Georg Stricker, Mathilde Galinier, Julien Gagneur, GenoGAM 2.0: Scalable and efficient implementation of genome-wide generalized additive models for gigabase-scale genomes, bioRxiv

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, bioRxiv


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, and Ilona C Grunwald Kadow, Inhibition of oxidative stress in cholinergic projection neurons fully rescues aging associated olfactory circuit degeneration in Drosophila, eLife, 2018


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

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 

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

Laura S Kremer*, Daniel M Bader*, Christian Mertes, Robert Kopajtich, Garwin Pichler, Arcangela Iuso, Tobias B Haack, Elisabeth Graf, Thomas Schwarzmayr, Caterina Terrile, Eliska Konafikova, Birgit Repp, Gabi Kastenmüller, Jerzy Adamski, Peter Lichtner, Christoph Leonhardt, Benoit Funalot, Alice Donati, Valeria Tiranti, Anne Lombes, Claude Jardel, Dieter Gläser, Robert W Taylor, Daniele Ghezzi, Johannes A Mayr, Agnes Rötig, Peter Freisinger, Felix Distelmaier, Tim M Strom, Thomas Meitinger, Julien Gagneur@, and Holger Prokisch@, Genetic diagnosis of Mendelian disorders via RNA sequencing, Nature communications, 2017

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

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

Witzel M., ..., Mertes C., Gagneur J., ..., Klein C., Chromatin remodelling factor SMARCD2 regulates transcriptional networks controlling early and late differentiation of neutrophil granulocytes, Nature Genetics, 2017

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, Jan 5

Zacher B., Michel M., Schwalb B., Cramer P., Tresch A., Gagneur J., Accurate promoter and enhancer identification in 127 ENCODE and Roadmap Epigenomics cell types and tissues by GenoSTAN, PLoS One, 2017, Jan 5


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

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 Aug 9;6(8):2255-63

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 Vol 352, Issue 6290

Eser P.*, Wachutka L*., Maier K., Demel C., Boroni M., Iyer S., Cramer P.@, Gagneur J.@, Determinants of RNA metabolism in the Schizosaccharomyces pombe genome, Molecular Systems Biology, 2016


Gupta S, Radhakrishnan A, Raharja-Liu P, Lin G, Steinmetz LM, Gagneur J, Sinha H. Temporal expression profiling identifies pathways mediating effect of causal variant on phenotypePLoS Genet., 2015

Glas J., Dumcke S., Zacher B., Poron D., Gagneur J., Tresch A. Simultaneous characterization of sense and antisense genomic processes by the double-stranded hidden Markov modelNucleic Acids Research, 2015

Haack T., Staufner C., Köpke M., Straub B., Kölker S., Thiel C., Freisinger P., Baric I., McKiernan P., Dikow N., Harting I., Beisse F., Burgard F., Kotzaeridou U., Kühr J., Himbert U., Taylor R., Distelmaier F., Vockley J., Ghaloul-Gonzalez L., Zschocke J., Kremer L., Graf E., Schwarzmayr T., Bader D., Gagneur J., Wieland T., Terrile C., Strom T., Meitinger T., Hoffmann G., Prokisch H. Biallelic Mutations in NBAS Cause Recurrent Acute Liver Failure with Onset in InfancyThe American Journal of Human Genetics, 2015

Bader, D., Wilkening, S., Lin, G., Tekkedil, M.M., Dietrich K., Steinmetz, L.M., & Gagneur J. Negative feedback buffers effects of regulatory variantsMolecular Systems Biology, 2015


Zacher, B., Lidschreiber, M., Cramer, P., Gagneur, J. & Tresch, A. Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycleMolecular Systems Biology 2014

Aiyar, R.S., Bohnert, M., Duvezin-Caubet, S., Voisset, C., Gagneur, J., Fritsch, E.S., Couplan, E., von der Malsburg, K., Funaya, C., Soubigou, F., Courtin, F., Suresh, S., Kucharczyk, R., Evrard, J., Antony, C., St. Onge, R.P., Blondel, M., di Rago, JP., van der Laan, M. & Steinmetz, L.M "Mitochondrial protein sorting as a therapeutic target for ATP synthase disorders", Nature communications, 2014

Bhatia A., Yadav A., Gagneur J., Zhu C., Steinmetz L.M., Bhanot G., Sinha H. Yeast Growth Plasticity Is Regulated by Environment Specific Multi-QTL Interactions. G3, 2014, 4(5):769-77


Wilkening S., Lin G., Fritsch E.S., Tekkedil M.M., Anders S., Kuehn R., Nguyen M., Aiyar R.S., Proctor M., Sakhanenko N.A., Galas D.J., Gagneur J., Deutschbauer A., Steinmetz L.M. "An Evaluation of High-Throughput Approaches to QTL Mapping in Saccharomyces cerevisiae.", Genetics, 2013

Schulz D., Schwalb B., Kiesel A., Baejen B.,Torkler P.,Gagneur J., Soeding J. and Cramer P. Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis. Cell (155)

Gagneur J.*, Stegle O.*, Zhu C., Jakob P., Tekkedil M. M., Aiyar R., Schuon AK., Pe'er D. and Steinmetz L.M. Genotype-Environment Interactions Reveal Causal Pathways That Mediate Genetic Effects on Phenotype, PLoS Genet 9(9): e1003803.

Landry J.J.M.*, Pyl P.T.*, Rausch T., Zichner T., Tekkedil M. M., Stütz A.M., Jauch A., Aiyar R.S., Pau G., Delhomme N., Gagneur J., Korbel J.O., Huber W. and Steinmetz L.M. The Genomic and Transcriptomic Landscape of a HeLa Cell Line, G3 2013 3 (3)

Wilkening S., Tekkedil M. M.†, Lin G., Fritsch E.S., Wei W., Gagneur J.,Lazinsk D.W., Camilli A. and Steinmetz L.M. Genotyping 1000 yeast strains by next-generation sequencing, BMC Genomics 2013


Bietenhader, M.*, Martos, A.*, Tetaud, E.*, Aiyar, R.S.*, Sellem, C.H., Kucharczyk, R., Clauder-Munster, S.,  Giraud, M.F., Godard, F., Salin, B., Sagot, I., Gagneur, J., Dequard-Chablat, M., Contamine, M., Denmat, S.H., Sainsard-Chanet,A., Steinmetz, L.M., & di Rago, J.P. Experimental relocation of the mitochondrial ATP9 gene to the nucleus reveals forces underlying mitochondrial genome evolution. PLoS genetics 2012

Izquierdo-Carrasco F., Gagneur J., Stamatakis A.: "Trading Memory for Running Time in Phylogenetic Likelihood Computations", 2012 Bioinformatics conference, Vilamoura, Portugal, 2012

Gagneur, J., Pelechano, V., Steinmetz, L. & Mertens, C. Methods and systems for tracking samples and sample combinations Int. Patent Application Nr. WO 2012/019765, 2012 Feb. 16


Gagneur, J., Elze, M.C. & Tresch A. Selective phenotyping, entropy reduction, and the mastermind game BMC Bioinformatics 2011 Oct 20;12:406

Couplan*, E., Aiyar*, R.S., Kucharczyk, R., Kabala, A., Ezkurdia, N., Gagneur, J., St Onge, R.P., Salin, B., Soubigou, F., Le Cann, M., Steinmetz, L.M., di Rago, J.P. & Blondel M. A yeast-based assay identifies drugs active against human mitochondrial disorders. Proc Natl Acad Sci U S A. 2011 Jun 29

Bauer, S., Robinson, P.N. & Gagneur, J. Model-based Gene Set Analysis for Bioconductor. Bioinformatics. 2011 May 10.

Xu*, Z., Wei*, W., Gagneur*, J., Clauder-Munster, S., Smolik, M., Huber, W. & Steinmetz, L.M. Antisense expression increases gene expression variability and locus interdependency. Mol Syst Biol. 2011


Bauer*, S., Gagneur*, J. & Robinson, P.N. GOing Bayesian: model-based gene set analysis of genome-scale data. Nucleic Acids Res. 2010


Zinzen*, R.P., Girardot*, C., Gagneur*, J., Braun, M. & Furlong, E.E. Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature. 2009

Blandin*, S.A., Wang-Sattler*, R., Lamacchia, M., Gagneur, J., Lycett, G., Ning, Y., Levashina, E.A. & Steinmetz, L.M. Dissecting the genetic basis of resistance to malaria parasites in Anopheles gambiae. Science. 2009

Gagneur, J., Sinha, H., Perocchi, F., Bourgon, R., Huber, W. & Steinmetz, L.M. Genome-wide allele- and strand-specific expression profiling. Mol Syst Biol. 2009

Xu*, Z., Wei*, W., Gagneur, J., Perocchi, F., Clauder-Munster, S., Camblong, J., Guffanti, E., Stutz, F., Huber, W. & Steinmetz, L.M. Bidirectional promoters generate pervasive transcription in yeast. Nature. 2009