Publications by authors named "Ion Moraru"

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Verification and reproducible curation of the BioModels repository.
Lucian P Smith, Rahuman S Malik-Sheriff, Tung V N Nguyen, Henning Hermjakob, Jonathan Karr, Ion I Moraru

PLoS Comput Biol· December 2025

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Visualizing mechanistic models by integrating site-specific molecular details into reaction networks.
Dan Vasilescu, James C Schaff, Ion I Moraru, Michael L Blinov

Front Mol Biosci· December 2025

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Scalable cyberinfrastructure for experimental NMR data.
Jeffrey C Hoch, Katherine Henzler-Wildman, Arthur S Edison, Chad M Rienstra, Christopher Bontempi, Ion I Moraru

Sci Data· December 2025

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Verification and reproducible curation of the BioModels repository.
Lucian Smith, Rahuman S Malik-Sheriff, Tung V N Nguyen, Henning Hermjakob, Jonathan Karr, Ion I Moraru

bioRxiv· June 2025

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From FAIR to CURE: Guidelines for Computational Models of Biological Systems.
Herbert M Sauro, Eran Agmon, Michael L Blinov, John H Gennari, Joe Hellerstein, Ion Moraru

ArXiv· February 2025

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

Front Netw Physiol· May 2023

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BioSimulators: a central registry of simulation engines and services for recommending specific tools.
Bilal Shaikh, Lucian P Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Ion I Moraru

Nucleic Acids Res· July 2022

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

Nucleic Acids Res· July 2021

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SBML Level 3: an extensible format for the exchange and reuse of biological models.
Sarah M Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Ion I Moraru

Mol Syst Biol· August 2020

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Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE).
Dagmar Waltemath, Frank T Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, Ion I Moraru

Stand Genomic Sci· August 2018

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Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).
Frank T Bergmann, Jonathan Cooper, Matthias König, Ion Moraru, David Nickerson

J Integr Bioinform· March 2018

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

Biophys J· October 2017

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NMRbox: A Resource for Biomolecular NMR Computation.
Mark W Maciejewski, Adam D Schuyler, Michael R Gryk, Ion I Moraru, Pedro R Romero

Biophys J· April 2017

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

Bioinformatics· September 2016

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

Cell Signal· September 2015

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Analysis of AKAP7γ Dimerization.
Arpita Singh, Marc Rigatti, Andrew V Le, Cathrine R Carlson, Ion I Moraru

J Signal Transduct· September 2015

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SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3.
Lucian Paul Smith, Michael Hucka, Stefan Hoops, Andrew Finney, Martin Ginkel, Ion Moraru

J Integr Bioinform· September 2015

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Computed tomography number changes observed during computed tomography-guided radiation therapy for head and neck cancer.
Mei Feng, Cungeng Yang, Xiaojian Chen, Shouping Xu, Ion Moraru

Int J Radiat Oncol Biol Phys· April 2015

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Radiation dose responses for chemoradiation therapy of pancreatic cancer: an analysis of compiled clinical data using biophysical models.
Ion C Moraru, An Tai, Beth Erickson, X Allen Li

Pract Radiat Oncol· January 2015

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Variability of target and normal structure delineation using multimodality imaging for radiation therapy of pancreatic cancer.
Entesar Dalah, Ion Moraru, Eric Paulson, Beth Erickson, X Allen Li

Int J Radiat Oncol Biol Phys· July 2014

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Pathway Commons at virtual cell: use of pathway data for mathematical modeling.
Michael L Blinov, James C Schaff, Oliver Ruebenacker, Xintao Wei, Dan Vasilescu, Ion I Moraru

Bioinformatics· January 2014

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Leveraging modeling approaches: reaction networks and rules.
Michael L Blinov, Ion I Moraru

Adv Exp Med Biol· January 2013

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

BMC Biol· November 2012

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Spatial modeling of cell signaling networks.
Ann E Cowan, Ion I Moraru, James C Schaff, Boris M Slepchenko, Leslie M Loew

Methods Cell Biol· July 2012

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Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.
Dagmar Waltemath, Richard Adams, Frank T Bergmann, Michael Hucka, Fedor Kolpakov, Ion I Moraru

BMC Syst Biol· December 2011

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