The single-cell transcriptional landscape of mammalian organogenesis

Ultraconserved Enhancers Are Required for Normal Development

(2018) Diane E. Dickel et al.   CELL

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Highly scalable generation of DNA methylation profiles in single cells

(2018) Ryan M Mulqueen et al.   NATURE BIOTECHNOLOGY

Defining the earliest step of cardiovascular lineage segregation by single-cell RNA-seq

(2018) Fabienne Lescroart et al.   SCIENCE

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

(2018) Alexander B. Rosenberg et al.   SCIENCE

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution

(2018) James A. Briggs et al.   SCIENCE

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

Developmental diversification of cortical inhibitory interneurons

(2018) Christian Mayer et al.   NATURE

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

RSPO2 inhibition of RNF43 and ZNRF3 governs limb development independently of LGR4/5/6

(2018) Emmanuelle Szenker-Ravi et al.   NATURE

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Principal Graph and Structure Learning Based on Reversed Graph Embedding

(2017) Qi Mao et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium

(2017) Terrence F Meehan et al.   NATURE GENETICS

Sequencing thousands of single-cell genomes with combinatorial indexing

(2017) Sarah A Vitak et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

Limb development: a paradigm of gene regulation

(2017) Florence Petit et al.   NATURE REVIEWS GENETICS

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

High-throughput discovery of novel developmental phenotypes

(2016) Mary E. Dickinson et al.   NATURE

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing

(2016) Graham Heimberg et al.   Cell Systems

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Identification and characterization of mouse otic sensory lineage genes

(2015) Byron H. Hartman et al.   Frontiers in Cellular Neuroscience

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

(2014) S. Anders et al.   BIOINFORMATICS

deML: robust demultiplexing of Illumina sequences using a likelihood-based approach

(2014) Gabriel Renaud et al.   BIOINFORMATICS

Variations in the Efficiency of Lineage Marking and Ablation Confound Distinctions between Myogenic Cell Populations

(2014) Glenda Comai et al.   DEVELOPMENTAL CELL

Formation of Proximal and Anterior Limb Skeleton Requires Early Function of Irx3 and Irx5 and Is Negatively Regulated by Shh Signaling

(2014) Danyi Li et al.   DEVELOPMENTAL CELL

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

(2014) Andrew Adey et al.   GENOME RESEARCH

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing

(2014) Sasan Amini et al.   NATURE GENETICS

Timing of developmental events in the early mouse embryo

(2014) Yoji Kojima et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Tbx20 acts upstream of Wnt signaling to regulate endocardial cushion formation and valve remodeling during mouse cardiogenesis

(2013) X. Cai et al.   DEVELOPMENT

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Skin melanocytes: biology and development

(2013) Mirosława Cichorek et al.   Postepy Dermatologii i Alergologii

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Insulin-Like Growth Factor 2 in Development and Disease: A Mini-Review

(2012) Daniel Bergman et al.   GERONTOLOGY

F-Spondin/spon1b Expression Patterns in Developing and Adult Zebrafish

(2012) Veronica Akle et al.   PLoS One

Sclerotome-derived Slit1 drives directional migration and differentiation of Robo2-expressing pioneer myoblasts

(2011) O. Halperin-Barlev et al.   DEVELOPMENT

Transcriptional mechanisms regulating skeletal muscle differentiation, growth and homeostasis

(2011) Thomas Braun et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Evidence of an epithelial stem/progenitor cell hierarchy in the adult mouse lung

(2010) J. L. McQualter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gpnmb is a melanosome-associated glycoprotein that contributes to melanocyte/keratinocyte adhesion in a RGD-dependent fashion

(2009) Mizuki Tomihari et al.   EXPERIMENTAL DERMATOLOGY

Hedgehog: functions and mechanisms

(2008) M. Varjosalo et al.   GENES & DEVELOPMENT

Efficient Array-Based Identification of Novel Cardiac Genes through Differentiation of Mouse ESCs

(2008) Ronald A. Miller et al.   PLoS One