Detecting signatures of selection on gene expression

[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.