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J

Julien Gagneur

technical university of munich

54H-index
240Paper Count
1.6WCitation Count
Published Papers 87
Publication Date
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Non-destructive transcriptomics via vesicular export
errNature Communications
IF15.7
err2026-04-25
err0
errOAAI
errNiklas Armbrust; Martin Grosshauser; Julian Geilenkeuser; Luisa Stroppel; Mattea Jozinovic; Hella Levermann; Tobias Panne; Jannick Wißmann; Lukas Goelitz; Sebastian Schmidt; Tanja Orschmann; Ejona Rusha; Emily Steinmaßl; Florenc Widenmeyer; Niklas Warsing; Melike Sabry; Asina Sultanbai; Tobias Santl; Arie Geerlof; Oleksandr Berezin; Silviu-Vasile Bodea; Alessandra Moretti; Steffen Schneider; Fabian Theis; Julien Gagneur; Dong-Jiunn Jeffery Truong; Gil Gregor Westmeyer
errShare
errSave
Author Correction: The Solve-RD Solvathons as a pan-European interdisciplinary collaboration to diagnose patients with rare disease
errNature Genetics
IF29
err2026-01-06
err0
errOAAI
errVicente A. Yépez; German Demidov; Kornelia Ellwanger; Steven Laurie; Rebeka Luknárová; Midhuna Immaculate Joseph Maran; Thomas Hentrich; Lydia Sagath; Bart van der Sanden; Galuh Astuti; Kornelia Neveling; Laura Batlle-Masó; Danique Beijer; Felix Brechtmann; Andrés Caballero-Oteyza; Marc Dabad; Anne-Sophie Denommé-Pichon; Cenna Doornbos; Zakaria Eddafir; Berta Estévez-Arias; Ozge Aksel Kilicarslan; Ingrid H. M. Kolen; Leon Kraß; Katja Lohmann; Shubhankar Londhe; Estrella López-Martín; Kars Maassen; William Macken; Beatriz Martínez-Delgado; Davide Mei; Christian Mertes; Raffaella Minardi; Heba Morsy; Juliane S. Mueller; Daniel Natera-de Benito; Isabelle Nelson; Machteld M. Oud; Ida Paramonov; Daniel Picó; Davide Piscia; Kiran Polavarapu; Emanuele Raineri; Marco Savarese; Noor Smal; Marloes Steehouwer; Wouter Steyaert; Morris A. Swertz; Mirja Thomsen; Ana Töpf; Liedewei Van de Vondel; Gerben van der Vries; Antonio Vitobello; Carlo Wilke; Birte Zurek; Peter-Bram t’ Hoen; Leslie Matalonga; Lisenka E. L. M. Vissers; Christian Gilissen; Julia Schulze-Hentrich; Sergi Beltran; Anna Esteve-Codina; Alexander Hoischen; Julien Gagneur; Holm Graessner
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errSave
Modanovo: A Unified Model for Post-Translational Modification-Aware de Novo Sequencing Using Experimental Spectra from In Vivo and Synthetic Peptides
errMolecular & Cellular Proteomics
IF5.5
err2025-12-24
err0
errOAAI
errDaniela Klaproth-Andrade; Yanik Bruns; Wassim Gabriel; Christian Nix; Valter Bergant; Andreas Pichlmair; Mathias Wilhelm; Julien Gagneur
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errSave
PROTRIDER: protein abundance outlier detection from mass spectrometry-based proteomics data with a conditional autoencoder
errBIOINFORMATICS
IF5.4
err2025-12-01
err0
PREAI
errKlaproth-Andrade, Daniela; Scheller, Ines F.; Tsitsiridis, Georgios; Loipfinger, Stefan; Mertes, Christian; Smirnov, Dmitrii; Prokisch, Holger; Yepez, Vicente A.; Gagneur, Julien
errShare
errSave
scooby: modeling multimodal genomic profiles from DNA sequence at single-cell resolution
errNature Methods
IF32.1
err2025-10-22
err0
errOAAI
errJohannes C. Hingerl; Laura D. Martens; Alexander Karollus; Trevor Manz; Jason D. Buenrostro; Fabian J. Theis; Julien Gagneur
errShare
errSave
Nucleotide dependency analysis of genomic language models detects functional elements
