Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures

(2017) Thalia E. Chan et al.   Cell Systems

Single-Cell RNA-Sequencing: Assessment of Differential Expression Analysis Methods

(2017) Alessandra Dal Molin et al.   Frontiers in Genetics

Beta-Poisson model for single-cell RNA-seq data analyses

(2016) Trung Nghia Vu et al.   BIOINFORMATICS

Pseudotime estimation: deconfounding single cell time series

(2016) John E. Reid et al.   BIOINFORMATICS

BTR: training asynchronous Boolean models using single-cell expression data

(2016) Chee Yee Lim et al.   BMC BIOINFORMATICS

Discrete distributional differential expression (D3E) - a tool for gene expression analysis of single-cell RNA-seq data

(2016) Mihails Delmans et al.   BMC BIOINFORMATICS

Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference

(2016) Kieran R. Campbell et al.   PLoS Computational Biology

Single-cell RNA-seq reveals distinct injury responses in different types of DRG sensory neurons

(2016) Ganlu Hu et al.   Scientific Reports

NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference

(2015) Pau Bellot et al.   BMC BIOINFORMATICS

Processing, visualising and reconstructing network models from single-cell data

(2015) Steven Woodhouse et al.   IMMUNOLOGY AND CELL BIOLOGY

Decoding the regulatory network of early blood development from single-cell gene expression measurements

(2015) Victoria Moignard et al.   NATURE BIOTECHNOLOGY

Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments

(2015) Ning Leng et al.   NATURE METHODS

Single-Cell Network Analysis Identifies DDIT3 as a Nodal Lineage Regulator in Hematopoiesis

(2015) Cristina Pina et al.   Cell Reports

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

(2015) Catalina A. Vallejos et al.   PLoS Computational Biology

Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal

(2015) Dmitri Papatsenko et al.   Stem Cell Reports

Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing

(2014) Fernando H. Biase et al.   GENOME RESEARCH

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase

(2012) Yosef Buganim et al.   CELL

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods

(2011) Thomas Schaffter et al.   BIOINFORMATICS

DREAM4: Combining Genetic and Dynamic Information to Identify Biological Networks and Dynamical Models

(2010) Alex Greenfield et al.   PLoS One