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• A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies.
• A Lasso multi-marker mixed model for association mapping with population structure correction.
• A Palaeolithic-type diet causes strong tissue-specific effects on ectopic fat deposition in obese postmenopausal women.
• A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative Promoters
• A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters.
• A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program.
• A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.
• A global reference for human genetic variation.
• A linear mixed-model approach to study multivariate gene-environment interactions.
• A random forest approach to capture genetic effects in the presence of population structure.
• A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series.
• A toolbox for predicting g-quadruplex formation and stability.
• Accounting for Non-genetic Factors Improves the Power of eQTL Studies
• Accurate detection of differential RNA processing.
• An integrated map of structural variation in 2,504 human genomes.
• Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis.
• Benchmarking single-cell RNA-sequencing protocols for cell atlas projects.
• Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes.
• Cell segmentation-free inference of cell types from in situ transcriptomics data.
• Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage.
• Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity.
• Common genetic variation drives molecular heterogeneity in human iPSCs.
• Comparative architectures of direct and social genetic effects from the genome-wide association study of 170 phenotypes in outbred laboratory mice
• Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients.
• Computational and analytical challenges in single-cell transcriptomics.
• Computational assignment of cell-cycle stage from single-cell transcriptome data.
• Computational principles and challenges in single-cell data integration.
• Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs.
• DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome.
• DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development.
• DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.
• Deep learning for computational biology.
• DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.
• Detecting regulatory gene-environment interactions with unmeasured environmental factors.
• Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats.
• Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients.
• Dissecting indirect genetic effects from peers in laboratory mice.
• Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19.
• Effects of the COVID-19 pandemic on life scientists.
• Eleven grand challenges in single-cell data science.
• Erosion of human X chromosome inactivation causes major remodeling of the iPSC proteome.
• Erratum to: DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.
• Estimation of Free-Living Energy Expenditure by Heart Rate and Movement Sensing: A Doubly-Labelled Water Study.
• Expression Atlas: gene and protein expression across multiple studies and organisms.
• Extensive cis-Regulatory Variation Robust to Environmental Perturbation in Arabidopsis.
• GWAS for executive function and processing speed suggests involvement of the CADM2 gene.
• Gaussian process robust regression for noisy heart rate data.
• Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.
• Genetic Variation in the Social Environment Contributes to Health and Disease.
• Genetic variants regulating expression levels and isoform diversity during embryogenesis.
• Genome-Scale Oscillations in DNA Methylation during Exit from Pluripotency.
• Genome-wide Studies of Verbal Declarative Memory in Nondemented Older People: The Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium.
• Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types.
• Genome-wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus.
• Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.
• Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits.
• Genomic basis for RNA alterations in cancer.
• Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types
• Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype.
• Haplotype-resolved diverse human genomes and integrated analysis of structural variation.
• High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.
• Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.
• IceR improves proteome coverage and data completeness in global and single-cell proteomics.
• Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics.
• Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors.
• Induction of Neural Crest Stem Cells From Bardet-Biedl Syndrome Patient Derived hiPSCs.
• Interactions between genetic variation and cellular environment in skeletal muscle gene expression
• Interactions between genetic variation and cellular environment in skeletal muscle gene expression.
• It is all in the noise: Efficient multi-task Gaussian process inference with structured residuals
• Joint Profiling Of Chromatin Accessibility, DNA Methylation And Transcription In Single Cells
• Joint genetic analysis of gene expression data with inferred cellular phenotypes.
• Joint genetic analysis using variant sets reveals polygenic gene-context interactions.
• Joint modelling of confounding factors and prominent genetic regulators provides increased accuracy in genetical genomics studies.
• LIMIX: genetic analysis of multiple traits
• Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression.
• LifeTime and improving European healthcare through cell-based interceptive medicine.
• Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana.
• Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.
• Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19.
• MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data.
• Mitochondrial DNA variants modulate N-formylmethionine, proteostasis and risk of late-onset human diseases.
• Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis.
• Modelling local gene networks increases power to detect trans-acting genetic effects on gene expression.
• Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.
• Multi-omics Characterization of Interaction-mediated Control of Human Protein Abundance levels.
• Multi-omics profiling of mouse gastrulation at single-cell resolution.
• Multi-tissue DNA methylation age predictor in mouse.
• Multiple reference genomes and transcriptomes for Arabidopsis thaliana.
• Naive Pluripotent Stem Cells Exhibit Phenotypic Variability that Is Driven by Genetic Variation.
• Pan-cancer analysis of whole genomes.
• Patterns of cis regulatory variation in diverse human populations.
• Platelet function is modified by common sequence variation in megakaryocyte super enhancers.
• Population-scale proteome variation in human induced pluripotent stem cells.
• Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
• Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation.
• Predicting and understanding the stability of G-quadruplexes.
• Promoter shape varies across populations and affects promoter evolution and expression noise.
• Properties of structural variants and short tandem repeats associated with gene expression and complex traits.
• Publisher Correction: Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression.
• Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
• Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data.
• Science Forum: The Human Cell Atlas.
• Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1.
• Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment.
• Sex differences in oncogenic mutational processes.
• ShapePheno: unsupervised extraction of shape phenotypes from biological image collections.
• Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria.
• Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression.
• Single-cell epigenomics: Recording the past and predicting the future.
• SpatialDE - Identification Of Spatially Variable Genes
• SpatialDE: identification of spatially variable genes.
• Spontaneous epigenetic variation in the Arabidopsis thaliana methylome.
• Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects.
• Swarm Learning for decentralized and confidential clinical machine learning.
• Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease.
• The Human Cell Atlas
• The Kipoi repository accelerates community exchange and reuse of predictive models for genomics.
• The Organoid Cell Atlas.
• The germline genetic component of drug sensitivity in cancer cell lines.
• The single-cell eQTLGen consortium.
• Transcriptome and genome sequencing uncovers functional variation in humans.
• Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses.
• Using the past to estimate sensory uncertainty.
• Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference.
• Vitamin A-Retinoic Acid Signaling Regulates Hematopoietic Stem Cell Dormancy.
• Warped Matrix Factorisation for Multi-view Data Integration
• Warped linear mixed models for the genetic analysis of transformed phenotypes.
• Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits.
• Whole-genome sequencing of multiple Arabidopsis thaliana populations.
• f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.
• scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells.
• scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation.