Florian R. Hölzlwimmer, Jonas Lindner, Nils Wagner, Vicente A. Yépez, Francesco Paolo Casale, Julien Gagneur. Aberrant expression prediction across human tissues. bioRxiv, 2023

Vicente A. Yépez@, Nicholas H. Smith, Ines Scheller, Julien Gagneur, Christian Mertes@. Predicting molecular events underlying rare diseases using variant annotation, aberrant gene expression events, and human phenotype ontology. Research Square, 2023

Muhammed Hasan Celik, Julien Gagneur, Ryan G Lim, Jie Wu, Leslie M Thompson, Xiaohui Xie. Identifying dysregulated regions in amyotrophic lateral sclerosis through DNA accessibility outliers. bioRxiv, 2023

Xueqi Cao, ..., Ata Jadid Ahari, Franziska R. Traube, ..., Polina Secheyko, Ines Scheller, Nils Wagner, Vicente A. Yépez, ..., Matthias Heinig, Leonhard Wachutka@, Stephan Hutter@, Julien Gagneur@. Aberrant transcriptome analysis of 3,760 hematologic malignancies reveals LRP1B as hairy cell leukemia variant biomarker. medRxiv, 2023

Brian Clarke*, Eva Holtkamp*, ..., Felix Brechtmann, Florian R. Hölzlwimmer, Julien Gagneur@, Oliver Stegle@. Integration of variant annotations using deep set networks boosts rare variant association genetics. bioRxiv, 2023

Pedro Tomaz da Silva, ..., Evangelos Theodorakis, Laura D. Martens, Vicente A. Yépez, Vicent Pelechano, Julien Gagneur. Cellular energy regulates mRNA translation and degradation in a codon-specific manner. bioRxiv, 2023

Alexander Karollus*, Johannes Hingerl*, Dennis Gankin*, Martin Grosshauser, Kristian Klemon, Julien Gagneur. Species-aware DNA language models capture regulatory elements and their evolution. bioRxiv 2023

Anne Dueck, ..., Julien Gagneur, ..., Evangelos Theodorakis, ..., Stefan Engelhardt. The lncRNA landscape of cardiac resident macrophages and identification of Schlafenlnc as a regulator of macrophage migratory function. bioRxiv, 2022

Sarah L Stenton, ..., Julien Gagneur, ..., Vicente A. Yépez, ..., Holger Prokisch. Diagnosing pediatric mitochondrial disease: lessons from 2,000 exomes. medRxiv, 2021

Robert Kopajtich, ..., Ines Scheller, ..., Christian Mertes, ..., Vicente Yépez, ..., Julien Gagneur, Holger Prokisch. Integration of proteomics with genomics and transcriptomics increases the diagnostic rate of Mendelian disorders. medRxiv, 2021


Daniela Klaproth-Andrade, Johannes Hingerl, Yanik Bruns, Nicholas H. Smith, Jakob Träuble, Mathias Wilhelm@, Julien Gagneur@. Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing. Nature Communications , 2024


Laura D. Martens, David S. Fischer, Vicente A. Yépez, Fabian J. Theis@, Julien Gagneur@. Modeling fragment counts improves single-cell ATAC-seq analysis. Nature Methods, 2023, PMID: 38049697 Sharedlt Link

Ines Scheller, Karoline Lutz, Christian Mertes, Vicente A. Yépez@, Julien Gagneur@. Improved detection of aberrant splicing and the Intron Jaccard Index. The American Journal of Human Genetics, 2023, PMID: 38006880 Sharedlt Link

Felix Brechtmann, Thibault Bechtler, Shubhankar Londhe, Christian Mertes, and Julien Gagneur. Evaluation of input data modality choices on functional gene embeddings. NAR Genomics and Bioinformatics, 2023, PMID: 37942285

Marc Horlacher, Nils Wagner, ..., Julien Gagneur, Ole Winther@, Annalisa Marsico@. Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning. Genome Biology, 2023, PMID: 37542318

