The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models

(2021) Chenling Xu et al.   Molecular Systems Biology

Cross-tissue organization of the fibroblast lineage

(2021) Matthew B. Buechler et al.   NATURE

Multimodal analysis for human ex vivo studies shows extensive molecular changes from delays in blood processing

(2021) Adam K. Savage et al.   iScience

Leveraging the Cell Ontology to classify unseen cell types

(2021) Sheng Wang et al.   Nature Communications

RNA splicing programs define tissue compartments and cell types at single cell resolution

(2021) Julia Eve Olivieri et al.   eLife

A single–cell type transcriptomics map of human tissues

(2021) Max Karlsson et al.   Science Advances

Single-cell transcriptional profiles in human skeletal muscle

(2020) Aliza B. Rubenstein et al.   Scientific Reports

Myofibroblast contraction is essential for generating and regenerating the gas-exchange surface

(2020) Rongbo Li et al.   JOURNAL OF CLINICAL INVESTIGATION

Construction of a human cell landscape at single-cell level

(2020) Xiaoping Han et al.   NATURE

Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data

(2020) Gregor Sturm et al.   BIOINFORMATICS

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

(2020)   NATURE

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

A reference single-cell transcriptomic atlas of human skeletal muscle tissue reveals bifurcated muscle stem cell populations

(2020) Andrea J. De Micheli et al.   Skeletal Muscle

Capillary cell-type specialization in the alveolus

(2020) Astrid Gillich et al.   NATURE

Single cell transcriptomics comes of age

(2020) Sarah Aldridge et al.   Nature Communications

A molecular cell atlas of the human lung from single-cell RNA sequencing

(2020) Kyle J. Travaglini et al.   NATURE

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

(2019) Brian Hie et al.   NATURE BIOTECHNOLOGY

CD24 signalling through macrophage Siglec-10 is a target for cancer immunotherapy

(2019) Amira A. Barkal et al.   NATURE

BBKNN: fast batch alignment of single cell transcriptomes

(2019) Krzysztof Polański et al.   BIOINFORMATICS

Single-Cell Transcriptomic Map of the Human and Mouse Bladders

(2019) Zhenyuan Yu et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

The biology and functional importance of MAIT cells

(2019) Dale I. Godfrey et al.   NATURE IMMUNOLOGY

CD47: role in the immune system and application to cancer therapy

(2019) Seyed Mohammad Gheibi Hayat et al.   CELLULAR ONCOLOGY

Immune Responses in Bladder Cancer-Role of Immune Cell Populations, Prognostic Factors and Therapeutic Implications

(2019) Magdalene Joseph et al.   Frontiers in Oncology

Hover-Net: Simultaneous segmentation and classification of nuclei in multi-tissue histology images

(2019) Simon Graham et al.   MEDICAL IMAGE ANALYSIS

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq

(2018) Ida Lindeman et al.   NATURE METHODS

The effects of death and post-mortem cold ischemia on human tissue transcriptomes

(2018) Pedro G. Ferreira et al.   Nature Communications

Detection and removal of barcode swapping in single-cell RNA-seq data

(2018) Jonathan A. Griffiths et al.   Nature Communications

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

An integrated method for quantitative morphometry and oxygen transport modelling in striated muscle

(2018) Abdullah A. Al-Shammari et al.   JOURNAL OF APPLIED PHYSIOLOGY

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

(2018) et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

Tales from the crypt: new insights into intestinal stem cells

(2018) Helmuth Gehart et al.   Nature Reviews Gastroenterology & Hepatology

Human skeletal muscle fibroblasts stimulate in vitro myogenesis and in vivo muscle regeneration

(2017) Abigail L. Mackey et al.   JOURNAL OF PHYSIOLOGY-LONDON

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

(2017) Susanne C van den Brink et al.   NATURE METHODS

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

Transcriptional Profiling of Quiescent Muscle Stem Cells In Vivo

(2017) Cindy T.J. van Velthoven et al.   Cell Reports

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

T cell fate and clonality inference from single-cell transcriptomes

(2016) Michael J T Stubbington et al.   NATURE METHODS

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability

(2016) Alexander D. Diehl et al.   Journal of Biomedical Semantics

Quantifying Memory CD8 T Cells Reveals Regionalization of Immunosurveillance

(2015) Elizabeth M. Steinert et al.   CELL

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

(2015) Evan Z. Macosko et al.   CELL

Tissue-resident macrophages: then and now

(2015) Luke C. Davies et al.   IMMUNOLOGY

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

The actinin family of actin cross-linking proteins – a genetic perspective

(2015) Anita C.H. Murphy et al.   Cell and Bioscience

Lymphocytes Infiltrate the Quadriceps Muscle in Lymphocytic Myocarditis Patients: A Potential New Diagnostic Tool

(2014) Reindert W. Emmens et al.   CANADIAN JOURNAL OF CARDIOLOGY

Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes

(2014) Alberto Santos et al.   NUCLEIC ACIDS RESEARCH

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

IgBLAST: an immunoglobulin variable domain sequence analysis tool

(2013) Jian Ye et al.   NUCLEIC ACIDS RESEARCH

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Three differentiation states risk-stratify bladder cancer into distinct subtypes

(2012) J.-P. Volkmer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pericytes: Developmental, Physiological, and Pathological Perspectives, Problems, and Promises

(2011) Annika Armulik et al.   DEVELOPMENTAL CELL

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Vascular smooth muscle phenotypic diversity and function

(2010) Steven A. Fisher   PHYSIOLOGICAL GENOMICS