Stochastic dynamics of Type-I interferon responses.

Autor: Benjamin D Maier, Luis U Aguilera, Sven Sahle, Pascal Mutz, Priyata Kalra, Christopher Dächert, Ralf Bartenschlager, Marco Binder, Ursula Kummer

Publikováno v: PLoS Computational Biology, Vol 18, Iss 10, p e1010623 (2022)

Interferon (IFN) activates the transcription of several hundred of IFN stimulated genes (ISGs) that constitute a highly effective antiviral defense program. Cell-to-cell variability in the induction of ISGs is well documented, but its source and effe

Externí odkaz: https://doaj.org/article/e723854cc75e40c39ccfcee145ce8af2

SBML Level 3: an extensible format for the exchange and reuse of biological models

Autor: Sarah M Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank T Bergmann, Andrew Finney, Colin S Gillespie, Tomáš Helikar, Stefan Hoops, Rahuman S Malik‐Sheriff, Stuart L Moodie, Ion I Moraru, Chris J Myers, Aurélien Naldi, Brett G Olivier, Sven Sahle, James C Schaff, Lucian P Smith, Maciej J Swat, Denis Thieffry, Leandro Watanabe, Darren J Wilkinson, Michael L Blinov, Kimberly Begley, James R Faeder, Harold F Gómez, Thomas M Hamm, Yuichiro Inagaki, Wolfram Liebermeister, Allyson L Lister, Daniel Lucio, Eric Mjolsness, Carole J Proctor, Karthik Raman, Nicolas Rodriguez, Clifford A Shaffer, Bruce E Shapiro, Joerg Stelling, Neil Swainston, Naoki Tanimura, John Wagner, Martin Meier‐Schellersheim, Herbert M Sauro, Bernhard Palsson, Hamid Bolouri, Hiroaki Kitano, Akira Funahashi, Henning Hermjakob, John C Doyle, Michael Hucka, SBML Level 3 Community members, Richard R Adams, Nicholas A Allen, Bastian R Angermann, Marco Antoniotti, Gary D Bader, Jan Červený, Mélanie Courtot, Chris D Cox, Piero Dalle Pezze, Emek Demir, William S Denney, Harish Dharuri, Julien Dorier, Dirk Drasdo, Ali Ebrahim, Johannes Eichner, Johan Elf, Lukas Endler, Chris T Evelo, Christoph Flamm, Ronan MT Fleming, Martina Fröhlich, Mihai Glont, Emanuel Gonçalves, Martin Golebiewski, Hovakim Grabski, Alex Gutteridge, Damon Hachmeister, Leonard A Harris, Benjamin D Heavner, Ron Henkel, William S Hlavacek, Bin Hu, Daniel R Hyduke, Hidde de Jong, Nick Juty, Peter D Karp, Jonathan R Karr, Douglas B Kell, Roland Keller, Ilya Kiselev, Steffen Klamt, Edda Klipp, Christian Knüpfer, Fedor Kolpakov, Falko Krause, Martina Kutmon, Camille Laibe, Conor Lawless, Lu Li, Leslie M Loew, Rainer Machne, Yukiko Matsuoka, Pedro Mendes, Huaiyu Mi, Florian Mittag, Pedro T Monteiro, Kedar Nath Natarajan, Poul MF Nielsen, Tramy Nguyen, Alida Palmisano, Jean‐Baptiste Pettit, Thomas Pfau, Robert D Phair, Tomas Radivoyevitch, Johann M Rohwer, Oliver A Ruebenacker, Julio Saez‐Rodriguez, Martin Scharm, Henning Schmidt, Falk Schreiber, Michael Schubert, Roman Schulte, Stuart C Sealfon, Kieran Smallbone, Sylvain Soliman, Melanie I Stefan, Devin P Sullivan, Koichi Takahashi, Bas Teusink, David Tolnay, Ibrahim Vazirabad, Axel von Kamp, Ulrike Wittig, Clemens Wrzodek, Finja Wrzodek, Ioannis Xenarios, Anna Zhukova, Jeremy Zucker

Publikováno v: Molecular Systems Biology, Vol 16, Iss 8, Pp 1-21 (2020)

Abstract Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edi

Externí odkaz: https://doaj.org/article/86e517962df24b21af078b7f951f7487

Inspecting the Solution Space of Genome-Scale Metabolic Models

Autor: Seyed Babak Loghmani, Nadine Veith, Sven Sahle, Frank T. Bergmann, Brett G. Olivier, Ursula Kummer

Publikováno v: Metabolites, Vol 12, Iss 1, p 43 (2022)

Genome-scale metabolic models are frequently used in computational biology. They offer an integrative view on the metabolic network of an organism without the need to know kinetic information in detail. However, the huge solution space which comes wi

Externí odkaz: https://doaj.org/article/76ab4049043d4d4e9231f435a2a8afa8

A20/TNFAIP3 Discriminates Tumor Necrosis Factor (TNF)-Induced NF-κB from JNK Pathway Activation in Hepatocytes

Autor: Federico Pinna, Michaela Bissinger, Katharina Beuke, Nicolas Huber, Thomas Longerich, Ursula Kummer, Peter Schirmacher, Sven Sahle, Kai Breuhahn

Publikováno v: Frontiers in Physiology, Vol 8 (2017)

In the liver tumor necrosis factor (TNF)-induced signaling critically regulates the immune response of non-parenchymal cells as well as proliferation and apoptosis of hepatocytes via activation of the NF-κB and JNK pathways. Especially, the inductio

Externí odkaz: https://doaj.org/article/f899ec503a3e4bee82139cb18a71fc4f

Minimum Information About a Simulation Experiment (MIASE).

Autor: Dagmar Waltemath, Richard Adams, Daniel A Beard, Frank T Bergmann, Upinder S Bhalla, Randall Britten, Vijayalakshmi Chelliah, Michael T Cooling, Jonathan Cooper, Edmund J Crampin, Alan Garny, Stefan Hoops, Michael Hucka, Peter Hunter, Edda Klipp, Camille Laibe, Andrew K Miller, Ion Moraru, David Nickerson, Poul Nielsen, Macha Nikolski, Sven Sahle, Herbert M Sauro, Henning Schmidt, Jacky L Snoep, Dominic Tolle, Olaf Wolkenhauer, Nicolas Le Novère

Publikováno v: PLoS Computational Biology, Vol 7, Iss 4, p e1001122 (2011)

Externí odkaz: https://doaj.org/article/13131c5d4d6c4638ab84981fd5e20ad9