Nils Wagner*, Muhammed H. Çelik*, Florian R. Hölzlwimmer, Christian Mertes, Holger Prokisch, Vicente A. Yépez, Julien Gagneur. Aberrant splicing prediction across human tissues. Nature Genetics, 2023, PMID: 37142848

Anna B. Meier*, Dorota Zawada*, Maria Teresa De Angelis*, Laura D. Martens*, ..., Julien Gagneur, ..., Alessandra Moretti. Epicardioid single-cell genomics uncovers principles of human epicardium biology in heart development and disease. Nature Biotechnology, 2023, PMID: 37012447

Alexander Karollus, Thomas Mauermeier, Julien Gagneur. Current sequence-based models capture gene expression determinants in promoters but mostly ignore distal enhancers. Genome Biology, 2023, PMID: 36973806

Dennis Hecker, ..., Alexander Karollus, Julien Gagneur, Marcel H. Schulz. The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data. Bioinformatics, 2023, PMID: 36708003

Carl Bredthauer, ..., Ata Jadid Ahari, Xueqi Cao, ..., Roland Rad, Leonhard Wachutka@, Julien Gagneur@. Transmicron: accurate prediction of insertion probabilities improves detection of cancer driver genes from transposon mutagenesis screens. Nucleic Acids Research, 2023, PMID: 36617985


Mianne Lee*, Anna K. Y. Kwong*, ..., Vicente A. Yépez, Julien Gagneur, ..., Brian H. Y. Chung. Diagnostic potential of the amniotic fluid cells transcriptome in deciphering mendelian disease: a proof-of-concept. npj Genomic Medicine, 2022, PMID: 36577754

Gerard Muñoz-Pujol, ..., Vicente A. Yépez, Mirjana Gusic, Julien Gagneur, Holger Prokisch, ..., Frederic Tort. Leigh syndrome is the main clinical characteristic of PTCD3 deficiency. Brain Pathology, 2022, PMID: 36450274

Gerard Muñoz-Pujol, ..., Vicente A. Yépez, Julien Gagneur, Mirjana Gusic, Holger Prokisch, ..., Antonia Ribes. Diagnostic Odyssey in an Adult Patient with Ophthalmologic Abnormalities and Hearing Loss: Contribution of RNA-Seq to the Diagnosis of a PEX1 Deficiency. International Journal of Molecular Sciences, 2022, PMID: 36293220

Francisca Rojas Ringeling, ..., Julien Gagneur, ..., Stefan Canzar. Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data. Nature Biotechnology, 2022, PMID: 35013600

Ling Li, ..., Julien Gagneur, ..., Heribert Schunkert. Transcriptome-wide association study of coronary artery disease identifies novel susceptibility genes. Basic Research in Cardiology, 2022, PMID: 35175464

Vicente A. Yépez*, Mirjana Gusic*, ..., Christian Mertes, Nicholas H. Smith, ..., Michaela F. Müller, ..., Julien Gagneur@, Holger Prokisch@. Clinical implementation of RNA sequencing for Mendelian disease diagnostics. Genome Medicine, 2022, PMID: 35379322


Andreas Walker, ..., German COVID-19 OMICS Initiative. 2021. Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection clusters based on integrated genomic surveillance, outbreak analysis and contact tracing in an urban setting. Clinical Infectious Diseases, 2021, PMID: 34181711

Yogesh Singh, ..., Julien Gagneur, ..., Christian Mertes, ..., Inti Alberto De La Rosa Velázquez. SARS-CoV-2 infection paralyzes cytotoxic and metabolic functions of the immune cells. Heliyon, 2021, PMID: 34075347 Sharedlt link.

Benjamin Krämer, ..., Julien Gagneur, ..., Christian Mertes, ..., Janne Vehreschild. Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19. Immunity, 2021, PMID: 34592166 Sharedlt link.

