Evolutionary dynamics of coding and non-coding transcriptomes

Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals

(2014) S. Washietl et al.   GENOME RESEARCH

PIWI proteins and PIWI-interacting RNAs in the soma

(2014) Robert J. Ross et al.   NATURE

Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators

(2014) Daniel W. Bellott et al.   NATURE

Origins and functional evolution of Y chromosomes across mammals

(2014) Diego Cortez et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

A molecular basis for classic blond hair color in Europeans

(2014) Catherine A Guenther et al.   NATURE GENETICS

X chromosome regulation: diverse patterns in development, tissues and disease

(2014) Xinxian Deng et al.   NATURE REVIEWS GENETICS

Cis and Trans Effects of Human Genomic Variants on Gene Expression

(2014) Julien Bryois et al.   PLoS Genetics

The Functional Consequences of Variation in Transcription Factor Binding

(2014) Darren A. Cusanovich et al.   PLoS Genetics

Conserved microRNA editing in mammalian evolution, development and disease

(2014) Maria Warnefors et al.   GENOME BIOLOGY

Developmental Basis of Phallus Reduction during Bird Evolution

(2013) Ana M. Herrera et al.   CURRENT BIOLOGY

Evolution of the Correlation between Expression Divergence and Protein Divergence in Mammals

(2013) Maria Warnefors et al.   Genome Biology and Evolution

Modeling Gene Expression Evolution with an Extended Ornstein–Uhlenbeck Process Accounting for Within-Species Variation

(2013) Rori V. Rohlfs et al.   MOLECULAR BIOLOGY AND EVOLUTION

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

Entering the era of single-cell transcriptomics in biology and medicine

(2013) Rickard Sandberg   NATURE METHODS

Biases in small RNA deep sequencing data

(2013) Carsten A. Raabe et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Expression quantitative trait loci: present and future

(2013) A. C. Nica et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolutionary and ontogenetic changes in RNA editing in human, chimpanzee, and macaque brains

(2013) Z. Li et al.   RNA

Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures

(2013) Z. Khan et al.   SCIENCE

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

Contributions of Protein-Coding and Regulatory Change to Adaptive Molecular Evolution in Murid Rodents

(2013) Daniel L. Halligan et al.   PLoS Genetics

Dynamics of DNA Methylation in Recent Human and Great Ape Evolution

(2013) Irene Hernando-Herraez et al.   PLoS Genetics

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

(2013) Ana C Marques et al.   GENOME BIOLOGY

Comparative modular analysis of gene expression in vertebrate organs

(2012) Barbara Piasecka et al.   BMC GENOMICS

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

Transcription Factors Are Targeted by Differentially Expressed miRNAs in Primates

(2012) Michael Dannemann et al.   Genome Biology and Evolution

A quantitative atlas of polyadenylation in five mammals

(2012) Adnan Derti et al.   GENOME RESEARCH

Birth and expression evolution of mammalian microRNA genes

(2012) J. Meunier et al.   GENOME RESEARCH

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

The H19 lincRNA is a developmental reservoir of miR-675 that suppresses growth and Igf1r

(2012) Andrew Keniry et al.   NATURE CELL BIOLOGY

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

Human-Specific Transcriptional Networks in the Brain

(2012) Genevieve Konopka et al.   NEURON

Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs

(2012) Julien Roux et al.   NUCLEIC ACIDS RESEARCH

A Selection Index for Gene Expression Evolution and Its Application to the Divergence between Humans and Chimpanzees

(2012) Maria Warnefors et al.   PLoS One

Expression reduction in mammalian X chromosome evolution refutes Ohno's hypothesis of dosage compensation

(2012) F. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Airn Transcriptional Overlap, But Not Its lncRNA Products, Induces Imprinted Igf2r Silencing

(2012) P. A. Latos et al.   SCIENCE

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

Evolution of the human-specific microRNA miR-941

(2012) Hai Yang Hu et al.   Nature Communications

Human-Specific Histone Methylation Signatures at Transcription Start Sites in Prefrontal Neurons

(2012) Hennady P. Shulha et al.   PLOS BIOLOGY

Mechanisms and Evolutionary Patterns of Mammalian and Avian Dosage Compensation

(2012) Philippe Julien et al.   PLOS BIOLOGY

Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression

(2012) Claudia Kutter et al.   PLoS Genetics

Microarrays, deep sequencing and the true measure of the transcriptome

(2011) John H Malone et al.   BMC BIOLOGY

A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

(2011) Marcella Cesana et al.   CELL

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Gene Expression Differences Among Primates Are Associated With Changes in a Histone Epigenetic Modification

