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List of works by Oliver Stegle

A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies

scientific article

A Lasso multi-marker mixed model for association mapping with population structure correction.

scientific article published on 22 November 2012

A Palaeolithic-type diet causes strong tissue-specific effects on ectopic fat deposition in obese postmenopausal women

scientific article published on 11 March 2013

A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative Promoters

A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters

scientific article published on 01 September 2019

A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program

scientific article published on 29 June 2020

A high-content platform to characterise human induced pluripotent stem cell lines

scientific article published on 19 November 2015

A linear mixed model approach to study multivariate gene-environment interactions

article

A linear mixed-model approach to study multivariate gene–environment interactions

article

A random forest approach to capture genetic effects in the presence of population structure

scientific article

A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series

scientific article published on March 2010

A toolbox for predicting g-quadruplex formation and stability

scientific article published on 8 June 2010

Accounting for Non-genetic Factors Improves the Power of eQTL Studies

article

Accurate detection of differential RNA processing

scientific article

Accurate prediction of single-cell DNA methylation states using deep learning

scholarly article published 27 May 2016

An integrated map of structural variation in 2,504 human genomes

scientific article

An omnibus test for differential distribution analysis of microbiome sequencing data

scientific article published on 12 October 2017

Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis

scientific article published on 28 September 2012

Assessing the Gene Regulatory Landscape in 1,188 Human Tumors

article

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

scientific article published on 06 April 2020

Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants

Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes

scientific article published on 16 March 2020

Cell segmentation-free inference of cell types from in situ transcriptomics data ⬇️

journal article from 'bioRxiv' published in 2020

Cell2location maps fine-grained cell types in spatial transcriptomics

scientific article published on 13 January 2022

Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage

scientific article

Combined single cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

scientific article published on 11 February 2019

Common genetic variation drives molecular heterogeneity in human iPSCs

scientific article published on 10 May 2017

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

article

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

scientific article

Computational and analytical challenges in single-cell transcriptomics

scientific article

Computational assignment of cell-cycle stage from single-cell transcriptome data

scientific article

Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs

scientific article published in Nature

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome.

scientific article

DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development.

scientific article

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.

scientific article published on 5 May 2015

Deep learning for computational biology

scientific article

DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning

scientific article

Detecting regulatory gene-environment interactions with unmeasured environmental factors

scientific article published on 4 April 2013

Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats

scientific article published on 10 June 2020

Effects of the COVID-19 pandemic on life scientists

scientific article published on 11 May 2020

Efficient branch-and-bound techniques for two-locus association mapping.

scientific article

Efficient inference in matrix-variate Gaussian models with \\iid observation noise ⬇️

scientific article published in January 2011

Efficient set tests for the genetic analysis of correlated traits.

scientific article

Eleven grand challenges in single-cell data science

scientific article published on 07 February 2020

Erratum to: DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning

scientific article published on 12 May 2017

Estimation of Free-Living Energy Expenditure by Heart Rate and Movement Sensing: A Doubly-Labelled Water Study

scientific article published on 8 September 2015

Expression Atlas: gene and protein expression across multiple studies and organisms.

scientific article

Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis

scientific article published on 26 November 2014

GWAS for executive function and processing speed suggests involvement of the CADM2 gene.

scientific article

Gaussian process robust regression for noisy heart rate data

scientific article

GeneCodeq: quality score compression and improved genotyping using a Bayesian framework.

scientific article published on 26 June 2016

Generalized correlation measure using count statistics for gene expression data with ordered samples.

scientific article published on 12 October 2017

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

scientific article

Genetic Variation in the Social Environment Contributes to Health and Disease

scientific article

Genetic variants regulating expression levels and isoform diversity during embryogenesis

scientific article published on 26 December 2016

Genome-Scale Oscillations in DNA Methylation during Exit from Pluripotency

scientific article published on 01 July 2018

Genome-wide Analysis of Differential Transcriptional and Epigenetic Variability Across Human Immune Cell Types

Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types

scientific article published on 26 January 2017

Genome-wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus

scientific article published on 15 November 2017

Genome-wide studies of verbal declarative memory in nondemented older people: the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium

scientific article

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

scientific article published on August 2017

Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits

scientific article published on 07 February 2017

Genomic basis for RNA alterations in cancer

scientific article published on 05 February 2020

Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types

Genomic determinants of protein abundance variation in colorectal cancer cells

Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype

scientific article

Germline determinants of the somatic mutation landscape in 2,642 cancer genomes

article

IceR improves proteome coverage and data completeness in global and single-cell proteomics

scientific article published on 09 August 2021

Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors

Identifying extrinsic versus intrinsic drivers of variation in cell behaviour in human iPS cell lines from healthy donors

Inference algorithms and learning theory for Bayesian sparse factor analysis

scholarly article by Magnus Rattray et al published 1 December 2009 in Journal of Physics: Conference Series

Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma

scientific article published on January 2015

Interactions between genetic variation and cellular environment in skeletal muscle gene expression

article

Interactions between genetic variation and cellular environment in skeletal muscle gene expression.

scientific article published on 16 April 2018

It is all in the noise: Efficient multi-task Gaussian process inference with structured residuals ⬇️

Joint genetic analysis of gene expression data with inferred cellular phenotypes

scientific article

Joint genetic analysis using variant sets reveals polygenic gene-context interactions

scientific article

Joint modelling of confounding factors and prominent genetic regulators provides increased accuracy in genetical genomics studies

scientific article

KMgene: a unified R package for gene-based association analysis for complex traits

scientific article published on 9 February 2018

Kipoi: accelerating the community exchange and reuse of predictive models for genomics

LIMIX: genetic analysis of multiple traits

article

LiMMBo: a simple, scalable approach for linear mixed models in high-dimensional genetic association studies

LifeTime and improving European healthcare through cell-based interceptive medicine

scientific article published on 07 September 2020

Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana

scientific article

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

scientific article

MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data

scientific article published on 11 May 2020

Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis

scientific article published on 01 October 2019

Modelling 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

scientific article published on 24 February 2016

Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.

scientific article published on 20 June 2018

Multi-omics Characterization of Interaction-mediated Control of Human Protein Abundance levels

scientific article published on 25 June 2019

Multi-omics profiling of mouse gastrulation at single-cell resolution

scientific article published on 11 December 2019

Multi-tissue DNA methylation age predictor in mouse

scientific article

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

scientific article published on 28 August 2011

Naive Pluripotent Stem Cells Exhibit Phenotypic Variability that Is Driven by Genetic Variation

scientific article published on 11 August 2020

OME-Zarr: a cloud-optimized bioimaging file format with international community support

scientific article published in 2023

Open Targets: a platform for therapeutic target identification and validation

scientific article

PERSONALIZED MEDICINE: FROM GENOTYPES AND MOLECULAR PHENOTYPES TOWARDS COMPUTED THERAPY.

scientific article

PERSONALIZED MEDICINE: FROM GENOTYPES AND MOLECULAR PHENOTYPES TOWARDS THERAPY.

scientific article published on January 2014

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

scientific article published on 11 January 2016

Patterns of cis regulatory variation in diverse human populations

scientific article

Personalized medicine: from genotypes and molecular phenotypes towards therapy- session introduction

Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine.

scientific article published in January 2015

Platelet function is modified by common sequence variation in megakaryocyte super enhancers

scientific article

Population-scale proteome variation in human induced pluripotent stem cells

Population-scale proteome variation in human induced pluripotent stem cells

scientific article published on 10 August 2020

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

scientific article published on 04 March 2021

Predicting and understanding the stability of G-quadruplexes

scientific article published on June 2009

Probabilistic latent variable models for distinguishing between cause and effect ⬇️

Promoter shape varies across populations and affects promoter evolution and expression noise

scientific article published on 13 February 2017

Properties of structural variants and short tandem repeats associated with gene expression and complex traits

scientific article published on 10 June 2020

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

scientific article published on 23 March 2020

Reply

scientific article published on 09 June 2018

Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data

scientific article published on 12 February 2020

Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1

scientific article published on 14 August 2019

Selenzyme: Enzyme selection tool for pathway design

scientific article published on 7 February 2018

ShapePheno: unsupervised extraction of shape phenotypes from biological image collections.

scientific article published on 13 February 2012

Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification: Supplementary Figures

Single-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-cell responses

scientific article published on 01 April 2022

Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria

scientific article published on March 2017

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

article

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

scientific article published on 10 February 2020

Single-cell epigenomics: Recording the past and predicting the future

scientific article

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

scientific article

SpatialDE - Identification of spatially variable genes

article

SpatialDE: identification of spatially variable genes

article

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

scientific article published on 20 September 2011

Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts

Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts

Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects

article

Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease

scientific article published on 20 November 2019

Temporal mixture modelling of single-cell RNA-seq data resolves a CD4+ T cell fate bifurcation

article

The Human Cell Atlas

scientific article

The Human Cell Atlas

The Kipoi repository accelerates community exchange and reuse of predictive models for genomics

scientific article published on 01 June 2019

The Organoid Cell Atlas

scientific article

The Organoid Cell Atlas: A Rosetta Stone for Biomedical Discovery and Regenerative Therapy ⬇️

journal article published in 2020

The Polygenic and Monogenic Basis of Blood Traits and Diseases

scientific article published on 01 September 2020

The future of genome-based medicine

scientific article published in January 2013

The germline genetic component of drug sensitivity in cancer cell lines

scientific article published in Nature Communications

The single-cell eQTLGen consortium

scientific article published on 09 March 2020

Transcriptome and genome sequencing uncovers functional variation in humans

scientific article

UC2 search: Using unique connectivity of uncharged compounds for metabolite annotation by database searching in mass spectrometry-based metabolomics.

scientific article published on 12 October 2017

Unraveling the polygenic architecture of complex traits using blood eQTL meta-analysis

scholarly article published 19 October 2018

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

scientific article

Using the past to estimate sensory uncertainty

scientific article published on 15 December 2020

Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference

scientific article published on 13 December 2019

Vitamin A-Retinoic Acid Signaling Regulates Hematopoietic Stem Cell Dormancy.

scientific article published on 3 May 2017

Warped Matrix Factorisation for Multi-view Data Integration

Warped linear mixed models for the genetic analysis of transformed phenotypes

scientific article

Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits

scientific article published on 23 May 2017

Whole-genome sequencing of multiple Arabidopsis thaliana populations

scientific article published on 28 August 2011

easyGWAS: A Cloud-Based Platform for Comparing the Results of Genome-Wide Association Studies.

scientific article published on 16 December 2016

f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.

scientific article

omicsPrint: DETECTION OF DATA LINKAGE ERRORS IN MULTIPLE OMICS STUDIES.

scientific article published on 6 February 2018

scDALI: modeling allelic heterogeneity in single cells reveals context-specific genetic regulation

scientific article published on 06 January 2022

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

scientific article published on 22 February 2018

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

scientific article published on 31 December 2019

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