Publications by authors named "Julien Gagneur"

60Publications

Quantification of Proteins and Histone Marks in Drosophila Embryos Reveals Stoichiometric Relationships Impacting Chromatin Regulation.

Dev Cell 2019 12 17;51(5):632-644.e6. Epub 2019 Oct 17.

Max-Planck Institute of Biochemistry, Laboratory of Chromatin Biology, Am Klopferspitz 18, 82152 Martinsried, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2019.09.011DOI Listing
December 2019

CAGI 5 splicing challenge: Improved exon skipping and intron retention predictions with MMSplice.

Hum Mutat 2019 09 29;40(9):1243-1251. Epub 2019 Jul 29.

Department of Informatics, Technical University of Munich, Garching, Germany.

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http://dx.doi.org/10.1002/humu.23788DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7241300PMC
September 2019

Global donor and acceptor splicing site kinetics in human cells.

Elife 2019 04 26;8. Epub 2019 Apr 26.

Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.

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http://dx.doi.org/10.7554/eLife.45056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6548502PMC
April 2019

Deep learning: new computational modelling techniques for genomics.

Nat Rev Genet 2019 07;20(7):389-403

Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.

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http://www.nature.com/articles/s41576-019-0122-6
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http://dx.doi.org/10.1038/s41576-019-0122-6DOI Listing
July 2019

MMSplice: modular modeling improves the predictions of genetic variant effects on splicing.

Genome Biol 2019 03 1;20(1):48. Epub 2019 Mar 1.

Department of Informatics, Technical University of Munich, Boltzmannstraße, Garching, 85748, Germany.

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http://dx.doi.org/10.1186/s13059-019-1653-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6396468PMC
March 2019

OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data.

Am J Hum Genet 2018 12 29;103(6):907-917. Epub 2018 Nov 29.

Department of Informatics, Technical University of Munich, Boltzmannstr. 3, 85748 Garching, Germany; Quantitative Biosciences Munich, Gene Center, Department of Biochemistry, Ludwig-Maximilians Universität München, Feodor-Lynen-Str. 25, 81377 München, Germany. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00029297183040
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http://dx.doi.org/10.1016/j.ajhg.2018.10.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6288422PMC
December 2018

GenoGAM 2.0: scalable and efficient implementation of genome-wide generalized additive models for gigabase-scale genomes.

BMC Bioinformatics 2018 06 27;19(1):247. Epub 2018 Jun 27.

Department of Informatics, Technical University Munich, Boltzmannstr. 3, Garching, Germany.

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http://dx.doi.org/10.1186/s12859-018-2238-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6020310PMC
June 2018

-regulatory elements explain most of the mRNA stability variation across genes in yeast.

RNA 2017 11 11;23(11):1648-1659. Epub 2017 Aug 11.

Department of Informatics, Technical University of Munich, 85748 Garching, Germany

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http://rnajournal.cshlp.org/lookup/doi/10.1261/rna.062224.11
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http://dx.doi.org/10.1261/rna.062224.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5648033PMC
November 2017

CES-1 Snail Represses MELK Expression To Control Asymmetric Cell Division.

Genetics 2017 08 26;206(4):2069-2084. Epub 2017 Jun 26.

Center for Integrated Protein Science Munich - CIPSM, Department Biology II, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany

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http://dx.doi.org/10.1534/genetics.117.202754DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5560807PMC
August 2017

GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis.

Bioinformatics 2017 Aug;33(15):2258-2265

Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 80333 Munich, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btx150DOI Listing
August 2017

TT-seq captures enhancer landscapes immediately after T-cell stimulation.

Mol Syst Biol 2017 03 7;13(3):920. Epub 2017 Mar 7.

Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5371733PMC
http://dx.doi.org/10.15252/msb.20167507DOI Listing
March 2017

Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN.

PLoS One 2017 5;12(1):e0169249. Epub 2017 Jan 5.

Gene Center and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität Munich, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0169249PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5215863PMC
August 2017

Measures of RNA metabolism rates: Toward a definition at the level of single bonds.

Transcription 2017 03 14;8(2):75-80. Epub 2016 Nov 14.

a Department of Informatics , Technical University of Munich, Garching bei München , Germany.

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http://dx.doi.org/10.1080/21541264.2016.1257972DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5423486PMC
March 2017

Meiotic Interactors of a Mitotic Gene TAO3 Revealed by Functional Analysis of its Rare Variant.

G3 (Bethesda) 2016 08 9;6(8):2255-63. Epub 2016 Aug 9.

Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India Initiative for Biological Systems Engineering, Indian Institute of Technology Madras, Chennai 600036, India

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http://dx.doi.org/10.1534/g3.116.029900DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978881PMC
August 2016

TT-seq maps the human transient transcriptome.

Science 2016 Jun;352(6290):1225-8

Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany. Department of Biosciences and Nutrition, Center for Innovative Medicine, and Science for Life Laboratory, Karolinska Institutet, Novum, Hälsovägen 7, 141 83 Huddinge, Sweden.

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http://dx.doi.org/10.1126/science.aad9841DOI Listing
June 2016

Determinants of RNA metabolism in the Schizosaccharomyces pombe genome.

Mol Syst Biol 2016 Feb 16;12(2):857. Epub 2016 Feb 16.

Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany

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http://biorxiv.org/content/biorxiv/early/2015/08/26/025585.f
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http://lyonsysbio2015.sciencesconf.org/conference/lyonsysbio
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4770384PMC
http://dx.doi.org/10.15252/msb.20156526DOI Listing
February 2016

Simultaneous characterization of sense and antisense genomic processes by the double-stranded hidden Markov model.

