Kidney Single-Cell Atlas Reveals Myeloid Heterogeneity in Progression and Regression of Kidney Disease

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments

(2020) H. Atakan Ekiz et al.   BMC BIOINFORMATICS

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

ApoE attenuates unresolvable inflammation by complex formation with activated C1q

(2019) Changjun Yin et al.   NATURE MEDICINE

Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution

(2019) Takahiro Masuda et al.   NATURE

Complementary Roles for Single-Nucleus and Single-Cell RNA Sequencing in Kidney Disease Research

(2019) Eoin D. O’Sullivan et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Single-Cell RNA Sequencing Identifies Candidate Renal Resident Macrophage Gene Expression Signatures across Species

(2019) Kurt A. Zimmerman et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury

(2019) Nona Farbehi et al.   eLife

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Tubular GM-CSF Promotes Late MCP-1/CCR2-Mediated Fibrosis and Inflammation after Ischemia/Reperfusion Injury

(2019) Leyuan Xu et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Chronic Kidney Disease Diagnosis and Management

(2019) Teresa K. Chen et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Spatiotemporal immune zonation of the human kidney

(2019) Benjamin J. Stewart et al.   SCIENCE

Resolving the fibrotic niche of human liver cirrhosis at single-cell level

(2019) P. Ramachandran et al.   NATURE

Single-cell immune landscape of human atherosclerotic plaques

(2019) Dawn M. Fernandez et al.   NATURE MEDICINE

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

(2018) Kelly Street et al.   BMC GENOMICS

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease

(2018) Jihwan Park et al.   SCIENCE

Advantages of Single-Nucleus over Single-Cell RNA Sequencing of Adult Kidney: Rare Cell Types and Novel Cell States Revealed in Fibrosis

(2018) Haojia Wu et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarction

(2018) Sarah A. Dick et al.   NATURE IMMUNOLOGY

A Single-Cell Sequencing Guide for Immunologists

(2018) Peter See et al.   Frontiers in Immunology

Breast Regression Protein–39/Chitinase 3–Like 1 Promotes Renal Fibrosis after Kidney InjuryviaActivation of Myofibroblasts

(2017) Tinika A. Montgomery et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Proliferation Drives Aging-Related Functional Decline in a Subpopulation of the Hematopoietic Stem Cell Compartment

(2017) Kristina Kirschner et al.   Cell Reports

Urinary peptidomics in a rodent model of diabetic nephropathy highlights epidermal growth factor as a biomarker for renal deterioration in patients with type 2 diabetes

(2016) Boris B. Betz et al.   KIDNEY INTERNATIONAL

A single heterochronic blood exchange reveals rapid inhibition of multiple tissues by old blood

(2016) Justin Rebo et al.   Nature Communications

destiny: diffusion maps for large-scale single-cell data in R

(2015) Philipp Angerer et al.   BIOINFORMATICS

A systematic analysis of worldwide population-based data on the global burden of chronic kidney disease in 2010

(2015) Katherine T. Mills et al.   KIDNEY INTERNATIONAL

Proximal tubule-derived colony stimulating factor-1 mediates polarization of renal macrophages and dendritic cells, and recovery in acute kidney injury

(2015) Yinqiu Wang et al.   KIDNEY INTERNATIONAL

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Tissue transcriptome-driven identification of epidermal growth factor as a chronic kidney disease biomarker

(2015) Wenjun Ju et al.   Science Translational Medicine

CX3CR1 deficiency promotes muscle repair and regeneration by enhancing macrophage ApoE production

(2015) Ludovic Arnold et al.   Nature Communications

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

(2014) Simone Picelli et al.   Nature Protocols

Tight blood glycaemic and blood pressure control in experimental diabetic nephropathy reduces extracellular matrix production without regression of fibrosis

(2014) Bryan R. Conway et al.   NEPHROLOGY

A Murine Model of Irreversible and Reversible Unilateral Ureteric Obstruction

(2014) Emily E. Hesketh et al.   Jove-Journal of Visualized Experiments

Nr4a1-Dependent Ly6Clow Monocytes Monitor Endothelial Cells and Orchestrate Their Disposal

(2013) Leo M. Carlin et al.   CELL

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

CSF-1 signaling mediates recovery from acute kidney injury

(2012) Ming-Zhi Zhang et al.   JOURNAL OF CLINICAL INVESTIGATION

Kidney Function Can Improve in Patients with Hypertensive CKD

(2012) B. Hu et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Differential Ly-6C expression identifies the recruited macrophage phenotype, which orchestrates the regression of murine liver fibrosis

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

Macrophages in Kidney Repair and Regeneration

(2011) J. S. Duffield   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

The Renal Mononuclear Phagocytic System

(2011) P. J. Nelson et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Distinct Macrophage Phenotypes Contribute to Kidney Injury and Repair

(2011) S. Lee et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Lower estimated glomerular filtration rate and higher albuminuria are associated with mortality and end-stage renal disease. A collaborative meta-analysis of kidney disease population cohorts

(2011) Brad C. Astor et al.   KIDNEY INTERNATIONAL

The transcription factor NR4A1 (Nur77) controls bone marrow differentiation and the survival of Ly6C− monocytes

(2011) Richard N Hanna et al.   NATURE IMMUNOLOGY

Macrophage Wnt7b is critical for kidney repair and regeneration

(2010) S.-L. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bone Marrow Ly6Chigh Monocytes Are Selectively Recruited to Injured Kidney and Differentiate into Functionally Distinct Populations

(2009) S. L. Lin et al.   JOURNAL OF IMMUNOLOGY

Macrophage diversity in renal injury and repair

(2008) Sharon D. Ricardo et al.   JOURNAL OF CLINICAL INVESTIGATION

Role of Remission Clinics in the Longitudinal Treatment of CKD

(2008) P. Ruggenenti et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY