Gene expression across mammalian organ development

Repurposing of promoters and enhancers during mammalian evolution

(2018) Francesco N. Carelli et al.   Nature Communications

Timing the developmental origins of mammalian limb diversity

(2017) Karen Sears et al.   GENESIS

Convergent origination of aDrosophila-like dosage compensation mechanism in a reptile lineage

(2017) Ray Marin et al.   GENOME RESEARCH

Comparative anatomy of neonates of the three major mammalian groups (monotremes, marsupials, placentals) and implications for the ancestral mammalian neonate morphotype

(2017) Kirsten Ferner et al.   JOURNAL OF ANATOMY

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Estimating the selective effects of heterozygous protein-truncating variants from human exome data

(2017) Christopher A Cassa et al.   NATURE GENETICS

WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit

(2017) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

Constrained vertebrate evolution by pleiotropic genes

(2017) Haiyang Hu et al.   Nature Ecology & Evolution

High-throughput discovery of novel developmental phenotypes

(2016) Mary E. Dickinson et al.   NATURE

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Patterns of genic intolerance of rare copy number variation in 59,898 human exomes

(2016) Douglas M Ruderfer et al.   NATURE GENETICS

The Cellular and Molecular Landscapes of the Developing Human Central Nervous System

(2016) John C. Silbereis et al.   NEURON

An interactive three-dimensional digital atlas and quantitative database of human development

(2016) Bernadette S. de Bakker et al.   SCIENCE

Fast Nonparametric Clustering of Structured Time-Series

(2015) James Hensman et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Computing and Visualizing Dynamic Time Warping Alignments inR: ThedtwPackage

(2015) Toni Giorgino   Journal of Statistical Software

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

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

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

BLIND ordering of large-scale transcriptomic developmental timecourses

(2014) L. Anavy et al.   DEVELOPMENT

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

(2014) Sophie Pantalacci et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors

(2014) Hong-Mei Zhang et al.   NUCLEIC ACIDS RESEARCH

Hierarchical Bayesian modelling of gene expression time series across irregularly sampled replicates and clusters

(2013) James Hensman et al.   BMC BIOINFORMATICS

Control of mammalian germ cell entry into meiosis

(2013) Chun-Wei Feng et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

mRNA expression, splicing and editing in the embryonic and adult mouse cerebral cortex

(2013) Allissa A Dillman et al.   NATURE NEUROSCIENCE

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data

(2013) Gautier Koscielny et al.   NUCLEIC ACIDS RESEARCH

von Baer's law for the ages: lost and found principles of developmental evolution

(2013) Arhat Abzhanov   TRENDS IN GENETICS

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

Signaling and Transcriptional Networks in Heart Development and Regeneration

(2013) B. G. Bruneau   Cold Spring Harbor Perspectives in Biology

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

(2013) Magali Soumillon et al.   Cell Reports

Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes

(2013) Slavé Petrovski et al.   PLoS Genetics

How to Make a Gonad: Cellular Mechanisms Governing Formation of the Testes and Ovaries

(2012) E.K. Ungewitter et al.   Sexual Development

The evolution of early animal embryos: conservation or divergence?

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

The HUDSEN Atlas: a three-dimensional (3D) spatial framework for studying gene expression in the developing human brain

(2010) Janet Kerwin et al.   JOURNAL OF ANATOMY

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

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

Gonad Morphogenesis in Vertebrates: Divergent Means to a Convergent End

(2009) Tony DeFalco et al.   Annual Review of Cell and Developmental Biology

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

Developmental Constraints on Vertebrate Genome Evolution

(2008) Julien Roux et al.   PLoS Genetics

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics