Integrated single cell data analysis reveals cell specific networks and novel coactivation markers

SCell: integrated analysis of single-cell RNA-seq data

(2016) Aaron Diaz et al.   BIOINFORMATICS

pcaReduce: hierarchical clustering of single cell transcriptional profiles

(2016) Justina žurauskienė et al.   BMC BIOINFORMATICS

Transcriptome Analysis of Murine Olfactory Sensory Neurons during Development Using Single Cell RNA-Seq

(2016) Paul Scholz et al.   CHEMICAL SENSES

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

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

(2015) Chen Xu et al.   BIOINFORMATICS

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Olfactory sensory neurons transiently express multiple olfactory receptors during development

(2015) L. Tan et al.   Molecular Systems Biology

Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes

(2015) János Fuzik et al.   NATURE BIOTECHNOLOGY

Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis

(2015) N. K. Hanchate et al.   SCIENCE

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

(2015) A. Zeisel et al.   SCIENCE

Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq

(2015) Luis R. Saraiva et al.   Scientific Reports

Transcriptional Bursting in Gene Expression: Analytical Results for General Stochastic Models

(2015) Niraj Kumar et al.   PLoS Computational Biology

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue

(2014) Ditte Lovatt et al.   NATURE METHODS

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing

(2014) Dmitry Usoskin et al.   NATURE NEUROSCIENCE

Single-cell RNA-seq: advances and future challenges

(2014) Antoine-Emmanuel Saliba et al.   NUCLEIC ACIDS RESEARCH

Neuronal carbonic anhydrase VII provides GABAergic excitatory drive to exacerbate febrile seizures

(2013) Eva Ruusuvuori et al.   EMBO JOURNAL

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

(2013) Alex K. Shalek et al.   NATURE

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data

(2013) Jong Kim et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Genomics of mature and immature olfactory sensory neurons

(2012) Melissa D. Nickell et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Sonic Hedgehog Expression in Corticofugal Projection Neurons Directs Cortical Microcircuit Formation

(2012) Corey C. Harwell et al.   NEURON

Heparan sulfate proteoglycan syndecan-3 is a novel receptor for GDNF, neurturin, and artemin

(2011) Maxim M. Bespalov et al.   JOURNAL OF CELL BIOLOGY

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

(2011) D. M. Suter et al.   SCIENCE

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS