Preprints
Ines Scheller*, Daniela Klaproth-Andrade*, Stefan Loipfinger, Christian Mertes, Dmitrii Smirnov, Holger Prokisch, Vicente Yépez, Julien Gagneur. PROTRIDER: Protein abundance outlier detection from mass spectrometry-based proteomics data with a conditional autoencoder. bioRxiv, 2025
Johannes Hingerl*, Alexander Karollus, Julien Gagneur*. Flashzoi: An enhanced Borzoi model for accelerated genomic analysis. bioRxiv, 2024
Niklas Armbrust, ..., Fabian Theis, Julien Gagneur, Dong-Jiunn Jeffrey Truong@, Gil Gregor Westmeyer@. Non-destructive transcriptomics via vesicular export. bioRxiv, 2024
Jinzhou Li, Benjamin B. Chu, Ines F. Scheller, Julien Gagneur, Marloes H. Maathuis. Root cause discovery via permutations and Cholesky decomposition. arXiv, 2024
Johannes Hingerl, Laura D. Martens, Alexander Karollus, Trevor Manz, Jason D. Buenrostro, Fabian J. Theis, Julien Gagneur. scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution. bioRxiv, 2024
Pedro Tomaz da Silva, Alexander Karollus, Johannes Hingerl, Gihanna Galindez, Nils Wagner, Xavier Hernandez-Alias, Danny Incarnato, Julien Gagneur. Nucleotide dependency analysis of DNA language models reveals genomic functional elements. bioRxiv, 2024
Shubhankar Londhe, Jonas Lindner, Zhifen Chen, Eva Holtkamp, Florian R. Hölzlwimmer, Francesco Paolo Casale, Felix Brechtmann, Julien Gagneur. Functional gene embeddings improve rare variant polygenic risk scores. bioRxiv, 2024
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
Anne Dueck, Lara Althaus, Kathrin Heise, Dena Esfandyari, Seren Baygün, Ralf P. Brandes, 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, Masaru Shimura, Dorota Piekutowska-Abramczuk, Peter Freisinger, Felix Distelmaier, Johannes A. Mayr, ..., Julien Gagneur, ..., Vicente A. Yépez, ..., Thomas Meitinger, 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
2025
Juliane S. Müller, Shira Rabinowicz, Irina Zaharieva, Veronica Pini, Vicente A. Yépez, Anna Esteve-Codina, …, Anna Sarkozy. Multi-omics approach identifies a novel recessive pathogenic variant in the TNNT3 gene in two siblings with congenital myopathy. J. Neuromuscul. Dis., 2025.
Martin MC Chui, Anna KY Kwong, Hiu YC Leung, Chingyiu Pang, Ines F. Scheller, Sheila SN Wong, Cheuk-Wing Fung, Vicente A. Yépez, Julien Gagneur, Christopher CY Mak, Brian HY Chung. An outlier approach: advancing diagnosis of neurological diseases through integrating proteomics into multi-omics guided exome reanalysis. npj Genomic Medicine, 2025. PMID: 40319040
Wouter Steyaert*, Lydia Sagath*, German Demidov, Vicente A. Yépez, Anna Esteve-Codina, Julien Gagneur, ..., Christian Gilissen@, Alexander Hoischen@, Solve-RD Consortium. Unravelling undiagnosed rare disease cases by HiFi long-read genome sequencing. Genome Research, 2025. PMID: 38746462
Florian R. Hölzlwimmer, Jonas Lindner, Georgios Tsitsiridis, Nils Wagner, Francesco Paolo Casale, Vicente A. Yépez, Julien Gagneur. Aberrant gene expression prediction across human tissues. Nature Communications, 2025. PMID: 40157914
2024
Charlotte Capitanchik, Oscar G. Wilkins, Nils Wagner, Julien Gagneur@, Jernej Ule@. From computational models of the splicing code to regulatory mechanisms and therapeutic implications. Nature Reviews Genetics, 2024, PMID: 39358547
Alba Segarra-Casas, Vicente A. Yépez, German Demidov, Steven Laurie, Anna Esteve-Codina, Julien Gagneur, Yolande Parkhurst, Robert Muni-Lofra, Elizabeth Harris, Chiara Marini-Bettolo, Volker Straub, Ana Töpf. An Integrated Transcriptomics and Genomics Approach Detects an X/Autosome Translocation in a Female with Duchenne Muscular Dystrophy. International Journal of Molecular Sciences, 2024, PMID: 39063034
Axel Schmidt, Nicolas Casadei, Fabian Brand, German Demidov, Elaheh Vojgani, Ayda Abolhassani, Rana Aldisi, Guillaume Butler-Laporte, DeCOI host genetics group, …., Julien Gagneur, …, Eva C. Schulte, Kerstin U. Ludwig. Systematic assessment of COVID-19 host genetics using whole genome sequencing data. PLOS Pathogens, 2024, PMID: 39715278
Angélica María Delgado-Vega, Helene Cederroth, Fulya Taylan, ..., Vicente A. Yépez, Valtteri Wirta, Anna Lindstrand, Orion J. Buske, Mikk Cederroth & Ann Nordgren. Pushing the boundaries of rare disease diagnostics with the help of the first Undiagnosed Hackathon. Nature Genetics, 2024, PMID: 39433890. SharedIt Link
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. Nature Genetics, 2024, PMID: 39322779
Berta Estévez-Arias, Leslie Matalonga, ..., Rebeka Luknárová, Anna Esteve-Codina, Marta Gut, Steven Laurie, German Demidov, Vicente A. Yépez, Sergi Beltran, Julien Gagneur, ..., Francesc Palau@ and Daniel Natera-de Benito@. Phenotype-driven genomics enhance diagnosis in children with unresolved neuromuscular diseases. European Journal of Human Genetics, 2024
Lucia Trastulla, Georgii Dolgalev, Sylvain Moser, Laura T. Jiménez-Barrón, Till F. M. Andlauer, ..., Julien Gagneur, Francesco Iorio, Bertram Müller-Myhsok, Heribert Schunkert, Michael J. Ziller. Distinct genetic liability profiles define clinically relevant patient strata across common diseases. Nature Communications, 2024, PMID: 37214898
Tina Meißgeier, Melanie Kappelmann-Fenzl, Sebastian Staebler, Ata Jadid Ahari, Christian Mertes, Julien Gagneur, Lisa Linck-Paulus, Anja Katrin Bosserhoff. Splicing control by PHF5A is crucial for melanoma cell survival. Cell Proliferation, 2024, PMID: 39212334
Muhammed Hasan Çelik, Julien Gagneur, Ryan G. Lim, Jie Wu, Leslie M. Thomposon, Xiaohui Xie. Identifying dysregulated regions in amyotrophic lateral sclerosis through chromatin accessibility outliers. Human Genetics and Genomics Advances, 2024, PMID: 38872308
Blai Morales-Romero, Gerard Muñoz-Pujol, Rafael Artuch, ..., Anna Esteve-Codina, Vicente A. Yépez, Julien Gagneur, Saskia B. Wortmann, Holger Prokisch, Antonia Ribes, Judit García-Villoria@, Frederic Tort@. Genome and RNA sequencing were essential to reveal cryptic intronic variants associated to defective ATP6AP1 mRNA processing. Molecular Genetics and Metabolism, 2024, PMID: 38878498
Xueqi Cao, Sandra Huber, Ata Jadid Ahari, Franziska R. Traube, Marc Seifer, Christopher C. Oakes, Polina Secheyko, Sergey Vilov, Ines F. Scheller, Nils Wagner, Vicente A. Yépez, Piers Blombery, Torsten Haferlach, Matthias Heinig, Leonhard Wachutka@, Stephan Hutter@, Julien Gagneur@. Analysis of 3760 hematologic malignancies reveals rare transcriptomic aberrations of driver genes. Genome Medicine, 2024, PMID: 38769532
Alexander Karollus*, Johannes Hingerl*, Dennis Gankin*, Martin Grosshauser, Kristian Klemon, Julien Gagneur. Species-aware DNA language models capture regulatory elements and their evolution. Genome Biology, 2024, PMID: 38566111
Pedro Tomaz da Silva, Yujie Zhang, Evangelos Theodorakis, Laura D. Martens, Vicente A. Yépez, Vicent Pelechano, Julien Gagneur. Cellular energy regulates mRNA translation and degradation in a codon-specific manner. Molecular Systems Biology, 2024, PMID: 38491213
Elisabeth Esser, Eva C. Schulte, Alexander Graf, Alexander Karollus, Nicholas H. Smith, Thomas Michler, Stefan Dvoretskii, Angel Angelov, ..., Julien Gagneur@, Ulrike Protzer@. Viral genome sequencing to decipher in-hospital SARS-CoV-2 transmission events. Scientific Reports, 2024, PMID: 38459123 Sharedlt Link
The Critical Assessment of Genome Interpretation Consortium. CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biology, 2024, PMID: 38389099
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, PMID: 38167372 Sharedlt Link
2023
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
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, Lambert Moyon, Klara Kuret, Nicolas Goedert, Marco Salvatore, Jernej Ule, 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*, ..., Fabian J. Theis, Julien Gagneur, Alexander Goedel, Karl-Ludwig Laugwitz, Tatjana Dorn, 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, Fatemeh Behjati Ardakani, 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, Anja Fischer, Ata Jadid Ahari, Xueqi Cao, Julia Weber, Lena Rad, 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
2022
Mianne Lee*, Anna K. Y. Kwong*, Martin M. C. Chui, Jeffrey F. T. Chau, Christopher C. Y. Mak, Sandy L. K. Au, Hei Man Lo, Kelvin Y. K. Chan, Vicente A. Yépez, Julien Gagneur, Anita S. Y. Kan, 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, Juan D. Ortigoza-Escobar, ..., Vicente A. Yépez, Mirjana Gusic, Julien Gagneur, Holger Prokisch, Rafael Artuch, Antonia Ribes, Roser Urreizti, Frederic Tort. Leigh syndrome is the main clinical characteristic of PTCD3 deficiency. Brain Pathology, 2022, PMID: 36450274
Gerard Muñoz-Pujol, Socorro Alforja-Castiella, Ricardo Casaroli-Marano, Blai Morales-Romero, Judit García-Villoria, Vicente A. Yépez, Julien Gagneur, Mirjana Gusic, Holger Prokisch, Frederic Tort, 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, Shounak Chakraborty, Caroline Vissers, Derek Reiman, Akshay M. Patel, Ki-Heon Lee, Ari Hong, Chan-Woo Park, Tim Reska, Julien Gagneur, ..., Stefan Canzar. Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data. Nature Biotechnology, 2022, PMID: 35013600
Ling Li, Zhifen Chen, Moritz von Scheidt, Shuangyue Li, ..., Julien Gagneur, Jeanette Erdmann, Jason C. Kovacic, Johan L. M. Björkegren, 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*, Robert Kopajtich, Christian Mertes, Nicholas H. Smith, ..., Michaela F. Müller, ..., Kei Murayama, Thomas Meitinger, Julien Gagneur@, Holger Prokisch@. Clinical implementation of RNA sequencing for Mendelian disease diagnostics. Genome Medicine, 2022, PMID: 35379322
2021
Andreas Walker, Torsten Houwaart, Patrick Finzer, Lutz Ehlkers, Alona Tyshaieva, Maximilian Damagnez, Daniel Strelow, Ashley Dupllessis, Jessica Nicolai,..., Alexander T. Dilthey, German COVID-19 OMICS Initiative (DeCOI). 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, Christoph Trautwein, Rolf Fendel, Naomi Krickeberg, Georgy Berezhnoy, Rosi Bissinger, Stephan Ossowski, Madhuri S. Salker, Nicolas Casadei, Olaf Riess and the Deutsche COVID-19 OMICS Initiate (DeCOI). SARS-CoV-2 infection paralyzes cytotoxic and metabolic functions of the immune cells. Heliyon, 2021, PMID: 34075347 Sharedlt link.
Benjamin Krämer, Rainer Knoll, Lorenzo Bonaguro, Michael ToVinh, Jan Raabe, Rosario Astaburuaga-García, Jonas Schulte-Schrepping, Kim Melanie Kaiser, ..., Deutsche COVID-19 OMICS Initiative (DeCOI) Anna C. Aschenbrenner, Joachim L. Schultze, Jacob Nattermann. 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, Melanie Weilert, Avanti Shrikumar, Sabrina Krueger, Amr Alexandari, Khyati, Robin Fropf, Charles McAnany, 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, Yingjjqiong Liang, Laura S. Kremer, 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, Laure Frésard, Mirjana Gusic, Ines Scheller, Patricia F. Goldberg, Holger Prokisch, Julien Gagneur. Detection of aberrant events in RNA-seq data. Nature Protocols , 2021, PMID: 33462443 Sharedlt link.
