Julien Gagneur

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 55

Top Venues

Nature communications

Molecular systems biology

Nature genetics

Nucleic acids research

Technische Universität München

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Technische Universität München Jan 01 2016

Germany

Associate Professor :: Informatics

Publications

Pedro Tomaz da Silva, Yujie Zhang, Evangelos Theodorakis, Laura D Martens, Vicente A Yépez, Vicent Pelechano, Julien Gagneur
Cellular energy regulates mRNA degradation in a codon-specific manner. Molecular systems biology 20 (5) (2024)
Lucia Trastulla, Georgii Dolgalev, Sylvain Moser, Laura T Jiménez-Barrón, Till F M Andlauer, Moritz von Scheidt, null null, Monika Budde, Urs Heilbronner, Sergi Papiol, Alexander Teumer, Georg Homuth, Henry Völzke, Marcus Dörr, Peter Falkai, Thomas G Schulze, 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 15 (1) (2024)
Pedro Tomaz da Silva, Yujie Zhang, Evangelos Theodorakis, Laura D Martens, Vicente A Yépez, Vicent Pelechano, Julien Gagneur
Cellular energy regulates mRNA degradation in a codon-specific manner. Molecular systems biology 20 (5) (2024)
Lucia Trastulla, Georgii Dolgalev, Sylvain Moser, Laura T Jiménez-Barrón, Till F M Andlauer, Moritz von Scheidt, null null, Monika Budde, Urs Heilbronner, Sergi Papiol, Alexander Teumer, Georg Homuth, Henry Völzke, Marcus Dörr, Peter Falkai, Thomas G Schulze, 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 15 (1) (2024)
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 15 (1) (2024)
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 25 (14) (2024)
Xueqi Cao, Sandra Huber, Ata Jadid Ahari, Franziska R Traube, Marc Seifert, 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 16 (1) (2024)
Xueqi Cao, Sandra Huber, Ata Jadid Ahari, Franziska R Traube, Marc Seifert, 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 16 (1) (2024)
Wouter Steyaert, Lydia Sagath, German Demidov, Vicente A Yépez, Anna Esteve-Codina, Julien Gagneur, Kornelia Ellwanger, Ronny Derks, Janneke M Weiss, Amber den Ouden, Simone van den Heuvel, Hilde Swinkels, Nick Zomer, Marloes Steehouwer, Luke O'Gorman, Galuh Astuti, Kornelia Neveling, Rebecca Schüle, Jishu Xu, Matthis Synofzik, Danique Beijer, Holger Hengel, Ludger Schöls, Kristl G Claeys, Jonathan Baets, Liedewei Van de Vondel, Alessandra Ferlini, Rita Selvatici, Heba Morsy, Marwa Saeed Abd Elmaksoud, Volker Straub, Juliane Müller, Veronica Pini, Luke Perry, Anna Sarkozy, Irina T Zaharieva, Francesco Muntoni, Enrico Bugiardini, Kiran Polavarapu, Rita Horvath, Evan Reid, Hanns Lochmüller, Marco Spinazzi, Marco Savarese, null null, null null, null null, null null, Leslie Matalonga, Steven Laurie, Han G Brunner, Holm Graessner, Sergi Beltran, Stephan Ossowski, Lisenka E L M Vissers, Christian Gilissen, Alexander Hoischen
Unravelling undiagnosed rare disease cases by HiFi long-read genome sequencing. medRxiv : the preprint server for health sciences (2024)
Domenico Di Fraia, Antonio Marino, Jae Ho Lee, Erika Kelmer Sacramento, Mario Baumgart, Sara Bagnoli, Pedro Tomaz da Silva, Amit Kumar Sahu, Giacomo Siano, Max Tiessen, Eva Terzibasi-Tozzini, Julien Gagneur, Judith Frydman, Alessandro Cellerino, Alessandro Ori
Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain. bioRxiv : the preprint server for biology (2024)
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 25 (14) (2024)
Pedro Tomaz da Silva, Yujie Zhang, Evangelos Theodorakis, Laura D Martens, Vicente A Yépez, Vicent Pelechano, Julien Gagneur
Cellular energy regulates mRNA degradation in a codon-specific manner. Molecular systems biology (2024)
Domenico Di Fraia, Antonio Marino, Jae Ho Lee, Erika Kelmer Sacramento, Mario Baumgart, Sara Bagnoli, Pedro Tomaz da Silva, Amit Kumar Sahu, Giacomo Siano, Max Tiessen, Eva Terzibasi-Tozzini, Julien Gagneur, Judith Frydman, Alessandro Cellerino, Alessandro Ori
Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain. bioRxiv : the preprint server for biology (2024)
Lucia Trastulla, Georgii Dolgalev, Sylvain Moser, Laura T Jiménez-Barrón, Till F M Andlauer, Moritz von Scheidt, null null, Monika Budde, Urs Heilbronner, Sergi Papiol, Alexander Teumer, Georg Homuth, Henry Völzke, Marcus Dörr, Peter Falkai, Thomas G Schulze, 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 15 (1) (2024)
Pedro Tomaz da Silva, Yujie Zhang, Evangelos Theodorakis, Laura D Martens, Vicente A Yépez, Vicent Pelechano, Julien Gagneur
Cellular energy regulates mRNA degradation in a codon-specific manner. Molecular systems biology 20 (5) (2024)
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 15 (1) (2024)
Pedro Tomaz da Silva, Yujie Zhang, Evangelos Theodorakis, Laura D Martens, Vicente A Yépez, Vicent Pelechano, Julien Gagneur
Cellular energy regulates mRNA degradation in a codon-specific manner. Molecular systems biology 20 (5) (2024)
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 25 (14) (2024)
Lucia Trastulla, Georgii Dolgalev, Sylvain Moser, Laura T Jiménez-Barrón, Till F M Andlauer, Moritz von Scheidt, null null, Monika Budde, Urs Heilbronner, Sergi Papiol, Alexander Teumer, Georg Homuth, Henry Völzke, Marcus Dörr, Peter Falkai, Thomas G Schulze, 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 15 (1) (2024)
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)
Xueqi Cao, Sandra Huber, Ata Jadid Ahari, Franziska R Traube, Marc Seifert, 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 16 (1) (2024)
Domenico Di Fraia, Antonio Marino, Jae Ho Lee, Erika Kelmer Sacramento, Mario Baumgart, Sara Bagnoli, Pedro Tomaz da Silva, Amit Kumar Sahu, Giacomo Siano, Max Tiessen, Eva Terzibasi-Tozzini, Julien Gagneur, Judith Frydman, Alessandro Cellerino, Alessandro Ori
Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain. bioRxiv : the preprint server for biology (2024)
Carl Justus Bredthauer, Anja Pfaus, 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 51 (4) (2023)
Laura D Martens, David S Fischer, Vicente A Yépez, Fabian Joachim Theis, Julien Gagneur
Modeling fragment counts improves single-cell ATAC-seq analysis. Nature methods (2023)
Carl Justus Bredthauer, Anja Pfaus, 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)
Felix Brechtmann, Thibault Bechtler, Shubhankar Londhe, Christian Mertes, Julien Gagneur
Evaluation of input data modality choices on functional gene embeddings. NAR genomics and bioinformatics 5 (4) (2023)
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 55 (5) (2023)
Ines F Scheller, Karoline Lutz, Christian Mertes, Vicente A Yépez, Julien Gagneur
Improved detection of aberrant splicing using the Intron Jaccard Index. medRxiv : the preprint server for health sciences (2023)
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 (Oxford, England) 39 (2) (2023)
Anna B Meier, Dorota Zawada, Maria Teresa De Angelis, Laura D Martens, Gianluca Santamaria, Sophie Zengerle, Monika Nowak-Imialek, Jessica Kornherr, Fangfang Zhang, Qinghai Tian, Cordula M Wolf, Christian Kupatt, Makoto Sahara, Peter Lipp, 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)
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 (Oxford, England) 39 (2) (2023)
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 (Oxford, England) 39 (2) (2023)
Carl Justus Bredthauer, Anja Pfaus, 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 51 (4) (2023)
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 55 (5) (2023)
Carl Justus Bredthauer, Anja Pfaus, 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 51 (4) (2023)
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 55 (5) (2023)
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 55 (5) (2023)
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)
Francisca Rojas Ringeling, Shounak Chakraborty, Caroline Vissers, Derek Reiman, Akshay M Patel, Ki-Heon Lee, Ari Hong, Chan-Woo Park, Tim Reska, Julien Gagneur, Hyeshik Chang, Maria L Spletter, Ki-Jun Yoon, Guo-Li Ming, Hongjun Song, Stefan Canzar
Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data. Nature biotechnology 40 (5) (2022)
Gerard Muñoz-Pujol, Socorro Alforja-Castiella, Ricardo-Pedro 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 23 (20) (2022)
Christian Mertes, Ines F Scheller, Vicente A Yépez, Muhammed H Çelik, Yingjiqiong Liang, Laura S Kremer, Mirjana Gusic, Holger Prokisch, Julien Gagneur
Author Correction: Detection of aberrant splicing events in RNA-seq data using FRASER. Nature communications 13 (1) (2022)
Christian Mertes, Ines F Scheller, Vicente A Yépez, Muhammed H Çelik, Yingjiqiong Liang, Laura S Kremer, Mirjana Gusic, Holger Prokisch, Julien Gagneur
Detection of aberrant splicing events in RNA-seq data using FRASER. Nature communications 12 (1) (2021)
Alexander Karollus, Žiga Avsec, Julien Gagneur
Predicting mean ribosome load for 5'UTR of any length using deep learning. PLoS computational biology 17 (5) (2021)
Vicente A Yépez, Christian Mertes, Michaela F Müller, Daniela Klaproth-Andrade, Leonhard Wachutka, Laure Frésard, Mirjana Gusic, Ines F Scheller, Patricia F Goldberg, Holger Prokisch, Julien Gagneur
Detection of aberrant gene expression events in RNA sequencing data. Nature protocols 16 (2) (2021)
Žiga Avsec, Melanie Weilert, Avanti Shrikumar, Sabrina Krueger, Amr Alexandari, Khyati Dalal, Robin Fropf, Charles McAnany, Julien Gagneur, Anshul Kundaje, Julia Zeitlinger
Base-resolution models of transcription-factor binding reveal soft motif syntax. Nature genetics 53 (3) (2021)
Basak Eraslan, Dongxue Wang, Mirjana Gusic, Holger Prokisch, Björn M Hallström, Mathias Uhlen, 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 15 (2) (2019)
Jun Cheng, Thi Yen Duong Nguyen, Kamil J Cygan, Muhammed Hasan Çelik, William G Fairbrother, Žiga Avsec, Julien Gagneur
MMSplice: modular modeling improves the predictions of genetic variant effects on splicing. Genome biology 20 (1) (2019)
Leonhard Wachutka, Livia Caizzi, Julien Gagneur, Patrick Cramer
Global donor and acceptor splicing site kinetics in human cells. eLife 8 (2019)
Stephen M Mount, Žiga Avsec, Liran Carmel, Rita Casadio, Muhammed Hasan Çelik, Ken Chen, Julien Gagneur, Noa E Cohen, William G Fairbrother, Tzila Fenesh, Julien Gagneur, Valer Gotea, Tamar Holzer, Chiao-Feng Lin, Pier Luigi Martelli, Tatsuhiko Naito, Thi Yen Duong Nguyen, Castrense Savojardo, Ron Unger, Robert Wang, Yuedong Yang, Huiying Zhao
Assessing predictions of the impact of variants on splicing in CAGI5. Human mutation 40 (9) (2019)
Dongxue Wang, Basak Eraslan, Thomas Wieland, Björn Hallström, Thomas Hopf, Daniel Paul Zolg, Jana Zecha, Anna Asplund, Li-Hua Li, Chen Meng, Martin Frejno, Tobias Schmidt, Karsten Schnatbaum, Mathias Wilhelm, Frederik Pontén, Mathias Uhlen, Julien Gagneur, Hannes Hahne, Bernhard Kuster
A deep proteome and transcriptome abundance atlas of 29 healthy human tissues. Molecular systems biology 15 (2) (2019)
Ashiq Hussain, Atefeh Pooryasin, Mo Zhang, Laura F Loschek, Marco La Fortezza, Anja B Friedrich, Catherine-Marie Blais, Habibe K Üçpunar, Vicente A Yépez, Martin Lehmann, Nicolas Gompel, 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 7 (2018)
Julien Gagneur, Kerstin C Maier, Žiga Avsec, Petra Rus, Julien Gagneur
Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast. RNA (New York, N.Y.) 23 (11) (2017)
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 13 (3) (2017)
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 12 (1) (2017)
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 (Bethesda, Md.) 6 (8) (2016)

Julien Gagneur.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Julien Gagneur