Model Reduction for the Chemical Master Equation: an Information-Theoretic Approach

Autor: Öcal, K., Sanguinetti, G., Grima, R.

The complexity of mathematical models in biology has rendered model reduction an essential tool in the quantitative biologist's toolkit. For stochastic reaction networks described using the Chemical Master Equation, commonly used methods include time

Externí odkaz: http://arxiv.org/abs/2210.05329

Efficient and scalable prediction of stochastic reaction-diffusion processes using graph neural networks.

Autor: Cao Z; State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Department of Chemical Engineering, Queen's University, Kingston, Canada K7L 3N6. Electronic address: z.cao@queensu.ca., Chen R; Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China., Xu L; State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China., Zhou X; State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China., Fu X; State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China., Zhong W; Key Laboratory of Smart Manufacturing in Energy Chemical Process, Ministry of Education, East China University of Science and Technology, Shanghai 200237, China., Grima R; School of Biological Sciences, the University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, Scotland, United Kingdom. Electronic address: ramon.grima@ed.ac.uk.

Publikováno v: Mathematical biosciences [Math Biosci] 2024 Sep; Vol. 375, pp. 109248. Date of Electronic Publication: 2024 Jul 08.

Holimap: an accurate and efficient method for solving stochastic gene network dynamics.

Autor: Jia C; Applied and Computational Mathematics Division, Beijing Computational Science Research Center, Beijing, China., Grima R; School of Biological Sciences, University of Edinburgh, Edinburgh, UK. Ramon.Grima@ed.ac.uk.

Publikováno v: Nature communications [Nat Commun] 2024 Aug 02; Vol. 15 (1), pp. 6557. Date of Electronic Publication: 2024 Aug 02.

Airway microbiota signals anabolic and catabolic remodeling in the transplanted lung

Autor: Jougon, J., Velly, J.-F., Rozé, H., Blanchard, E., Dromer, C., Antoine, M., Cappello, M., Ruiz, M., Sokolow, Y., Vanden Eynden, F., Van Nooten, G., Barvais, L., Berré, J., Brimioulle, S., De Backer, D., Créteur, J., Engelman, E., Huybrechts, I., Ickx, B., Preiser, T.J.C., Tuna, T., Van Obberghe, L., Vancutsem, N., Vincent, J.-L., De Vuyst, P., Etienne, I., Féry, F., Jacobs, F., Knoop, C., Vachiéry, J.L., Van den Borne, P., Wellemans, I., Amand, G., Collignon, L., Giroux, M., Angelescu, D., Chavanon, O., Hacini, R., Pirvu, A., Porcu, P., Albaladejo, P., Allègre, C., Bataillard, A., Bedague, D., Briot, E., Casez-Brasseur, M., Colas, D., Dessertaine, G., Durand, M., Francony, G., Hebrard, A., Marino, M.R., Oummahan, B., Protar, D., Rehm, D., Robin, S., Rossi-Blancher, M., Augier, C., Bedouch, P., Boignard, A., Bouvaist, H., Briault, A., Camara, B., Claustre, J., Chanoine, S., Dubuc, M., Quétant, S., Maurizi, J., Pavèse, P., Pison, C., Saint-Raymond, C., Wion, N., Chérion, C., Grima, R., Jegaden, O., Maury, J.-M., Tronc, F., Flamens, C., Paulus, S., Mornex, J.-F., Philit, F., Senechal, A., Glérant, J.-C., Turquier, S., Gamondes, D., Chalabresse, L., Thivolet-Bejui, F., Barnel, C., Dubois, C., Tiberghien, A., Le Pimpec-Barthes, F., Bel, A., Mordant, P., Achouh, P., Boussaud, V., Guillemain, R., Méléard, D., Bricourt, M.O., Cholley, B., Pezella, V., Brioude, G., D'Journo, X.B., Doddoli, C., Thomas, P., Trousse, D., Dizier, S., Leone, M., Papazian, L., Bregeon, F., Basire, A., Coltey, B., Dufeu, N., Dutau, H., Garcia, S., Gaubert, J.Y., Gomez, C., Laroumagne, S., Nieves, A., Picard, L.C., Reynaud-Gaubert, M., Secq, V., Mouton, G., Baron, O., Lacoste, P., Perigaud, C., Roussel, J.C., Danner, I., Haloun, A., Magnan, A., Tissot, A., Lepoivre, T., Treilhaud, M., Botturi-Cavaillès, K., Brouard, S., Danger, R., Loy, J., Morisset, M., Pain, M., Pares, S., Reboulleau, D., Royer, P.-J., Fabre, D., Fadel, E., Mercier, O., Mussot, S., Stephan, F., Viard, P., Cerrina, J., Dorfmuller, P., Ghigna, S.M., Hervén, Ph., Le Roy Ladurie, F., Le Pavec, J., Thomas de Montpreville, V., Lamrani, L., Castier, Y., Cerceau, P., Augustin, P., Jean-Baptiste, S., Boudinet, S., Montravers, P., Brugière, O., Dauriat, G., Jébrak, G., Mal, H., Marceau, A., Métivier, A.-C., Thabut, G., Lhuillier, E., Dupin, C., Bunel, V., Falcoz, P., Massard, G., Santelmo, N., Ajob, G., Collange, O., Helms, O., Hentz, J., Roche, A., Bakouboula, B., Degot, T., Dory, A., Hirschi, S., Ohlmann-Caillard, S., Kessler, L., Kessler, R., Schuller, A., Bennedif, K., Vargas, S., Stauder, J., Ali-Azouaou, S., Bonnette, P., Chapelier, A., Puyo, P., Sage, E., Bresson, J., Caille, V., Cerf, C., Devaquet, J., Dumans-Nizard, V., Felten, M.-L., Fischler, M., Si Larbi, A.-G., Leguen, M., Ley, L., Liu, N., Trebbia, G., De Miranda, S., Douvry, B., Gonin, F., Grenet, D., Hamid, A.M., Neveu, H., Parquin, F., Picard, C., Roux, A., Stern, M., Bouillioud, F., Cahen, P., Colombat, M., Dautricourt, C., Delahousse, M., D'Urso, B., Gravisse, J., Guth, A., Hillaire, S., Honderlick, P., Lequintrec, M., Longchampt, E., Mellot, F., Scherrer, A., Temagoult, L., Tricot, L., Vasse, M., Veyrie, C., Zemoura, L., Berjaud, J., Brouchet, L., Dahan, M., Mathe, F.O., Benahoua, H., DaCosta, M., Serres, I., Merlet-Dupuy, V., Grigoli, M., Didier, A., Murris, M., Crognier, L., Fourcade, O., Krueger, T., Ris, H.B., Gonzalez, M., Jolliet, Ph., Marcucci, C., Chollet, M., Gronchi, F., Courbon, C., Berutto, C., Manuel, O., Koutsokera, A., Aubert, J.-D., Nicod, L.P., Mouraux, S., Bernasconi, E., Pattaroni, C., Marsland, B.J., Soccal, P.M., Rochat, T., Lücker, L.M., Hillinger, S., Inci, I., Weder, W., Schuepbach, R., Zalunardo, M., Benden, C., Schuurmans, M.M., Gaspert, A., Holzmann, D., Müller, N., Schmid, C., Vrugt, B., Fritz, A., Maier, D., Deplanche, K., Koubi, D., Ernst, F., Paprotka, T., Schmitt, M., Wahl, B., Boissel, J.-P., Olivera-Botello, G., Trocmé, C., Toussaint, B., Bourgoin-Voillard, S., Sève, M., Benmerad, M., Siroux, V., Slama, R., Auffray, C., Charron, D., Lefaudeux, D., Pellet, J., Mouraux, Stéphane, Bernasconi, Eric, Pattaroni, Céline, Koutsokera, Angela, Aubert, John-David, Claustre, Johanna, Pison, Christophe, Royer, Pierre-Joseph, Magnan, Antoine, Kessler, Romain, Benden, Christian, Soccal, Paola M., Marsland, Benjamin J., Nicod, Laurent P.

Publikováno v: In The Journal of Allergy and Clinical Immunology February 2018 141(2):718-729

Analysis of a detailed multi-stage model of stochastic gene expression using queueing theory and model reduction.

Autor: Ma M; School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK., Szavits-Nossan J; School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK., Singh A; Department of Electrical and Computer Engineering, University of Delaware, Newark DE 19716, USA., Grima R; School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK. Electronic address: ramon.grima@ed.ac.uk.

Publikováno v: Mathematical biosciences [Math Biosci] 2024 Jul; Vol. 373, pp. 109204. Date of Electronic Publication: 2024 May 06.