Detecting signatures of selection on gene expression
暂无分享,去创建一个
Christopher R. Cooney | J. Mank | E. Place | C. Cooney | Jessica A. Taylor | Thea F. Rogers | A. Wright | Alison E. Wright | Daniela H. Palmer Droguett | D. W. Kim | Peter D. Price
[1] Pooja Singh,et al. The importance of alternative splicing in adaptive evolution , 2021, Molecular ecology.
[2] D. Silver,et al. Human brain evolution: Emerging roles for regulatory DNA and RNA , 2021, Current Opinion in Neurobiology.
[3] Evan Z. Macosko,et al. Comparative cellular analysis of motor cortex in human, marmoset and mouse , 2021, Nature.
[4] A. Gutiérrez-Adán,et al. Role of Alternative Splicing in Sex Determination in Vertebrates , 2021, Sexual Development.
[5] S. Pfister,et al. Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells , 2021, Science.
[6] J. Good,et al. Molecular Evolution across Mouse Spermatogenesis , 2021, bioRxiv.
[7] I. Mathieson. The omnigenic model and polygenic prediction of complex traits. , 2021, American journal of human genetics.
[8] J. Good,et al. Unraveling patterns of disrupted gene expression across a complex tissue , 2021, bioRxiv.
[9] James K. Bull,et al. Innovative mark–recapture experiment shows patterns of selection on transcript abundance in the wild , 2021, Molecular ecology.
[10] P. Khaitovich,et al. Alternative splicing during mammalian organ development , 2021, Nature Genetics.
[11] P. Hof,et al. Tempo and mode of gene expression evolution in the brain across primates , 2021, bioRxiv.
[12] B. Koop,et al. Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication , 2021, Genome biology.
[13] E. Place,et al. Single-cell analysis of early chick hypothalamic development reveals that hypothalamic cells are induced from prethalamic-like progenitors , 2021, bioRxiv.
[14] Francisco A. Cubillos,et al. A comprehensive fitness landscape model reveals the evolutionary history and future evolvability of eukaryotic cis-regulatory DNA sequences , 2021, bioRxiv.
[15] T. Przytycka,et al. Modeling gene expression evolution with EvoGeneX uncovers differences in evolution of species, organs and sexes , 2020, bioRxiv.
[16] P. Wittkopp,et al. Molecular and evolutionary processes generating variation in gene expression , 2020, Nature Reviews Genetics.
[17] W. Salzburger,et al. Gene expression dynamics during rapid organismal diversification in African cichlid fishes , 2020, Nature Ecology & Evolution.
[18] Alice S. Naftaly,et al. Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish , 2020, bioRxiv.
[19] H. Kaessmann,et al. Transcriptome and translatome co-evolution in mammals , 2020, Nature.
[20] D. Palmer,et al. Sex-Specific Selection Drives the Evolution of Alternative Splicing in Birds , 2020, Molecular biology and evolution.
[21] A. Spradling,et al. Two distinct pathways of pregranulosa cell differentiation support follicle formation in the mouse ovary , 2020, Proceedings of the National Academy of Sciences.
[22] Hunter B. Fraser,et al. Detecting selection with a genetic cross , 2020, Proceedings of the National Academy of Sciences.
[23] E. Buckler,et al. Local adaptation contributes to gene expression divergence in maize , 2020, bioRxiv.
[24] Y. Gilad,et al. Gene expression variability in human and chimpanzee populations share common determinants , 2020, bioRxiv.
[25] Abhijeet R. Sonawane,et al. Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues. , 2020, Cell reports.
[26] A. Wu,et al. Effect of methanol fixation on single-cell RNA sequencing data , 2020, bioRxiv.
[27] Rahulsimham Vegesna,et al. Ampliconic Genes on the Great Ape Y Chromosomes: Rapid Evolution of Copy Number but Conservation of Expression Levels , 2020, Genome biology and evolution.
[28] D. Adhikari,et al. Insights into Gonadal Sex Differentiation Provided by Single-Cell Transcriptomics in the Chicken Embryo. , 2020, Cell reports.
[29] Jun Z. Li,et al. Single-cell RNA sequencing of human, macaque, and mouse testes uncovers conserved and divergent features of mammalian spermatogenesis , 2020, bioRxiv.
[30] Joanna L. Kelley,et al. Convergent evolution of conserved mitochondrial pathways underlies repeated adaptation to extreme environments , 2020, Proceedings of the National Academy of Sciences.
[31] P. Debes,et al. The strength and form of natural selection on transcript abundance in the wild , 2020, bioRxiv.
[32] William M. Mauck,et al. The strength and pattern of natural selection on gene expression in rice , 2020, Nature.
