Architectural Principles for Characterizing the Performance of Antithetic Integral Feedback Networks

Autor: Noah Olsman, Fangzhou Xiao, John C. Doyle

Publikováno v: iScience, Vol 14, Iss , Pp 277-291 (2019)

Summary: As we begin to design increasingly complex synthetic biomolecular systems, it is essential to develop rational design methodologies that yield predictable circuit performance. Here we apply mathematical tools from the theory of control and d

Externí odkaz: https://doaj.org/article/f764f0f14a584c268232e98c0ece11fc

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

Convex robust performance with structured uncertainties in System Level Synthesis

Autor: Anish A. Sarma, John C. Doyle

Publikováno v: 2022 IEEE 61st Conference on Decision and Control (CDC).

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::4fdb550f4a4bacb9f3abce9e333946d0
https://doi.org/10.1109/cdc51059.2022.9993137

Mathematics and the Internet

Autor: Walter Willinger, David L. Alderson, John C. Doyle

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ddf21e1aa8c9d3679a86e4b308f3a193
https://doi.org/10.2307/j.ctv1t1kg73.17

Module-based analysis of robustness tradeoffs in the heat shock response system.

Autor: Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C Doyle, Irina Grigorova, Carol A Gross, Mustafa Khammash

Publikováno v: PLoS Computational Biology, Vol 2, Iss 7, p e59 (2006)

Biological systems have evolved complex regulatory mechanisms, even in situations where much simpler designs seem to be sufficient for generating nominal functionality. Using module-based analysis coupled with rigorous mathematical comparisons, we pr

Externí odkaz: https://doaj.org/article/23455b0dcce64f1a8fb1bd33b56841f1