Screening single-cell trajectories via continuity assessments for cell transition potential

Three tissue resident macrophage subsets coexist across organs with conserved origins and life cycles

(2022) Sarah A. Dick et al.   Science Immunology

Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury

(2022) Christian Hinze et al.   Genome Medicine

Context-dependent gene regulatory network reveals regulation dynamics and cell trajectories using unspliced transcripts

(2022) Yueh-Hua Tu et al.   BRIEFINGS IN BIOINFORMATICS

Non-canonical Wnt/PCP signalling regulates intestinal stem cell lineage priming towards enteroendocrine and Paneth cell fates

(2021) Anika Böttcher et al.   NATURE CELL BIOLOGY

Generalized and scalable trajectory inference in single-cell omics data with VIA

(2021) Shobana V. Stassen et al.   Nature Communications

The reactome pathway knowledgebase 2022

(2021) Marc Gillespie et al.   NUCLEIC ACIDS RESEARCH

Construction of a human cell landscape at single-cell level

(2020) Xiaoping Han et al.   NATURE

Deciphering human macrophage development at single-cell resolution

(2020) Zhilei Bian et al.   NATURE

Lineage tracing meets single-cell omics: opportunities and challenges

(2020) Daniel E. Wagner et al.   NATURE REVIEWS GENETICS

A single-cell transcriptomic atlas characterizes ageing tissues in the mouse

(2020)   NATURE

Single-cell sequencing reveals clonal expansions of pro-inflammatory synovial CD8 T cells expressing tissue-homing receptors in psoriatic arthritis

(2020) Frank Penkava et al.   Nature Communications

Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis

(2020) Anna Maria Ranzoni et al.   Cell Stem Cell

A single-cell molecular map of mouse gastrulation and early organogenesis

(2019) Blanca Pijuan-Sala et al.   NATURE

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

scSLAM-seq reveals core features of transcription dynamics in single cells

(2019) Florian Erhard et al.   NATURE

TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8 T Cell-Fate Decision

(2019) Zeyu Chen et al.   IMMUNITY

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Synovial IL‐17A+ CD8+ T cells display a polyfunctional, pro‐inflammatory and tissue‐resident memory phenotype and function in psoriatic arthritis

(2019) Kathryn J.A. Steel et al.   Arthritis & Rheumatology

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

(2018) Kelly Street et al.   BMC GENOMICS

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

The pathogenesis of psoriatic arthritis

(2018) Douglas J Veale et al.   LANCET

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

(2018) Bushra Raj et al.   NATURE BIOTECHNOLOGY

Distinct progenitor lineages contribute to the heterogeneity of plasmacytoid dendritic cells

(2018) Patrick Fernandes Rodrigues et al.   NATURE IMMUNOLOGY

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

(2018) James A. Briggs et al.   SCIENCE

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

(2018) et al.   NATURE

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber et al.   NATURE

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

(2017) Peter See et al.   SCIENCE

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

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

Migration of encephalitogenic CD8 T cells into the central nervous system is dependent on the α4β1-integrin

(2015) Guillaume Martin-Blondel et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Differential effects of α4β7 and GPR15 on homing of effector and regulatory T cells from patients with UC to the inflamed gut in vivo

(2015) Anika Fischer et al.   GUT

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

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

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Acute kidney injury

(2012) Rinaldo Bellomo et al.   LANCET

Mechanisms of T Cell Development and Transformation

(2011) Ute Koch et al.   Annual Review of Cell and Developmental Biology

Distinct ATOH1 and Neurog3 requirements define tuft cells as a new secretory cell type in the intestinal epithelium

(2011) François Gerbe et al.   JOURNAL OF CELL BIOLOGY

On the Composition of the Preimmune Repertoire of T Cells Specific for Peptide–Major Histocompatibility Complex Ligands

(2010) Marc K. Jenkins et al.   Annual Review of Immunology

Intestinal Crypt Homeostasis Results from Neutral Competition between Symmetrically Dividing Lgr5 Stem Cells

(2010) Hugo J. Snippert et al.   CELL

Intestinal Stem Cell Replacement Follows a Pattern of Neutral Drift

(2010) C. Lopez-Garcia et al.   SCIENCE