David R. Murdock, Hongzheng Dai, Lindsay C. Burrage, Jill A. Rosenfeld, Shamika Ketkar, Michaela F. Müller, Vicente A. Yépez, Julien Gagneur, ..., Undiagnosed Diseases Network, Brendan Lee. Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing. The Journal of Clinical Investigation, 2021, PMID: 33001864
2019
Jacques Bonnet, Rik G. H. Lindeboom, Daniil Pokrovsky, Georg Stricker, Muhammed Hasan Çelik, Ralp A. W. Rupp, Julien Gagneur, Michiel Vermeulen, Axel Imhof, 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*, Johnny Israeli, Nancy Xu, Jun Cheng, Avanti Shrikumar, Abhimanyu Banerjee, Daniel S. Kim, Thorsten Beier, Lara Urban, 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, Thi Yen Duong Nguyen, 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, Björn M. Hallström, Mathias Uhlén, Anna Asplund, Frederik Pontén, Thomas Wieland, Thomas Hopf, 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*, Thomas Wieland, Björn M. Hallström, Thomas Hopf, Daniel Paul Zolg, Jana Zecha, ..., Julien Gagneur, Hannes Hahne@, Bernhard Kuster@, A deep proteome and transcriptome abundance atlas of 29 healthy human tissues, Molecular Systems Biology 2019, PMID: 30777892
Jun Cheng, Thi Yen Duong Nguyen, Kamil J. Cygan, Muhammed Hasan Celik, William G. Fairbrother, Žiga Avsec, Julien Gagneur, MMSplice: modular modeling improves the predictions of genetic variant effects on splicing, Genome Biology. 2019, PMID: 30823901
2018
Felix Brechtmann*, Christian Mertes*, Agne Matuseviciute*, Vicente A Yépez, Ziga Avsec, Maximilian Herzog, Daniel M. Bader, Holger Prokisch, Julien Gagneur, OUTRIDER: A statistical method for detecting aberrantly expressed genes in RNA sequencing data, The American Journal of Human Genetics, 2018, PMID: 30503520
Beate Hagl, Benedikt D. Spielberger, Silvia Thoene, Sophie Bonnal, ..., Christian Mertes, ..., Thomas Meitinger, Julien Gagneur, Jordan S. Orange, Marielle E. van Gijn, 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, Laura S. Kremer, Arcangela Iuso, Mirjana Gusic, Robert Kopajtich, Eliška Koňaříková, Agnieszka Nadel, 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, Atefeh Pooryasin, Mo Zhang, Laura F. Loschek, Marco La Fortezza, Anja B. Friedrich, ..., Vicente A. Yépez, ..., Julien Gagneur, Stephan J. Sigrist, 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
2017
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, 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@, 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, Robert Kopajtich, Garwin Pichler, Arcangela Iuso, Tobias B. Haack, ..., Thomas Meitinger, Julien Gagneur@, Holger Prokisch@. Genetic diagnosis of Mendelian disorders via RNA sequencing, Nature communications, 2017. PMID: 28604674
Julien Gagneur, Caroline Friedel, Volker Heun, Ralf Zimmer, Burkhard Rost. Bioinformatics advances biology and medicine by turning big data troves into knowledge, Informatik-Spektrum, 2017
Georg Stricker*, Alexander Engelhardt*, Daniel Schulz, Matthias Schmid, Achim Tresch, Julien Gagneur. GenoGAM: Genome-wide generalized additive models for ChIP-seq analysis, Bioinformatics, 2017. PMID: 28369277
Margaux Michel*, Carina Demel*, Benedikt Zacher, Björn Schwalb, Stefan Krebs, Helmut Blum, Julien Gagneur@, Patrick Cramer@, TT-seq captures enhancer landscapes immediately after T cell stimulation, Molecular Systems Biology, 2017. PMID: 28270558