Alexander Karollus, Žiga Avsec, Julien Gagneur. Predicting mean ribosome load for 5’UTR of any length using deep learning. PLOS Computational Biology, 2021, PMID: 33970899

Jun Cheng@, Muhammed Hasan Çelik, Anshul Kundaje, Julien Gagneur@. MTSplice predicts effects of genetic variants on tissue-specific splicing. Genome Biology, 2021, PMID: 33789710 Sharedlt link.

Žiga Avsec, ..., Julien Gagneur, Anshul Kundaje@, Julia Zeitlinger@. Base-resolution models of transcription factor binding reveal soft motif syntax. Nature Genetics, 2021, PMID: 33603233 Sharedlt link.

Christian Mertes*, Ines Scheller*, Vicente A. Yépez, Muhammed H. Çelik, ..., Mirjana Gusic, Holger Prokisch, Julien Gagneur. Detection of aberrant splicing events in RNA-Seq data with FRASER. Nature Communications, 2021, PMID: 33483494 Sharedlt link.

Vicente A. Yépez, Christian Mertes, Michaela F. Müller, Daniela S. Andrade, Leonhard Wachutka,..., Mirjana Gusic, Ines Scheller, ..., Holger Prokisch, Julien Gagneur. Detection of aberrant events in RNA-seq data. Nature Protocols , 2021, PMID: 33462443 Sharedlt link.

David R. Murdock, ..., Michaela F. Müller, Vicente A. Yépez, Julien Gagneur, ..., Brendan Lee. Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing. The Journal of Clinical Investigation, 2021, PMID: 33001864


Jacques Bonnet,..., Georg Stricker, Muhammed Hasan Çelik, ..., Julien Gagneur, ..., Jürg Müller. Quantification of proteins and histone marks in Drosophila embryos reveals stoichiometric relationships impacting chromatin regulation. Cell Development, 2019, PMID: 31630981

Žiga Avsec@*, Roman Kreuzhuber*, ..., Jun Cheng, Avanti Shrikumar, ..., Anshul Kundaje@, Oliver Stegle@, Julien Gagneur@, The Kipoi repository accelerates community exchange and reuse of predictive models for genomics, Nature Biotechnology, 2019, PMID: 31138913

Jun Cheng@, Muhammed Hasan Çelik,  ..., Žiga Avsec,  Julien Gagneur@, CAGI5 splicing challenge: Improved exon skipping and intron retention predictions with MMSplice, Human Mutation, 2019, PMID: 31070280

Leonhard Wachutka*, Livia Caizzi*, Julien Gagneur@, Patrick Cramer@, Global donor and acceptor splicing site kinetics in human cells, eLife, 2019, PMID: 31025937

Gökcen Eraslan*, Žiga Avsec*, Julien Gagneur@, Fabian Theis@, Deep learning: New computational modeling techniques for genomics, Nature Reviews Genetics, 2019, PMID: 30971806 SharedIt link.

Basak Eraslan*, Dongxue Wang*, Mirjana Gusic, Holger Prokisch,..., Hannes Hahne@, Bernhard Kuster@, Julien Gagneur@, Quantification and discovery of sequence determinants of protein per mRNA amount in 29 human tissues, Molecular Systems Biology 2019, PMID: 30777893

Dongxue Wang*, Basak Eraslan*, ..., Julien Gagneur, Hannes Hahne@, Bernhard Kuster@, A deep proteome and transcriptome abundance atlas of 29 healthy human tissuesMolecular Systems Biology 2019, PMID: 30777892

Jun Cheng, ..., Muhammed Hasan Celik, ..., Žiga Avsec, Julien Gagneur, MMSplice: modular modeling improves the predictions of genetic variant effects on splicing, Genome Biology. 2019, PMID: 30823901


Felix Brechtmann*, Agne Matuseviciute*, Christian Mertes*, Vicente A Yépez, Ziga Avsec, ..., Daniel Magnus Bader, Holger Prokisch, Julien Gagneur, OUTRIDER: A statistical method for detecting aberrantly expressed genes in RNA sequencing data, AJHG, 2018, PMID: 30503520

