Cellular diversity and lineage trajectory: insights from mouse single cell transcriptomes

Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development

(2019) Shangli Cheng et al.   Cell Reports

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

(2019) Samuel G. Rodriques et al.   SCIENCE

Cell lineage inference from SNP and scRNA-Seq data

(2019) Jun Ding et al.   NUCLEIC ACIDS RESEARCH

Characterization of cell fate probabilities in single-cell data with Palantir

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

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

(2019) Blanca Pijuan-Sala et al.   NATURE

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming

(2019) Geoffrey Schiebinger et al.   CELL

Transcription Factor Stoichiometry Drives Cell Fate: Single-Cell Proteomics to the Rescue

(2019) Thomas Graf   Cell Stem Cell

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

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments

(2019) Luyi Tian et al.   NATURE METHODS

scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets

(2019) Yingxin Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA

(2019) Jin Xu et al.   eLife

Integration of Single-Cell Genomics Datasets

(2019) Andrew C. Adey   CELL

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

Recording development with single cell dynamic lineage tracing

(2019) Aaron McKenna et al.   DEVELOPMENT

Gene expression across mammalian organ development

(2019) Margarida Cardoso-Moreira et al.   NATURE

Simultaneous quantification of protein–DNA contacts and transcriptomes in single cells

(2019) Koos Rooijers et al.   NATURE BIOTECHNOLOGY

High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer

(2019) Kevin Grosselin et al.   NATURE GENETICS

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

(2019) Guangdun Peng et al.   NATURE

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

(2019)   NATURE

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

(2019) Ricard Argelaguet et al.   NATURE

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

Highly scalable generation of DNA methylation profiles in single cells

(2018) Ryan M Mulqueen 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

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

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

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

(2018) et al.   NATURE

Single-cell analysis reveals lineage segregation in early post-implantation mouse embryos

(2017) Jing Wen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation

(2017) Hisham Mohammed et al.   Cell Reports

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

(2016) Guangdun Peng et al.   DEVELOPMENTAL CELL

Resolving early mesoderm diversification through single-cell expression profiling

(2016) Antonio Scialdone et al.   NATURE

Timing of developmental events in the early mouse embryo

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

The Dynamics of Morphogenesis in the Early Mouse Embryo

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

The Transcriptional and Functional Properties of Mouse Epiblast Stem Cells Resemble the Anterior Primitive Streak

(2013) Yoji Kojima et al.   Cell Stem Cell

Gastrulation: Making and Shaping Germ Layers

(2011) Lila Solnica-Krezel et al.   Annual Review of Cell and Developmental Biology

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