Stegle, Oliver

A global reference for human genetic variation

The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature

Genetic Associations and EpidemiologyForensic and Genetic Research

Cited by 18,247

The repertoire of mutational signatures in human cancer

Alexandrov, L. B., Kim, J., Haradhvala, N. J., Huang, M. N., Tian Ng, A. W., Wu, Y., Boot, A., Covington, K. R., Gordenin, D. A., Bergstrom, E. N., et al. (2020) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 3,496

Pan-cancer analysis of whole genomes

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S.-M., Aikata, H., et al. (2020) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 3,064

Unraveling the polygenic architecture of complex traits using blood eQTL metaanalysis

Võsa, U., Claringbould, A., Westra, H.-J., Bonder, M. J., Deelen, P., Zeng, B., Kirsten, H., Saha, A., Kreuzhuber, R., Kasela, S., et al. (2018) · Nature Genetics

Genetic Associations and EpidemiologyGenetic Mapping and Diversity in Plants and Animals

Cited by 2,607

Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression

Võsa, U., Claringbould, A., Westra, H.-J., Bonder, M. J., Deelen, P., Zeng, B., Kirsten, H., Saha, A., Kreuzhuber, R., Yazar, S., et al. (2021) · Nature Genetics

Genetic Associations and EpidemiologyGenetic Mapping and Diversity in Plants and Animals

Cited by 2,607

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

Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Hsi-Yang Fritz, M., et al. (2015) · Nature

Genomic variations and chromosomal abnormalitiesGenome Rearrangement Algorithms

Cited by 2,354

The human cell atlas

Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C., Birney, E., Bodenmiller, B., Campbell, P., Carninci, P., Clatworthy, M., et al. (2017) · eLife

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 2,232

Transcriptome and genome sequencing uncovers functional variation in humans

The Geuvadis Consortium, Lappalainen, T., Sammeth, M., Friedländer, M. R., ‘t Hoen, P. A. C., Monlong, J., Rivas, M. A., Gonzàlez-Porta, M., Kurbatova, N., Griebel, T., et al. (2013) · Nature

Genetic Associations and EpidemiologyRNA Research and Splicing

Cited by 1,888

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

Argelaguet, R., Velten, B., Arnol, D., Dietrich, S., Zenz, T., Marioni, J. C., Buettner, F., Huber, W., & Stegle, O. (2018) · Molecular Systems Biology

Bioinformatics and Genomic NetworksSingle-cell and spatial transcriptomics

Cited by 1,510

Deep learning for computational biology

Angermueller, C., Pärnamaa, T., Parts, L., & Stegle, O. (2016) · Molecular Systems Biology

Machine Learning in BioinformaticsBioinformatics and Genomic Networks

Cited by 1,473

Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment

Schulte-Schrepping, J., Reusch, N., Paclik, D., Baßler, K., Schlickeiser, S., Zhang, B., Krämer, B., Krammer, T., Brumhard, S., Bonaguro, L., et al. (2020) · Cell

COVID-19 Clinical Research StudiesSARS-CoV-2 and COVID-19 Research

Cited by 1,461

Eleven grand challenges in single-cell data science

Lähnemann, D., Köster, J., Szczurek, E., McCarthy, D. J., Hicks, S. C., Robinson, M. D., Vallejos, C. A., Campbell, K. R., Beerenwinkel, N., Mahfouz, A., et al. (2020) · Genome Biology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 1,327

Cell2location maps fine-grained cell types in spatial transcriptomics

Kleshchevnikov, V., Shmatko, A., Dann, E., Aivazidis, A., King, H. W., Li, T., Elmentaite, R., Lomakin, A., Kedlian, V., Gayoso, A., et al. (2022) · Nature Biotechnology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 1,279

Computational and analytical challenges in single-cell transcriptomics

Stegle, O., Teichmann, S. A., & Marioni, J. C. (2015) · Nature Reviews Genetics

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 1,170

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

Buettner, F., Natarajan, K. N., Casale, F. P., Proserpio, V., Scialdone, A., Theis, F. J., Teichmann, S. A., Marioni, J. C., & Stegle, O. (2015) · Nature Biotechnology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 1,136

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

Smallwood, S. A., Lee, H. J., Angermueller, C., Krueger, F., Saadeh, H., Peat, J., Andrews, S. R., Stegle, O., Reik, W., & Kelsey, G. (2014) · Nature Methods

Epigenetics and DNA MethylationSingle-cell and spatial transcriptomics

Cited by 1,125

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

Argelaguet, R., Arnol, D., Bredikhin, D., Deloro, Y., Velten, B., Marioni, J. C., & Stegle, O. (2020) · Genome Biology

Single-cell and spatial transcriptomicsBioinformatics and Genomic Networks

Cited by 1,091

The evolutionary history of 2,658 cancers

Gerstung, M., Jolly, C., Leshchiner, I., Dentro, S. C., Gonzalez, S., Rosebrock, D., Mitchell, T. J., Rubanova, Y., Anur, P., Yu, K., et al. (2020) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 1,057

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

Stegle, O., Parts, L., Piipari, M., Winn, J., & Durbin, R. (2012) · Nature Protocols

Genetic Associations and EpidemiologyGene expression and cancer classification

Cited by 1,049

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

Javierre, B. M., Burren, O. S., Wilder, S. P., Kreuzhuber, R., Hill, S. M., Sewitz, S., Cairns, J., Wingett, S. W., Várnai, C., Thiecke, M. J., et al. (2016) · Cell

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 1,046

Swarm Learning for decentralized and confidential clinical machine learning

Warnat-Herresthal, S., Schultze, H., Shastry, K. L., Manamohan, S., Mukherjee, S., Garg, V., Sarveswara, R., Händler, K., Pickkers, P., Aziz, N. A., et al. (2021) · Nature

Privacy-Preserving Technologies in DataBlockchain Technology Applications and Security

Cited by 884

Patterns of somatic structural variation in human cancer genomes

Li, Y., Roberts, N. D., Wala, J. A., Shapira, O., Schumacher, S. E., Kumar, K., Khurana, E., Waszak, S., Korbel, J. O., Haber, J. E., et al. (2020) · Nature

Cancer Genomics and DiagnosticsGenomic variations and chromosomal abnormalities

Cited by 867

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

Angermueller, C., Clark, S. J., Lee, H. J., Macaulay, I. C., Teng, M. J., Hu, T. X., Krueger, F., Smallwood, S. A., Ponting, C. P., Voet, T., et al. (2016) · Nature Methods

Epigenetics and DNA MethylationSingle-cell and spatial transcriptomics

Cited by 717

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Cortés-Ciriano, I., Lee, J. J.-K., Xi, R., Jain, D., Jung, Y. L., Yang, L., Gordenin, D., Klimczak, L. J., Zhang, C.-Z., Pellman, D. S., et al. (2020) · Nature Genetics

Cancer Genomics and DiagnosticsGenomic variations and chromosomal abnormalities

Cited by 712