RNA velocity—current challenges and future perspectives

Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data

(2020) Aditya Pratapa et al.   NATURE METHODS

Sequencing metabolically labeled transcripts in single cells reveals mRNA turnover strategies

(2020) Nico Battich et al.   SCIENCE

Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe

(2020) Xiaojie Qiu et al.   Cell Systems

Sci-fate characterizes the dynamics of gene expression in single cells

(2020) Junyue Cao et al.   NATURE BIOTECHNOLOGY

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

(2020) Michal Slyper et al.   NATURE MEDICINE

The emergence and promise of single-cell temporal-omics approaches

(2020) Alex R Lederer et al.   CURRENT OPINION IN BIOTECHNOLOGY

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

(2020) Sai Ma et al.   CELL

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

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

(2019) Geoffrey Schiebinger et al.   CELL

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

(2019) Florian Erhard et al.   NATURE

Spatiotemporal structure of cell fate decisions in murine neural crest

(2019) Ruslan Soldatov et al.   SCIENCE

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

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Massively parallel digital transcriptional profiling of single cells

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

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

A Comparison of Deterministic and Stochastic Modeling Approaches for Biochemical Reaction Systems: On Fixed Points, Means, and Modes

(2016) Sayuri K. Hahl et al.   Frontiers in Genetics

Control of Transcript Variability in Single Mammalian Cells

(2015) Nico Battich et al.   CELL

Listening to the noise: random fluctuations reveal gene network parameters

(2009) Brian Munsky et al.   Molecular Systems Biology

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

(2008) Arjun Raj et al.   CELL