Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

(2022) Ao Chen et al.   CELL

High-resolution 3D spatiotemporal transcriptomic maps of developing Drosophila embryos and larvae

(2022) Mingyue Wang et al.   DEVELOPMENTAL CELL

Alignment and integration of spatial transcriptomics data

(2022) Ron Zeira et al.   NATURE METHODS

Hijacking of transcriptional condensates by endogenous retroviruses

(2022) Vahid Asimi et al.   NATURE GENETICS

Robust decomposition of cell type mixtures in spatial transcriptomics

(2021) Dylan M. Cable et al.   NATURE BIOTECHNOLOGY

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis

(2021) T. Lohoff et al.   NATURE BIOTECHNOLOGY

Embryo-scale, single-cell spatial transcriptomics

(2021) Sanjay R. Srivatsan et al.   SCIENCE

Diverse epigenetic mechanisms maintain parental imprints within the embryonic and extraembryonic lineages

(2021) Daniel Andergassen et al.   DEVELOPMENTAL CELL

A single cell transcriptome atlas of the developing zebrafish hindbrain

(2020) Monica Tambalo et al.   DEVELOPMENT

Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids

(2020) Susanne C. van den Brink et al.   NATURE

Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas

(2020) Reuben Moncada et al.   NATURE BIOTECHNOLOGY

Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies

(2020) Shiquan Sun et al.   NATURE METHODS

Epigenetic regulator function through mouse gastrulation

(2020) Stefanie Grosswendt et al.   NATURE

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma

(2020) Andrew L. Ji et al.   CELL

Redundant type II cadherins define neuroepithelial cell states for cytoarchitectonic robustness

(2020) Kou Hiraga et al.   Communications Biology

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

(2020) Robert R. Stickels et al.   NATURE BIOTECHNOLOGY

Mouse embryonic stem cells self-organize into trunk-like structures with neural tube and somites

(2020) Jesse V. Veenvliet et al.   SCIENCE

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

(2019) Samuel G. Rodriques et al.   SCIENCE

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord

(2019) Julien Delile et al.   DEVELOPMENT

Molecular recording of mammalian embryogenesis

(2019) Michelle M. Chan et al.   NATURE

Spatiotemporal structure of cell fate decisions in murine neural crest

(2019) Ruslan Soldatov et al.   SCIENCE

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

(2019) Guangdun Peng et al.   NATURE

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

FOXG1 Dose in Brain Development

(2019) Nuwan C. Hettige et al.   Frontiers in Pediatrics

Multi-omics profiling of mouse gastrulation at single-cell resolution

(2019) Ricard Argelaguet et al.   NATURE

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

The neural border: Induction, specification and maturation of the territory that generates neural crest cells

(2018) Patrick Pla et al.   DEVELOPMENTAL BIOLOGY

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation

(2018) Ximena Ibarra-Soria et al.   NATURE CELL BIOLOGY

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

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity

(2018) Emelie Berglund et al.   Nature Communications

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

In Toto Imaging and Reconstruction of Post-Implantation Mouse Development at the Single-Cell Level

(2018) Katie McDole et al.   CELL

Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer

(2017) Zachary D. Smith et al.   NATURE

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

(2017) Terrence F Meehan et al.   NATURE GENETICS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Sfrp5 identifies murine cardiac progenitors for all myocardial structures except for the right ventricle

(2017) Masayuki Fujii et al.   Nature Communications

Collinear Hox-Hox interactions are involved in patterning the vertebrate anteroposterior (A-P) axis

(2017) Kongju Zhu et al.   PLoS One

Expression of Barhl2 and its relationship with Pax6 expression in the forebrain of the mouse embryo

(2016) Elisa V. Parish et al.   BMC NEUROSCIENCE

High-throughput discovery of novel developmental phenotypes

(2016) Mary E. Dickinson et al.   NATURE

Transgenic increase of Wnt7b in neural progenitor cells decreases expression of T-domain transcription factors and impairs neuronal differentiation

(2014) Panagiotis Papachristou et al.   BRAIN RESEARCH

The Dynamics of Morphogenesis in the Early Mouse Embryo

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

Novel mechanisms that pattern and shape the midbrain-hindbrain boundary

(2013) Sebastian Dworkin et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Wnt Signal Specifies the Intrathalamic Limit and Its Organizer Properties by Regulating Shh Induction in the Alar Plate

(2013) A. Martinez-Ferre et al.   JOURNAL OF NEUROSCIENCE

Large-scale gene function analysis with the PANTHER classification system

(2013) Huaiyu Mi et al.   Nature Protocols

Morphogenetic movements in the neural plate and neural tube: mouse

(2013) R'ada Massarwa et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Shh and Gli3 regulate formation of the telencephalic–diencephalic junction and suppress an isthmus-like signaling source in the forebrain

(2011) Brian G. Rash et al.   DEVELOPMENTAL BIOLOGY

Tbx6-dependent Sox2 regulation determines neural or mesodermal fate in axial stem cells

(2011) Tatsuya Takemoto et al.   NATURE

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

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

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

Pattern formation in the vertebrate neural tube: a sonic hedgehog morphogen-regulated transcriptional network

(2008) E. Dessaud et al.   DEVELOPMENT