errNature Genetics
IF29
err2025-10-10
err0
errOAAI
errPedro Tomaz da Silva; Alexander Karollus; Johannes Hingerl; Gihanna Sta. Teresa Galindez; Nils Wagner; Xavier Hernandez-Alias; Danny Incarnato; Julien Gagneur
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errSave
Flashzoi: an enhanced Borzoi for accelerated genomic analysis
errBIOINFORMATICS
IF5.4
err2025-09-01
err1
errOAAI
errHingerl, Johannes C.; Karollus, Alexander; Gagneur, Julien
errShare
errSave
Altered translation elongation contributes to key hallmarks of aging in the killifish brain
errScience
IF45.8
err2025-07-31
err0
PREAI
errDomenico Di Fraia; Antonio Marino; Jae Ho Lee; Erika Kelmer Sacramento; Mario Baumgart; Sara Bagnoli; Till Balla; Felix Schalk; Stephan Kamrad; Rui Guan; Cinzia Caterino; Chiara Giannuzzi; Pedro Tomaz da Silva; Amit Kumar Sahu; Hanna Gut; Giacomo Siano; Max Tiessen; Eva Terzibasi-Tozzini; Eugenio F. Fornasiero; Julien Gagneur; Christoph Englert; Kiran R. Patil; Clara Correia-Melo; Danny D. Nedialkova; Judith Frydman; Alessandro Cellerino; Alessandro Ori
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errSave
Spatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data
errBIOINFORMATICS
IF5.4
err2025-07-01
err0
errOAAI
errOuologuem, Sarah; Martens, Laura D.; Schaar, Anna C.; Shulman, Maiia; Gagneur, Julien; Theis, Fabian J.
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errSave
An outlier approach: advancing diagnosis of neurological diseases through integrating proteomics into multi-omics guided exome reanalysis
errNPJ GENOMIC MEDICINE
IF4.8
err2025-05-03
err0
errOAAI
errMartin Man-Chun Chui; Anna Ka-Yee Kwong; Hiu Yu Cherie Leung; Chingyiu Pang; Ines F. Scheller; Sheila Suet-Na Wong; Cheuk-Wing Fung; Vicente A. Yépez; Julien Gagneur; Christopher Chun-Yu Mak; Brian Hon-Yin Chung
errShare
errSave
Aberrant gene expression prediction across human tissues
errNATURE COMMUNICATIONS
IF15.7
err2025-03-29
err0
errOAAI
errHoelzlwimmer, Florian R.; Lindner, Jonas; Tsitsiridis, Georgios; Wagner, Nils; Casale, Francesco Paolo; Yepez, Vicente A.; Gagneur, Julien
errShare
errSave
Phenotype-driven genomics enhance diagnosis in children with unresolved neuromuscular diseases (27 Sept, 10.1038/s41431-024-01699-4, 2024)
errEUROPEAN JOURNAL OF HUMAN GENETICS
IF4.6
err2024-12-10
err0
PREAI
errEstevez-Arias, Berta; Matalonga, Leslie; Yubero, Delia; Polavarapu, Kiran; Codina, Anna; Ortez, Carlos; Carrera-Garcia, Laura; Exposito-Escudero, Jesica; Jou, Cristina; Meyer, Stefanie; Kilicarslan, Ozge Aksel; Aleman, Alberto; Thompson, Rachel; Luknarova, Rebeka; Esteve-Codina, Anna; Gut, Marta; Laurie, Steven; Demidov, German; Yepez, Vicente A.; Beltran, Sergi; Gagneur, Julien; Topf, Ana; Lochmueller, Hanns; Nascimento, Andres; Hoenicka, Janet; Palau, Francesc; Benito, Daniel Natera-de
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errSave
From computational models of the splicing code to regulatory mechanisms and therapeutic implications
errNATURE REVIEWS GENETICS
IF52
err2024-10-02
err0
PREAI
errCapitanchik, Charlotte; Wilkins, Oscar G.; Wagner, Nils; Gagneur, Julien; Ule, Jernej
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errSave
GENETICS MEETS TRANSCRIPTOMICS: EXPRESSION AND SPLICING OUTLIER ANALYSIS IN WHOLE TRANSCRIPTOMES OF INDIVIDUALS WITH SCHIZOPHRENIA
