A sparse differential clustering algorithm for tracing cell type changes via single-cell RNA-sequencing data

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

(2017) Huipeng Li et al.   NATURE GENETICS

SCOUP: a probabilistic model based on the Ornstein–Uhlenbeck process to analyze single-cell expression data during differentiation

(2016) Hirotaka Matsumoto et al.   BMC BIOINFORMATICS

pcaReduce: hierarchical clustering of single cell transcriptional profiles

(2016) Justina žurauskienė et al.   BMC BIOINFORMATICS

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

(2016) Dominic Grün et al.   Cell Stem Cell

Emerging roles for long noncoding RNAs in skeletal biology and disease

(2016) Nguyen P. T. Huynh et al.   CONNECTIVE TISSUE RESEARCH

A comparative transcriptomic analysis of astrocytes differentiation from human neural progenitor cells

(2016) Marco Magistri et al.   EUROPEAN JOURNAL OF NEUROSCIENCE

Intravitreal implantation of TPP1-transduced stem cells delays retinal degeneration in canine CLN2 neuronal ceroid lipofuscinosis

(2016) Christopher J. Tracy et al.   EXPERIMENTAL EYE RESEARCH

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

The origin and evolution of cell types

(2016) Detlev Arendt et al.   NATURE REVIEWS GENETICS

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

Dynamics of the mouse brain cortical synaptic proteome during postnatal brain development

(2016) Miguel A. Gonzalez-Lozano et al.   Scientific Reports

Normalization and noise reduction for single cell RNA-seq experiments

(2015) Bo Ding et al.   BIOINFORMATICS

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

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

(2015) Jaehoon Shin et al.   Cell Stem Cell

Single-Cell Transcriptomics Reveals a Population of Dormant Neural Stem Cells that Become Activated upon Brain Injury

(2015) Enric Llorens-Bobadilla et al.   Cell Stem Cell

Zic2 Is an Enhancer-Binding Factor Required for Embryonic Stem Cell Specification

(2015) Zhuojuan Luo et al.   MOLECULAR CELL

Genome-wide gene expression profiling of ischemia-reperfusion injury in rat kidney, intestine and skeletal muscle implicate a common involvement of MAPK signaling pathway

(2015) NAI-JEN CHANG et al.   Molecular Medicine Reports

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

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

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

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

(2015) A. Zeisel et al.   SCIENCE

Single-Cell Analysis in Cancer Genomics

(2015) Assieh Saadatpour et al.   TRENDS IN GENETICS

Brain development is impaired in c-fos -/- mice

(2015) Fabiola N. Velazquez et al.   Oncotarget

MLLT11/AF1q is differentially expressed in maturing neurons during development

(2014) Makiko Yamada et al.   GENE EXPRESSION PATTERNS

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

Glial Scar Formation Occurs in the Human Brain after Ischemic Stroke

(2014) Lijie Huang et al.   International Journal of Medical Sciences

Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells

(2014) Jichang Wang et al.   NATURE

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

(2014) Alex K. Shalek et al.   NATURE

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

(2014) Alex A Pollen et al.   NATURE BIOTECHNOLOGY

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

Time-variant clustering model for understanding cell fate decisions

(2014) W. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

(2014) Eugenio Marco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

Discovery of Consensus Gene Signature and Intermodular Connectivity Defining Self-Renewal of Human Embryonic Stem Cells

(2014) Jeffrey J. Kim et al.   STEM CELLS

SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization

(2013) Shintaro Katayama et al.   BIOINFORMATICS

Human iPSC models of neuronal ceroid lipofuscinosis capture distinct effects of TPP1 and CLN3 mutations on the endocytic pathway

(2013) Xenia Lojewski et al.   HUMAN MOLECULAR GENETICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Quantitative assessment of single-cell RNA-sequencing methods

(2013) Angela R Wu et al.   NATURE METHODS

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features

(2012) Chih-yu Chen et al.   BMC GENOMICS

A Sparse-Group Lasso

(2012) Noah Simon et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

The X-Linked Intellectual Disability Protein TSPAN7 Regulates Excitatory Synapse Development and AMPAR Trafficking

(2012) Silvia Bassani et al.   NEURON

Comparison of the effect of lps and pam3 on ventilated lungs

(2012) Hans P Hauber et al.   BMC Pulmonary Medicine

Glypican-5 stimulates rhabdomyosarcoma cell proliferation by activating Hedgehog signaling

(2011) Fuchuan Li et al.   JOURNAL OF CELL BIOLOGY

Single-cell dissection of transcriptional heterogeneity in human colon tumors

(2011) Piero Dalerba et al.   NATURE BIOTECHNOLOGY

Persistent Sonic Hedgehog Signaling in Adult Brain Determines Neural Stem Cell Positional Identity

(2011) Rebecca A. Ihrie et al.   NEURON

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Cis interaction between Semaphorin6A and Plexin-A4 modulates the repulsive response to Sema6A

(2010) Liat Haklai-Topper et al.   EMBO JOURNAL

The Unique Transcriptional Activation Domain of Nuclear Factor-I-X3 Is Critical to Specifically Induce Marker Gene Expression in Astrocytes

(2010) Sandeep K. Singh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Intelligent Choice of the Number of Clusters in K-Means Clustering: An Experimental Study with Different Cluster Spreads

(2010) Mark Ming-Tso Chiang et al.   JOURNAL OF CLASSIFICATION

A Framework for Feature Selection in Clustering

(2010) Daniela M. Witten et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Rapid and dynamic alterations of gene expression profiles of adult porcine bone marrow-derived stem cell in response to hypoxia

(2010) Suna Wang et al.   Stem Cell Research

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and "antibodyome" measures

(2009) L. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nuclear Factor I Isoforms Regulate Gene Expression During the Differentiation of Human Neural Progenitors to Astrocytes

(2009) Katarzyna M. Wilczynska et al.   STEM CELLS

Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling

(2009) King-Hwa Ling et al.   GENOME BIOLOGY

Identification of Genes Particularly Sensitive to Lipopolysaccharide (LPS) in Human Monocytes Induced by Wild-Type versus LPS-Deficient Neisseria meningitidis Strains

(2008) R. Ovstebo et al.   INFECTION AND IMMUNITY

Neuronal differentiation elicited by glial cell line-derived neurotrophic factor and ciliary neurotrophic factor in adrenal chromaffin cell line tsAM5D immortalized with temperature-sensitive SV40 T-antigen

(2008) Tomiyasu Murata et al.   JOURNAL OF NEUROSCIENCE RESEARCH

The Wnt modulator sFRP2 enhances mesenchymal stem cell engraftment, granulation tissue formation and myocardial repair

(2008) M. P. Alfaro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of genes up-regulated by retinoic-acid-induced differentiation of the human neuronal precursor cell line NTERA-2 cl.D1

(2003) Frank Leypoldt et al.   JOURNAL OF NEUROCHEMISTRY