The roles of different gene expression regulators in acoustic variation in the intermediate horseshoe bat revealed by long-read and short-read RNA sequencing data

Two Forms of Sexual Dimorphism in Gene Expression in Drosophila melanogaster: Their Coincidence and Evolutionary Genetics

(2023) Amardeep Singh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The importance of alternative splicing in adaptive evolution

(2022) Pooja Singh et al.   MOLECULAR ECOLOGY

A model for isoform-level differential expression analysis using RNA-seq data without pre-specifying isoform structure

(2022) Yang Liu et al.   PLoS One

Transcriptome innovations in primates revealed by single-molecule long-read sequencing

(2022) Luis Ferrández-Peral et al.   GENOME RESEARCH

Alternative splicing as a source of phenotypic diversity

(2022) Charlotte J. Wright et al.   NATURE REVIEWS GENETICS

Characterization of microRNA and gene expression in the cochlea of an echolocating bat ( Rhinolophus affinis )

(2022) Qianqian Li et al.   Ecology and Evolution

The 3D-Evo Space: Evolution of Gene Expression and Alternative Splicing Regulation

(2022) Federica Mantica et al.   Annual Review of Genetics

Genome-Wide Expression and Alternative Splicing in Domesticated Sunflowers (Helianthus annuus L.) under Flooding Stress

(2021) Joon Seon Lee et al.   Agronomy-Basel

Alternative splicing and gene expression play contrasting roles in the parallel phenotypic evolution of a salmonid fish

(2021) Arne Jacobs et al.   MOLECULAR ECOLOGY

Large-Scale Annotation and Evolution Analysis of MiRNA in Insects

(2021) Xingzhou Ma et al.   Genome Biology and Evolution

Evolution after whole genome duplication: teleost microRNAs

(2021) Thomas Desvignes et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cochlear hair cells of echolocating bats are immune to intense noise

(2021) Zhen Liu et al.   Journal of Genetics and Genomics

Comparative genomics provides insights into the aquatic adaptations of mammals

(2021) Yuan Yuan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule, full-length transcript isoform sequencing reveals disease-associated RNA isoforms in cardiomyocytes

(2021) Chenchen Zhu et al.   Nature Communications

The role of alternative splicing in adaptation and evolution

(2021) Jukka-Pekka Verta et al.   TRENDS IN ECOLOGY & EVOLUTION

Integrated Analysis of lncRNA and mRNA Reveals Novel Insights into Wool Bending in Zhongwei Goat

(2021) Xiaobo Li et al.   Animals

The origins of acoustic communication in vertebrates

(2020) Zhuo Chen et al.   Nature Communications

Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns

(2020) Alison D. Tang et al.   Nature Communications

Six reference-quality genomes reveal evolution of bat adaptations

(2020) David Jebb et al.   NATURE

Sex-specific selection drives the evolution of alternative splicing in birds

(2020) Thea F Rogers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide data reveal discordant mitonuclear introgression in the intermediate horseshoe bat (Rhinolophus affinis)

(2020) Xiuguang Mao et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Echolocation call frequency variation in horseshoe bats: molecular basis revealed by comparative transcriptomics

(2020) Haijian Sun et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mechanisms of Hair Cell Damage and Repair

(2019) Elizabeth L. Wagner et al.   TRENDS IN NEUROSCIENCES

Modulation and Evolution of Animal Development through microRNA Regulation of Gene Expression

(2019) Kittelmann et al.   Genes

Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing

(2019) Bo Wang et al.   Frontiers in Genetics

RNA sequencing: the teenage years

(2019) Rory Stark et al.   NATURE REVIEWS GENETICS

Conservation, acquisition, and functional impact of sex-biased gene expression in mammals

(2019) Sahin Naqvi et al.   SCIENCE

Gene expression vs. sequence divergence: comparative transcriptome sequencing among natural Rhinolophus ferrumequinum populations with different acoustic phenotypes

(2019) Hanbo Zhao et al.   Frontiers in Zoology

MicroRNA Gene Regulation in Extremely Young and Parallel Adaptive Radiations of Crater Lake Cichlid Fish

