RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats von Shaikh, Bilal, Marupilla, Gnaneswara, Wilson, Mike, Blinov, Michael L, Moraru, Ion I, Karr, Jonathan R

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Cell Shape and Negative Links in Regulatory Motifs Together Control Spatial Information Flow in Signaling Networks von 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

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NMRbox: A Resource for Biomolecular NMR Computation von 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.

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Logic modeling and the ridiculome under the rug von Blinov, Michael L, Moraru, Ion I

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Virtual cell modeling and simulation software von Blinov, Michael L., Moraru, Ion I., Schaff, James C., Loew, Leslie M.

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Compartmental and Spatial Rule-Based Modeling with Virtual Cell von Blinov, Michael L., Schaff, James C., Vasilescu, Dan, Moraru, Ion I., Bloom, Judy E., Loew, Leslie M.

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Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE) von Waltemath, Dagmar, Bergmann, Frank T, Chaouiya, Claudine, Czauderna, Tobias, Gleeson, Padraig, Goble, Carole, Golebiewski, Martin, Hucka, Michael, Juty, Nick, Krebs, Olga, Le Novère, Nicolas, Mi, Huaiyu, Moraru, Ion I, Myers, Chris J, Nickerson, David, Olivier, Brett G, Rodriguez, Nicolas, Schreiber, Falk, Smith, Lucian, Zhang, Fengkai, Bonnet, Eric

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Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language von 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

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Modeling and Analysis of Calcium Signaling Events Leading to Long-Term Depression in Cerebellar Purkinje Cells von Hernjak, Nicholas, Slepchenko, Boris M., Fernald, Kathleen, Fink, Charles C., Fortin, Dale, Moraru, Ion I., Watras, James, Loew, Leslie M.

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Rule-based modeling with Virtual Cell von Schaff, James C, Vasilescu, Dan, Moraru, Ion I, Loew, Leslie M, Blinov, Michael L

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Dynamic model assuming mutually inhibitory biomarkers of frailty suggests bistability with contrasting mobility phenotypes von Schaumburger, Nathan, Pally, Joel, Moraru, Ion I, Kositsawat, Jatupol, Kuchel, George A, Blinov, Michael L

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Phosphorylation state-dependent interaction between AKAP7δ/γ and phospholamban increases phospholamban phosphorylation von Rigatti, Marc, Le, Andrew V., Gerber, Claire, Moraru, Ion I., Dodge-Kafka, Kimberly L.

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Pathway Commons at virtual cell: use of pathway data for mathematical modeling von 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

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Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling von Brown, Sherry-Ann, Moraru, Ion I., Schaff, James C., Loew, Leslie M.

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Topology of the Mitochondrial Inner Membrane: Dynamics and Bioenergetic Implications von Mannella, Carmen A., Pfeiffer, Douglas R., Bradshaw, Patrick C., Moraru, Ion I., Slepchenko, Boris, Loew, Leslie M., Hsieh, Chyong‐ere, Buttle, Karolyn, Marko, Michael

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An Image-Based Model of Calcium Waves in Differentiated Neuroblastoma Cells von Fink, Charles C., Slepchenko, Boris, Moraru, Ion I., Watras, James, Schaff, James C., Loew, Leslie M.

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A wave of IP3 production accompanies the fertilization Ca2+ wave in the egg of the frog, Xenopus laevis: theoretical and experimental support von Wagner, John, Fall, Christopher P, Hong, Feng, Sims, Christopher E, Allbritton, Nancy L, Fontanilla, Ray A, Moraru, Ion I, Loew, Leslie M, Nuccitelli, Richard

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Intracellular Signaling: Spatial and Temporal Control von Moraru, Ion I, Loew, Leslie M

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Virtual FRAP - an Experiment-Oriented Simulation Tool von Schaff, James C., Cowan, Ann E., Loew, Leslie M., Moraru, Ion I.

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The virtual cell: an integrated modeling environment for experimental and computational cell biology von Moraru, Ion I, Schaff, James C, Slepchenko, Boris M, Loew, Leslie M

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