2022
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*, Robert Kopajtich, 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
2021
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, and 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, 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, Yingjiqiong 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, ..., 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
2019
Jacques Bonnet, Rik G.H. Lindeboom, Daniil Pokrovsky, Georg Stricker, Muhammed Hasan Çelik, Ralph A.W. Rupp, Julien Gagneur, Michiel Vermeulen, Axel Imhof and 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, 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, Bjorn M Hallstrom, Mathias Uhlen, Anna Asplund, Fredrik Ponten, 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, Mol. Syst. Biol. 2019, PMID: 30777893
Dongxue Wang*, Basak Eraslan*, ..., Julien Gagneur, Hannes Hahne@, Bernhard Kuster@, A deep proteome and transcriptome abundance atlas of 29 healthy human tissues, Mol. Syst. Biol. 2019, PMID: 30777892
Jun Cheng, Thi Yen Duong Nguyen, Kamil J Cygan, Muhammed Hasan Celik, William Fairbrother, Žiga Avsec, Julien Gagneur, MMSplice: modular modeling improves the predictions of genetic variant effects on splicing, Genome Biol. 2019, PMID: 30823901
2018
Felix Brechtmann*, Agne Matuseviciute*, Christian Mertes*, Vicente A Yépez, Ziga Avsec, Maximilian Herzog, 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, Laura S Kremer, Arcangela Iuso, Mirjana Gusic, Robert Kopajtich, Eliska Konarikova, 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, ..., 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
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, 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 knowledge, Informatik-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, Björn Schwalb, Stefan Krebs, Helmut Blum, 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, 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, Gen Lin, Lars M. Steinmetz, Julien Gagneur, Himanshu Sinha, Temporal expression profiling identifies pathways mediating effect of causal variant on phenotype, PLoS Genet., 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, ..., Daniel M. Bader, Julien Gagneur, ..., 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, ..., Julien Gagneur, ..., 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, ..., Julien Gagneur, ..., 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 (155). 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 Genet 9(9) 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, 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*, ..., 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
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*, ..., 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*, Sandra Clauder-Münster, Milosz Smolik, Wolfgang Huber, Lars M. Steinmetz, Antisense expression increases gene expression variability and locus interdependency. Mol Syst Biol. 2011. PMID: 21326235
2010
Sebastian Bauer*, Julien Gagneur*, Peter N. Robinson, GOing Bayesian: model-based gene set analysis of genome-scale data. Nucleic Acids Res. 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. Mol Syst Biol. 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, ..., Julien Gagneur, ..., Thorsten Henrich, 4DXpress: a database for cross-species expression pattern comparisons. Nucleic Acids Research 2008. PMID: 17916571
2006
Fabiana Perocci, 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 Genet, 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, ..., 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