(2019) Paolo Franchini et al.   MOLECULAR BIOLOGY AND EVOLUTION

Echolocation call divergence in bats: a comparative analysis

(2019) Bo Luo et al.   BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY

Nanopore native RNA sequencing of a human poly(A) transcriptome

(2019) Rachael E. Workman et al.   NATURE METHODS

Regulation of gene expression by cis-acting long non-coding RNAs

(2019) Noa Gil et al.   NATURE REVIEWS GENETICS

ShinyGO: a graphical gene-set enrichment tool for animals and plants

(2019) Steven Xijin Ge et al.   BIOINFORMATICS

Genome-wide analyses reveal the role of noncoding variation in complex traits during rice domestication

(2019) X. M. Zheng et al.   Science Advances

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

Extensive Differential Splicing Underlies Phenotypically Plastic Aphid Morphs

(2018) Mary E Grantham et al.   MOLECULAR BIOLOGY AND EVOLUTION

Alternative splicing associated with phenotypic plasticity in the bumble bee Bombus terrestris

(2018) J. Price et al.   MOLECULAR ECOLOGY

Transcriptomic analysis of skin pigmentation variation in the Virginia opossum (Didelphis virginiana )

(2018) Sergio F. Nigenda-Morales et al.   MOLECULAR ECOLOGY

Essential nucleotide- and protein-dependent functions ofActb/β-actin

(2018) Xiaobai Patrinostro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential gene regulation underlies variation in melanic plumage coloration in the dark-eyed junco (Junco hyemalis )

(2018) Mikus Abolins-Abols et al.   MOLECULAR ECOLOGY

Integrated analysis of lncRNA and mRNA expression in rainbow trout families showing variation in muscle growth and fillet quality traits

(2018) Ali Ali et al.   Scientific Reports

Comparative cochlear transcriptomics of echolocating bats provides new insights into different nervous activities of CF bat species

(2018) Hui Wang et al.   Scientific Reports

The effects of cultural drift on geographic variation in echolocation calls of the Chinese rufous horseshoe bat (Rhinolophus sinicus )

(2017) Lifen Xie et al.   ETHOLOGY

The Role of Alternative Splicing and Differential Gene Expression in Cichlid Adaptive Radiation

(2017) Pooja Singh et al.   Genome Biology and Evolution

Cellular mechanisms of noise-induced hearing loss

(2017) Arwa Kurabi et al.   HEARING RESEARCH

The transcriptional landscape of seasonal coat colour moult in the snowshoe hare

(2017) Mafalda S. Ferreira et al.   MOLECULAR ECOLOGY

Detecting alternatively spliced transcript isoforms from single-molecule long-read sequences without a reference genome

(2017) Xiaoxian Liu et al.   Molecular Ecology Resources

The transcriptional architecture of phenotypic dimorphism

(2017) Judith E. Mank   Nature Ecology & Evolution

Testing the Sensory Drive Hypothesis: Geographic variation in echolocation frequencies of Geoffroy's horseshoe bat (Rhinolophidae: Rhinolophus clivosus)

(2017) David S. Jacobs et al.   PLoS One

The Role of microRNAs in the Repeated Parallel Diversification of Lineages of Midas Cichlid Fish from Nicaragua

(2016) Paolo Franchini et al.   Genome Biology and Evolution

The role of isoforms in the evolution of cryptic coloration inPeromyscusmice

(2016) Ricardo Mallarino et al.   MOLECULAR ECOLOGY

The power and promise of RNA-seq in ecology and evolution

(2016) Erica V. Todd et al.   MOLECULAR ECOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Alternative splicing and the evolution of phenotypic novelty

(2016) Stephen J. Bush et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

RNA splicing is a primary link between genetic variation and disease

(2016) Yang I. Li et al.   SCIENCE

Sensory Drive Mediated by Climatic Gradients Partially Explains Divergence in Acoustic Signals in Two Horseshoe Bat Species, Rhinolophus swinnyi and Rhinolophus simulator

(2016) Gregory L. Mutumi et al.   PLoS One

Global Transcriptional Profiling of Diapause and Climatic Adaptation inDrosophila melanogaster

(2015) Xiaqing Zhao et al.   MOLECULAR BIOLOGY AND EVOLUTION

Differentially expressed genes match bill morphology and plumage despite largely undifferentiated genomes in a Holarctic songbird

(2015) Nicholas A. Mason et al.   MOLECULAR ECOLOGY

Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution?

