Single-cell transcriptional diversity is a hallmark of developmental potential

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

(2019) Brian Hie et al.   NATURE BIOTECHNOLOGY

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

Concepts and limitations for learning developmental trajectories from single cell genomics

(2019) Sophie Tritschler et al.   DEVELOPMENT

Clinical and Therapeutic Implications of Cancer Stem Cells

(2019) Michael F. Clarke   NEW ENGLAND JOURNAL OF MEDICINE

Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM

(2019) Huidong Chen et al.   Nature Communications

A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution

(2019) Jonathan S. Packer et al.   SCIENCE

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

(2018) Kelly Street et al.   BMC GENOMICS

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

(2018) Tathiane M. Malta et al.   CELL

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

A Single-Cell Transcriptomic Atlas of Thymus Organogenesis Resolves Cell Types and Developmental Maturation

(2018) Eric M. Kernfeld et al.   IMMUNITY

Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing

(2018) Hannah Hochgerner et al.   NATURE NEUROSCIENCE

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics

(2018) Mireya Plass et al.   SCIENCE

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution

(2018) James A. Briggs et al.   SCIENCE

Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

(2018) Tetsutaro Hayashi et al.   Nature Communications

CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo

(2018) Gabriel N Aughey et al.   eLife

Identification of the Human Skeletal Stem Cell

(2018) Charles K.F. Chan et al.   CELL

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency

(2018) Aleksandra Pękowska et al.   Cell Systems

Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons

(2017) Jiaxu Wang et al.   GENOME RESEARCH

A single-cell transcriptomic analysis reveals precise pathways and regulatory mechanisms underlying hepatoblast differentiation

(2017) Li Yang et al.   HEPATOLOGY

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber et al.   NATURE

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Transcriptional landscape of the human cell cycle

(2017) Yin Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multipotent peripheral glial cells generate neuroendocrine cells of the adrenal medulla

(2017) Alessandro Furlan et al.   SCIENCE

Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling

(2017) Bhupinder Pal et al.   Nature Communications

Transcriptomic and anatomic parcellation of 5-HT3AR expressing cortical interneuron subtypes revealed by single-cell RNA sequencing

(2017) Sarah Frazer et al.   Nature Communications

Single-cell entropy for accurate estimation of differentiation potency from a cell’s transcriptome

(2017) Andrew E. Teschendorff et al.   Nature Communications

Role of epithelial to mesenchymal transition associated genes in mammary gland regeneration and breast tumorigenesis

(2017) Shaheen S. Sikandar et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Single-cell RNA sequencing identifies distinct mouse medial ganglionic eminence cell types

(2017) Ying-Jiun J. Chen et al.   Scientific Reports

Developmental Emergence of Adult Neural Stem Cells as Revealed by Single-Cell Transcriptional Profiling

(2017) Scott A. Yuzwa et al.   Cell Reports

Mouse embryonic stem cells can differentiate via multiple paths to the same state

(2017) James Alexander Briggs et al.   eLife

Reconstructing Lineage Hierarchies of Mouse Uterus Epithelial Development Using Single-Cell Analysis

(2017) Bingbing Wu et al.   Stem Cell Reports

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Mapping the Pairwise Choices Leading from Pluripotency to Human Bone, Heart, and Other Mesoderm Cell Types

(2016) Kyle M. Loh et al.   CELL

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

(2016) Dominic Grün et al.   Cell Stem Cell

Single-cell analysis of mixed-lineage states leading to a binary cell fate choice

(2016) Andre Olsson et al.   NATURE

Tracing haematopoietic stem cell formation at single-cell resolution

(2016) Fan Zhou et al.   NATURE

Hoxb5 marks long-term haematopoietic stem cells and reveals a homogenous perivascular niche

(2016) James Y. Chen et al.   NATURE

A developmental coordinate of pluripotency among mice, monkeys and humans

(2016) Tomonori Nakamura et al.   NATURE

Tissue-specific designs of stem cell hierarchies

(2016) Jane E. Visvader et al.   NATURE CELL BIOLOGY

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

SLICE: determining cell differentiation and lineage based on single cell entropy

(2016) Minzhe Guo et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system

(2016) S. Marques et al.   SCIENCE

Activation of PKA leads to mesenchymal-to-epithelial transition and loss of tumor-initiating ability

(2016) D. R. Pattabiraman et al.   SCIENCE

Single-Cell Transcript Profiles Reveal Multilineage Priming in Early Progenitors Derived from Lgr5 + Intestinal Stem Cells

(2016) Tae-Hee Kim et al.   Cell Reports

Widespread Chromatin Accessibility at Repetitive Elements Links Stem Cells with Human Cancer

(2016) Nicholas C. Gomez et al.   Cell Reports

Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells

(2016) Iain C. Macaulay et al.   Cell Reports

Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity

(2016) Simon Joost et al.   Cell Systems

Induction of Pluripotency in Mouse Somatic Cells with Lineage Specifiers

(2015) Jian Shu et al.   CELL

Identification and Specification of the Mouse Skeletal Stem Cell

(2015) Charles K.F. Chan et al.   CELL

A Unique Gene Regulatory Network Resets the Human Germline Epigenome for Development

(2015) Walfred W.C. Tang 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 RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells

(2015) Monika S. Kowalczyk et al.   GENOME RESEARCH

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrow

(2015) Andreas Schlitzer et al.   NATURE IMMUNOLOGY

Direct Detection of Transcription Factors in Cotyledons during Seedling Development Using Sensitive Silicon-Substrate Photonic Crystal Protein Arrays

(2015) Sarah I. Jones et al.   PLANT PHYSIOLOGY

‘LungGENS’: a web-based tool for mapping single-cell gene expression in the developing lung: Figure 1

(2015) Yina Du et al.   THORAX

Primed and ready: understanding lineage commitment through single cell analysis

(2015) Rachael A. Nimmo et al.   TRENDS IN CELL BIOLOGY

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Fgd5identifies hematopoietic stem cells in the murine bone marrow

(2014) Roi Gazit et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

(2013) G. K. Marinov et al.   GENOME RESEARCH

Type 2 alveolar cells are stem cells in adult lung

(2013) Christina E. Barkauskas et al.   JOURNAL OF CLINICAL INVESTIGATION

Gene-pair expression signatures reveal lineage control

(2013) Merja Heinäniemi et al.   NATURE METHODS

Molecular regulation of stem cell quiescence

(2013) Tom H. Cheung et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MET: A Critical Player in Tumorigenesis and Therapeutic Target

(2013) C. R. Graveel et al.   Cold Spring Harbor Perspectives in Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Lineage Tracing

(2012) Kai Kretzschmar et al.   CELL

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Gene Expression Commons: An Open Platform for Absolute Gene Expression Profiling

(2012) Jun Seita et al.   PLoS One

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

(2010) Alexander Lachmann et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Chromatin plasticity in pluripotent cells

(2010) Shai Melcer et al.   Essays in Biochemistry

Hematopoietic stem cell: self-renewal versus differentiation

(2010) Jun Seita et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

The Glial Nature of Embryonic and Adult Neural Stem Cells

(2009) Arnold Kriegstein et al.   Annual Review of Neuroscience

Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers

(2009) Elgene Lim et al.   NATURE MEDICINE

Hematopoietic Stem Cells Reversibly Switch from Dormancy to Self-Renewal during Homeostasis and Repair

(2008) Anne Wilson et al.   CELL

Stem Cells, the Molecular Circuitry of Pluripotency and Nuclear Reprogramming

(2008) Rudolf Jaenisch et al.   CELL

Transcriptome Analysis of the Normal Human Mammary Cell Commitment and Differentiation Process

(2008) Afshin Raouf et al.   Cell Stem Cell

Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells

(2008) L. V. Sharova et al.   DNA RESEARCH

Regulatory networks define phenotypic classes of human stem cell lines

(2008) Franz-Josef Müller et al.   NATURE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY