-
Dynamic model assuming mutually inhibitory biomarkers of frailty suggests bistability with contrasting mobility phenotypes.
Schaumburger, Nathan; Pally, Joel; Moraru, Ion I; Kositsawat, Jatupol; Kuchel, George A; Blinov, Michael L. Frontiers in Network Physiology. 2023 May;31079070
-
BioSimulators: a central registry of simulation engines and services for recommending specific tools.
Shaikh, Bilal; Smith, Lucian P; Vasilescu, Dan; Marupilla, Gnaneswara; Wilson, Michael; Agmon, Eran; Agnew, Henry; Andrews, Steven S; Anwar, Azraf; Beber, Moritz E; Bergmann, Frank T; Brooks, David; Brusch, Lutz; Calzone, Laurence; Choi, Kiri; Cooper, Joshua; Detloff, John; Drawert, Brian; Dumontier, Michel; Ermentrout, G Bard; Faeder, James R; Freiburger, Andrew P; Fröhlich, Fabian; Funahashi, Akira; Garny, Alan; Gennari, John H; Gleeson, Padraig; Goelzer, Anne; Haiman, Zachary; Hasenauer, Jan; Hellerstein, Joseph L; Hermjakob, Henning; Hoops, Stefan; Ison, Jon C; Jahn, Diego; Jakubowski, Henry V; Jordan, Ryann; Kalaš, Matúš; König, Matthias; Liebermeister, Wolfram; Sheriff, Rahuman S Malik; Mandal, Synchon; McDougal, Robert; Medley, J Kyle; Mendes, Pedro; Müller, Robert; Myers, Chris J; Naldi, Aurelien; Nguyen, Tung V N; Nickerson, David P; Olivier, Brett G; Patoliya, Drashti; Paulevé, Loïc; Petzold, Linda R; Priya, Ankita; Rampadarath, Anand K; Rohwer, Johann M; Saglam, Ali S; Singh, Dilawar; Sinha, Ankur; Snoep, Jacky; Sorby, Hugh; Spangler, Ryan; Starruß, Jörn; Thomas, Payton J; van Niekerk, David; Weindl, Daniel; Zhang, Fengkai; Zhukova, Anna; Goldberg, Arthur P; Schaff, James C; Blinov, Michael L; Sauro, Herbert M; Moraru, Ion I; Karr, Jonathan R Nucleic acids research 2022 May;
-
RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats.
Shaikh, Bilal; Marupilla, Gnaneswara; Wilson, Mike; Blinov, Michael L; Moraru, Ion I; Karr, Jonathan R Nucleic acids research 2021 May;
-
Quantifying the Roles of Space and Stochasticity in Computer Simulations for Cell Biology and Cellular Biochemistry.
Johnson, M E; Chen, A; Faeder, J R; Henning, P; Moraru, I I; Meier-Schellersheim, M; Murphy, R F; Prüstel, T; Theriot, J A; Uhrmacher, A M Molecular biology of the cell 2020 Nov;mbcE20080530
-
SBML Level 3: an extensible format for the exchange and reuse of biological models.
Keating, Sarah M; Waltemath, Dagmar; König, Matthias; Zhang, Fengkai; Dräger, Andreas; Chaouiya, Claudine; Bergmann, Frank T; Finney, Andrew; Gillespie, Colin S; Helikar, Tomáš; Hoops, Stefan; Malik-Sheriff, Rahuman S; Moodie, Stuart L; Moraru, Ion I; Myers, Chris J; Naldi, Aurélien; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Swat, Maciej J; Thieffry, Denis; Watanabe, Leandro; Wilkinson, Darren J; Blinov, Michael L; Begley, Kimberly; Faeder, James R; Gómez, Harold F; Hamm, Thomas M; Inagaki, Yuichiro; Liebermeister, Wolfram; 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; Bolouri, Hamid; Kitano, Hiroaki; Funahashi, Akira; Hermjakob, Henning; Doyle, John C; Hucka, Michael; SBML Level 3 Community members Molecular systems biology 2020 Aug;16(8):e9110
-
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).
Bergmann, Frank T; Cooper, Jonathan; König, Matthias; Moraru, Ion; Nickerson, David; Le Novère, Nicolas; Olivier, Brett G; Sahle, Sven; Smith, Lucian; Waltemath, Dagmar Journal of integrative bioinformatics 2018 Mar;15(1):
-
Compartmental and Spatial Rule-Based Modeling with Virtual Cell.
Blinov, Michael L; Schaff, James C; Vasilescu, Dan; Moraru, Ion I; Bloom, Judy E; Loew, Leslie M Biophysical journal 2017 Oct;113(7):1365-1372
-
NMRbox: A Resource for Biomolecular NMR Computation.
Maciejewski, Mark W; Schuyler, Adam D; Gryk, Michael R; Moraru, Ion I; Romero, Pedro R; Ulrich, Eldon L; Eghbalnia, Hamid R; Livny, Miron; Delaglio, Frank; Hoch, Jeffrey C Biophysical journal 2017 Apr;112(8):1529-1534
-
Rule-based modeling with Virtual Cell.
Schaff, James C; Vasilescu, Dan; Moraru, Ion I; Loew, Leslie M; Blinov, Michael L Bioinformatics (Oxford, England) 2016 Sep;32(18):2880-2
-
Phosphorylation state-dependent interaction between AKAP7δ/γ and phospholamban increases phospholamban phosphorylation.
Rigatti, Marc; Le, Andrew V; Gerber, Claire; Moraru, Ion I; Dodge-Kafka, Kimberly L Cellular signalling 2015 May;27(9):1807-15
-
Pathway Commons at virtual cell: use of pathway data for mathematical modeling.
Blinov, Michael L; Schaff, James C; Ruebenacker, Oliver; Wei, Xintao; Vasilescu, Dan; Gao, Fei; Morgan, Frank; Ye, Li; Lakshminarayana, Anuradha; Moraru, Ion I; Loew, Leslie M Bioinformatics (Oxford, England) 2013 Nov;30(2):292-4
-
Leveraging modeling approaches: reaction networks and rules.
Blinov, Michael L; Moraru, Ion I Advances in experimental medicine and biology 2012 Jan;736517-30
-
Logic modeling and the ridiculome under the rug.
Blinov, Michael L; Moraru, Ion I BMC biology 2012 Jan;1092
-
Spatial modeling of cell signaling networks.
Cowan, Ann E; Moraru, Ion I; Schaff, James C; Slepchenko, Boris M; Loew, Leslie M Methods in cell biology 2012 Jan;110195-221
-
Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling.
Brown, Sherry-Ann; Moraru, Ion I; Schaff, James C; Loew, Leslie M Journal of computational neuroscience 2011 Oct;31(2):385-400
-
Minimum Information About a Simulation Experiment (MIASE).
Waltemath, Dagmar; Adams, Richard; Beard, Daniel A; Bergmann, Frank T; Bhalla, Upinder S; Britten, Randall; Chelliah, Vijayalakshmi; Cooling, Michael T; Cooper, Jonathan; Crampin, Edmund J; Garny, Alan; Hoops, Stefan; Hucka, Michael; Hunter, Peter; Klipp, Edda; Laibe, Camille; Miller, Andrew K; Moraru, Ion; Nickerson, David; Nielsen, Poul; Nikolski, Macha; Sahle, Sven; Sauro, Herbert M; Schmidt, Henning; Snoep, Jacky L; Tolle, Dominic; Wolkenhauer, Olaf; Le Novère, Nicolas PLoS computational biology 2011 Apr;7(4):e1001122
-
Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.
Waltemath, Dagmar; Adams, Richard; Bergmann, Frank T; Hucka, Michael; Kolpakov, Fedor; Miller, Andrew K; Moraru, Ion I; Nickerson, David; Sahle, Sven; Snoep, Jacky L; Le Novère, Nicolas BMC systems biology 2011 Jan;5198
-
Modeling without borders: Creating and annotating Vcell models using the web.
Blinov M.L., Ruebenacker O., Schaff J.C., Moraru I.I. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2010 Jan;6053 LNBI3-17
-
Integrating BioPAX pathway knowledge with SBML models.
Ruebenacker, O; Moraru, I I; Schaff, J C; Blinov, M L IET systems biology 2009 Sep;3(5):317-28
-
Complexity and modularity of intracellular networks: a systematic approach for modelling and simulation.
Blinov, M L; Ruebenacker, O; Moraru, I I IET systems biology 2008 Sep;2(5):363-8
-
Virtual Cell modelling and simulation software environment.
Moraru, I I; Schaff, J C; Slepchenko, B M; Blinov, M L; Morgan, F; Lakshminarayana, A; Gao, F; Li, Y; Loew, L M IET systems biology 2008 Sep;2(5):352-62
-
Cell shape and negative links in regulatory motifs together control spatial information flow in signaling networks.
Neves, Susana R; Tsokas, Panayiotis; Sarkar, Anamika; Grace, Elizabeth A; Rangamani, Padmini; Taubenfeld, Stephen M; Alberini, Cristina M; Schaff, James C; Blitzer, Robert D; Moraru, Ion I; Iyengar, Ravi Cell 2008 May;133(4):666-80
-
Modeling and analysis of calcium signaling events leading to long-term depression in cerebellar Purkinje cells.
Hernjak, Nicholas; Slepchenko, Boris M; Fernald, Kathleen; Fink, Charles C; Fortin, Dale; Moraru, Ion I; Watras, James; Loew, Leslie M Biophysical journal 2005 Dec;89(6):3790-806
-
A wave of IP3 production accompanies the fertilization Ca2+ wave in the egg of the frog, Xenopus laevis: theoretical and experimental support.
Wagner, John; Fall, Christopher P; Hong, Feng; Sims, Christopher E; Allbritton, Nancy L; Fontanilla, Ray A; Moraru, Ion I; Loew, Leslie M; Nuccitelli, Richard Cell calcium 2004 May;35(5):433-47
-
An image-based model of calcium waves in differentiated neuroblastoma cells.
Fink, C C; Slepchenko, B; Moraru, I I; Watras, J; Schaff, J C; Loew, L M Biophysical journal 2000 Jul;79(1):163-83
-
An endogenous sulfated inhibitor of neuronal inositol trisphosphate receptors.
Watras, J; Orlando, R; Moraru, I I Biochemistry 2000 Mar;39(12):3452-60
-
Morphological control of inositol-1,4,5-trisphosphate-dependent signals.
Fink, C C; Slepchenko, B; Moraru, I I; Schaff, J; Watras, J; Loew, L M The Journal of cell biology 1999 Nov;147(5):929-36
-
Regulation of type 1 inositol 1,4,5-trisphosphate-gated calcium channels by InsP3 and calcium: Simulation of single channel kinetics based on ligand binding and electrophysiological analysis.
Moraru, I I; Kaftan, E J; Ehrlich, B E; Watras, J The Journal of general physiology 1999 Jun;113(6):837-49
-
Molecular adaptation of vascular endothelial cells to oxidative stress.
Lu, D; Maulik, N; Moraru, I I; Kreutzer, D L; Das, D K The American journal of physiology 1993 Mar;264(3 Pt 1):C715-22