Maximilian Witzel, Daniel Petersheim, Yanxin Fan, Ehsan Bahrami, Tomas Racek, Meino Rohlfs, Jacek Puchałka, ..., 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, Manal Dayem-Quere, Mirjana Gusic, Annabelle Chaussenot, Sylvie Bannwarth, Bérengère François, ..., Ziga Avsec, Christian Mertes, ..., Julien Gagneur, ..., Véronique Paquis-Flucklinger. Mutations in MDH2, Encoding a Krebs Cycle Enzyme, Cause Early-Onset Severe Encephalopathy, The American Journal of Human Genetics, 2017. PMID: 27989324
Benedikt Zacher, Margaux Michel, Björn Schwalb, Patrick Cramer, Achim Tresch, Julien Gagneur. Accurate promoter and enhancer identification in 127 ENCODE and Roadmap Epigenomics cell types and tissues by GenoSTAN, PLoS One, 2017. PMID: 28056037
2016
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, Aparna Radhakrishnan, Rachana Nitin, Pandu Raharja-Liu, Gen Lin, Lars M. Steinmetz, 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*, Katja Frühauf, Carina Demel, Achim Tresch, Julien Gagneur@, Patrick Cramer@. TT-seq maps the human transient transcriptome, Science, 2016. PMID: 27257258
Philipp Eser*, Leonhard Wachutka*, Kerstin C. Maier, Carina Demel, Mariana Boroni, Srignanakshi Iyer, Patrick Cramer@, Julien Gagneur@. Determinants of RNA metabolism in the Schizosaccharomyces pombe genome, Molecular Systems Biology, 2016. PMID: 26883383
2015
Saumya Gupta, Aparna Radhakrishnan, Pandu Raharja-Liu, Lars M. Steinmetz, Julien Gagneur, Himanshu Sinha. Temporal expression profiling identifies pathways mediating effect of causal variant on phenotype, PLoS Genetics, 2015. PMID: 26039065
Julia Glas, Sebastian Dümcke, Benedikt Zacher, Don Poron, Julien Gagneur, Achim Tresch. Simultaneous characterization of sense and antisense genomic processes by the double-stranded hidden Markov model, Nucleic Acids Research, 2015. PMID: 26578558
Tobias B. Haack, Christian Staufner, Marlies G. Köpke, Beate K. Straub, Stefan Kölker, ..., Daniel M. Bader, Julien Gagneur, ..., Thomas Meitinger, Georg F. Hoffmann, Holger Prokisch. Biallelic Mutations in NBAS Cause Recurrent Acute Liver Failure with Onset in Infancy, The American Journal of Human Genetics, 2015. PMID: 26073778
Daniel M. Bader, Stefan Wilkening, Gen Lin, Manu M. Tekkedil, Kim Dietrich, Lars M. Steinmetz, Julien Gagneur. Negative feedback buffers effects of regulatory variants, Molecular Systems Biology, 2015. PMID: 25634765
2014
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 cycle. Molecular Systems Biology 2014. PMID: 25527639
Raeka S. Aiyar, Maria Bohnert, Stéphane Duvezin-Caubet, Cécile Voisset, Julien Gagneur, Emilie S. Fritsch, Elodie Couplan, Karina von der Malsburg, ..., Martin van der Laan, Lars M. Steinmetz. Mitochondrial protein sorting as a therapeutic target for ATP synthase disorders, Nature communications, 2014. PMID: 25519239
Aatish Bhatia, Anupama Yadav, Chenchen Zhu, Julien Gagneur, Aparna Radhakrishnan, Lars M. Steinmetz, Gyan Bhanot, Himanshu Sinha. Yeast Growth Plasticity Is Regulated by Environment Specific Multi-QTL Interactions. G3Journal, 2014. PMID: 24474169
2013
Stefan Wilkening, Gen Lin, Emilie S. Fritsch, Manu M. Tekkedil, Simon Anders, Raquel Kuehn, Michelle Nguyen, Raeka S. Aiyar, Michael Proctor, Nikita A. Sakhanenko, David J. Galas, Julien Gagneur, Adam Deutschbauer, Lars M. Steinmetz. An Evaluation of High-Throughput Approaches to QTL Mapping in Saccharomyces cerevisiae. Genetics, 2013, PMID: 24374355
Daniel Schulz, Björn Schwalb, Anja Kiesel, Carlo Baejen, Phillipp Torkler, Julien Gagneur, Johannes Soeding, Patrick Cramer. Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis. Cell. PMID: 24210918
