Vicente A. Yépez, Mirjana Gusic, Robert Kopajtich, Christian Mertes, Nicholas H. Smith, Charlotte Alston, Riccardo Berutti, Holger Blessing, Elzbieta Ciara, Fang Fang, Peter Freisinger, Daniele Ghezzi, Susan J. Hayflick, Yoshihito Kishita, Thomas Klopstock, Constanza Lamperti, Dominic Lenz, Christine C. Makowski, Johannes A. Mayr, Signe Mosegaard, Michaela F. Müller, Gerard Munoz-Pujol, Kei Murayama, Agnieszka Nadel, Akira Ohtake, Yasushi Okazaki, Dorota Piekutowska-Abramczuk, Elena Procopio, Antonia Ribes, Agnes Rotig, Thomas Schwarzmayr, Christian Staufner, Sarah L. Stenton, Tim M. Strom, Robert W. Taylor, Caterina Terrile, Frederic Tort, Rudy Van Coster, Matias Wagner, Saskia B. Wortmann, Manting Xu, Thomas Meitinger, Julien Gagneur@, Holger Prokisch@. Clinical implementation of RNA sequencing for Mendelian disease diagnostics. medRxiv, 2021

Robert Kopajtich, Dmitrii Smirnov, Sarah Louise Stenton, Stefan Loipfinger, Chen Meng, Ines Scheller, Peter Freisinger, Robert Baski, Riccardo Berutti, Juergen Behr, Martina Bucher, Felix Distelmaier, Mirjana Gusic, Maja Hempel, Lea Kulterer, Hans Mayr, Thomas Meitinger, Christian Mertes, Metodi Metodiev, Alessia Nasca, Agnieszka Nadel, Akira Ohtake, Yasushi Okazaki, Rikke Olsen, Dorota Piekutowska-Abramczuk, Agnes Roetig, Rene Santer, Detlev Schindler, Abdelhamid Slama, Christian Staufner, Tim Strom, Patrick Verloo, Juergen-Christoph von Kleist-Retzow, Saskia Wortmann, Vicente Yepez, Costanza Lamperti, Daniele Ghezzi, Kei Murayama, Christina Ludwig, Julien Gagneur, Holger Prokisch. Integration of proteomics with genomics and transcriptomics increases the diagnostic rate of Mendelian disorders. medRxiv, 2021

2021

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. Nat Commun, 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. Nat Protoc , 2021, PMID: 33462443 Sharedlt link.

David R. Murdock, Hongzheng Dai, Lindsay C. Burrage, Jill A. Rosenfeld, Shamika Ketkar, Michaela F. Müller, Vicente A. Yépez, Julien Gagneur, Pengfei Liu, Shan Chen, Mahim Jain, Gladys Zapata, Carlos A. Bacino, Hsiao-Tuan Chao, Paolo Moretti, William J. Craigen, Neil A. Hanchard, and Brendan Lee. Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing. JCI, 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*, 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 tissuesMol. 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 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, AJHG, 2018, PMID: 30503520

Beate Hagl, Benedikt D. Spielberger, Silvia Thoene, Sophie Bonnal, Christian Mertes, Christof Winter, Isaac J.Nijman, Shira Verduin, Andreas C. Eberherr, Anne Puel, Detlev Schindler, Jürgen Ruland, Thomas Meitinger, Julien Gagneur, Jordan S. Orange, Marielle E. van Gijn, Ellen D. Renner, Somatic alterations compromised molecular diagnosis of DOCK8 hyper-IgE syndrome caused by a novel intronic splice site mutation., Sci Rep. 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, 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. 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

Maximilian Witzel, Daniel Petersheim, Yanxin Fan, Ehsan Bahrami, Tomas Racek, Meino Rohlfs, Jacek Puchałka, Christian Mertes, Julien Gagneur, Christoph Ziegenhain, Wolfgang Enard,  Asbjørg Stray-Pedersen, Peter D Arkwright, Miguel R Abboud, Vahid Pazhakh, Graham J Lieschke, Peter M Krawitz, Maik Dahlhoff, Marlon R Schneider, Eckhard Wolf, Hans-Peter Horny, Heinrich Schmidt, Alejandro A Schäffer, 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, Manal Dayem-Quere, Mirjana Gusic, Annabelle Chaussenot, Sylvie Bannwarth, Bérengère François, Emmanuelle C Genin, Konstantina Fragaki, Chatarina L M Volker-Touw, Christelle Vasnier, Valérie Serre, Koen L I van Gassen, Françoise Lespinasse, Susan Richter, Graeme Eisenhofer, Cécile Rouzier, Fanny Mochel, Anne De Saint-Martin, Marie-Thérèse Abi Warde, Monique G M de Sain-van der Velde, Judith J M Jans, Jeanne Amiel, Ziga Avsec, Christian Mertes, Tobias B Haack, Tim Strom, Thomas Meitinger, Penelope E Bonnen, Robert W Taylor, Julien Gagneur, Peter M van Hasselt, Agnès Rötig, Agnès Delahodde, Holger Prokisch, Sabine A Fuchs, 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 phenotypePLoS 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 modelNucleic Acids Research, 2015. PMID: 26578558

Tobias B. Haack, Christian Staufner, Marlies G. Köpke, Beate K. Straub, Stefan Kölker, Christian Thiel, Peter Freisinger, Ivo Baric, Patrick J. McKiernan, Nicola Dikow, Inga Harting, Flemming Beisse, Peter Burgard, Urania Kotzaeridou, Joachim Kühr, Urban Himbert, Robert W. Taylor, Felix Distelmaier, Jerry Vockley, Lina Ghaloul-Gonzalez, Johannes Zschocke, Laura S. Kremer, Elisabeth Graf, Thomas Schwarzmayr, Daniel M. Bader, Julien Gagneur, Thomas Wieland, Caterina Terrile, Tim M. Strom, Thomas Meitinger, Georg F. Hoffmann, Holger Prokisch, Biallelic Mutations in NBAS Cause Recurrent Acute Liver Failure with Onset in InfancyThe 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 variantsMolecular 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 cycleMolecular Systems Biology 2014. PMID: 25527639

Raeka S. Aiyar, Maria Bohnert, Stéphane Duvezin-Caubet, Cécile Voisset, Julien Gagneur, Emilie S. Fritsch, Elodie Couplan, Karina von der Malsburg, Charlotta Funaya, Flavie Soubigou, Florence Courtin, Sundari Suresh, Roza Kucharczyk, Justine Evrard, Claude Antony, Robert P. St. Onge, Marc Blondel, Jean-Paul di Rago, Martin van der Laan, 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, Gen Lin, Emilie S. Fritsch, Manu M. Tekkedil, Simon Anders, Raquel Kuehn, Michelle Nguyen, Raeka S. Aiyar, Michael Proctor, Nikita A. Sakhanenko, David J. Galas, Julien Gagneur, Adam Deutschbauer, 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*, Tobias Rausch, Thomas Zichner, Manu M. Tekkedil, Adrian M. Stütz, Anna Jauch, Raeka S. Aiyar, Gregoire Pau, Nicolas Delhomme, Julien Gagneur, Jan O. Korbel, Wolfgang Huber, 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*, Carole H. Sellem, Roza Kucharczyk, Sandra Clauder-Münster, Marie-France Giraud, François Godard, Bénédict Salin, Isabelle Sagot, Julien Gagneur, Michelle Déquard-Chablat, Véronique Contamine, Sylvie Hermann-Le Denmat, Annie Sainsard-Chanet, Lars M. Steinmetz, 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*, Roza Kucharczyk, Anna Kabala, Nahia Ezkurdia, Julien Gagneur, Robert P. St Onge, Bénédicte Salin, Flavie Soubigou, Marie Le Cann, Lars M. Steinmetz, Jean-Paul di Rago, 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, Hugo Berube, Ivica Letunic, Paul-Daniel Weeber, Julien Gagneur, Charles Girardot, Misha Kapushesky, Detlev Arendt, Peer Bork, Alvis Brazma, Eileen E. M. Furlong, Joachim Wittbrodt, 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, Angela Bauch, Heinz Ruffner, Pierre-Olivier Angrand, Giovanna Bergamini, Karen Croughton, Cristina Cruciat, Dirk Eberhard, Julien Gagneur, Sonja Ghidelli, Carsten Hopf, Bettina Huhse, Raffaella Mangano, Anne-Marie Michon, Markus Schirle, Judith Schlegl, Markus Schwab, Martin A. Stein, Andreas Bauer, Georg Casari, Gerard Drewes, Anne-Claude Gavin, David B. Jackson, Gerard Joberty, Gitte Neubauer, Jens Rick, Bernhard Kuster, 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

Gagneur@ J, Jackson DB, Casari G. Hierarchical analysis of dependency in metabolic networks. Bioinformatics, 19(8):1027–34, 2003.