Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq

Interpretable dimensionality reduction of single cell transcriptome data with deep generative models

(2018) Jiarui Ding et al.   Nature Communications

Dissection of Influenza Infection In Vivo by Single-Cell RNA Sequencing

(2018) Yael Steuerman et al.   Cell Systems

Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain

(2018) Arpiar Saunders et al.   CELL

Enter the Matrix: Factorization Uncovers Knowledge from Omics

(2018) Genevieve L. Stein-O’Brien et al.   TRENDS IN GENETICS

Distinct Roles of Different Presynaptic and Postsynaptic NCAM Isoforms in Early Motoneuron–Myotube Interactions Required for Functional Synapse Formation

(2017) Katsusuke Hata et al.   JOURNAL OF NEUROSCIENCE

Cell diversity and network dynamics in photosensitive human brain organoids

(2017) Giorgia Quadrato et al.   NATURE

Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex

(2017) Sinisa Hrvatin et al.   NATURE NEUROSCIENCE

RTN1-C mediates cerebral ischemia/reperfusion injury via ER stress and mitochondria-associated apoptosis pathways

(2017) Lingli Gong et al.   Cell Death & Disease

Controlling for Confounding Effects in Single Cell RNA Sequencing Studies Using both Control and Target Genes

(2017) Mengjie Chen et al.   Scientific Reports

Dishing out mini-brains: Current progress and future prospects in brain organoid research

(2016) Iva Kelava et al.   DEVELOPMENTAL BIOLOGY

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

Long noncoding RNA MEG3 activation of p53 mediates ischemic neuronal death in stroke

(2016) Honglin Yan et al.   NEUROSCIENCE

MEF2C regulates cortical inhibitory and excitatory synapses and behaviors relevant to neurodevelopmental disorders

(2016) Adam J Harrington et al.   eLife

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure

(2016) Maayan Baron et al.   Cell Systems

Inhibition of 14-3-3 Proteins Leads to Schizophrenia-Related Behavioral Phenotypes and Synaptic Defects in Mice

(2015) Molly Foote et al.   BIOLOGICAL PSYCHIATRY

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

(2015) Allon M. Klein et al.   CELL

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

Computational assignment of cell-cycle stage from single-cell transcriptome data

(2015) Antonio Scialdone et al.   METHODS

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Hypoxia-induced gene expression results from selective mRNA partitioning to the endoplasmic reticulum

(2015) Jonas J. Staudacher et al.   NUCLEIC ACIDS RESEARCH

14-3-3ζ deficient mice in the BALB/c background display behavioural and anatomical defects associated with neurodevelopmental disorders

(2015) Xiangjun Xu et al.   Scientific Reports

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

(2014) Alex K. Shalek 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

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

Deciphering Signatures of Mutational Processes Operative in Human Cancer

(2013) Ludmil B. Alexandrov et al.   Cell Reports

A Framework for Regularized Non-Negative Matrix Factorization, with Application to the Analysis of Gene Expression Data

(2012) Leo Taslaman et al.   PLoS One

C. elegans bicd-1, homolog of the Drosophila dynein accessory factor Bicaudal D, regulates the branching of PVD sensory neuron dendrites

(2011) C. Aguirre-Chen et al.   DEVELOPMENT

Bicaudal-D binds clathrin heavy chain to promote its transport and augments synaptic vesicle recycling

(2010) Xuan Li et al.   EMBO JOURNAL

SynCAM 1 Adhesion Dynamically Regulates Synapse Number and Impacts Plasticity and Learning

(2010) Elissa M. Robbins et al.   NEURON

The 14-3-3ζ Protein Binds to the Cell Adhesion Molecule L1, Promotes L1 Phosphorylation by CKII and Influences L1-Dependent Neurite Outgrowth

(2010) Elisa M. Ramser et al.   PLoS One

Analysis of human muscle stem cells reveals a differentiation-resistant progenitor cell population expressing Pax7 capable of self-renewal

(2008) Bradley Pawlikowski et al.   DEVELOPMENTAL DYNAMICS

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Hypoxic Inhibition of Nonsense-Mediated RNA Decay Regulates Gene Expression and the Integrated Stress Response

(2008) L. B. Gardner   MOLECULAR AND CELLULAR BIOLOGY

Genome-Wide Analysis of MEF2 Transcriptional Program Reveals Synaptic Target Genes and Neuronal Activity-Dependent Polyadenylation Site Selection

(2008) Steven W. Flavell et al.   NEURON

MEF2C, a transcription factor that facilitates learning and memory by negative regulation of synapse numbers and function

(2008) A. C. Barbosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA