Gagneur, Julien

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

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

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

Wang, D., Eraslan, B., Wieland, T., Hallström, B., Hopf, T., Zolg, D. P., Zecha, J., Asplund, A., Li, L., Meng, C., et al. (2019) · Molecular Systems Biology

Advanced Proteomics Techniques and ApplicationsBioinformatics and Genomic Networks

Cited by 750

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

Wang, D., Eraslan, B., Wieland, T., Hallström, B., Hopf, T., Zolg, D. P., Zecha, J., Asplund, A., Li, L.-H., Meng, C., et al. (2018) · Molecular Systems Biology

Advanced Proteomics Techniques and ApplicationsBioinformatics and Genomic Networks

Cited by 750

Base-resolution models of transcription-factor binding reveal soft motif syntax

Avsec, Ž., Weilert, M., Shrikumar, A., Krueger, S., Alexandari, A., Dalal, K., Fropf, R., McAnany, C., Gagneur, J., Kundaje, A., et al. (2021) · Nature Genetics

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 610

Genetic diagnosis of Mendelian disorders via RNA sequencing

Kremer, L. S., Bader, D. M., Mertes, C., Kopajtich, R., Pichler, G., Iuso, A., Haack, T. B., Graf, E., Schwarzmayr, T., Terrile, C., et al. (2017) · Nature Communications

Genomics and Rare DiseasesMitochondrial Function and Pathology

Cited by 590

MMSplice: modular modeling improves the predictions of genetic variant effects on splicing

Cheng, J., Nguyen, T. Y. D., Cygan, K. J., Çelik, M. H., Fairbrother, W. G., Avsec, Ž., & Gagneur, J. (2019) · Genome Biology

RNA Research and SplicingGenomics and Rare Diseases

Cited by 235

Current sequence-based models capture gene expression determinants in promoters but mostly ignore distal enhancers

Karollus, A., Mauermeier, T., & Gagneur, J. (2023) · Genome Biology

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 128

Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN

Zacher, B., Michel, M., Schwalb, B., Cramer, P., Tresch, A., & Gagneur, J. (2017) · PLOS ONE

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 91

Cis -regulatory elements explain most of the mRNA stability variation across genes in yeast

Cheng, J., Maier, K. C., Avsec, Ž., Rus, P., & Gagneur, J. (2017) · RNA

RNA Research and SplicingRNA and protein synthesis mechanisms

Cited by 79

Predicting mean ribosome load for 5’UTR of any length using deep learning

Karollus, A., Avsec, Ž., & Gagneur, J. (2021) · PLOS Computational Biology

RNA and protein synthesis mechanismsRNA Research and Splicing

Cited by 57

Predicting Mean Ribosome Load for 5’UTR of any length using Deep Learning

Karollus, A., Avsec, Ž., & Gagneur, J. (2020) · PLoS Computational Biology

RNA and protein synthesis mechanismsRNA Research and Splicing

Cited by 57

PROTRIDER: Protein abundance outlier detection from mass spectrometry-based proteomics data with a conditional autoencoder

Klaproth-Andrade, D., Scheller, I. F., Tsitsiridis, G., Loipfinger, S., Mertes, C., Smirnov, D., Prokisch, H., Yépez, V. A., & Gagneur, J. (2025) · Bioinformatics

Advanced Proteomics Techniques and ApplicationsAnomaly Detection Techniques and Applications

Cited by 4

Modanovo: A Unified Model for Post-Translational Modification-Aware de Novo Sequencing Using Experimental Spectra from In Vivo and Synthetic Peptides

Klaproth-Andrade, D., Bruns, Y., Gabriel, W., Nix, C., Bergant, V., Pichlmair, A., Wilhelm, M., & Gagneur, J. (2025) · Molecular & Cellular Proteomics

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 4

Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast

Cheng, J., Maier, K. C., Avsec, Ž., Rus, P., & Gagneur, J. (2016) · bioRxiv (Cold Spring Harbor Laboratory)

RNA Research and SplicingRNA and protein synthesis mechanisms

Cited by 1