List of works - Oliver Stegle

Transcriptome and genome sequencing uncovers functional variation in humans

scientific article

Common genetic variation drives molecular heterogeneity in human iPSCs

scientific article published on 10 May 2017

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

scientific article

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

scientific article

Whole-genome sequencing of multiple Arabidopsis thaliana populations

scientific article published on 28 August 2011

Computational and analytical challenges in single-cell transcriptomics

scientific article published on January 28, 2015

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

scientific article published on 28 August 2011

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

scientific article

The Human Cell Atlas

scientific article

Patterns of cis regulatory variation in diverse human populations

scientific article

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

scientific article published on 20 September 2011

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

scientific article

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

scientific article

Deep learning for computational biology

scientific article

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

scientific article

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

article

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

scientific article published on 11 January 2016

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

scientific article published on 5 May 2015

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

scientific article

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

scientific article published on 28 September 2012

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

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

scientific article published on July 2, 2015

Open Targets: a platform for therapeutic target identification and validation

scientific article

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

scientific article

Gaussian process robust regression for noisy heart rate data

scientific article

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

scientific article published on August 2017

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

scientific article

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

scientific article published on 22 February 2018

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

scientific article published on 3 May 2017

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

scientific article published on March 2017

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

scientific article

Multi-tissue DNA methylation age predictor in mouse

scientific article

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

scientific article published on 20 June 2018

Eleven grand challenges in single-cell data science

scientific article published on 07 February 2020

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

scientific article

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

scientific article published on 8 September 2015

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

scientific article

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

scientific article

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

scientific article published on 22 November 2012

Predicting and understanding the stability of G-quadruplexes

scientific article published on June 2009

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

scientific article published on March 2010

Joint genetic analysis of gene expression data with inferred cellular phenotypes

scientific article

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

scientific article

Efficient set tests for the genetic analysis of correlated traits.

scientific article

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

scientific article

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

Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis

scientific article published on 26 November 2014

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

scientific article published on 13 February 2017

Accurate detection of differential RNA processing

scientific article

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

scientific article published on 23 May 2017

List of works by Oliver Stegle

Transcriptome and genome sequencing uncovers functional variation in humans

Common genetic variation drives molecular heterogeneity in human iPSCs

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

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

Whole-genome sequencing of multiple Arabidopsis thaliana populations

Computational and analytical challenges in single-cell transcriptomics

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

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

The Human Cell Atlas

Patterns of cis regulatory variation in diverse human populations

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

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

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

Deep learning for computational biology

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

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

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

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

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

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

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

Open Targets: a platform for therapeutic target identification and validation

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

Gaussian process robust regression for noisy heart rate data

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

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

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

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

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

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

Multi-tissue DNA methylation age predictor in mouse

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

Eleven grand challenges in single-cell data science

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

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

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

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

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

Predicting and understanding the stability of G-quadruplexes

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

Joint genetic analysis of gene expression data with inferred cellular phenotypes

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

Efficient set tests for the genetic analysis of correlated traits.

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

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

Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis

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

Accurate detection of differential RNA processing

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