The single-cell eQTLGen consortium

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

(2020) Anna S. E. Cuomo et al.   Nature Communications

Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments

(2020) Christopher A Jackson et al.   eLife

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

(2019) Molly Gasperini et al.   CELL

C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

(2019) Tsukasa Kouno et al.   Nature Communications

Probabilistic fine-mapping of transcriptome-wide association studies

(2019) Nicholas Mancuso et al.   NATURE GENETICS

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

(2019) Emily R. Miraldi et al.   GENOME RESEARCH

The Missing Diversity in Human Genetic Studies

(2019) Giorgio Sirugo et al.   CELL

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Abundant associations with gene expression complicate GWAS follow-up

(2019) Boxiang Liu et al.   NATURE GENETICS

Evaluating measures of association for single-cell transcriptomics

(2019) Michael A. Skinnider et al.   NATURE METHODS

Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments

(2019) Luyi Tian et al.   NATURE METHODS

Spatial transcriptomics coming of age

(2019) Darren J. Burgess   NATURE REVIEWS GENETICS

Discovery and characterization of variance QTLs in human induced pluripotent stem cells

(2019) Abhishek K. Sarkar et al.   PLoS Genetics

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

(2019) Christopher S. Smillie et al.   CELL

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

Genetic analyses of diverse populations improves discovery for complex traits

(2019) Genevieve L. Wojcik et al.   NATURE

Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility

(2019) Caleb A. Lareau et al.   NATURE BIOTECHNOLOGY

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

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

Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits

(2019) Eleonora Porcu et al.   Nature Communications

Spatial transcriptomics: putting genome-wide expression on the map

(2019) K. R. Maynard et al.   NEUROPSYCHOPHARMACOLOGY

Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data

(2018) Shuonan Chen et al.   BMC BIOINFORMATICS

Mapping gene regulatory networks from single-cell omics data

(2018) Mark W E J Fiers et al.   Briefings in Functional Genomics

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs

(2018) Monique G. P. van der Wijst et al.   NATURE GENETICS

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

(2018) Farhad Hormozdiari et al.   NATURE GENETICS

Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

(2018) Tetsutaro Hayashi et al.   Nature Communications

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

(2018) Stephen J. Clark et al.   Nature Communications

Gene-by-environment interactions in urban populations modulate risk phenotypes

(2018) Marie-Julie Favé et al.   Nature Communications

PolyQTL: Bayesian multiple eQTL detection with control for population structure and sample relatedness

(2018) Biao Zeng et al.   BIOINFORMATICS

Meta-analysis of genome-wide association studies for height and body mass index in ∼700000 individuals of European ancestry

(2018) Loic Yengo et al.   HUMAN MOLECULAR GENETICS

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Genome-wide association analyses identify 143 risk variants and putative regulatory mechanisms for type 2 diabetes

(2018) Angli Xue et al.   Nature Communications

Single cell molecular alterations reveal target cells and pathways of concussive brain injury

(2018) Douglas Arneson et al.   Nature Communications

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data

(2018) Nils Eling et al.   Cell Systems

The UK Biobank resource with deep phenotyping and genomic data

(2018) Clare Bycroft et al.   NATURE

Comprehensive functional genomic resource and integrative model for the human brain

(2018) Daifeng Wang et al.   SCIENCE

An integrative approach for building personalized gene regulatory networks for precision medicine

(2018) Monique G. P. van der Wijst et al.   Genome Medicine

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

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

(2017) Kazuyoshi Ishigaki et al.   NATURE GENETICS

Allele-specific expression reveals interactions between genetic variation and environment

(2017) David A Knowles et al.   NATURE METHODS

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

SCnorm: robust normalization of single-cell RNA-seq data

(2017) Rhonda Bacher et al.   NATURE METHODS

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

The European Nucleotide Archive in 2017

(2017) Nicole Silvester et al.   NUCLEIC ACIDS RESEARCH

Exploring regulation in tissues with eQTL networks

(2017) Maud Fagny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

Genetic correlations reveal the shared genetic architecture of transcription in human peripheral blood

(2017) Samuel W. Lukowski et al.   Nature Communications

A review of active learning approaches to experimental design for uncovering biological networks

