Generalizing RNA velocity to transient cell states through dynamical modeling

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics

(2019) Leif S. Ludwig et al.   CELL

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis

(2019) Aimée Bastidas-Ponce et al.   DEVELOPMENT

Concepts and limitations for learning developmental trajectories from single cell genomics

(2019) Sophie Tritschler et al.   DEVELOPMENT

scSLAM-seq reveals core features of transcription dynamics in single cells

(2019) Florian Erhard et al.   NATURE

scGen predicts single-cell perturbation responses

(2019) Mohammad Lotfollahi et al.   NATURE METHODS

Beyond bulk: a review of single cell transcriptomics methodologies and applications

(2019) Ashwinikumar Kulkarni et al.   CURRENT OPINION IN BIOTECHNOLOGY

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

(2019) Chenglong Xia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

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

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

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

(2018) Bushra Raj et al.   NATURE BIOTECHNOLOGY

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing

(2018) Hannah Hochgerner et al.   NATURE NEUROSCIENCE

Fundamental limits on dynamic inference from single-cell snapshots

(2018) Caleb Weinreb et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Understanding human fetal pancreas development using subpopulation sorting, RNA sequencing and single-cell profiling

(2018) Cyrille Ramond et al.   DEVELOPMENT

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Lineage dynamics of murine pancreatic development at single-cell resolution

(2018) Lauren E. Byrnes et al.   Nature Communications

Single-Cell Transcriptome Profiling of Mouse and hESC-Derived Pancreatic Progenitors

(2018) Nicole A.J. Krentz et al.   Stem Cell Reports

Efficient and Robust Approximate Nearest Neighbor Search Using Hierarchical Navigable Small World Graphs

(2018) Yu A. Malkov et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Synthetic recording and in situ readout of lineage information in single cells

(2017) Kirsten L. Frieda et al.   NATURE

A Single-Cell RNA Sequencing Study Reveals Cellular and Molecular Dynamics of the Hippocampal Neurogenic Niche

(2017) Benedetta Artegiani et al.   Cell Reports

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

(2017) Fabian Fröhlich et al.   PLoS Computational Biology

Computational methods for trajectory inference from single-cell transcriptomics

(2016) Robrecht Cannoodt et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Precommitment low-levelNeurog3expression defines a long-lived mitotic endocrine-biased progenitor pool that drives production of endocrine-committed cells

(2016) Matthew E. Bechard et al.   GENES & DEVELOPMENT

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion

(2016) Fabian Fröhlich et al.   PLoS Computational Biology

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Insulin regulates carboxypeptidase E by modulating translation initiation scaffolding protein eIF4G1 in pancreatic   cells

(2014) C. W. Liew et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Status epilepticus triggers early and late alterations in brain-derived neurotrophic factor and NMDA glutamate receptor Grin2b DNA methylation levels in the hippocampus

(2013) R. Ryley Parrish et al.   NEUROSCIENCE

Altered expression of synapse and glutamate related genes in post-mortem hippocampus of depressed subjects

(2012) Vanja Duric et al.   INTERNATIONAL JOURNAL OF NEUROPSYCHOPHARMACOLOGY

Listening to the noise: random fluctuations reveal gene network parameters

(2009) Brian Munsky et al.   Molecular Systems Biology

Stochastic modelling for quantitative description of heterogeneous biological systems

(2009) Darren J. Wilkinson   NATURE REVIEWS GENETICS

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT