Transcriptomics of developing embryos and organs: A raising tool for evo-devo

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series

(2014) M. J. Nueda et al.   BIOINFORMATICS

Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation

(2014) Tarmo Äijö et al.   BIOINFORMATICS

Integrated transcriptome analysis of mouse spermatogenesis

(2014) Gennady Margolin et al.   BMC GENOMICS

Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia)

(2014) Gong-Hua Lin et al.   BMC GENOMICS

BLIND ordering of large-scale transcriptomic developmental timecourses

(2014) L. Anavy et al.   DEVELOPMENT

Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data

(2014) J. J. Li et al.   GENOME RESEARCH

Interspecific Variation in Rx1 Expression Controls Opsin Expression and Causes Visual System Diversity in African Cichlid Fishes

(2014) Jane E. Schulte et al.   MOLECULAR BIOLOGY AND EVOLUTION

Natural selection and the genetic basis of osmoregulation in heteromyid rodents as revealed by RNA-seq

(2014) Nicholas J. Marra et al.   MOLECULAR ECOLOGY

Patterning and post-patterning modes of evolutionary digit loss in mammals

(2014) Kimberly L. Cooper et al.   NATURE

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

Genomic basis for the convergent evolution of electric organs

(2014) J. R. Gallant et al.   SCIENCE

CellMix: a comprehensive toolbox for gene expression deconvolution

(2013) R. Gaujoux et al.   BIOINFORMATICS

The genome of Romanomermis culicivorax: revealing fundamental changes in the core developmental genetic toolkit in Nematoda

(2013) Philipp H Schiffer et al.   BMC GENOMICS

Comparative transcriptomics of early dipteran development

(2013) Eva Jiménez-Guri et al.   BMC GENOMICS

Antennal transcriptome profiles of anopheline mosquitoes reveal human host olfactory specialization in Anopheles gambiae

(2013) David C Rinker et al.   BMC GENOMICS

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

(2013) Justin Cotney et al.   CELL

Dictyostelium Development Shows a Novel Pattern of Evolutionary Conservation

(2013) Xiangjun Tian et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of the Eye Transcriptome under Constant Darkness in Sinocyclocheilus Cavefish

(2013) Fanwei Meng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene Coexpression Networks Reveal Key Drivers of Phenotypic Divergence in Lake Whitefish

(2013) Marie Filteau et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative Analysis of the Transcriptome in Tissues Secreting Purple and White Nacre in the Pearl Mussel Hyriopsis cumingii

(2013) Zhiyi Bai et al.   PLoS One

An Integrated Transcriptome-Wide Analysis of Cave and Surface Dwelling Astyanax mexicanus

(2013) Joshua B. Gross et al.   PLoS One

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

(2013) Magali Soumillon et al.   Cell Reports

Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate–Invertebrate Gap

(2013) Philippe Gayral et al.   PLoS Genetics

The Hourglass and the Early Conservation Models—Co-Existing Patterns of Developmental Constraints in Vertebrates

(2013) Barbara Piasecka et al.   PLoS Genetics

DIFFERENCES IN THE REGULATION OF GROWTH AND BIOMINERALIZATION GENES REVEALED THROUGH LONG-TERM COMMON-GARDEN ACCLIMATION AND EXPERIMENTAL GENOMICS IN THE PURPLE SEA URCHIN

(2012) Melissa H. Pespeni et al.   EVOLUTION

RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development

(2012) M. H. Tan et al.   GENOME RESEARCH

Next-generation phylogenomics using a Target Restricted Assembly Method

(2012) Kevin P. Johnson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A transcriptomic hourglass in plant embryogenesis

(2012) Marcel Quint et al.   NATURE

Closely related bird species demonstrate flexibility between beak morphology and underlying developmental programs

(2012) R. Mallarino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The evolution of early animal embryos: conservation or divergence?

(2012) Alex T. Kalinka et al.   TRENDS IN ECOLOGY & EVOLUTION

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

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

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin 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

Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

(2011) Naoki Irie et al.   Nature Communications

Gene expression divergence recapitulates the developmental hourglass model

(2010) Alex T. Kalinka et al.   NATURE

A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns

(2010) Tomislav Domazet-Lošo et al.   NATURE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

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

Highly Divergent Gene Expression Programs Can Lead to Similar Chordate Larval Body Plans

(2009) Daniel Sobral et al.   CURRENT BIOLOGY

Early origin of the bilaterian developmental toolkit

(2009) D. H. Erwin   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

The evolution of cell types in animals: emerging principles from molecular studies

(2008) Detlev Arendt   NATURE REVIEWS GENETICS

Developmental Constraints on Vertebrate Genome Evolution

(2008) Julien Roux et al.   PLoS Genetics