Felix Brechtmann, Agne Matuseviciute, Christian Mertes, Vicente A Yepez, Ziga Avsec, Maximilian Herzog, Daniel Magnus Bader, Holger Prokisch, Julien Gagneur, OUTRIDER: A statistical method for detecting aberrantly expressed genes in RNA sequencing data, bioRxiv

Ziga Avsec, Roman Kreuzhuber, Johnny Israeli, Nancy Xu, Jun Cheng, Avanti Shrikumar, Abhimanyu Banerjee, Daniel S Kim, Lara Urban, Anshul Kundaje, Oliver Stegle, Julien Gagneur, Kipoi: accelerating the community exchange and reuse of predictive models for genomics bioRxiv

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, bioRxiv

Dongxue Wang, Basak Eraslan, Thomas Wieland, Bjorn M Hallstrom, Thomas Hopf, Daniel Paul Zolg, Jana Zecha, Anna Asplund, Li-hua Li, Chen Meng, Martin Frejno, Tobias Schmidt, Karsten Schnatbaum, Mathias Wilhelm, Fredrik Ponten, Mathias Uhlen, Julien Gagneur, Hannes Hahne, Bernhard Kuster, A deep proteome and transcriptome abundance atlas of 29 healthy human tissues, bioRxiv

2018

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 Jul 11;13(7):e0199938. PMID: 29995917

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. 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 Jun 27;19(1):247. 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, 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. PMID: 28604674

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. 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

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. 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, Jan 5. PMID: 27989324

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. PMID: 28056037

2016

Leonhard Wachutka and Julien Gagneur, Measures of RNA metabolism rates: Toward a definition at the level of single bonds, Transcription, 2016, Nov. 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 Aug 9;6(8):2255-63. 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 Vol 352, Issue 6290. PMID: 27257258

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. PMID: 26883383

2015

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. PMID: 26039065

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. PMID: 26578558

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. PMID: 26073778

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. PMID: 25634765

2014

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. PMID: 25527639

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. PMID: 25519239

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 . PMID: 24474169

2013

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. PMID: 24374355

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). PMID: 24210918

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. PMID: 24068968

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). PMID: 23550136

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

2012

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. PMID: 22916027

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

2011

Gagneur, J., Elze, M.C. & Tresch A. Selective phenotyping, entropy reduction, and the mastermind game BMC Bioinformatics 2011 Oct 20;12:406. PMID: 22014271

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. PMID: 21715656

Bauer, S., Robinson, P.N. & Gagneur, J. Model-based Gene Set Analysis for Bioconductor. Bioinformatics. 2011 May 10. PMID: 21561920

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. PMID: 21326235

2010

Bauer*, S., Gagneur*, J. & Robinson, P.N. GOing Bayesian: model-based gene set analysis of genome-scale data. Nucleic Acids Res. 2010. PMID: 20172960

2009

Zinzen*, R.P., Girardot*, C., Gagneur*, J., Braun, M. & Furlong, E.E. Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature. 2009. PMID: 19890324

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. 200. PMID: 19797663

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. PMID: 19536197

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. PMID: 19169243