. 3104-3107
-
-
Chen, X.1
Zhang, J.2
-
4
-
-
79960405019
-
The variant call format and VCFtools
-
Danecek P, et al. 2011. The variant call format and VCFtools. Bioinformatics 27:2156–2158.
-
(2011)
Bioinformatics
, vol.27
, pp. 2156-2158
-
-
Danecek, P.1
-
5
-
-
84859256941
-
Critical evaluation of imprinted gene expression by RNA-Seq: A new perspective
-
DeVeale B, van der Kooy D, Babak T. 2012. Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective. PLoS Genet. 8:e1002600.
-
(2012)
PLoS Genet
, vol.8
-
-
DeVeale, B.1
Van Der Kooy, D.2
Babak, T.3
-
6
-
-
84961755772
-
Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data
-
Dozmorov MG, et al. 2015. Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data. BMC Bioinformatics 16 Suppl 13:S10.
-
(2015)
BMC Bioinformatics
, vol.16
, pp. S10
-
-
Dozmorov, M.G.1
-
7
-
-
36849094065
-
Faced with inequality: Chicken do not have a general dosage compensation of sex-linked genes
-
Ellegren H, et al. 2007. Faced with inequality: chicken do not have a general dosage compensation of sex-linked genes. BMC Biol. 5:40.
-
(2007)
BMC Biol
, vol.5
, pp. 40
-
-
Ellegren, H.1
-
8
-
-
84899023759
-
Transcriptome-wide investigation of genomic imprinting in chicken
-
Fresard L, et al. 2014. Transcriptome-wide investigation of genomic imprinting in chicken. Nucleic Acids Res. 42:3768–3782.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 3768-3782
-
-
Fresard, L.1
-
9
-
-
84900417384
-
Avian sex, sex chromosomes, and dosage compensation in the age of genomics
-
Graves JA. 2014. Avian sex, sex chromosomes, and dosage compensation in the age of genomics. Chromosome Res. 22:45–57.
-
(2014)
Chromosome Res
, vol.22
, pp. 45-57
-
-
Graves, J.A.1
-
10
-
-
77955285002
-
Sex-specific parent-of-origin allelic expression in the mouse brain
-
Gregg C, Zhang J, Butler JE, Haig D, Dulac C. 2010a. Sex-specific parent-of-origin allelic expression in the mouse brain. Science 329:682–685.
-
(2010)
Science
, vol.329
, pp. 682-685
-
-
Gregg, C.1
Zhang, J.2
Butler, J.E.3
Haig, D.4
Dulac, C.5
-
11
-
-
77955299096
-
High-resolution analysis of parent-of-origin allelic expression in the mouse brain
-
Gregg C, et al. 2010b. High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science 329:643–648.
-
(2010)
Science
, vol.329
, pp. 643-648
-
-
Gregg, C.1
-
12
-
-
85016219024
-
X-Chromosome dosage compensation
-
Chichester: John Wiley & Sons, Ltd.
-
He X, Zhang J. 2016. X-Chromosome dosage compensation. In: eLS. Chichester: John Wiley & Sons, Ltd. p. 1–7.
-
(2016)
eLS
, pp. 1-7
-
-
He, X.1
Zhang, J.2
-
13
-
-
84901675746
-
Genetic degeneration of old and young Y chromosomes in the flowering plant Rumex hastatulus
-
Hough J, Hollister JD, Wang W, Barrett SC, Wright SI. 2014. Genetic degeneration of old and young Y chromosomes in the flowering plant Rumex hastatulus. Proc Natl Acad Sci U S A. 111:7713–7718.
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, pp. 7713-7718
-
-
Hough, J.1
Hollister, J.D.2
Wang, W.3
Barrett, S.C.4
Wright, S.I.5
-
14
-
-
33947528380
-
Dosage compensation is less effective in birds than in mammals
-
Itoh Y, et al. 2007. Dosage compensation is less effective in birds than in mammals. J Biol. 6:2.
-
(2007)
J Biol
, vol.6
, pp. 2
-
-
Itoh, Y.1
-
15
-
-
77950657563
-
Sex bias and dosage compensation in the zebra finch versus chicken genomes: General and specialized patterns among birds
-
Itoh Y, et al. 2010. Sex bias and dosage compensation in the zebra finch versus chicken genomes: general and specialized patterns among birds. Genome Res. 20:512–518.
-
(2010)
Genome Res
, vol.20
, pp. 512-518
-
-
Itoh, Y.1
-
16
-
-
38949090440
-
Large-scale population study of human cell lines indicates that dosage compensation is virtually complete
-
Johnston CM, et al. 2008. Large-scale population study of human cell lines indicates that dosage compensation is virtually complete. PLoS Genet. 4:e9.