Julien Gagneur*, Oliver Stegle*, Chenchen Zhu, Petra Jakob, Manu M. Tekkedil, Raeka S. Aiyar, Ann-Kathrin Schuon, Dana Pe'er, 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*, Tobias Rausch, Thomas Zichner, Manu M. Tekkedil, Adrian M. Stütz, Anna Jauch, Raeka S. Aiyar, Gregoire Pau, Nicolas Delhomme, Julien Gagneur, Jan O. Korbel, Wolfgang Huber, Lars M. Steinmetz. The Genomic and Transcriptomic Landscape of a HeLa Cell Line, G3 2013. PMID: 23550136
Stefan Wilkening, Manu M. Tekkedil, Gen Lin, Emilie S. Fritsch, Wu Wei, Julien Gagneur, David W. Lazinski, Andrew Camilli, Lars M. Steinmetz. Genotyping 1000 yeast strains by next-generation sequencing, BMC Genomics 2013. PMID: 23394869
2012
Maïlis Bietenhader*, Alexandre Martos*, Emmanuel Tetaud*, Raeka S. Aiyar*, Carole H. Sellem, Roza Kucharczyk, Sandra Clauder-Münster, ..., Julien Gagneur, ..., Lars M. Steinmetz, 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
2011
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*, Roza Kucharczyk, Anna Kabala, Nahia Ezkurdia, Julien Gagneur, Robert P. St. Onge, Bénédicte Salin, Flavie Soubigou, Marie Le Cann, Lars M. Steinmetz, Jean-Paul di Rago, 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*, Sandra Clauder-Münster, Milosz Smolik, Wolfgang Huber, Lars M. Steinmetz. Antisense expression increases gene expression variability and locus interdependency. Molecular Systems Biology 2011. PMID: 21326235
2010
Sebastian Bauer*, Julien Gagneur*, Peter N. Robinson, GOing Bayesian: model-based gene set analysis of genome-scale data. Nucleic Acids Research 2010. PMID: 20172960
2009
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*, Marina Lamacchia, Julien Gagneur, Gareth Lycett, Ye Ning, Elena A. Levashina, Lars M. Steinmetz. Dissecting the genetic basis of resistance to malaria parasites in Anopheles gambiae. Science. 2009. PMID: 19797663
Gagneur, Julien, Himanshu Sinha, Fabiana Perocchi, Richard Bourgon, Wolfgang Huber, Lars M. Steinmetz. Genome-wide allele- and strand-specific expression profiling. Molecular Systems Biology. 2009. PMID: 19536197
Zhenyu Xu*, Wu Wei*, Julien Gagneur, Fabiana Perocchi, Sandra Clauder-Münster, Jurgi Camblong, Elisa Guffanti, Françoise Stutz, Wolfgang Huber, Lars M. Steinmetz. Bidirectional promoters generate pervasive transcription in yeast. Nature. 2009. PMID: 19169243
2008
Katarzyna Oktaba, Luis Gutiérrez, Julien Gagneur, Charles Girardot, Aditya K. Sengupta, Eileen E. M. Furlong, 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, Hugo Berube, Ivica Letunic, Paul-Daniel Weeber, Julien Gagneur, Charles Girardot, Misha Kapushesky, Detlef Arendt, Peer Bork, Alvis Brazma, Eileen E. M. Furlong, Joachim Wittbrodt, Thorsten Henrich. 4DXpress: a database for cross-species expression pattern comparisons. Nucleic Acids Research 2008. PMID: 17916571
2006
Fabiana Perocchi, Lars J. Jensen, Julien Gagneur, Uwe Ahting, Christian von Mering, Peer Bork, 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
2005
Julien Gagneur, Georg Casari, From molecular networks to qualitative cell behavior. FEBS Letters, 2005. PMID: 15763565
2004
Tewis Bouwemeester, Angela Bauch, Heinz Ruffner, Pierre-Olivier Angrand, Giovanna Bergamini, Karen Croughton, Cristina Cruciat, Dirk Eberhard, 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
2003
Julien Gagneur@, David B Jackson, Georg Casari, Hierarchical analysis of dependency in metabolic networks. Bioinformatics, 19(8):1027–34, 2003., PMID: 12761067