• 2016

  • 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, bioRxiv


  • 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


  • 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 phenotype. PLoS Genet. 2015 Jun 3;11(6):e1005195. doi: 10.1371/journal.pgen.1005195. eCollection 2015 Jun.


  • 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 model Nucleic 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 Infancy The 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)


  • 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 10:768


  • 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 5:5585


  • 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


  • 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 (Epub ahead of print)


  • 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) 5:1075-1087


  • 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 (14) 90


  • 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 8 (8) 


  • 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


  • 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 Feb 15;7:468.


  • 2010

  • Bauer*, S., Gagneur*, J. & Robinson, P.N.

    GOing Bayesian: model-based gene set analysis of genome-scale data.

    Nucleic Acids Res. 2010 Feb 19


  • 2009

  • Zinzen*, R.P., Girardot*, C., Gagneur*, J., Braun, M. & Furlong, E.E.

    Combinatorial binding predicts spatio-temporal cis-regulatory activity.

    Nature. 2009 Nov 5;462(7269):65-70


  • 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 Oct 2;326(5949):147-50


  • 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;5:274. Epub 2009 Jun 16


  • 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 Feb 19;457(7232):1033-7. Epub 2009 Jan 25


  • 2008

  • Oktaba*, K., Gutierrez*, L., Gagneur, J., Girardot, C., Sengupta, A.K., Furlong, E.E. & Muller, J.

    Dynamic regulation by polycomb group protein complexes controls pattern formation and the cell cycle in Drosophila.

    Dev Cell. 2008 Dec;15(6):877-89. Epub 2008 Nov 6


  • Aiyar, R.S., Gagneur, J. & Steinmetz, L.M.

    Identification of mitochondrial disease genes through integrative analysis of multiple datasets.

    Methods. 2008 Dec;46(4):248-55. Epub 2008 Oct 16


  • 2007

  • Haudry, Y., Berube, H., Letunic, I., Weeber, P.D., Gagneur, J., Girardot, C., Kapushesky, M., Arendt, D., Bork, P., Brazma, A., Furlong, E., Wittbrodt, J. & Henrich, T.

    4DXpress: a database for cross-species expression pattern comparisons.

    Nucleic Acids Res. 2007 Oct 4


  • 2006

  • Perocchi, F., Jensen, L.J., Gagneur, J., Ahting, U., von Mering, C., Bork, P., Prokisch, H. & Steinmetz, L.M.

    Assessing systems properties of yeast mitochondria through an interaction map of the organelle.

    PLoS Genet. 2006 Oct 20;2(10):e170


  • Gagneur*, J., David*, L. & Steinmetz, L.M.

    Capturing cellular machines by systematic screens of protein complexes.

    Trends Microbiol. 2006 Aug;14(8):336-9. Epub 2006 Jun 16


  • 2005

  • Gagneur, J. & Casari, G.

    From molecular networks to qualitative cell behavior.

    FEBS Lett. 2005 Mar 21;579(8):1867-71


  • Klamt*, S., Gagneur* J., von Kamp*, A.

    Algorithmic approaches for computing elementary modes in large biochemical reaction networks.

    IEE Proceedings - Systems Biology 2005 Dec;152(4):249-255.

  • 2004

  • Bouwmeester, T., Bauch, A., Ruffner, H., Angrand, P.O., Bergamini, G., Croughton, K., Cruciat, C., Eberhard, D., Gagneur, J., Ghidelli, S., Hopf, C., Huhse, B., Mangano, R., Michon, A.M., Schirle, M., Schlegl, J., Schwab, M., Stein, M.A., Bauer, A., Casari, G., Drewes, G., Gavin, A.C., Jackson, D.B., Joberty, G., Neubauer, G., Rick, J., Kuster, B. & Superti-Furga, G.

    A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway.

    Nat Cell Biol 2004 Feb;6(2):97-105. Epub 2004 Jan 25.


  • Gagneur, J., Krause, R., Bouwmeester, T. & Casari, G.

    Modular decomposition of protein-protein interaction networks.

    Genome Biol 2004;5(8):R57. Epub 2004 Jul 21


  • Gagneur*, J. & Klamt*, S.

    Computation of elementary modes: a unifying framework and the new binary approach.

    BMC Bioinformatics. 2004 Nov 4;5:175


  • 2003

  • Gagneur, J., Jackson, D.B. & Casari, G.

    Hierarchical analysis of dependency in metabolic networks.

    Bioinformatics. 2003 May 22;19(8):1027-34.


↑ to the top
  • -