(2015) Mariano Alvarez et al.   MOLECULAR ECOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Deficiency of Angulin-2/ILDR1, a Tricellular Tight Junction-Associated Membrane Protein, Causes Deafness with Cochlear Hair Cell Degeneration in Mice

(2015) Tomohito Higashi et al.   PLoS One

Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species

(2015) Hadas Hezroni et al.   Cell Reports

ILDR1 deficiency causes degeneration of cochlear outer hair cells and disrupts the structure of the organ of Corti: a mouse model for human DFNB42

(2015) Q. Sang et al.   Biology Open

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Multicore and GPU algorithms for Nussinov RNA folding

(2014) Junjie Li et al.   BMC BIOINFORMATICS

Sensory trait variation in an echolocating bat suggests roles for both selection and plasticity

(2014) Lizelle J Odendaal et al.   BMC EVOLUTIONARY BIOLOGY

ATOH8: a novel marker in human muscle fiber regeneration

(2014) Anne-K. Güttsches et al.   HISTOCHEMISTRY AND CELL BIOLOGY

ILDR1 null mice, a model of human deafness DFNB42, show structural aberrations of tricellular tight junctions and degeneration of auditory hair cells

(2014) Eva L. Morozko et al.   HUMAN MOLECULAR GENETICS

Genetic Variants of CDH23 Associated With Noise-Induced Hearing Loss

(2014) Tomasz Jarema Kowalski et al.   OTOLOGY & NEUROTOLOGY

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AmotL2 links VE-cadherin to contractile actin fibres necessary for aortic lumen expansion

(2014) Sara Hultin et al.   Nature Communications

Comparative inner ear transcriptome analysis between the Rickett’s big-footed bats (Myotis ricketti) and the greater short-nosed fruit bats (Cynopterus sphinx)

(2013) Dong Dong et al.   BMC GENOMICS

Alternative splicing: a pivotal step between eukaryotic transcription and translation

(2013) Alberto R. Kornblihtt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Geographic Variation in the Acoustic Traits of Greater Horseshoe Bats: Testing the Importance of Drift and Ecological Selection in Evolutionary Processes

(2013) Keping Sun et al.   PLoS One

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Identification of new altered genes in rat cochleae with noise-induced hearing loss

(2012) Yu Han et al.   GENE

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders 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

Historical introgression and the persistence of ghost alleles in the intermediate horseshoe bat (Rhinolophus affinis)

(2012) Xiuguang Mao et al.   MOLECULAR ECOLOGY

Comparative studies of gene expression and the evolution of gene regulation

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

The evolution of gene expression and the transcriptome–phenotype relationship

(2011) Peter W. Harrison et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Molecular Evolution: Gene Convergence in Echolocating Mammals

(2010) Gareth Jones   CURRENT BIOLOGY

The communicative potential of bat echolocation pulses

(2010) Gareth Jones et al.   JOURNAL OF COMPARATIVE PHYSIOLOGY A-NEUROETHOLOGY SENSORY NEURAL AND BEHAVIORAL PHYSIOLOGY

Pleistocene climatic cycling drives intra-specific diversification in the intermediate horseshoe bat (Rhinolophus affinis) in Southern China

(2010) XIU GUANG MAO et al.   MOLECULAR ECOLOGY

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

Variability in Echolocation Call Intensity in a Community of Horseshoe Bats: A Role for Resource Partitioning or Communication?

(2010) Maike Schuchmann et al.   PLoS One

β-Actin and γ-Actin Are Each Dispensable for Auditory Hair Cell Development But Required for Stereocilia Maintenance

(2010) Benjamin J. Perrin et al.   PLoS Genetics

Recent Surveys of Bats (Mammalia: Chiroptera) from China. I. Rhinolophidae and Hipposideridae

(2009) Libiao Zhang et al.   ACTA CHIROPTEROLOGICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

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

(2008) Sean B. Carroll   CELL