Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments

Anomalous collapses of Nares Strait ice arches leads to enhanced export of Arctic sea ice

(2021) G. W. K. Moore et al.   Nature Communications

Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation

(2021) Julie Jerber et al.   NATURE GENETICS

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

(2021) Yoshiharu Muto et al.   Nature Communications

Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets

(2021) Zhen Miao et al.   Nature Communications

Accurate estimation of cell composition in bulk expression through robust integration of single-cell information

(2020) Brandon Jew et al.   Nature Communications

Integration of GWAS Summary Statistics and Gene Expression Reveals Target Cell Types Underlying Kidney Function Traits

(2020) Yong Li et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

A simple new approach to variable selection in regression, with application to genetic fine mapping

(2020) Gao Wang et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Cell type–specific genetic regulation of gene expression across human tissues

(2020) Sarah Kim-Hellmuth et al.   SCIENCE

Author Correction: Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants

(2020) Margaret K. R. Donovan et al.   Nature Communications

The Nuclear Receptor ESRRA Protects from Kidney Disease by Coupling Metabolism and Differentiation

(2020) Poonam Dhillon et al.   Cell Metabolism

Bulk tissue cell type deconvolution with multi-subject single-cell expression reference

(2019) Xuran Wang et al.   Nature Communications

Genetic characterization of maize germplasm derived from Suwan population and temperate resources

(2019) Xun Wu et al.   HEREDITAS

Analysis from the EMPA-REG OUTCOME® trial indicate empagliflozin may assist in preventing the progression of chronic kidney disease in patients with type 2 diabetes irrespective of medications that alter intrarenal hemodynamics

(2019) Gert J. Mayer et al.   KIDNEY INTERNATIONAL

The kidney transcriptome, from single cells to whole organs and back

(2019) Shizheng Huang et al.   CURRENT OPINION IN NEPHROLOGY AND HYPERTENSION

Cell-Type Heterogeneity in Adipose Tissue Is Associated with Complex Traits and Reveals Disease-Relevant Cell-Specific eQTLs

(2019) Craig A. Glastonbury et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Determining cell type abundance and expression from bulk tissues with digital cytometry

(2019) Aaron M. Newman et al.   NATURE BIOTECHNOLOGY

A transcriptome-wide association study of high-grade serous epithelial ovarian cancer identifies new susceptibility genes and splice variants

(2019) Alexander Gusev et al.   NATURE GENETICS

A catalog of genetic loci associated with kidney function from analyses of a million individuals

(2019) Matthias Wuttke et al.   NATURE GENETICS

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

A single number for advocacy and communication—worldwide more than 850 million individuals have kidney diseases

(2019) Kitty J. Jager et al.   KIDNEY INTERNATIONAL

The single-cell transcriptomic landscape of early human diabetic nephropathy

(2019) Parker C. Wilson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility

(2019)   SCIENCE

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

(2019) Andrew Ransick et al.   DEVELOPMENTAL CELL

Prioritizing Functional Goals as We Rebuild the Kidney

(2019) Benjamin D. Humphreys et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Target genes, variants, tissues and transcriptional pathways influencing human serum urate levels

(2019) Adrienne Tin et al.   NATURE GENETICS

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

GWAS for urinary sodium and potassium excretion highlights pathways shared with cardiovascular traits

(2019) Raha Pazoki et al.   Nature Communications

Mapping eGFR loci to the renal transcriptome and phenome in the VA Million Veteran Program

(2019) Jacklyn N. Hellwege et al.   Nature Communications

Genome-wide association meta-analyses and fine-mapping elucidate pathways influencing albuminuria

(2019) Alexander Teumer et al.   Nature Communications

Are drug targets with genetic support twice as likely to be approved? Revised estimates of the impact of genetic support for drug mechanisms on the probability of drug approval

(2019) Emily A. King et al.   PLoS Genetics

A Bayesian framework for multiple trait colocalization from summary association statistics

(2018) Claudia Giambartolomei et al.   BIOINFORMATICS

Genetic determinants of co-accessible chromatin regions in activated T cells across humans

(2018) Rachel E. Gate et al.   NATURE GENETICS

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

(2018) Hilary K. Finucane et al.   NATURE GENETICS

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

(2018) Jihwan Park et al.   SCIENCE

Renal compartment–specific genetic variation analyses identify new pathways in chronic kidney disease

(2018) Chengxiang Qiu et al.   NATURE MEDICINE

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors

(2018) Matthew D. Young et al.   SCIENCE

Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions

(2018) Sarah M. Urbut et al.   NATURE GENETICS

Trans-ethnic association study of blood pressure determinants in over 750,000 individuals

(2018) Ayush Giri et al.   NATURE GENETICS

Diagnostic Utility of Exome Sequencing for Kidney Disease

(2018) Emily E. Groopman et al.   NEW ENGLAND JOURNAL OF MEDICINE

Trans-ethnic kidney function association study reveals putative causal genes and effects on kidney-specific disease aetiologies

(2018) Andrew P. Morris et al.   Nature Communications

Chronic Kidney Disease

(2017) Angela C Webster et al.   LANCET

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Polygenic burdens on cell-specific pathways underlie the risk of rheumatoid arthritis

(2017) Kazuyoshi Ishigaki et al.   NATURE GENETICS

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Pathogenic implications for autoimmune mechanisms derived by comparative eQTL analysis of CD4+ versus CD8+ T cells

(2017) Silva Kasela et al.   PLoS Genetics

gkmSVM: an R package for gapped-kmer SVM

(2016) Mahmoud Ghandi et al.   BIOINFORMATICS

LS-GKM: a new gkm-SVM for large-scale datasets

(2016) Dongwon Lee   BIOINFORMATICS

Identification of Vulnerable Cell Types in Major Brain Disorders Using Single Cell Transcriptomes and Expression Weighted Cell Type Enrichment

(2016) Nathan G. Skene et al.   Frontiers in Neuroscience

Fast and efficient QTL mapper for thousands of molecular phenotypes

(2015) Halit Ongen et al.   BIOINFORMATICS

GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach

(2015) Ellen M. Schmidt et al.   BIOINFORMATICS

Diffusion maps for high-dimensional single-cell analysis of differentiation data

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

The support of human genetic evidence for approved drug indications

(2015) Matthew R Nelson et al.   NATURE GENETICS

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

(2015) Brendan K Bulik-Sullivan et al.   NATURE GENETICS

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

SLC transporters as therapeutic targets: emerging opportunities

(2015) Lawrence Lin et al.   NATURE REVIEWS DRUG DISCOVERY

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

MAGMA: Generalized Gene-Set Analysis of GWAS Data

(2015) Christiaan A. de Leeuw et al.   PLoS Computational Biology

A Kenward-Roger Approximation and Parametric Bootstrap Methods for Tests in Linear Mixed Models - TheRPackagepbkrtest

(2015) Ulrich Halekoh et al.   Journal of Statistical Software

Diabetic nephropathy—emerging epigenetic mechanisms

(2014) Mitsuo Kato et al.   Nature Reviews Nephrology

Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics

(2014) Claudia Giambartolomei et al.   PLoS Genetics

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Metabolic memory and diabetic nephropathy: potential role for epigenetic mechanisms

(2010) Stephen Tonna et al.   Nature Reviews Nephrology

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

1000 Genomes project

(2008) Nayanah Siva   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY