Molecular architecture of lineage allocation and tissue organization in early mouse embryo

Lung regeneration by multipotent stem cells residing at the bronchioalveolar-duct junction

(2019) Qiaozhen Liu et al.   NATURE GENETICS

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

Molecular recording of mammalian embryogenesis

(2019) Michelle M. Chan et al.   NATURE

The emergent landscape of the mouse gut endoderm at single-cell resolution

(2019) Sonja Nowotschin et al.   NATURE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Using single‐cell genomics to understand developmental processes and cell fate decisions

(2018) Jonathan A Griffiths et al.   Molecular Systems Biology

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

(2018) James A. Briggs et al.   SCIENCE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq

(2017) Jun Chen et al.   Nature Protocols

Lineage specification of early embryos and embryonic stem cells at the dawn of enabling technologies

(2017) Guangdun Peng et al.   National Science Review

Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo

(2016) Guangdun Peng et al.   DEVELOPMENTAL CELL

Notochord morphogenesis in mice: Current understanding & open questions

(2016) Sophie Balmer et al.   DEVELOPMENTAL DYNAMICS

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Neuromesodermal progenitors and the making of the spinal cord

(2015) D. Henrique et al.   DEVELOPMENT

Lineage-Specific Profiling Delineates the Emergence and Progression of Naive Pluripotency in Mammalian Embryogenesis

(2015) Thorsten Boroviak et al.   DEVELOPMENTAL CELL

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Statistical significance of variables driving systematic variation in high-dimensional data

(2014) Neo Christopher Chung et al.   BIOINFORMATICS

The developmental hourglass model: a predictor of the basic body plan?

(2014) N. Irie et al.   DEVELOPMENT

SOX17 links gut endoderm morphogenesis and germ layer segregation

(2014) Manuel Viotti et al.   NATURE CELL BIOLOGY

The Dynamics of Morphogenesis in the Early Mouse Embryo

(2014) Jaime A. Rivera-Pérez et al.   Cold Spring Harbor Perspectives in Biology

Using networks to measure similarity between genes: association index selection

(2013) Juan I Fuxman Bass et al.   NATURE METHODS

EMAGE mouse embryo spatial gene expression database: 2014 update

(2013) Lorna Richardson et al.   NUCLEIC ACIDS RESEARCH

Integrating Genomic, Epigenomic, and Transcriptomic Features Reveals Modular Signatures Underlying Poor Prognosis in Ovarian Cancer

(2013) Wei Zhang et al.   Cell Reports

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets

(2010) Hanchuan Peng et al.   NATURE BIOTECHNOLOGY

The Hippo Signaling Pathway Components Lats and Yap Pattern Tead4 Activity to Distinguish Mouse Trophectoderm from Inner Cell Mass

(2009) Noriyuki Nishioka et al.   DEVELOPMENTAL CELL

Making a commitment: cell lineage allocation and axis patterning in the early mouse embryo

(2009) Sebastian J. Arnold et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

The Endoderm of the Mouse Embryo Arises by Dynamic Widespread Intercalation of Embryonic and Extraembryonic Lineages

(2008) Gloria S. Kwon et al.   DEVELOPMENTAL CELL