Single-cell profiling of healthy human kidney reveals features of sex-based transcriptional programs and tissue-specific immunity

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

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

Wanted: An endothelial cell targeting atlas for nanotherapeutic delivery in allograft organs

(2022) Samuel T. Liburd et al.   AMERICAN JOURNAL OF TRANSPLANTATION

Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling

(2021) Tracy M. Yamawaki et al.   BMC GENOMICS

A Comprehensive Map of mRNAs and Their Isoforms across All 14 Renal Tubule Segments of Mouse

(2021) Lihe Chen et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

A practical solution to pseudoreplication bias in single-cell studies

(2021) Kip D. Zimmerman et al.   Nature Communications

Inference and analysis of cell-cell communication using CellChat

(2021) Suoqin Jin et al.   Nature Communications

Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney

(2021) Yoshiharu Muto et al.   Nature Communications

Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response

(2021) Yuping Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extracellular Granzyme K Modulates Angiogenesis by Regulating Soluble VEGFR1 Release From Endothelial Cells

(2021) Shuang Li et al.   Frontiers in Oncology

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

(2020) Mirjana Efremova et al.   Nature Protocols

Single-cell RNA sequencing of human kidney

(2020) Jinling Liao et al.   Scientific Data

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

(2020) Michal Slyper et al.   NATURE MEDICINE

BREM-SC: a bayesian random effects mixture model for joint clustering single cell multi-omics data

(2020) Xinjun Wang et al.   NUCLEIC ACIDS RESEARCH

SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics

(2020) Simon Cabello-Aguilar et al.   NUCLEIC ACIDS RESEARCH

Distinct fate, dynamics and niches of renal macrophages of bone marrow or embryonic origins

(2020) Fengming Liu et al.   Nature Communications

Sex differences in the response to oxidative and proteolytic stress

(2020) John Tower et al.   Redox Biology

Sex diversity in proximal tubule and endothelial gene expression in mice with ischemic acute kidney injury

(2020) Jose L. Viñas et al.   CLINICAL SCIENCE

Mapping systemic lupus erythematosus heterogeneity at the single-cell level

(2020) Djamel Nehar-Belaid et al.   NATURE IMMUNOLOGY

Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury

(2020) Yuhei Kirita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fatty acid transport protein-2 regulates glycemic control and diabetic kidney disease progression

(2020) Shenaz Khan et al.   JCI Insight

Kidney GATA3+ regulatory T cells play roles in the convalescence stage after antibody-mediated renal injury

(2020) Ryota Sakai et al.   Cellular & Molecular Immunology

Extracellular Matrix Injury of Kidney Allografts in Antibody-Mediated Rejection: A Proteomics Study

(2020) Sergi Clotet-Freixas et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Predicting cell-to-cell communication networks using NATMI

(2020) Rui Hou et al.   Nature Communications

SCENITH: A Flow Cytometry-Based Method to Functionally Profile Energy Metabolism with Single-Cell Resolution

(2020) Rafael J. Argüello et al.   Cell Metabolism

Comprehensive Profiling of an Aging Immune System Reveals Clonal GZMK+ CD8+ T Cells as Conserved Hallmark of Inflammaging

(2020) Denis A. Mogilenko et al.   IMMUNITY

SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data

(2020) Matthew D Young et al.   GigaScience

Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

(2019) Tianyu Wang et al.   BMC BIOINFORMATICS

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

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap

(2019) Jüri Reimand et al.   Nature Protocols

Differential isoform expression and alternative splicing in sex determination in mice

(2019) Benjamín Planells et al.   BMC GENOMICS

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

Representation and relative abundance of cell-type selective markers in whole-kidney RNA-Seq data

(2019) Jevin Z. Clark et al.   KIDNEY INTERNATIONAL

ChEA3: transcription factor enrichment analysis by orthogonal omics integration

(2019) Alexandra B Keenan et al.   NUCLEIC ACIDS RESEARCH

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

c-Kit-positive ILC2s exhibit an ILC3-like signature that may contribute to IL-17-mediated pathologies