[33] Giovanni Parmigiani,et al. ComBat-seq: batch effect adjustment for RNA-seq count data , 2020, bioRxiv.
[34] C. Danko,et al. Bayesian cell-type deconvolution and gene expression inference reveals tumor-microenvironment interactions , 2020, bioRxiv.
[35] M. E. Shafer. Cross-Species Analysis of Single-Cell Transcriptomic Data , 2019, Front. Cell Dev. Biol..
[36] J. Baker,et al. Gene expression across mammalian organ development , 2019, Nature.
[37] Li Zhao,et al. Testis single-cell RNA-seq reveals the dynamics of de novo gene transcription and germline mutational bias in Drosophila , 2019, bioRxiv.
[38] Jae Hoon Sul,et al. Accurate estimation of cell composition in bulk expression through robust integration of single-cell information , 2019, Nature Communications.
[39] P. Wittkopp,et al. Empirical measures of mutational effects define neutral models of regulatory evolution in Saccharomyces cerevisiae , 2019, Proceedings of the National Academy of Sciences.
[40] Morris A. Swertz,et al. Deconvolution of bulk blood eQTL effects into immune cell subpopulations , 2019, BMC Bioinformatics.
[41] M. Ceccarelli,et al. RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types , 2019, Cell reports.
[42] Beryl B. Cummings,et al. A quantitative framework for characterizing the evolutionary history of mammalian gene expression , 2018, Genome research.
[43] A. Catalán,et al. Drift and Directional Selection Are the Evolutionary Forces Driving Gene Expression Divergence in Eye and Brain Tissue of Heliconius Butterflies , 2018, Genetics.
[44] Yang I Li,et al. Trans Effects on Gene Expression Can Drive Omnigenic Inheritance , 2018, Cell.
[45] Ellen K. Velte,et al. The Mammalian Spermatogenesis Single-Cell Transcriptome, from Spermatogonial Stem Cells to Spermatids. , 2018, Cell reports.
[46] N. Patterson,et al. Extreme Polygenicity of Complex Traits Is Explained by Negative Selection. , 2019, American journal of human genetics.
[47] Saher Sue Hammoud,et al. A Comprehensive Roadmap of Murine Spermatogenesis Defined by Single-Cell RNA-Seq. , 2018, Developmental cell.
[48] S. Allen,et al. Genetic constraints on microevolutionary divergence of sex-biased gene expression , 2018, Philosophical Transactions of the Royal Society B: Biological Sciences.
[49] E. King,et al. Pan-cancer deconvolution of tumour composition using DNA methylation , 2018, Nature Communications.
[50] S. Nuzhdin,et al. The Evolution of Gene Expression in cis and trans. , 2018, Trends in genetics : TIG.
[51] Tracy M. Yamawaki,et al. Evolution of pallium, hippocampus, and cortical cell types revealed by single-cell transcriptomics in reptiles , 2018, Science.
[52] Felipe Zapata,et al. Pairwise comparisons across species are problematic when analyzing functional genomic data , 2018, Proceedings of the National Academy of Sciences.
[53] Michael Lässig,et al. Adaptive Evolution of Gene Expression in Drosophila. , 2017, Cell reports.
[54] H. Kaessmann,et al. The evolution of duplicate gene expression in mammalian organs , 2017, Genome research.
[55] M. Robinson‐Rechavi,et al. Developmental Constraints on Genome Evolution in Four Bilaterian Model Species , 2017, bioRxiv.
[56] Yang I Li,et al. An Expanded View of Complex Traits: From Polygenic to Omnigenic , 2017, Cell.
[57] Jing Wang,et al. Gene co-expression network connectivity is an important determinant of selective constraint , 2017, bioRxiv.
[58] J. Mank. The transcriptional architecture of phenotypic dimorphism , 2017, Nature Ecology &Evolution.
[59] Qi Zhou,et al. Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages , 2016, PLoS genetics.
[60] Lars E. Borm,et al. Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells , 2016, Cell.
[61] J. Mank,et al. Inferring regulatory change from gene expression: the confounding effects of tissue scaling , 2016, Molecular ecology.
[62] G. Thomas,et al. The impact of rate heterogeneity on inference of phylogenetic models of trait evolution , 2016, Journal of evolutionary biology.
[63] J. Mank,et al. Tissue Specificity and Sex-Specific Regulatory Variation Permit the Evolution of Sex-Biased Gene Expression , 2016, The American Naturalist.
[64] Christine B. Peterson,et al. Controlling the Rate of GWAS False Discoveries , 2016, Genetics.
[65] T. Mackay,et al. Spontaneous mutations and the origin and maintenance of quantitative genetic variation , 2016, eLife.
[66] P. Wittkopp,et al. Contrasting Frequencies and Effects of cis- and trans-Regulatory Mutations Affecting Gene Expression. , 2016, Molecular biology and evolution.
[67] R. Freckleton,et al. A cautionary note on the use of Ornstein Uhlenbeck models in macroevolutionary studies , 2015, Biological journal of the Linnean Society. Linnean Society of London.
[68] Terence P. Speed,et al. Correcting gene expression data when neither the unwanted variation nor the factor of interest are observed , 2012, Biostatistics.
[69] R. Nielsen,et al. Phylogenetic ANOVA: The Expression Variance and Evolution Model for Quantitative Trait Evolution. , 2015, Systematic biology.
[70] V. Anne Smith,et al. Relationship between differentially expressed mRNA and mRNA-protein correlations in a xenograft model system , 2015 .
[71] Marie Sémon,et al. Transcriptomics of developing embryos and organs: A raising tool for evo-devo. , 2015, Journal of experimental zoology. Part B, Molecular and developmental evolution.
[72] Peter W. Harrison,et al. Sexual selection drives evolution and rapid turnover of male gene expression , 2015, Proceedings of the National Academy of Sciences.
[73] D. Silvestro,et al. Measurement errors should always be incorporated in phylogenetic comparative analysis , 2015 .
[74] P. Wittkopp,et al. Selection on noise constrains variation in a eukaryotic promoter , 2015, Nature.
[75] J. Merilä,et al. The Evolution and Adaptive Potential of Transcriptional Variation in Sticklebacks—Signatures of Selection and Widespread Heritability , 2014, Molecular biology and evolution.
[76] Lam Si Tung Ho,et al. Intrinsic inference difficulties for trait evolution with Ornstein‐Uhlenbeck models , 2014 .
[77] Henrik Kaessmann,et al. Evolutionary dynamics of coding and non-coding transcriptomes , 2014, Nature Reviews Genetics.
[78] Craig R. Primmer,et al. Gene pleiotropy constrains gene expression changes in fish adapted to different thermal conditions , 2014, Nature Communications.
[79] Matthew W Pennell,et al. Robust regression and posterior predictive simulation increase power to detect early bursts of trait evolution. , 2014, Systematic biology.
[80] C. Ané,et al. A linear-time algorithm for Gaussian and non-Gaussian trait evolution models. , 2014, Systematic biology.
[81] Richard G FitzJohn,et al. Model Adequacy and the Macroevolution of Angiosperm Functional Traits , 2014, bioRxiv.
[82] R. Scott,et al. Phylogenetic comparative methods complement discriminant function analysis in ecomorphology. , 2014, American journal of physical anthropology.
[83] James B. Brown,et al. Diversity and dynamics of the Drosophila transcriptome , 2014, Nature.
[84] John P. Huelsenbeck,et al. Probabilistic Graphical Model Representation in Phylogenetics , 2013, Systematic biology.
[85] Rasmus Nielsen,et al. Modeling gene expression evolution with an extended Ornstein-Uhlenbeck process accounting for within-species variation. , 2014, Molecular biology and evolution.
[86] Jonathan K. Pritchard,et al. Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures , 2013, Science.
[87] Matthew W. Pennell,et al. An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology , 2013, Annals of the New York Academy of Sciences.
[88] R. O’Hara,et al. QST–FST comparisons: evolutionary and ecological insights from genomic heterogeneity , 2013, Nature Reviews Genetics.
[89] J. Parsch,et al. The evolutionary causes and consequences of sex-biased gene expression , 2013, Nature Reviews Genetics.
[90] B. O’Meara,et al. MODELING STABILIZING SELECTION: EXPANDING THE ORNSTEIN–UHLENBECK MODEL OF ADAPTIVE EVOLUTION , 2012, Evolution; international journal of organic evolution.
[91] Y. Gilad,et al. Comparative studies of gene expression and the evolution of gene regulation , 2012, Nature Reviews Genetics.
[92] J. Mank,et al. W chromosome expression responds to female-specific selection , 2012, Proceedings of the National Academy of Sciences.
[93] A. Eyre-Walker,et al. A Selection Index for Gene Expression Evolution and Its Application to the Divergence between Humans and Chimpanzees , 2012, PloS one.
[94] Liam J. Revell,et al. phytools: an R package for phylogenetic comparative biology (and other things) , 2012 .
[95] Peter W. Harrison,et al. The evolution of gene expression and the transcriptome-phenotype relationship. , 2012, Seminars in cell & developmental biology.
[96] E. Marcotte,et al. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses , 2012, Nature Reviews Genetics.
[97] Andrew E. Jaffe,et al. Bioinformatics Applications Note Gene Expression the Sva Package for Removing Batch Effects and Other Unwanted Variation in High-throughput Experiments , 2022 .
[98] S. Bergmann,et al. The evolution of gene expression levels in mammalian organs , 2011, Nature.
[99] L. Keller,et al. Evolution of gene expression in fire ants: the effects of developmental stage, caste, and species. , 2011, Molecular biology and evolution.
[100] Dave T. Gerrard,et al. Gene expression divergence recapitulates the developmental hourglass model , 2010, Nature.
[101] Mark M. Davis,et al. Cell type–specific gene expression differences in complex tissues , 2010, Nature Methods.
[102] D. Tautz,et al. A TEST OF THE NEUTRAL MODEL OF EXPRESSION CHANGE IN NATURAL POPULATIONS OF HOUSE MOUSE SUBSPECIES , 2010, Evolution; international journal of organic evolution.
[103] M. Stephens,et al. Sex-specific and lineage-specific alternative splicing in primates. , 2010, Genome research.
[104] B. Nickel,et al. Transcriptional neoteny in the human brain , 2009, Proceedings of the National Academy of Sciences.
[105] T. Birkhead,et al. SPERM COMPETITION SELECTS BEYOND RELATIVE TESTES SIZE IN BIRDS , 2009, Evolution; international journal of organic evolution.
[106] D. Hartl,et al. Optimization of gene expression by natural selection , 2009, Proceedings of the National Academy of Sciences.
[107] B. Pujol,et al. Are QST–FST comparisons for natural populations meaningful? , 2008, Molecular ecology.
[108] Alicia Oshlack,et al. Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures , 2008, PLoS genetics.
[109] S. Carroll. Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution , 2008, Cell.
[110] Chung-I Wu,et al. Decoupled differentiation of gene expression and coding sequence among Drosophila populations. , 2008, Genes & genetic systems.
[111] Justin C. Fay,et al. Evaluating the role of natural selection in the evolution of gene regulation , 2008, Heredity.
[112] G. Wray. The evolutionary significance of cis-regulatory mutations , 2007, Nature Reviews Genetics.
[113] Michael Lachmann,et al. Evolution of primate gene expression , 2006, Nature Reviews Genetics.
[114] Scott A. Rifkin,et al. Natural selection on gene expression. , 2006, Trends in genetics : TIG.
[115] A. Whitehead,et al. Neutral and adaptive variation in gene expression. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[116] S. Carroll,et al. Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene , 2006, Nature.
[117] Terence P. Speed,et al. Expression profiling in primates reveals a rapid evolution of human transcription factors , 2006, Nature.
[118] Kevin P. White,et al. A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression , 2005, Nature.
[119] M. Lynch,et al. The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans , 2005, Nature Genetics.
[120] A. Graham. Faculty Opinions recommendation of Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila. , 2005 .
[121] S. Carroll,et al. Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila , 2005, Nature.
[122] D. Hartl,et al. RATES OF DIVERGENCE IN GENE EXPRESSION PROFILES OF PRIMATES, MICE, AND FLIES: STABILIZING SELECTION AND VARIABILITY AMONG FUNCTIONAL CATEGORIES , 2005, Evolution; international journal of organic evolution.
[123] Todd H. Oakley,et al. Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data. , 2005, Molecular biology and evolution.
[124] A. King,et al. Phylogenetic Comparative Analysis: A Modeling Approach for Adaptive Evolution , 2004, The American Naturalist.
[125] X. Gu. Statistical Framework for Phylogenomic Analysis of Gene Family Expression Profiles , 2004, Genetics.
[126] S. Pääbo,et al. A Neutral Model of Transcriptome Evolution , 2004, PLoS biology.
[127] Scott A. Rifkin,et al. Evolution of gene expression in the Drosophila melanogaster subgroup , 2003, Nature Genetics.
[128] G. Churchill,et al. Variation in gene expression within and among natural populations , 2002, Nature Genetics.
[129] S. Pääbo,et al. Intra- and Interspecific Variation in Primate Gene Expression Patterns , 2002, Science.
[130] T. F. Hansen. STABILIZING SELECTION AND THE COMPARATIVE ANALYSIS OF ADAPTATION , 1997, Evolution; international journal of organic evolution.
[131] R. Hudson,et al. A test of neutral molecular evolution based on nucleotide data. , 1987, Genetics.
[132] J. Felsenstein. Phylogenies and the Comparative Method , 1985, The American Naturalist.
[133] S. J. Arnold,et al. THE MEASUREMENT OF SELECTION ON CORRELATED CHARACTERS , 1983, Evolution; international journal of organic evolution.
[134] J. Felsenstein. Maximum-likelihood estimation of evolutionary trees from continuous characters. , 1973, American journal of human genetics.
[135] M. Kimura. Genetic variability maintained in a finite population due to mutational production of neutral and nearly neutral isoalleles. , 1968, Genetical research.