Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

(2021) Christoph Muus et al.   NATURE MEDICINE

Genome-wide enhancer maps link risk variants to disease genes

(2021) Joseph Nasser et al.   NATURE

Pathway paradigms revealed from the genetics of inflammatory bowel disease

(2020) Daniel B. Graham et al.   NATURE

Mechanisms of tissue and cell-type specificity in heritable traits and diseases

(2020) Idan Hekselman et al.   NATURE REVIEWS GENETICS

Transcriptional and Cellular Diversity of the Human Heart

(2020) Nathan R. Tucker et al.   CIRCULATION

The COVID-19 Host Genetics Initiative, a global initiative to elucidate the role of host genetic factors in susceptibility and severity of the SARS-CoV-2 virus pandemic

(2020)   EUROPEAN JOURNAL OF HUMAN GENETICS

Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinson’s disease

(2020) Julien Bryois et al.   NATURE GENETICS

Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19

(2020) Mingfeng Liao et al.   NATURE MEDICINE

Tubular secretion of creatinine and kidney function: an observational study

(2020) Xuehan Zhang et al.   BMC Nephrology

Expansion of Neutrophils and Classical and Nonclassical Monocytes as a Hallmark in Relapsing-Remitting Multiple Sclerosis

(2020) David Haschka et al.   Frontiers in Immunology

TREM2 activation on microglia promotes myelin debris clearance and remyelination in a model of multiple sclerosis

(2020) Francesca Cignarella et al.   ACTA NEUROPATHOLOGICA

Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis

(2020) Arun C. Habermann et al.   Science Advances

Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations

(2020) Ming-Huei Chen et al.   CELL

The Human and Mouse Enteric Nervous System at Single-Cell Resolution

(2020) Eugene Drokhlyansky et al.   CELL

Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases

(2020) M. Ryan Corces et al.   NATURE GENETICS

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

(2020) Kyle J. Travaglini et al.   NATURE

In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes

(2020) Xin Jin et al.   SCIENCE

Interrogation of human hematopoiesis at single-cell and single-variant resolution

(2019) Jacob C. Ulirsch et al.   NATURE GENETICS

Disruption of TCF4 regulatory networks leads to abnormal cortical development and mental disabilities

(2019) Hong Li et al.   MOLECULAR PSYCHIATRY

Chronic Inflammation Permanently Reshapes Tissue-Resident Immunity in Celiac Disease

(2019) Toufic Mayassi et al.   CELL

Molecular Classification and Comparative Taxonomics of Foveal and Peripheral Cells in Primate Retina

(2019) Yi-Rong Peng et al.   CELL

Genomic Medicine–Progress, Pitfalls, and Promise

(2019) Jay Shendure et al.   CELL

Tumour Necrosis Factor Alpha in Intestinal Homeostasis and Gut Related Diseases

(2019) Barbara Ruder et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Single-cell transcriptomic analysis of Alzheimer’s disease

(2019) Hansruedi Mathys et al.   NATURE

A Bayesian framework that integrates multi-omics data and gene networks predicts risk genes from schizophrenia GWAS data

(2019) Quan Wang et al.   NATURE NEUROSCIENCE

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

(2019) Christopher S. Smillie et al.   CELL

Neuronal vulnerability and multilineage diversity in multiple sclerosis

(2019) Lucas Schirmer et al.   NATURE

Reconciling S-LDSC and LDAK functional enrichment estimates

(2019) Steven Gazal et al.   NATURE GENETICS

A genetics-led approach defines the drug target landscape of 30 immune-related traits

(2019) Hai Fang et al.   NATURE GENETICS

A cellular census of human lungs identifies novel cell states in health and in asthma

(2019) Felipe A. Vieira Braga et al.   NATURE MEDICINE

Translational genomics and precision medicine: Moving from the lab to the clinic

(2019) Eleftheria Zeggini et al.   SCIENCE

Spatiotemporal immune zonation of the human kidney

(2019) Benjamin J. Stewart et al.   SCIENCE

Microglia in Alzheimer Disease: Well-Known Targets and New Opportunities

(2019) Anne-Laure Hemonnot et al.   Frontiers in Aging Neuroscience

Annotations capturing cell-type-specific TF binding explain a large fraction of disease heritability

(2019) Bryce van de Geijn et al.   HUMAN MOLECULAR GENETICS

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

Leveraging molecular quantitative trait loci to understand the genetic architecture of diseases and complex traits

(2018) Farhad Hormozdiari et al.   NATURE GENETICS

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk

(2018) Jian Zhou 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

The importance of TCF4 gene in the etiology of recurrent depressive disorders

(2018) Joanna Mossakowska-Wójcik et al.   PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY

Langerhans Cells: Sensing the Environment in Health and Disease

(2018) Julie Deckers et al.   Frontiers in Immunology

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

(2018) Daniel T. Montoro et al.   NATURE

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

(2018) Livnat Jerby-Arnon et al.   CELL

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

Large-scale genome-wide enrichment analyses identify new trait-associated genes and pathways across 31 human phenotypes

(2018) Xiang Zhu et al.   Nature Communications

Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution

(2018) Jeffrey B. Cheng et al.   Cell Reports

Late onset Alzheimer’s disease genetics implicates microglial pathways in disease risk

(2017) Anastasia G. Efthymiou et al.   Molecular Neurodegeneration

Scaling single-cell genomics from phenomenology to mechanism

(2017) Amos Tanay et al.   NATURE

Linkage disequilibrium–dependent architecture of human complex traits shows action of negative selection

(2017) Steven Gazal et al.   NATURE GENETICS

Estimating the causal tissues for complex traits and diseases

(2017) Halit Ongen et al.   NATURE GENETICS

Genome-Wide Significance for PCLO as a Gene for Major Depressive Disorder

(2017) Hamdi Mbarek et al.   Twin Research and Human Genetics

Adipose tissue deficiency of hormone-sensitive lipase causes fatty liver in mice

(2017) Bo Xia et al.   PLoS Genetics

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

Microglial genes regulating neuroinflammation in the progression of Alzheimer's disease

(2016) Claudio Villegas-Llerena et al.   CURRENT OPINION IN NEUROBIOLOGY

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

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

(2015) Hilary K Finucane et al.   NATURE GENETICS

Progress and promise in understanding the genetic basis of common diseases

(2015) Alkes L. Price et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genetics of inflammatory bowel disease from multifactorial to monogenic forms

(2015) Anna Monica Bianco   WORLD JOURNAL OF GASTROENTEROLOGY

The dynamics of monocytes and microglia in Alzheimer’s disease

(2015) Peter Thériault et al.   Alzheimers Research & Therapy

MAGMA: Generalized Gene-Set Analysis of GWAS Data

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

Regulation of T Cell Immunity in Atopic Dermatitis by Microbes: The Yin and Yang of Cutaneous Inflammation

(2015) Tilo Biedermann et al.   Frontiers in Immunology

Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits

(2014) Joseph K. Pickrell   AMERICAN JOURNAL OF HUMAN GENETICS

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

Ndfip1 mediates peripheral tolerance to self and exogenous antigen by inducing cell cycle exit in responding CD4+T cells

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

Inflammatory demyelination induces glia alterations and ganglion cell loss in the retina of an experimental autoimmune encephalomyelitis model

(2013) Lioba Horstmann et al.   Journal of Neuroinflammation

Dendritic cells in multiple sclerosis: key players in the immunopathogenesis, key players for new cellular immunotherapies?

(2013) AH Nuyts et al.   Multiple Sclerosis Journal

Proximal Tubular Secretion of Creatinine by Organic Cation Transporter OCT2 in Cancer Patients

(2012) G. Ciarimboli et al.   CLINICAL CANCER RESEARCH

Inflammation inhibits GABA transmission in multiple sclerosis

(2012) Silvia Rossi et al.   Multiple Sclerosis Journal

Chromatin marks identify critical cell types for fine mapping complex trait variants

(2012) Gosia Trynka et al.   NATURE GENETICS

Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system

(2012) Susan M. Sunkin et al.   NUCLEIC ACIDS RESEARCH

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Role of the endothelium in inflammatory bowel diseases

(2011) Walter E Cromer   WORLD JOURNAL OF GASTROENTEROLOGY

Genetic variants in thymic stromal lymphopoietin are associated with atopic dermatitis and eczema herpeticum

(2010) Pei-Song Gao et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

The Ets-1 transcription factor controls the development and function of natural regulatory T cells

(2010) Enguerran Mouly et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The GABAergic deficit hypothesis of major depressive disorder

(2010) B Luscher et al.   MOLECULAR PSYCHIATRY

Cardiac Metabolism and Arrhythmias

(2009) Andreas S. Barth et al.   Circulation-Arrhythmia and Electrophysiology

Adipocyte metabolism and obesity: Fig. 1.

(2008) Alan D. Attie et al.   JOURNAL OF LIPID RESEARCH