(2019) Jochem H. Bernink et al.   NATURE IMMUNOLOGY

Metabolic consequences of cystinuria

(2019) Lauren E. Woodard et al.   BMC Nephrology

SingleCellNet: A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species

(2019) Yuqi Tan et al.   Cell Systems

Proximal Tubule Translational Profiling during Kidney Fibrosis Reveals Proinflammatory and Long Noncoding RNA Expression Patterns with Sexual Dimorphism

(2019) Haojia Wu et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Spatiotemporal immune zonation of the human kidney

(2019) Benjamin J. Stewart et al.   SCIENCE

Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney

(2019) Andrew Ransick et al.   DEVELOPMENTAL CELL

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

(2019) P. Ramachandran et al.   NATURE

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

Molecular determinants of nephron vascular specialization in the kidney

(2019) David M. Barry et al.   Nature Communications

Sexual dimorphism in glutathione metabolism and glutathione-dependent responses

(2019) Luxi Wang et al.   Redox Biology

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

(2018) Kelly Street et al.   BMC GENOMICS

Glycine Amidinotransferase (GATM), Renal Fanconi Syndrome, and Kidney Failure

(2018) Markus Reichold et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Sex dimorphism in ANGII-mediated crosstalk between ACE2 and ACE in diabetic nephropathy

(2018) Sergi Clotet-Freixas et al.   LABORATORY INVESTIGATION

Bias, robustness and scalability in single-cell differential expression analysis

(2018) Charlotte Soneson et al.   NATURE METHODS

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

(2018) Jihwan Park et al.   SCIENCE

Clinical significance of Th17 cells in kidney transplantation

(2018) Byung Ha Chung et al.   KOREAN JOURNAL OF INTERNAL MEDICINE

M3Drop: dropout-based feature selection for scRNASeq

(2018) Tallulah S Andrews et al.   BIOINFORMATICS

Comparative Analysis and Refinement of Human PSC-Derived Kidney Organoid Differentiation with Single-Cell Transcriptomics

(2018) Haojia Wu et al.   Cell Stem Cell

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Female sex reduces the risk of hospital-associated acute kidney injury: a meta-analysis

(2018) Joel Neugarten et al.   BMC Nephrology

Prolonged Ischemia Triggers Necrotic Depletion of Tissue-Resident Macrophages To Facilitate Inflammatory Immune Activation in Liver Ischemia Reperfusion Injury

(2017) Shi Yue et al.   JOURNAL OF IMMUNOLOGY

Stable Isotope Labeling with Amino Acids (SILAC)-Based Proteomics of Primary Human Kidney Cells Reveals a Novel Link between Male Sex Hormones and Impaired Energy Metabolism in Diabetic Kidney Disease

(2017) Sergi Clotet et al.   MOLECULAR & CELLULAR PROTEOMICS

Landscape of X chromosome inactivation across human tissues

(2017) Taru Tukiainen et al.   NATURE

Renal effects of metallothionein induction by zinc in vitro and in vivo

(2017) Moritz Schanz et al.   BMC Nephrology

Comprehensive analysis of normal adjacent to tumor transcriptomes

(2017) Dvir Aran et al.   Nature Communications

mixOmics: An R package for ‘omics feature selection and multiple data integration

(2017) Florian Rohart et al.   PLoS Computational Biology

A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA

(2017) Blue B. Lake et al.   Scientific Reports

Extracellular granzyme K mediates endothelial activation through the cleavage of protease-activated receptor-1

(2016) Mehul Sharma et al.   FEBS Journal

Improved renal ischemia tolerance in females influences kidney transplantation outcomes

(2016) David D. Aufhauser et al.   JOURNAL OF CLINICAL INVESTIGATION

Endogenous Nur77 Is a Specific Indicator of Antigen Receptor Signaling in Human T and B Cells

(2016) Judith F. Ashouri et al.   JOURNAL OF IMMUNOLOGY

OmniPath: guidelines and gateway for literature-curated signaling pathway resources

(2016) Dénes Türei et al.   NATURE METHODS

Mosaic expression of claudins in thick ascending limbs of Henle results in spatial separation of paracellular Na+and Mg2+transport

(2016) Susanne Milatz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hobit and Blimp1 instruct a universal transcriptional program of tissue residency in lymphocytes

(2016) L. K. Mackay et al.   SCIENCE

NAD+ Metabolism and the Control of Energy Homeostasis: A Balancing Act between Mitochondria and the Nucleus

(2015) Carles Cantó et al.   Cell Metabolism

The emerging role of resident memory T cells in protective immunity and inflammatory disease

(2015) Chang Ook Park et al.   NATURE MEDICINE

Resident memory T cells in human health and disease

(2015) R. A. Clark   Science Translational Medicine

Metallothionein deletion exacerbates intermittent hypoxia-induced renal injury in mice

(2015) Hao Wu et al.   TOXICOLOGY LETTERS

Hypoxia and Complement-and-Coagulation Pathways in the Deceased Organ Donor as the Major Target for Intervention to Improve Renal Allograft Outcome

(2015) Jeffrey Damman et al.   TRANSPLANTATION

The Debate about Dendritic Cells and Macrophages in the Kidney

(2015) Catherine Gottschalk et al.   Frontiers in Immunology

Esm1 Modulates Endothelial Tip Cell Behavior and Vascular Permeability by Enhancing VEGF Bioavailability

(2014) Susana F. Rocha et al.   CIRCULATION RESEARCH

Origin and Functions of Tissue Macrophages

(2014) Slava Epelman et al.   IMMUNITY

Dendritic cells and macrophages in the kidney: a spectrum of good and evil

(2014) Natasha M. Rogers et al.   Nature Reviews Nephrology

Origin of regenerating tubular cells after acute kidney injury

(2014) K. Berger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Granzyme K synergistically potentiates LPS-induced cytokine responses in human monocytes

(2014) A. C. Wensink et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Comparison of Inflammatory, Cytoprotective and Injury Gene Expression Profiles in Kidneys From Brain Death and Cardiac Death Donors

(2014) Tanja C. Saat et al.   TRANSPLANTATION

The Role of Metallothionein in Oxidative Stress

(2013) Branislav Ruttkay-Nedecky et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Determination of an Angiotensin II-regulated Proteome in Primary Human Kidney Cells by Stable Isotope Labeling of Amino Acids in Cell Culture (SILAC)

(2013) Ana Konvalinka et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system

(2013) Leo C. K. Wan et al.   NUCLEIC ACIDS RESEARCH

Proximal tubular cells contain a phenotypically distinct, scattered cell population involved in tubular regeneration

(2012) Bart Smeets et al.   JOURNAL OF PATHOLOGY

Tat-enhanced delivery of metallothionein can partially prevent the development of diabetes

(2011) Leejin Park et al.   FREE RADICAL BIOLOGY AND MEDICINE

Human natural killer cells expressing the memory-associated marker CD45RO from tuberculous pleurisy respond more strongly and rapidly than CD45RO− natural killer cells following stimulation with interleukin-12

(2011) Xiaoying Fu et al.   IMMUNOLOGY

Choosing between glycolysis and oxidative phosphorylation: A tumor's dilemma?

(2010) Caroline Jose et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

The Th17 immune response in renal inflammation

(2010) Jan-Eric Turner et al.   KIDNEY INTERNATIONAL

Prostaglandin E2 regulates Th17 cell differentiation and function through cyclic AMP and EP2/EP4 receptor signaling

(2009) Katia Boniface et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Human and Murine Kidneys Show Gender- and Species-Specific Gene Expression Differences in Response to Injury

(2009) Han Si et al.   PLoS One

A Mitochondrial Protein Compendium Elucidates Complex I Disease Biology

(2008) David J. Pagliarini et al.   CELL

ATF3 Protects against Renal Ischemia-Reperfusion Injury

(2008) T. Yoshida et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

SLC2A9 influences uric acid concentrations with pronounced sex-specific effects

(2008) Angela Döring et al.   NATURE GENETICS