(2017) Yuriy Sverchkov et al.   PLoS Computational Biology

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

An integrative imputation method based on multi-omics datasets

(2016) Dongdong Lin et al.   BMC BIOINFORMATICS

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

(2016) Lu Chen et al.   CELL

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

(2016) William J. Astle et al.   CELL

A reference panel of 64,976 haplotypes for genotype imputation

(2016)   NATURE GENETICS

Identification of context-dependent expression quantitative trait loci in whole blood

(2016) Daria V Zhernakova et al.   NATURE GENETICS

Integrative approaches for large-scale transcriptome-wide association studies

(2016) Alexander Gusev et al.   NATURE GENETICS

A prior-based integrative framework for functional transcriptional regulatory network inference

(2016) Alireza F. Siahpirani et al.   NUCLEIC ACIDS RESEARCH

HASE: Framework for efficient high-dimensional association analyses

(2016) G. V. Roshchupkin et al.   Scientific Reports

Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data

(2015) Andrea Ocone et al.   BIOINFORMATICS

Optimal design of gene knockout experiments for gene regulatory network inference

(2015) S. M. Minhaz Ud-Dean et al.   BIOINFORMATICS

Reconstruction of gene networks using prior knowledge

(2015) Mahsa Ghanbari et al.   BMC Systems Biology

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Personalized medicine: Time for one-person trials

(2015) Nicholas J. Schork   NATURE

Decoding the regulatory network of early blood development from single-cell gene expression measurements

(2015) Victoria Moignard et al.   NATURE BIOTECHNOLOGY

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

(2015) et al.   SCIENCE

Cohort profile: LifeLines DEEP, a prospective, general population cohort study in the northern Netherlands: study design and baseline characteristics

(2015) Ettje F Tigchelaar et al.   BMJ Open

Cell Specific eQTL Analysis without Sorting Cells

(2015) Harm-Jan Westra et al.   PLoS Genetics

Inferring gene regulatory networks by integrating ChIP-seq/chip and transcriptome data via LASSO-type regularization methods

(2014) Jing Qin et al.   METHODS

Intersection of population variation and autoimmunity genetics in human T cell activation

(2014) C. J. Ye et al.   SCIENCE

Predicting expression: the complementary power of histone modification and transcription factor binding data

(2014) David M Budden et al.   Epigenetics & Chromatin

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

(2014) Claudia Giambartolomei et al.   PLoS Genetics

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

(2013) A. Battle et al.   GENOME RESEARCH

Systematic identification of trans eQTLs as putative drivers of known disease associations

(2013) Harm-Jan Westra et al.   NATURE GENETICS

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Generalization and Dilution of Association Results from European GWAS in Populations of Non-European Ancestry: The PAGE Study

(2013) Christopher S. Carlson et al.   PLOS BIOLOGY

Integrative Modeling of eQTLs and Cis-Regulatory Elements Suggests Mechanisms Underlying Cell Type Specificity of eQTLs

(2013) Christopher D. Brown et al.   PLoS Genetics

Genetics of gene expression in primary immune cells identifies cell type–specific master regulators and roles of HLA alleles

(2012) Benjamin P Fairfax et al.   NATURE GENETICS

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

Unraveling the Regulatory Mechanisms Underlying Tissue-Dependent Genetic Variation of Gene Expression

(2012) Jingyuan Fu et al.   PLoS Genetics

Cytokine Gene Polymorphisms and the Outcome of Invasive Candidiasis: A Prospective Cohort Study

(2011) Melissa D. Johnson et al.   CLINICAL INFECTIOUS DISEASES

Demographic history and rare allele sharing among human populations

(2011) S. Gravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling expression quantitative trait loci in data combining ethnic populations

(2010) Ching-Lin Hsiao et al.   BMC BIOINFORMATICS

Genotype imputation for genome-wide association studies

(2010) Jonathan Marchini et al.   NATURE REVIEWS GENETICS

Complex nature of SNP genotype effects on gene expression in primary human leucocytes

(2009) Graham A Heap et al.   BMC Medical Genomics

Detection and interpretation of expression quantitative trait loci (eQTL)

(2009) Jacob J. Michaelson et al.   METHODS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS