FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

Human haematopoietic stem cell lineage commitment is a continuous process

(2017) Lars Velten et al.   NATURE CELL BIOLOGY

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

(2017) Huipeng Li et al.   NATURE GENETICS

Power analysis of single-cell RNA-sequencing experiments

(2017) Valentine Svensson et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Mapping the human DC lineage through the integration of high-dimensional techniques

(2017) Peter See et al.   SCIENCE

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

Massively parallel digital transcriptional profiling of single cells

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

A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation

(2016) S. Nestorowa et al.   BLOOD

Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells

(2016) Vionnie W.C. Yu 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

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Distinct myeloid progenitor–differentiation pathways identified through single-cell RNA sequencing

(2016) Roy Drissen et al.   NATURE IMMUNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development

(2016) Jinmiao Chen et al.   Nature Communications

The Branching Point in Erythro-Myeloid Differentiation

(2015) Leïla Perié et al.   CELL

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

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

(2015) Evan Z. Macosko et al.   CELL

Functionally Distinct Subsets of Lineage-Biased Multipotent Progenitors Control Blood Production in Normal and Regenerative Conditions

(2015) Eric M. Pietras et al.   Cell Stem Cell

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Fundamental properties of unperturbed haematopoiesis from stem cells in vivo

(2015) Katrin Busch et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Distinct routes of lineage development reshape the human blood hierarchy across ontogeny

(2015) F. Notta et al.   SCIENCE

Fate Mapping of Dendritic Cells

(2015) Mateusz Pawel Poltorak et al.   Frontiers in Immunology

Identification of Regulatory Networks in HSCs and Their Immediate Progeny via Integrated Proteome, Transcriptome, and DNA Methylome Analysis

(2014) Nina Cabezas-Wallscheid et al.   Cell Stem Cell

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

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

A Clonogenic Progenitor with Prominent Plasmacytoid Dendritic Cell Developmental Potential

(2013) Nobuyuki Onai et al.   IMMUNITY

Separation of Plasmacytoid Dendritic Cells from B-Cell-Biased Lymphoid Progenitor (BLP) and Pre-Pro B Cells Using PDCA-1

(2013) Kay L. Medina et al.   PLoS One

Convergent differentiation: myeloid and lymphoid pathways to murine plasmacytoid dendritic cells

(2012) P. Sathe et al.   BLOOD

Re(de)fining the dendritic cell lineage

(2012) Ansuman T Satpathy et al.   NATURE IMMUNOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Ly6d marks the earliest stage of B-cell specification and identifies the branchpoint between B-cell and T-cell development

(2009) M. A. Inlay et al.   GENES & DEVELOPMENT

Asynchronous RAG-1 Expression during B Lymphopoiesis

(2009) R. S. Welner et al.   JOURNAL OF IMMUNOLOGY

Hematopoiesis: An Evolving Paradigm for Stem Cell Biology

(2008) Stuart H. Orkin et al.   CELL