The changing mouse embryo transcriptome at whole tissue and single-cell resolution

Spatiotemporal DNA methylome dynamics of the developing mouse fetus

(2020) Yupeng He et al.   NATURE

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

An atlas of dynamic chromatin landscapes in mouse fetal development

(2020) David U. Gorkin et al.   NATURE

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

A single-cell molecular map of mouse gastrulation and early organogenesis

(2019) Blanca Pijuan-Sala et al.   NATURE

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

Dynamics of microRNA expression during mouse prenatal development

(2019) Sorena Rahmanian et al.   GENOME RESEARCH

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Expression reflects population structure

(2018) Brielin C. Brown et al.   PLoS Genetics

A Twist2-dependent progenitor cell contributes to adult skeletal muscle

(2017) Ning Liu et al.   NATURE CELL BIOLOGY

Multimodal profiling of single-cell morphology, electrophysiology, and gene expression using Patch-seq

(2017) Cathryn R Cadwell et al.   Nature Protocols

seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus

(2017) Sheel Shah et al.   NEURON

Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation

(2017) Yu Zhang et al.   NUCLEIC ACIDS RESEARCH

Transcriptional control of chondrocyte specification and differentiation

(2017) Chia-Feng Liu et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Odd skipped-related 1 identifies a population of embryonic fibro-adipogenic progenitors regulating myogenesis during limb development

(2017) Pedro Vallecillo-García et al.   Nature Communications

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells

(2016) Gioele La Manno et al.   CELL

Resolving early mesoderm diversification through single-cell expression profiling

(2016) Antonio Scialdone et al.   NATURE

Jointly characterizing epigenetic dynamics across multiple human cell types

(2016) Yu Zhang et al.   NUCLEIC ACIDS RESEARCH

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

A pathway to bone: signaling molecules and transcription factors involved in chondrocyte development and maturation

(2015) E. Kozhemyakina et al.   DEVELOPMENT

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

PAX3 and PAX7 as upstream regulators of myogenesis

(2015) Margaret Buckingham et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

A promoter-level mammalian expression atlas

(2014)   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype

(2014) James C McGann et al.   eLife

From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

(2013) G. K. Marinov et al.   GENOME RESEARCH

Satellite Cells and the Muscle Stem Cell Niche

(2013) Hang Yin et al.   PHYSIOLOGICAL REVIEWS

B-Cell Progenitors and Precursors Change Their Microenvironment in Fetal Liver During Early Development

(2013) Motokazu Tsuneto et al.   STEM CELLS

Genetic and Epigenetic Determinants of Neurogenesis and Myogenesis

(2012) Abraham P. Fong et al.   DEVELOPMENTAL CELL

Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting

(2012) P. Arnold et al.   GENOME RESEARCH

Integrative analysis of gene expression and copy number alterations using canonical correlation analysis

(2010) Charlotte Soneson et al.   BMC BIOINFORMATICS

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

Transcriptome analyses based on genetic screens for Pax3 myogenic targets in the mouse embryo

(2010) Mounia Lagha et al.   BMC GENOMICS

Connective tissue fibroblasts and Tcf4 regulate myogenesis

(2010) S. J. Mathew et al.   DEVELOPMENT

Identification and characterization of a non-satellite cell muscle resident progenitor during postnatal development

(2010) Kathryn J. Mitchell et al.   NATURE CELL BIOLOGY

Transcriptional networks controlling skeletal development

(2009) Christine Hartmann   CURRENT OPINION IN GENETICS & DEVELOPMENT

All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues

(2008) Julian M Rozenberg et al.   BMC GENOMICS