-
(2008)
PLoS Genet
, vol.4
-
-
Johnston, C.M.1
-
17
-
-
84861541065
-
Mechanisms and evolutionary patterns of mammalian and avian dosage compensation
-
Julien P, et al. 2012. Mechanisms and evolutionary patterns of mammalian and avian dosage compensation. PLoS Biol. 10:e1001328.
-
(2012)
PLoS Biol
, vol.10
-
-
Julien, P.1
-
18
-
-
77949587649
-
Fast and accurate long-read alignment with Burrows-Wheeler transform
-
Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26:589–595.
-
(2010)
Bioinformatics
, vol.26
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
19
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li H, et al. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
20
-
-
84863955476
-
Expression reduction in mammalian X chromosome evolution refutes Ohno’s hypothesis of dosage compensation
-
Lin F, Xing K, Zhang J, He X. 2012. Expression reduction in mammalian X chromosome evolution refutes Ohno’s hypothesis of dosage compensation. Proc Natl Acad Sci U S A. 109:11752–11757.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 11752-11757
-
-
Lin, F.1
Xing, K.2
Zhang, J.3
He, X.4
-
21
-
-
38749117957
-
Dosage compensation in the mouse balances up-regulation and silencing of X-linked genes
-
Lin H, et al. 2007. Dosage compensation in the mouse balances up-regulation and silencing of X-linked genes. PLoS Biol. 5:e326.
-
(2007)
PLoS Biol
, vol.5
-
-
Lin, H.1
-
22
-
-
84880770271
-
Independent evolution of transcriptional inactivation on sex chromosomes in birds and mammals
-
Livernois AM, Waters SA, Deakin JE, Marshall Graves JA, Waters PD. 2013. Independent evolution of transcriptional inactivation on sex chromosomes in birds and mammals. PLoS Genet. 9:e1003635.
-
(2013)
PLoS Genet
, vol.9
-
-
Livernois, A.M.1
Waters, S.A.2
Deakin, J.E.3
Marshall Graves, J.A.4
Waters, P.D.5
-
23
-
-
0033535478
-
X-chromosome inactivation
-
Lyon MF. 1999. X-chromosome inactivation. Curr Biol. 9:R235–R237.
-
(1999)
Curr Biol
, vol.9
, pp. R235-R237
-
-
Lyon, M.F.1
-
24
-
-
84859934498
-
Mediation of Drosophila autosomal dosage effects and compensation by network interactions
-
Malone JH, et al. 2012. Mediation of Drosophila autosomal dosage effects and compensation by network interactions. Genome Biol. 13:r28.
-
(2012)
Genome Biol
, vol.13
, pp. r28
-
-
Malone, J.H.1
-
25
-
-
85011854458
-
The transcriptional architecture of phenotypic dimorphism
-
Mank JE. 2017. The transcriptional architecture of phenotypic dimorphism. Nat Ecol Evol. 1:0006.
-
(2017)
Nat Ecol Evol
, vol.1
, pp. 0006
-
-
Mank, J.E.1
-
26
-
-
84888136375
-
Sex chromosome dosage compensation: Definitely not for everyone
-
Mank JE. 2013. Sex chromosome dosage compensation: definitely not for everyone. Trends Genet. 29:677–683.
-
(2013)
Trends Genet
, vol.29
, pp. 677-683
-
-
Mank, J.E.1
-
27
-
-
65349150546
-
The W, X, Y and Z of sex-chromosome dosage compensation
-
Mank JE. 2009. The W, X, Y and Z of sex-chromosome dosage compensation. Trends Genet. 25:226–233.
-
(2009)
Trends Genet
, vol.25
, pp. 226-233
-
-
Mank, J.E.1
-
28
-
-
60549110047
-
All dosage compensation is local: Gene-by-gene regulation of sex-biased expression on the chicken Z chromosome
-
Mank JE, Ellegren H. 2009. All dosage compensation is local: gene-by-gene regulation of sex-biased expression on the chicken Z chromosome. Heredity (Edinburgh) 102:312–320.
-
(2009)
Heredity (Edinburgh)
, vol.102
, pp. 312-320
-
-
Mank, J.E.1
Ellegren, H.2
-
29
-
-
77956295988
-
The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
-
McKenna A, et al. 2010. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297–1303.
-
(2010)
Genome Res
, vol.20
, pp. 1297-1303
-
-
McKenna, A.1
-
30
-
-
77955188336
-
Random X inactivation and extensive mosaicism in human placenta revealed by analysis of allele-specific gene expression along the X chromosome
-
Moreira de Mello JC, et al. 2010. Random X inactivation and extensive mosaicism in human placenta revealed by analysis of allele-specific gene expression along the X chromosome. PLoS One 5:e10947.