Beate Hagl, ..., Christian Mertes, ..., Julien Gagneur, ..., Ellen D. Renner, Somatic alterations compromised molecular diagnosis of DOCK8 hyper-IgE syndrome caused by a novel intronic splice site mutation., Scientific Reports 2018. PMID: 30425284

Vicente A. Yépez M, ..., Mirjana Gusic, Robert Kopajtich,..., Leonhard Wachutka, Holger Prokisch, Julien Gagneur, OCR-Stats: Robust estimation and statistical testing of mitochondrial respiration activities using Seahorse XF Analyzer, PLoS One. 2018. PMID: 29995917

Ashiq Hussain, ..., Vicente A. Yépez, ..., Julien Gagneur, ..., Ilona C Grunwald Kadow, Inhibition of oxidative stress in cholinergic projection neurons fully rescues aging associated olfactory circuit degeneration in Drosophila, eLife, 2018. PMID: 29345616

Georg Stricker, Mathilde Galinier, Julien Gagneur, GenoGAM 2.0: Scalable and efficient implementation of genome-wide generalized additive models for gigabase-scale genomes, BMC Bioinformatics. 2018. PMID: 29945559


Žiga Avsec, Mohammadamin Barekatain, Jun Cheng, Julien Gagneur, Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks, Bioinformatics, 2017. PMID: 29155928

Jun Cheng, Kerstin C. Maier, Žiga Avsec, Petra Rus, and Julien Gagneur, Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast, RNA, 2017. PMID: 28802259

Hai Wei, Bo Yan, Julien Gagneur@, and Barbara Conradt@ Caenorhabditis elegans CES-1 Snail Represses pig-1 MELK Expression To Control Asymmetric Cell Division, Genetics, 2017. PMID: 28652378

Laura S Kremer*, Daniel M Bader*, Christian Mertes,..., Julien Gagneur@, and Holger Prokisch@, Genetic diagnosis of Mendelian disorders via RNA sequencing, Nature communications, 2017. PMID: 28604674

Julien Gagneur, Caroline Friedel, Volker Heun, Ralf Zimmer, and Burkhard Rost, Bioinformatics advances biology and medicine by turning big data troves into knowledgeInformatik-Spektrum, 2017

Georg Stricker*, Alexander Engelhardt*, Daniel Schulz, Matthias Schmid, Achim Tresch, and Julien Gagneur GenoGAM: Genome-wide generalized additive models for ChIP-seq analysis, Bioinformatics, 2017. PMID: 28369277

Margaux Michel*, Carina Demel*, Benedikt Zacher, ..., Julien Gagneur@, and Patrick Cramer@, TT-seq captures enhancer landscapes immediately after T cell stimulation, Molecular Systems Biology, 2017. PMID: 28270558

Maximilian Witzel, ..., Christian Mertes, Julien Gagneur, ..., Christoph Klein, Chromatin remodelling factor SMARCD2 regulates transcriptional networks controlling early and late differentiation of neutrophil granulocytes, Nature Genetics, 2017. PMID: 28369036

Samira Ait-El-Makdem, ..., Ziga Avsec, Christian Mertes, ..., Julien Gagneur, ..., Véronique Paquis-Flucklinger, Mutations in MDH2, Encoding a Krebs Cycle Enzyme, Cause Early-Onset Severe Encephalopathy, AJHG, 2017. PMID: 27989324

Benedikt Zacher, ..., Julien Gagneur, Accurate promoter and enhancer identification in 127 ENCODE and Roadmap Epigenomics cell types and tissues by GenoSTAN, PLoS One, 2017. PMID: 28056037


Leonhard Wachutka and Julien Gagneur, Measures of RNA metabolism rates: Toward a definition at the level of single bonds, Transcription, 2016. PMID: 27841720

