Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data

Challenges in unsupervised clustering of single-cell RNA-seq data

(2019) Vladimir Yu Kiselev et al.   NATURE REVIEWS GENETICS

Single-Cell Transcriptome Analysis Maps the Developmental Track of the Human Heart

(2019) Yueli Cui et al.   Cell Reports

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

Continuous-state HMMs for modeling time-series single-cell RNA-Seq data

(2019) Chieh Lin et al.   BIOINFORMATICS

TSEE: an elastic embedding method to visualize the dynamic gene expression patterns of time series single-cell RNA sequencing data

(2019) Shaokun An et al.   BMC GENOMICS

Childhood cerebellar tumours mirror conserved fetal transcriptional programs

(2019) Maria C. Vladoiu et al.   NATURE

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Inferring population dynamics from single-cell RNA-sequencing time series data

(2019) David S. Fischer et al.   NATURE BIOTECHNOLOGY

Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex

(2019) L. Telley et al.   SCIENCE

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation

(2018) Zhisong He et al.   BMC GENOMICS

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

(2018) Kelly Street et al.   BMC GENOMICS

Reconstructing differentiation networks and their regulation from time series single-cell expression data

(2018) Jun Ding et al.   GENOME RESEARCH

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

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

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

Dissecting the Global Dynamic Molecular Profiles of Human Fetal Kidney Development by Single-Cell RNA Sequencing

(2018) Ping Wang et al.   Cell Reports

TGF-β Family Signaling in Neural and Neuronal Differentiation, Development, and Function

(2017) Emily A. Meyers et al.   Cold Spring Harbor Perspectives in Biology

Developmental Emergence of Adult Neural Stem Cells as Revealed by Single-Cell Transcriptional Profiling

(2017) Scott A. Yuzwa et al.   Cell Reports

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

(2016) Dominic Grün et al.   Cell Stem Cell

Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms Regulating Progenitor Behavior and Productivity

(2016) Noelle D. Dwyer et al.   JOURNAL OF NEUROSCIENCE

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

IGF-I: A Key Growth Factor that Regulates Neurogenesis and Synaptogenesis from Embryonic to Adult Stages of the Brain

(2016) Vanesa Nieto-Estévez et al.   Frontiers in Neuroscience

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Pathway and network analysis of cancer genomes

(2015)   NATURE METHODS

Proliferation control in neural stem and progenitor cells

(2015) Catarina C. F. Homem et al.   NATURE REVIEWS NEUROSCIENCE

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Characterization of primary human skeletal muscle cells from multiple commercial sources

(2013) Jane Owens et al.   IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-ANIMAL

An essential role for p38 MAPK in cerebellar granule neuron precursor proliferation

(2012) Cemile G. Guldal et al.   ACTA NEUROPATHOLOGICA

Building Muscle: Molecular Regulation of Myogenesis

(2012) C. F. Bentzinger et al.   Cold Spring Harbor Perspectives in Biology

Molecular Control of Neurogenesis: A View from the Mammalian Cerebral Cortex

(2012) B. Martynoga et al.   Cold Spring Harbor Perspectives in Biology

Dedifferentiation, transdifferentiation and reprogramming: three routes to regeneration

(2011) Chris Jopling et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A survey of graph edit distance

(2009) Xinbo Gao et al.   PATTERN ANALYSIS AND APPLICATIONS