Nucleic Acids Res 2016 Mar 17;44(5):e44. Epub 2015 Nov 17.

Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany Institute for Genetics, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany

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http://dx.doi.org/10.1093/nar/gkv1184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4797261PMC
March 2016

Temporal expression profiling identifies pathways mediating effect of causal variant on phenotype.

PLoS Genet 2015 Jun 3;11(6):e1005195. Epub 2015 Jun 3.

Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India.

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http://dx.doi.org/10.1371/journal.pgen.1005195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4454590PMC
June 2015

Negative feedback buffers effects of regulatory variants.

Mol Syst Biol 2015 Jan 29;11(1):785. Epub 2015 Jan 29.

Computational Genomics, Gene Center, Ludwig Maximilians University, Munich, Germany

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332157PMC
http://dx.doi.org/10.15252/msb.20145844DOI Listing
January 2015

Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle.

Mol Syst Biol 2014 Dec 19;10:768. Epub 2014 Dec 19.

Gene Center and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany Institute for Genetics, University of Cologne, Cologne, Germany Max Planck Institute for Plant Breeding Research, Cologne, Germany

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http://msb.embopress.org/cgi/doi/10.15252/msb.20145654
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300491PMC
http://dx.doi.org/10.15252/msb.20145654DOI Listing
December 2014

Mitochondrial protein sorting as a therapeutic target for ATP synthase disorders.

Nat Commun 2014 Dec 18;5:5585. Epub 2014 Dec 18.

1] European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany [2] Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA [3] Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.

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http://dx.doi.org/10.1038/ncomms6585DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4284804PMC
December 2014

Yeast growth plasticity is regulated by environment-specific multi-QTL interactions.

G3 (Bethesda) 2014 Jan 28;4(5):769-77. Epub 2014 Jan 28.

Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India

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http://dx.doi.org/10.1534/g3.113.009142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4025475PMC
January 2014

Transcriptome surveillance by selective termination of noncoding RNA synthesis.

Cell 2013 Nov 7;155(5):1075-87. Epub 2013 Nov 7.

Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.

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http://dx.doi.org/10.1016/j.cell.2013.10.024DOI Listing
November 2013

Genotyping 1000 yeast strains by next-generation sequencing.

BMC Genomics 2013 Feb 9;14:90. Epub 2013 Feb 9.

Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany.

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http://dx.doi.org/10.1186/1471-2164-14-90DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575377PMC
February 2013

Selective phenotyping, entropy reduction, and the mastermind game.

BMC Bioinformatics 2011 Oct 20;12:406. Epub 2011 Oct 20.

European Molecular Biology Lab, 69122 Heidelberg, Germany.

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http://dx.doi.org/10.1186/1471-2105-12-406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3258278PMC
October 2011

A yeast-based assay identifies drugs active against human mitochondrial disorders.

Proc Natl Acad Sci U S A 2011 Jul 29;108(29):11989-94. Epub 2011 Jun 29.

INSERM U613; Université de Brest, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; Centre Hospitalier Régional Universitaire Brest, Hop Morvan, Laboratoire de Génétique Moléculaire, F-29200 Brest, France.

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http://dx.doi.org/10.1073/pnas.1101478108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141935PMC
July 2011

Model-based gene set analysis for Bioconductor.

Bioinformatics 2011 Jul 10;27(13):1882-3. Epub 2011 May 10.

Institute for Medical Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btr296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117381PMC
July 2011

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

Nucleic Acids Res 2010 Jun 19;38(11):3523-32. Epub 2010 Feb 19.

Institute for Medical Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.

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http://dx.doi.org/10.1093/nar/gkq045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2887944PMC
June 2010

Combinatorial binding predicts spatio-temporal cis-regulatory activity.

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

European Molecular Biology Laboratory, D-69117 Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature08531DOI Listing
November 2009

Genome-wide allele- and strand-specific expression profiling.

Mol Syst Biol 2009 16;5:274. Epub 2009 Jun 16.

Gene Expression Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1038/msb.2009.31DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2710863PMC
September 2009

Bidirectional promoters generate pervasive transcription in yeast.

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

European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature07728DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2766638PMC
February 2009

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

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

European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.ymeth.2008.10.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774125PMC
December 2008

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

Nucleic Acids Res 2008 Jan 4;36(Database issue):D847-53. Epub 2007 Oct 4.

European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1093/nar/gkm797DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238840PMC
January 2008

Capturing cellular machines by systematic screens of protein complexes.

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

European Molecular Biology Laboratory, Heidelberg 69117, Germany.

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http://linkinghub.elsevier.com/retrieve/pii/S0966842X0600132
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http://dx.doi.org/10.1016/j.tim.2006.06.002DOI Listing
August 2006

From molecular networks to qualitative cell behavior.

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

Cellzome AG, Meyerhofstr. 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.febslet.2005.02.007DOI Listing
March 2005

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

BMC Bioinformatics 2004 Nov 4;5:175. Epub 2004 Nov 4.

Cellzome AG, Meyerhofstr. 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1186/1471-2105-5-175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC544875PMC
November 2004

Modular decomposition of protein-protein interaction networks.

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

Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1186/gb-2004-5-8-r57DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC507882PMC
February 2005

Hierarchical analysis of dependency in metabolic networks.

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

Lion Bioscience AG, Waldhoferstr. 98, 69123 Heidelberg, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btg115DOI Listing
May 2003