errEUROPEAN NEUROPSYCHOPHARMACOLOGY
IF6.7
err2024-10-01
err0
PREAI
errSchulte, Eva; Yepez, Vicente A.; Kilarski, Laura L.; Claus, Isabelle; Degenhardt, Franziska; Adorjan, Kristina; Budde, Monika; Kalman, Janos L.; Papiol, Sergi; Senner, Fanny; Forstner, Andreas J.; Heilbronner, Urs; Nothen, Markus; Gagneur, Julien; Schulze, Thomas
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errSave
Phenotype-driven genomics enhance diagnosis in children with unresolved neuromuscular diseases
errEUROPEAN JOURNAL OF HUMAN GENETICS
IF4.6
err2024-09-27
err2
PREAI
errEstevez-Arias, Berta; Matalonga, Leslie; Yubero, Delia; Polavarapu, Kiran; Codina, Anna; Ortez, Carlos; Carrera-Garcia, Laura; Exposito-Escudero, Jesica; Jou, Cristina; Meyer, Stefanie; Kilicarslan, Ozge Aksel; Aleman, Alberto; Thompson, Rachel; Luknarova, Rebeka; Esteve-Codina, Anna; Gut, Marta; Laurie, Steven; Demidov, German; Yepez, Vicente A.; Beltran, Sergi; Gagneur, Julien; Topf, Ana; Lochmueller, Hanns; Nascimento, Andres; Hoenicka, Janet; Palau, Francesc; Natera-de Benito, Daniel
errShare
errSave
Integration of variant annotations using deep set networks boosts rare variant association testing
errNATURE GENETICS
IF31.8
err2024-09-25
err0
errOAAI
errClarke, Brian; Holtkamp, Eva; Oeztuerk, Hakime; Mueck, Marcel; Wahlberg, Magnus; Meyer, Kayla; Munzlinger, Felix; Brechtmann, Felix; Hoelzlwimmer, Florian R.; Lindner, Jonas; Chen, Zhifen; Gagneur, Julien; Stegle, Oliver
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errSave
Splicing control by PHF5A is crucial for melanoma cell survival
errCELL PROLIFERATION
IF5.6
err2024-08-30
err0
errOAAI
errMeissgeier, Tina; Kappelmann-Fenzl, Melanie; Staebler, Sebastian; Ahari, Ata Jadid; Mertes, Christian; Gagneur, Julien; Linck-Paulus, Lisa; Bosserhoff, Anja Katrin
errShare
errSave
Identifying dysregulated regions in amyotrophic lateral sclerosis through chromatin accessibility outliers
errHUMAN GENETICS AND GENOMICS ADVANCES
IF3.6
err2024-07-01
err0
errOAAI
errCelik, Muhammed Hasan; Gagneur, Julien; Lim, Ryan G.; Wu, Jie; Thompson, Leslie M.; Xie, Xiaohui
errShare
errSave
Genome and RNA sequencing were essential to reveal cryptic intronic variants associated to defective ATP6AP1 mRNA processing
errMOLECULAR GENETICS AND METABOLISM
IF3.5
err2024-07-01
err2
PREAI
errMorales-Romero, Blai; Munoz-Pujol, Gerard; Artuch, Rafael; Garcia-Cazorla, Angels; O'Callaghan, Mar; Sykut-Cegielska, Jolanta; Campistol, Jaume; Moreno-Lozano, Pedro Juan; Oud, Machteld M.; Wevers, Ron A.; Lefeber, Dirk J.; Esteve-Codina, Anna; Yepez, Vicente A.; Gagneur, Julien; Wortmann, Saskia B.; Prokisch, Holger; Ribes, Antonia; Garcia-Villoria, Judit; Tort, Frederic
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Species-aware DNA language models capture regulatory elements and their evolution
errGENOME BIOLOGY
IF9.4
err2024-04-02
err3
errOAAI
errKarollus, Alexander; Hingerl, Johannes; Gankin, Dennis; Grosshauser, Martin; Klemon, Kristian; Gagneur, Julien
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errSave

Research Directions

No research directions
Co-authors
Cooperation Journals
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Thomas Meitinger
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H-index: 161 · Papers: 2.0K
M
Marta Gut
H-index: 157 · Papers: 1.1K
A
Aldons J. Lusis
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