Stegle, Oliver

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., et al. (2021) · Science

Genomic variations and chromosomal abnormalitiesGenomics and Phylogenetic Studies

Cited by 702

SpatialDE: identification of spatially variable genes

Svensson, V., Teichmann, S. A., & Stegle, O. (2018) · Nature Methods

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 695

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

Chen, L., Ge, B., Casale, F. P., Vasquez, L., Kwan, T., Garrido-Martín, D., Watt, S., Yan, Y., Kundu, K., Ecker, S., et al. (2016) · Cell

Genetic Associations and EpidemiologyEpigenetics and DNA Methylation

Cited by 679

The Polygenic and Monogenic Basis of Blood Traits and Diseases

Vuckovic, D., Bao, E. L., Akbari, P., Lareau, C. A., Mousas, A., Jiang, T., Chen, M.-H., Raffield, L. M., Tardaguila, M., Huffman, J. E., et al. (2020) · Cell

Genetic Associations and EpidemiologyGenetic Mapping and Diversity in Plants and Animals

Cited by 671

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

Clark, S. J., Argelaguet, R., Kapourani, C.-A., Stubbs, T. M., Lee, H. J., Alda-Catalinas, C., Krueger, F., Sanguinetti, G., Kelsey, G., Marioni, J. C., et al. (2018) · Nature Communications

Epigenetics and DNA MethylationSingle-cell and spatial transcriptomics

Cited by 657

Common genetic variation drives molecular heterogeneity in human iPSCs

Kilpinen, H., Goncalves, A., Leha, A., Afzal, V., Alasoo, K., Ashford, S., Bala, S., Bensaddek, D., Casale, F. P., Culley, O. J., et al. (2017) · Nature

Pluripotent Stem Cells ResearchGenetic Associations and Epidemiology

Cited by 586

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

Angermueller, C., Lee, H. J., Reik, W., & Stegle, O. (2017) · Genome Biology

Epigenetics and DNA MethylationSingle-cell and spatial transcriptomics

Cited by 536

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

Mereu, E., Lafzi, A., Moutinho, C., Ziegenhain, C., McCarthy, D. J., Álvarez-Varela, A., Batlle, E., Sagar, Grün, D., Lau, J. K., et al. (2020) · Nature Biotechnology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 499

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

Stegle, O., Parts, L., Durbin, R., & Winn, J. (2010) · PLoS Computational Biology

Genetic Associations and EpidemiologyGenetic Mapping and Diversity in Plants and Animals

Cited by 497

Computational principles and challenges in single-cell data integration

Argelaguet, R., Cuomo, A. S. E., Stegle, O., & Marioni, J. C. (2021) · Nature Biotechnology

Single-cell and spatial transcriptomicsBioinformatics and Genomic Networks

Cited by 472

Patterns of Cis Regulatory Variation in Diverse Human Populations

Stranger, B. E., Montgomery, S. B., Dimas, A. S., Parts, L., Stegle, O., Ingle, C. E., Sekowska, M., Smith, G. D., Evans, D., Gutierrez-Arcelus, M., et al. (2012) · PLoS Genetics

Genetic Associations and EpidemiologyGenetic Mapping and Diversity in Plants and Animals

Cited by 470

Vitamin A-Retinoic Acid Signaling Regulates Hematopoietic Stem Cell Dormancy

Cabezas-Wallscheid, N., Buettner, F., Sommerkamp, P., Klimmeck, D., Ladel, L., Thalheimer, F. B., Pastor-Flores, D., Roma, L. P., Renders, S., Zeisberger, P., et al. (2017) · Cell

Hematopoietic Stem Cell TransplantationRetinoids in leukemia and cellular processes

Cited by 454

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

Rodriguez-Martin, B., Alvarez, E. G., Baez-Ortega, A., Zamora, J., Supek, F., Demeulemeester, J., Santamarina, M., Ju, Y. S., Temes, J., Garcia-Souto, D., et al. (2020) · Nature Genetics

Genomic variations and chromosomal abnormalitiesCancer Genomics and Diagnostics

Cited by 451

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

Kelsey, G., Stegle, O., & Reik, W. (2017) · Science

Epigenetics and DNA MethylationSingle-cell and spatial transcriptomics

Cited by 415

Multi-tissue DNA methylation age predictor in mouse

BI Ageing Clock Team, Stubbs, T. M., Bonder, M. J., Stark, A.-K., Krueger, F., von Meyenn, F., Stegle, O., & Reik, W. (2017) · Genome Biology

Epigenetics and DNA MethylationGenetics, Aging, and Longevity in Model Organisms

Cited by 384

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

Huang, Y., McCarthy, D. J., & Stegle, O. (2019) · Genome Biology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 348

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

Cuomo, A. S. E., Seaton, D. D., McCarthy, D. J., Martinez, I., Bonder, M. J., Garcia-Bernardo, J., Amatya, S., Madrigal, P., Isaacson, A., Buettner, F., et al. (2020) · Nature Communications

Pluripotent Stem Cells ResearchSingle-cell and spatial transcriptomics

Cited by 331

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

Holland, C. H., Tanevski, J., Perales-Patón, J., Gleixner, J., Kumar, M. P., Mereu, E., Joughin, B. A., Stegle, O., Lauffenburger, D. A., Heyn, H., et al. (2020) · Genome Biology

Single-cell and spatial transcriptomicsBioinformatics and Genomic Networks

Cited by 323

Effect of predicted protein-truncating genetic variants on the human transcriptome

Rivas, M. A., Pirinen, M., Conrad, D. F., Lek, M., Tsang, E. K., Karczewski, K. J., Maller, J. B., Kukurba, K. R., DeLuca, D. S., Fromer, M., et al. (2015) · Science

Genomics and Rare DiseasesRNA Research and Splicing

Cited by 313

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

Akdemir, K. C., Le, V. T., Chandran, S., Li, Y., Verhaak, R. G., Beroukhim, R., Campbell, P. J., Chin, L., Dixon, J. R., Futreal, P. A., et al. (2020) · Nature Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 283

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

Demircioğlu, D., Cukuroglu, E., Kindermans, M., Nandi, T., Calabrese, C., Fonseca, N. A., Kahles, A., Lehmann, K.-V., Stegle, O., Brazma, A., et al. (2019) · Cell

Genomics and Chromatin DynamicsCancer-related molecular mechanisms research

Cited by 250

A spatially resolved atlas of the human lung characterizes a gland-associated immune niche

Madissoon, E., Oliver, A. J., Kleshchevnikov, V., Wilbrey-Clark, A., Polanski, K., Richoz, N., Ribeiro Orsi, A., Mamanova, L., Bolt, L., Elmentaite, R., et al. (2023) · Nature Genetics

Single-cell and spatial transcriptomicsAsthma and respiratory diseases

Cited by 219

MUON: multimodal omics analysis framework

Bredikhin, D., Kats, I., & Stegle, O. (2022) · Genome Biology

Bioinformatics and Genomic NetworksGenomics and Phylogenetic Studies

Cited by 216

Gaussian process robust regression for noisy heart rate data

Stegle, O., Fallert, S. V., MacKay, D. J. C., & Brage, S. (2008) · IEEE Transactions on Biomedical Engineering

Non-Invasive Vital Sign MonitoringGaussian Processes and Bayesian Inference

Cited by 213