-
(2010)
PLoS One
, vol.5
-
-
Moreira De Mello, J.C.1
-
31
-
-
0001732966
-
Why polyploidy is rare in animals than in plants
-
Muller HJ. 1925. Why polyploidy is rare in animals than in plants. Am Nat. 59:346–353.
-
(1925)
Am Nat
, vol.59
, pp. 346-353
-
-
Muller, H.J.1
-
32
-
-
84938379720
-
Evolution of dosage compensation under sexual selection differs between X and Z chromosomes
-
Mullon C, Wright AE, Reuter M, Pomiankowski A, Mank JE. 2015. Evolution of dosage compensation under sexual selection differs between X and Z chromosomes. Nat Commun. 6:7720.
-
(2015)
Nat Commun
, vol.6
, pp. 7720
-
-
Mullon, C.1
Wright, A.E.2
Reuter, M.3
Pomiankowski, A.4
Mank, J.E.5
-
33
-
-
29444455049
-
Dosage compensation of the active X chromosome in mammals
-
Nguyen DK, Disteche CM. 2006. Dosage compensation of the active X chromosome in mammals. Nat Genet. 38:47–53.
-
(2006)
Nat Genet
, vol.38
, pp. 47-53
-
-
Nguyen, D.K.1
Disteche, C.M.2
-
35
-
-
70349673635
-
Lessons from comparative analysis of X-chromosome inactivation in mammals
-
Okamoto I, Heard E. 2009. Lessons from comparative analysis of X-chromosome inactivation in mammals. Chromosome Res. 17:659–669.
-
(2009)
Chromosome Res
, vol.17
, pp. 659-669
-
-
Okamoto, I.1
Heard, E.2
-
36
-
-
0942268864
-
Epigenetic dynamics of imprinted X inactivation during early mouse development
-
Okamoto I, Otte AP, Allis CD, Reinberg D, Heard E. 2004. Epigenetic dynamics of imprinted X inactivation during early mouse development. Science 303:644–649.
-
(2004)
Science
, vol.303
, pp. 644-649
-
-
Okamoto, I.1
Otte, A.P.2
Allis, C.D.3
Reinberg, D.4
Heard, E.5
-
37
-
-
84859448442
-
Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome
-
Pessia E, Makino T, Bailly-Bechet M, McLysaght A, Marais GA. 2012. Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome. Proc Natl Acad Sci U S A. 109:5346–5351.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 5346-5351
-
-
Pessia, E.1
Makino, T.2
Bailly-Bechet, M.3
McLysaght, A.4
Marais, G.A.5
-
38
-
-
2942538192
-
Reduced variation on the chicken Z chromosome
-
Sundstrom H, Webster MT, Ellegren H. 2004. Reduced variation on the chicken Z chromosome. Genetics 167:377–385.
-
(2004)
Genetics
, vol.167
, pp. 377-385
-
-
Sundstrom, H.1
Webster, M.T.2
Ellegren, H.3
-
39
-
-
65449136284
-
Tophat: Discovering splice junctions with RNA-Seq
-
Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
40
-
-
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
-
41
-
-
84891706153
-
Chromosome-wide profiling of X-chromosome inactivation and epi-genetic states in fetal brain and placenta of the opossum, Monodelphis domestica
-
Wang X, Douglas KC, Vandeberg JL, Clark AG, Samollow PB. 2014. Chromosome-wide profiling of X-chromosome inactivation and epi-genetic states in fetal brain and placenta of the opossum, Monodelphis domestica. Genome Res. 24:70–83.
-
(2014)
Genome Res
, vol.24
, pp. 70-83
-
-
Wang, X.1
Douglas, K.C.2
Vandeberg, J.L.3
Clark, A.G.4
Samollow, P.B.5
-
42
-
-
84924872784
-
Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution
-
Wright AE, et al. 2015a. Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution. Mol Ecol. 24:1218–1235.
-
(2015)
Mol Ecol
, vol.24
, pp. 1218-1235
-
-
Wright, A.E.1
-
43
-
-
84943650369
-
Conservation of regional variation in sex-specific sex chromosome regulation
-
Wright AE, Zimmer F, Harrison PW, Mank JE. 2015b. Conservation of regional variation in sex-specific sex chromosome regulation. Genetics 201:587–598.
-
(2015)
Genetics
, vol.201
, pp. 587-598
-
-
Wright, A.E.1
Zimmer, F.2
Harrison, P.W.3
Mank, J.E.4
|