Saumya Gupta,..., Julien Gagneur, Himanshu Sinha, Meiotic Interactors of a Mitotic Gene TAO3 Revealed by Functional Analysis of its Rare Variant, G3, 2016. PMID: 27317780

Björn Schwalb*, Margaux Michel*, Benedikt Zacher*, ..., Julien Gagneur@, Patrick Cramer@, TT-seq maps the human transient transcriptome, Science, 2016. PMID: 27257258

Philipp Eser*, Leonhard Wachutka*, ..., Mariana Boroni, ..., Patrick Cramer@, Julien Gagneur@, Determinants of RNA metabolism in the Schizosaccharomyces pombe genome, Molecular Systems Biology, 2016. PMID: 26883383


Saumya Gupta, ..., Julien Gagneur, Himanshu Sinha, Temporal expression profiling identifies pathways mediating effect of causal variant on phenotypePLoS Genetics, 2015. PMID: 26039065

Julia Glas, ..., Benedikt Zacher, ..., Julien Gagneur, Achim Tresch, Simultaneous characterization of sense and antisense genomic processes by the double-stranded hidden Markov modelNucleic Acids Research, 2015. PMID: 26578558

Tobias B. Haack, ..., Daniel M. Bader, Julien Gagneur, ..., Holger Prokisch, Biallelic Mutations in NBAS Cause Recurrent Acute Liver Failure with Onset in InfancyThe American Journal of Human Genetics, 2015. PMID: 26073778

Daniel M. Bader, ..., Julien Gagneur, Negative feedback buffers effects of regulatory variantsMolecular Systems Biology, 2015. PMID: 25634765


Benedikt Zacher, Michael Lidschreiber, Patrick Cramer, Julien Gagneur, Achim Tresch, Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycleMolecular Systems Biology 2014. PMID: 25527639

Raeka S. Aiyar, ..., Julien Gagneur, ..., Lars M. Steinmetz, "Mitochondrial protein sorting as a therapeutic target for ATP synthase disorders", Nature communications, 2014. PMID: 25519239

Aatish Bhatia, ..., Julien Gagneur, ..., Himanshu Sinha, Yeast Growth Plasticity Is Regulated by Environment Specific Multi-QTL Interactions. G3Journal, 2014. PMID: 24474169


Stefan Wilkening, ..., Julien Gagneur, ..., Lars M. Steinmetz, An Evaluation of High-Throughput Approaches to QTL Mapping in Saccharomyces cerevisiae. Genetics, 2013, PMID: 24374355

Daniel Schulz, ..., Julien Gagneur, ..., Patrick Cramer, Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis. Cell. PMID: 24210918

Julien Gagneur*, Oliver Stegle*, ..., Lars M. Steinmetz, Genotype-Environment Interactions Reveal Causal Pathways That Mediate Genetic Effects on Phenotype, PLoS Genetics PMID: 24068968

Jonathan J. M. Landry*, Paul Theodor Pyl*, ..., Julien Gagneur, ..., Lars M. Steinmetz, The Genomic and Transcriptomic Landscape of a HeLa Cell Line, G3 2013. PMID: 23550136

Stefan Wilkening, ..., Julien Gagneur, ..., Lars M. Steinmetz, Genotyping 1000 yeast strains by next-generation sequencing, BMC Genomics 2013. PMID: 23394869


Maïlis Bietenhader*, Alexandre Martos*, Emmanuel Tetaud*, Raeka S. Aiyar*, ..., Julien Gagneur, ..., Jean-Paul di Rago, Experimental relocation of the mitochondrial ATP9 gene to the nucleus reveals forces underlying mitochondrial genome evolution. PLoS genetics 2012. PMID: 22916027

Fernando Izquierdo-Carrasco, Julien Gagneur, Alexandros Stamatakis, Trading Memory for Running Time in Phylogenetic Likelihood Computations, 2012 Bioinformatics conference, Vilamoura, Portugal, 2012

