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

A general and flexible method for signal extraction from single-cell RNA-seq data

(2018) Davide Risso et al.   Nature Communications

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

Pseudotime estimation: deconfounding single cell time series

(2016) John E. Reid et al.   BIOINFORMATICS

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

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

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

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

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 with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis

(2015) Jaehoon Shin et al.   Cell Stem Cell

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall 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

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Multiobjective evolutionary algorithms to identify highly autocorrelated areas: the case of spatial distribution in financially compromised farms

(2011) Carlos R. García-Alonso et al.   ANNALS OF OPERATIONS RESEARCH