Julien Gagneur
Professor
Develops statistical and machine learning models to interpret genomes, including RNA-seq based diagnostics of rare diseases and models of gene regulation.
Julien Gagneur's lab at TUM works on medical imaging & healthcare AI, genomics & computational biology and learning theory & optimization. 40 papers since 2023, 5 at top venues, mostly Bioinformatics and Nature Communications. 12 PhD students and 3 master's students. 9 alumni, most often to Chief Technical at Officer at OmicsDiscoveries GmbH.
At a glance
- papers, 2023–2026
- 10/ year
- at T1 venues
- 13%
- PhD students
- 12
- MS students
- 3
- alumni listed
- 9
Papers by yearfrom the lab homepage, 2023–2026
- 4 papers2026 · T1 0 · collecting
- 11 papers2025 · T1 2
- 16 papers2024 · T1 2
- 9 papers2023 · T1 1
T1 venuesOtherVenues: Bioinformatics, Nature Communications, Nature Methods, Nucleic Acids Research, DIS
Research focuspaper titles that use each topic's words
- Genomics & computational biology8 papers
- rare5 papers
- Learning theory & optimization2 papers
- Medical imaging & healthcare AI0 papers
- genomes0 papers
Paper list
From the lab homepage.
20264 papers
- Annals of Neurology, , PMID: 41623120Fibroblast transcriptomics in molecular diagnostics of a comprehensive dystonia cohort
- Nucleic Acids ResearchIntron location and sequence modulate gene expression in Yarrowia lipolytica
- The American Journal of Human Genetics, , PMID: 41570816MDGA2 homozygous loss-of-function variants cause developmental and epileptic encephalopathy
- ProteomicsModanovo: A Unified Model for Post-Translational Modification-Aware de Novo Sequencing Using Experimental Spectra from in Vivo and Synthetic Peptides
202511 papers
- Nature Communications (T1)Aberrant gene expression prediction across human tissues
- BioinformaticsAn enhanced Borzoi model for accelerated genomic analysis
- npj Genomic MedicineAn outlier approach: advancing diagnosis of neurological diseases through integrating proteomics into multi-omics guided exome reanalysis
- DISMulti-omics approach identifies a novel recessive pathogenic variant in the TNNT3 gene in two siblings with congenital myopathy
- Nature Genetics, , PMID: 41073788Nucleotide dependency analysis of DNA language models reveals genomic functional elements
- BioinformaticsPROTRIDER: Protein abundance outlier detection from mass spectrometry-based proteomics data with a conditional autoencoder
- Journal of the Royal Statistical Society, , PMID: 42459558Root cause discovery via permutations and Cholesky decomposition
- Nature Methods (T1)scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution
- BioinformaticsSpatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data
- —The Solve-RD Solvathons as a pan-European interdisciplinary collaboration to diagnose patients with rare diseases
- Genome ResearchUnravelling undiagnosed rare disease cases by HiFi long-read genome sequencing
202416 papers
- International Journal of Molecular Sciences, , PMID: 39063034An Integrated Transcriptomics and Genomics Approach Detects an X/Autosome Translocation in a Female with Duchenne Muscular Dystrophy
- Genome Medicine, , PMID: 38769532Analysis of 3760 hematologic malignancies reveals rare transcriptomic aberrations of driver genes
- Genome Biology, , PMID: 38389099CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
- Molecular Systems Biology, , PMID: 38491213Cellular energy regulates mRNA translation and degradation in a codon-specific manner
- Nature Communications (T1)Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing
- Nature Communications (T1)Distinct genetic liability profiles define clinically relevant patient strata across common diseases
- Nature Reviews Genetics, , PMID: 39358547From computational models of the splicing code to regulatory mechanisms and therapeutic implications
- Molecular Genetics and Metabolism, , PMID: 38878498Genome and RNA sequencing were essential to reveal cryptic intronic variants associated to defective ATP6AP1 mRNA processing
- Human Genetics and Genomics Advances, , PMID: 38872308Identifying dysregulated regions in amyotrophic lateral sclerosis through chromatin accessibility outliers
- Nature Genetics, , PMID: 39322779Integration of variant annotations using deep set networks boosts rare variant association genetics
- European Journal of Human GeneticsPhenotype-driven genomics enhance diagnosis in children with unresolved neuromuscular diseases
- Nature Genetics, , PMID: 39433890Pushing the boundaries of rare disease diagnostics with the help of the first Undiagnosed Hackathon
20239 papers
- Nature Genetics, , PMID: 37142848Aberrant splicing prediction across human tissues
- Genome Biology, , PMID: 36973806Current sequence-based models capture gene expression determinants in promoters but mostly ignore distal enhancers
- Nature Biotechnology, , PMID: 37012447Epicardioid single-cell genomics uncovers principles of human epicardium biology in heart development and disease
- NAR Genomics and Bioinformatics, , PMID: 37942285Evaluation of input data modality choices on functional gene embeddings
- The American Journal of Human Genetics, , PMID: 38006880 Sharedlt LinkImproved detection of aberrant splicing and the Intron Jaccard Index
- Nature Methods (T1)Modeling fragment counts improves single-cell ATAC-seq analysis
- BioinformaticsThe adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data
- Genome Biology, , PMID: 37542318Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning
- Nucleic Acids ResearchTransmicron: accurate prediction of insertion probabilities improves detection of cancer driver genes from transposon mutagenesis screens
Where alumni went9 listed, 50% to industry
Industry 1Academia 1
Most often to
- Chief Technical at Officer at OmicsDiscoveries GmbH
Also to
- TUM
Apply to TUMRolling
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Computer Science Doctorate (CIT)
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- Rolling (position-based)
- Opens
- —
- GRE
- See program page
- English
- Very good written and spoken English; no minimum test score
- Fee
- See program page
Confirmed on the program page.
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