Using neural networks for reducing the dimensions of single-cell RNA-Seq data

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

(2017) Bo Wang et al.   NATURE METHODS

Gene expression inference with deep learning

(2016) Yifei Chen et al.   BIOINFORMATICS

pcaReduce: hierarchical clustering of single cell transcriptional profiles

(2016) Justina žurauskienė et al.   BMC BIOINFORMATICS

Disentangling neural cell diversity using single-cell transcriptomics

(2016) Jean-Francois Poulin et al.   NATURE NEUROSCIENCE

Computational genomics tools for dissecting tumour–immune cell interactions

(2016) Hubert Hackl et al.   NATURE REVIEWS GENETICS

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages

(2016) Robert J. Kimmerling et al.   Nature Communications

Identification of cell types from single-cell transcriptomes using a novel clustering method

(2015) Chen Xu et al.   BIOINFORMATICS

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Somatosensory neuron types identified by high-coverage single-cell RNA-sequencing and functional heterogeneity

(2015) Chang-Lin Li et al.   CELL RESEARCH

Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis

(2015) Jaehoon Shin et al.   Cell Stem Cell

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

(2015) Aleksandra A. Kolodziejczyk et al.   Cell Stem Cell

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

A survey of human brain transcriptome diversity at the single cell level

(2015) Spyros Darmanis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis

(2015) Minzhe Guo et al.   PLoS Computational Biology

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Single-Cell Gene Expression Profiles Define Self-Renewing, Pluripotent, and Lineage Primed States of Human Pluripotent Stem Cells

(2014) Shelley R. Hough et al.   Stem Cell Reports

Identifying proteins controlling key disease signaling pathways

(2013) Anthony Gitter et al.   BIOINFORMATICS

The role of focal adhesion complexes in fibroblast mechanotransduction during scar formation

(2013) Kristine C. Rustad et al.   DIFFERENTIATION

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

(2012) Marcel H Schulz et al.   BMC Systems Biology

Detecting overlapping protein complexes in protein-protein interaction networks

(2012) Tamás Nepusz et al.   NATURE METHODS

IRF6 in development and disease: A mediator of quiescence and differentiation

(2011) Caleb M. Bailey et al.   CELL CYCLE

Mouse chimeras as a system to investigate development, cell and tissue function, disease mechanisms and organ regeneration

(2011) Sigrid Eckardt et al.   CELL CYCLE