Search Results - "Naldi, Aurélien"

SBML Level 3: an extensible format for the exchange and reuse of biological models by Waltemath, Dagmar, König, Matthias, Zhang, Fengkai, Dräger, Andreas, Chaouiya, Claudine, Bergmann, Frank T, Finney, Andrew, Helikar, Tomáš, Hoops, Stefan, Malik‐Sheriff, Rahuman S, Moraru, Ion I, Naldi, Aurélien, Olivier, Brett G, Sahle, Sven, Smith, Lucian P, Swat, Maciej J, Watanabe, Leandro, Wilkinson, Darren J, Begley, Kimberly, Faeder, James R, Gómez, Harold F, Inagaki, Yuichiro, Lister, Allyson L, Lucio, Daniel, Mjolsness, Eric, Proctor, Carole J, Raman, Karthik, Rodriguez, Nicolas, Shaffer, Clifford A, Shapiro, Bruce E, Stelling, Joerg, Swainston, Neil, Tanimura, Naoki, Wagner, John, Meier‐Schellersheim, Martin, Sauro, Herbert M, Palsson, Bernhard, Kitano, Hiroaki, Funahashi, Akira, Hermjakob, Henning, Doyle, John C, Hucka, Michael, Adams, Richard R, Allen, Nicholas A, Angermann, Bastian R, Antoniotti, Marco, Courtot, Mélanie, Cox, Chris D, Dalle Pezze, Piero, Demir, Emek, Denney, William S, Dharuri, Harish, Dorier, Julien, Drasdo, Dirk, Ebrahim, Ali, Eichner, Johannes, Elf, Johan, Flamm, Christoph, Fleming, Ronan MT, Fröhlich, Martina, Gonçalves, Emanuel, Golebiewski, Martin, Grabski, Hovakim, Heavner, Benjamin D, de Jong, Hidde, Juty, Nick, Karp, Peter D, Kiselev, Ilya, Klipp, Edda, Knüpfer, Christian, Kolpakov, Fedor, Lawless, Conor, Li, Lu, Machne, Rainer, Mendes, Pedro, Mittag, Florian, Monteiro, Pedro T, Natarajan, Kedar Nath, Nguyen, Tramy, Pfau, Thomas, Phair, Robert D, Radivoyevitch, Tomas, Rohwer, Johann M, Saez‐Rodriguez, Julio, Scharm, Martin, Schmidt, Henning, Schreiber, Falk, Schubert, Michael, Sealfon, Stuart C, Soliman, Sylvain, Stefan, Melanie I, Sullivan, Devin P, Takahashi, Koichi, Teusink, Bas, Tolnay, David, Vazirabad, Ibrahim, von Kamp, Axel, Wittig, Ulrike, Wrzodek, Clemens, Zucker, Jeremy

“…Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models,…”
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Sex Dimorphism of Nonalcoholic Fatty Liver Disease (NAFLD) in Pparg -Null Mice by Schiffrin, Mariano, Winkler, Carine, Quignodon, Laure, Naldi, Aurélien, Trötzmüller, Martin, Köfeler, Harald, Henry, Hugues, Parini, Paolo, Desvergne, Béatrice, Gilardi, Federica

“…Men with nonalcoholic fatty liver disease (NAFLD) are more exposed to nonalcoholic steatohepatitis (NASH) and liver fibrosis than women. However, the…”
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Contribution of ROS and metabolic status to neonatal and adult CD8+ T cell activation by Sánchez-Villanueva, José Antonio, Rodríguez-Jorge, Otoniel, Ramírez-Pliego, Oscar, Rosas Salgado, Gabriela, Abou-Jaoudé, Wassim, Hernandez, Céline, Naldi, Aurélien, Thieffry, Denis, Santana, María Angélica

“…In neonatal T cells, a low response to infection contributes to a high incidence of morbidity and mortality of neonates. Here we have evaluated the impact of…”
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The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks by Naldi, Aurélien, Hernandez, Céline, Levy, Nicolas, Stoll, Gautier, Monteiro, Pedro T, Chaouiya, Claudine, Helikar, Tomáš, Zinovyev, Andrei, Calzone, Laurence, Cohen-Boulakia, Sarah, Thieffry, Denis, Paulevé, Loïc

“…Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many…”
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Cooperative development of logical modelling standards and tools with CoLoMoTo by Naldi, Aurélien, Monteiro, Pedro T, Müssel, Christoph, Kestler, Hans A, Thieffry, Denis, Xenarios, Ioannis, Saez-Rodriguez, Julio, Helikar, Tomas, Chaouiya, Claudine

“…The identification of large regulatory and signalling networks involved in the control of crucial cellular processes calls for proper modelling approaches…”
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Genome-wide analysis of SREBP1 activity around the clock reveals its combined dependency on nutrient and circadian signals by Gilardi, Federica, Migliavacca, Eugenia, Naldi, Aurélien, Baruchet, Michaël, Canella, Donatella, Le Martelot, Gwendal, Guex, Nicolas, Desvergne, Béatrice

“…In mammals, the circadian clock allows them to anticipate and adapt physiology around the 24 hours. Conversely, metabolism and food consumption regulate the…”
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Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells by Naldi, Aurélien, Larive, Romain M, Czerwinska, Urszula, Urbach, Serge, Montcourrier, Philippe, Roy, Christian, Solassol, Jérôme, Freiss, Gilles, Coopman, Peter J, Radulescu, Ovidiu

“…The ability to build in-depth cell signaling networks from vast experimental data is a key objective of computational biology. The spleen tyrosine kinase (Syk)…”
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Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop by Niarakis, Anna, Kuiper, Martin, Ostaszewski, Marek, Malik Sheriff, Rahuman S, Casals-Casas, Cristina, Thieffry, Denis, Freeman, Tom C, Thomas, Paul, Touré, Vasundra, Noël, Vincent, Stoll, Gautier, Saez-Rodriguez, Julio, Naldi, Aurélien, Oshurko, Eugenia, Xenarios, Ioannis, Soliman, Sylvain, Chaouiya, Claudine, Helikar, Tomáš, Calzone, Laurence

“…Abstract The fast accumulation of biological data calls for their integration, analysis and exploitation through more systematic approaches. The generation of…”
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SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools by Chaouiya, Claudine, Bérenguier, Duncan, Keating, Sarah M, Naldi, Aurélien, van Iersel, Martijn P, Rodriguez, Nicolas, Dräger, Andreas, Büchel, Finja, Cokelaer, Thomas, Kowal, Bryan, Wicks, Benjamin, Gonçalves, Emanuel, Dorier, Julien, Page, Michel, Monteiro, Pedro T, von Kamp, Axel, Xenarios, Ioannis, de Jong, Hidde, Hucka, Michael, Klamt, Steffen, Thieffry, Denis, Le Novère, Nicolas, Saez-Rodriguez, Julio, Helikar, Tomáš

“…Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major…”
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Differential regulation of RNA polymerase III genes during liver regeneration by Yeganeh, Meghdad, Praz, Viviane, Carmeli, Cristian, Villeneuve, Dominic, Rib, Leonor, Guex, Nicolas, Herr, Winship, Delorenzi, Mauro, Hernandez, Nouria

“…Abstract Mouse liver regeneration after partial hepatectomy involves cells in the remaining tissue synchronously entering the cell division cycle. We have used…”
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PTPN13 induces cell junction stabilization and inhibits mammary tumor invasiveness by Hamyeh, Mohamed, Bernex, Florence, Larive, Romain M, Naldi, Aurélien, Urbach, Serge, Simony-Lafontaine, Joelle, Puech, Carole, Bakhache, William, Solassol, Jérome, Coopman, Peter J, Hendriks, Wiljan J A J, Freiss, Gilles

“…Clinical data suggest that the protein tyrosine phosphatase PTPN13 exerts an anti-oncogenic effect. Its exact role in tumorigenesis remains, however, unclear…”
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BioLQM: A Java Toolkit for the Manipulation and Conversion of Logical Qualitative Models of Biological Networks by Naldi, Aurélien

“…Here we introduce bioLQM, a new Java software toolkit for the conversion, modification, and analysis of Logical Qualitative Models of biological regulatory…”
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Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer by Cantini, Laura, Zakeri, Pooya, Hernandez, Celine, Naldi, Aurelien, Thieffry, Denis, Remy, Elisabeth, Baudot, Anaïs

“…High-dimensional multi-omics data are now standard in biology. They can greatly enhance our understanding of biological systems when effectively integrated. To…”
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Automated inference of Boolean models from molecular interaction maps using CaSQ by Aghamiri, Sara Sadat, Singh, Vidisha, Naldi, Aurélien, Helikar, Tomáš, Soliman, Sylvain, Niarakis, Anna

“…Abstract Motivation Molecular interaction maps have emerged as a meaningful way of representing biological mechanisms in a comprehensive and systematic manner…”
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GOATOOLS: A Python library for Gene Ontology analyses by Klopfenstein, D. V., Zhang, Liangsheng, Pedersen, Brent S., Ramírez, Fidel, Warwick Vesztrocy, Alex, Naldi, Aurélien, Mungall, Christopher J., Yunes, Jeffrey M., Botvinnik, Olga, Weigel, Mark, Dampier, Will, Dessimoz, Christophe, Flick, Patrick, Tang, Haibao

“…The biological interpretation of gene lists with interesting shared properties, such as up- or down-regulation in a particular experiment, is typically…”
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Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle by Fauré, Adrien, Naldi, Aurélien, Chaouiya, Claudine, Thieffry, Denis

“…Motivation: To understand the behaviour of complex biological regulatory networks, a proper integration of molecular data into a full-fledge formal dynamical…”
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Diversity and plasticity of Th cell types predicted from regulatory network modelling by Naldi, Aurélien, Carneiro, Jorge, Chaouiya, Claudine, Thieffry, Denis

“…Alternative cell differentiation pathways are believed to arise from the concerted action of signalling pathways and transcriptional regulatory networks…”
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Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0 by Naldi, Aurélien, Hernandez, Céline, Abou-Jaoudé, Wassim, Monteiro, Pedro T, Chaouiya, Claudine, Thieffry, Denis

“…The logical formalism is well adapted to model large cellular networks, in particular when detailed kinetic data are scarce. This tutorial focuses on this…”
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Linear cuts in Boolean networks by Naldi, Aurélien, Richard, Adrien, Tonello, Elisa

“…Boolean networks are popular tools for the exploration of qualitative dynamical properties of biological systems. Several dynamical interpretations have been…”
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Computational Verification of Large Logical Models-Application to the Prediction of T Cell Response to Checkpoint Inhibitors by Hernandez, Céline, Thomas-Chollier, Morgane, Naldi, Aurélien, Thieffry, Denis

“…At the crossroad between biology and mathematical modeling, computational systems biology can contribute to a mechanistic understanding of high-level…”
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