(2011) C. E. Cain et al.   GENETICS

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

(2011) G. H. Perry et al.   GENOME RESEARCH

Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB

(2011) Vincent J. Lynch et al.   NATURE

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes

(2011) Claudia Kutter et al.   NATURE GENETICS

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Gene silencing by microRNAs: contributions of translational repression and mRNA decay

(2011) Eric Huntzinger et al.   NATURE REVIEWS GENETICS

The Developmental Role of Agouti in Color Pattern Evolution

(2011) M. Manceau et al.   SCIENCE

Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

(2011) Naoki Irie et al.   Nature Communications

MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates

(2011) Mehmet Somel et al.   PLOS BIOLOGY

A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues

(2011) Athma A. Pai et al.   PLoS Genetics

MicroRNA Expression and Regulation in Human, Chimpanzee, and Macaque Brains

(2011) Hai Yang Hu et al.   PLoS Genetics

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

Comprehensive Polyadenylation Site Maps in Yeast and Human Reveal Pervasive Alternative Polyadenylation

(2010) Fatih Ozsolak et al.   CELL

Evolution of Neuronal and Endothelial Transcriptomes in Primates

(2010) Thomas Giger et al.   Genome Biology and Evolution

Both Noncoding and Protein-Coding RNAs Contribute to Gene Expression Evolution in the Primate Brain

(2010) Courtney C. Babbitt et al.   Genome Biology and Evolution

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain

(2010) M. Somel et al.   GENOME RESEARCH

Evolution of alternative splicing in primate brain transcriptomes

(2010) Lan Lin et al.   HUMAN MOLECULAR GENETICS

Evolutionary history of regulatory variation in human populations

(2010) T. Lappalainen et al.   HUMAN MOLECULAR GENETICS

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Next-generation genomics: an integrative approach

(2010) R. David Hawkins et al.   NATURE REVIEWS GENETICS

Contrasts between adaptive coding and noncoding changes during human evolution

(2010) Ralph Haygood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic signatures of diet-related shifts during human origins

(2010) C. C. Babbitt et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome

(2010) Yong E. Zhang et al.   PLOS BIOLOGY

Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes

(2010) Rebecca A Chodroff et al.   GENOME BIOLOGY

Estimating accuracy of RNA-Seq and microarrays with proteomics

(2009) Xing Fu et al.   BMC GENOMICS

Sex-specific and lineage-specific alternative splicing in primates

(2009) R. Blekhman et al.   GENOME RESEARCH

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Optimization of gene expression by natural selection

(2009) T. Bedford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional neoteny in the human brain

(2009) M. Somel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comment on "Human-Specific Gain of Function in a Developmental Enhancer"

(2009) L. Duret et al.   SCIENCE

Evolutionary Processes Acting on Candidate cis-Regulatory Regions in Humans Inferred from Patterns of Polymorphism and Divergence

(2009) Dara G. Torgerson et al.   PLoS Genetics

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes

(2008) F. Veyrunes et al.   GENOME RESEARCH

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Genome analysis of the platypus reveals unique signatures of evolution

(2008) Wesley C. Warren et al.   NATURE

Rapidly evolving human promoter regions

(2008) Martin S Taylor et al.   NATURE GENETICS

The mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression

(2008) Jacob L Mueller et al.   NATURE GENETICS

The functional repertoires of metazoan genomes

(2008) Chris P. Ponting   NATURE REVIEWS GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

RNA-based gene duplication: mechanistic and evolutionary insights

(2008) Henrik Kaessmann et al.   NATURE REVIEWS GENETICS

Human-Specific Gain of Function in a Developmental Enhancer

(2008) S. Prabhakar et al.   SCIENCE

GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates

(2008) Nicolas Galtier et al.   TRENDS IN GENETICS

Selective Constraints in Experimentally Defined Primate Regulatory Regions

(2008) Daniel J. Gaffney et al.   PLoS Genetics

Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures

(2008) Ran Blekhman et al.   PLoS Genetics

An Evolutionarily Conserved Sexual Signature in the Primate Brain

(2008) Björn Reinius et al.   PLoS Genetics