Julien Gagneur, Vicente José Pelechano Garcia, Lars M. Steinmetz, Christian Mertens, Methods and systems for tracking samples and sample combinations Int. Patent Application Nr. WO 2012/019765, 2012 Feb. 16


Julien Gagneur, Markus C. Elze, Achim Tresch, Selective phenotyping, entropy reduction, and the mastermind game BMC Bioinformatics 2011. PMID: 22014271

Elodie Couplan*, Raeka S.  Aiyar*, ..., Julien Gagneur, ..., Marc Blondel, A yeast-based assay identifies drugs active against human mitochondrial disorders. PNAS 2011. PMID: 21715656

Sebastian Bauer, Peter N. Robinson, Julien Gagneur, Model-based Gene Set Analysis for Bioconductor. Bioinformatics. 2011. PMID: 21561920

Zhenyu Xu*, Wu Wei*, Julien Gagneur*, ..., Lars M. Steinmetz, Antisense expression increases gene expression variability and locus interdependency. Molecular Systems Biology 2011. PMID: 21326235


Sebastian Bauer*, Julien Gagneur*, Peter N. Robinson, GOing Bayesian: model-based gene set analysis of genome-scale data. Nucleic Acids Research 2010. PMID: 20172960


Robert P. Zinzen*, Charles Girardot*, Julien Gagneur*, Martina Braun, Eileen E. M. Furlong, E.E. Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature. 2009. PMID: 19890324

Stephanie A. Blandin*, Rui Wang-Sattler*, ..., Julien Gagneur, ..., Lars M. Steinmetz, Dissecting the genetic basis of resistance to malaria parasites in Anopheles gambiae. Science. 2009. PMID: 19797663

Gagneur, Julien, ..., Lars M. Steinmetz, Genome-wide allele- and strand-specific expression profiling.  Molecular Systems Biology. 2009. PMID: 19536197

Zhenyu Xu*, Wu Wei*, Julien Gagneur, ..., Lars M. Steinmetz, Bidirectional promoters generate pervasive transcription in yeast. Nature.  2009. PMID: 19169243


Katarzyna Oktaba, ..., Julien Gagneur, ..., Jürg Müller, Dynamic regulation by polycomb group protein complexes controls pattern formation and the cell cycle in Drosophila. Developmental Cell 2008. PMID: 18993116

Raeka S. Aiyar, Julien Gagneur, Lars M. Steinmetz, Identification of mitochondrial disease genes through integrative analysis of multiple datasets. Methods 2008. PMID: 18930150

Yannick Haudry, ..., Julien Gagneur, ..., Thorsten Henrich, 4DXpress: a database for cross-species expression pattern comparisons. Nucleic Acids Research 2008. PMID: 17916571


Fabiana Perocci, ..., Julien Gagneur, ..., Holger Prokisch, Lars M. Steinmetz, Assessing systems properties of yeast mitochondria through an interaction map of the organelle. PLoS Genetics, 2006. PMID:  17054397

Julien Gagneur*, Lior David*, Lars M. Steinmetz, Capturing cellular machines by systematic screens of protein complexes. Trends in Microbiology, 2006. PMID: 16782340


Julien Gagneur, Georg Casari, From molecular networks to qualitative cell behavior. FEBS Letters, 2005. PMID: 15763565


Tewis Bouwemeester, ..., Julien Gagneur, ..., Giulio Superti-Furga, A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nature Cell Biology, 2004. PMID: 14743216

Julien Gagneur*, Stefan Klamt*, Computation of elementary modes: a unifying framework and the new binary approach. BMC Bioinformatics, 2004. PMID: 15527509

Julien Gagneur@, Roland Krause, Tewis Bouwmeester, Georg Casari, Modular decomposition of protein-protein interaction networks. Genome Biology, 2004. PMID: 15287979


Julien Gagneur@, David B Jackson, Georg Casari, Hierarchical analysis of dependency in metabolic networks. Bioinformatics, 19(8):1027–34, 2003., PMID: 12761067