Ion I. Moraru, M.D., Ph.D.Professor, Department of Cell Biology
Center for Cell Analysis and Modeling
|M.D.||Bucharest Institute for Medicine & Pharmacy||Medicine|
|Ph.D.||Carol Davila University of Medicine||Cell Biology|
|Fellowship||NIH||John E. Fogarty Research Fellowship|
|Postdoctoral||University of Connecticut Health Center||Cell Biology|
|Name of Award/Honor||Awarding Organization|
|Young Investigator Award, Scientific Conference on the Molecular Biology of the Normal, Hypertrophied, and Failing Heart||AHA|
|Mariana Constantinescu Memorial Award for Medical Excellence||Davila University|
|Senate Award, National Conference on Student Medical Research||Davila University|
|National Scholarship of Romania, 1985-88||Romania|
|First Prize, International Mathematical Competition||Germany|
|Bronze Medal, International Mathematical Olympiad||USA|
|Name & Description||Category||Role||Type||Scope||Start Year||End Year|
|MD/PhD Steering Committee||Education Committee||Member||UConn Health||Local||2016|
|Health Center Research Advisory Committee||Advisory Committee||Member||UConn Health||University||2015|
|High Performance Computing Facility||Other||Director||UConn Health||University||2015|
Biology: My general research interests center on understanding signal transduction mechanisms, in particular related to calcium and phosphoinositides. Examples are quantitative experimental and modeling studies of signaling networks in neuronal cells, such as the nonlinear response and spatial modulation of calcium signaling, and the regulation of IP3 receptor activity.
Computer Science: My general interest is focused on the design and development of computational cell biology software tools geared towards the biologist, non-mathematical expert, user. I have been involved since 1998 in theVirtual Cell project, and I am currently responsible for the design and development of the biological user interface and data export and analysis tools. Another recent project, in collaboration with Bill Mohler, is automated and/or interactive processing and VR visualization of 4D fluorescence microscopy data (gene expression during C. elegans embryonic development).
I oversee our Computational Facility, which provides High Performance Computing support to the National Center for Cell Analysis and Modeling, the Technology Center for Polarity in Networks and Pathways, the CCAM Microscopy Facility, and other research projects of individual CCAM faculty members.
Accepting Lab Rotation Students: Summer 2022, Fall 2022, and Spring 2023
BioSimulators: a central registry of simulation engines and services for recommending specific tools.
Nucleic acids research 2022 May;
RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats.
Nucleic acids research 2021 May;
Quantifying the Roles of Space and Stochasticity in Computer Simulations for Cell Biology and Cellular Biochemistry.
Molecular biology of the cell 2020 Nov;mbcE20080530
SBML Level 3: an extensible format for the exchange and reuse of biological models.
Molecular systems biology 2020 Aug;16(8):e9110
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).
Journal of integrative bioinformatics 2018 Mar;15(1):
Compartmental and Spatial Rule-Based Modeling with Virtual Cell.
Biophysical journal 2017 Oct;113(7):1365-1372
NMRbox: A Resource for Biomolecular NMR Computation.
Biophysical journal 2017 Apr;112(8):1529-1534
Rule-based modeling with Virtual Cell.
Bioinformatics (Oxford, England) 2016 Sep;32(18):2880-2
Phosphorylation state-dependent interaction between AKAP7δ/γ and phospholamban increases phospholamban phosphorylation.
Cellular signalling 2015 May;27(9):1807-15
Pathway Commons at virtual cell: use of pathway data for mathematical modeling.
Bioinformatics (Oxford, England) 2013 Nov;30(2):292-4
Leveraging modeling approaches: reaction networks and rules.
Advances in experimental medicine and biology 2012 Jan;736517-30
Logic modeling and the ridiculome under the rug.
BMC biology 2012 Jan;1092
Spatial modeling of cell signaling networks.
Methods in cell biology 2012 Jan;110195-221
Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling.
Journal of computational neuroscience 2011 Oct;31(2):385-400
Minimum Information About a Simulation Experiment (MIASE).
PLoS computational biology 2011 Apr;7(4):e1001122
Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.
BMC systems biology 2011 Jan;5198
Modeling without borders: Creating and annotating Vcell models using the web.
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.
IET systems biology 2009 Sep;3(5):317-28
Complexity and modularity of intracellular networks: a systematic approach for modelling and simulation.
IET systems biology 2008 Sep;2(5):363-8
Virtual Cell modelling and simulation software environment.
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.
Cell 2008 May;133(4):666-80
Modeling and analysis of calcium signaling events leading to long-term depression in cerebellar Purkinje cells.
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.
Cell calcium 2004 May;35(5):433-47
An image-based model of calcium waves in differentiated neuroblastoma cells.
Biophysical journal 2000 Jul;79(1):163-83
An endogenous sulfated inhibitor of neuronal inositol trisphosphate receptors.
Biochemistry 2000 Mar;39(12):3452-60
Morphological control of inositol-1,4,5-trisphosphate-dependent signals.
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.
The Journal of general physiology 1999 Jun;113(6):837-49
Molecular adaptation of vascular endothelial cells to oxidative stress.
The American journal of physiology 1993 Mar;264(3 Pt 1):C715-22
The Virtual Cell Project.
Systems Biomedicine 2009 Jan;
XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes.
Proceedings / Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE). IEEE International Symposium on Bioinformatics and Bioengineering 2007 Nov;987-994
Kinetic Modeling using BioPAX ontology
Proceedings - 2007 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2007 2007 Jan;339-346
Think simulation - Think experiment: The virtual cell paradigm
Proceedings - Winter Simulation Conference 2006 Jan;1713-1719
The virtual cell: an integrated modeling environment for experimental and computational cell biology.
Annals of the New York Academy of Sciences 2002 Oct;971595-6
Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE).
Standards in genomic sciences 2018 Jan;1317
Another barrier to reproducibility
Science 2017 Jan;354(6317):1240-1241
Intracellular signaling: spatial and temporal control.
Physiology (Bethesda, Md.) 2005 Jun;20(3):169-79
VCell CLI, 5 published versions
Virtual Cell version 7.3
Virtual Cell version 7.2
|Title or Abstract||Type||Sponsor/Event||Date/Year||Location|
|BioSimulations: integrated models, model languages, model repositories, simulation experiments, simulation tools and data visualization||Talk||2022||Berlin, Germany|
|Modeling and Simulation from Quantitative Imaging to Systems Biology||Talk||Systems Imaging: Applications in Immunology and Cancer||2012||Albuquerque, NM|
|Stochastic and Deterministic Spatial Modeling using VCell||Talk||12th International Conference for Systems Biology||2011||Heidelberg, Germany|
|Spatial Modeling of Signaling Networks||Talk||Experimental Biology 2010 Conference||2010||Anaheim, CA|
|VCell - A Platform for Quantitative Modeling||Talk||Neuron Simulator Meeting||2010||Tucson, AZ|
|Advanced Modeling and Simulation using VCell and SyBiL||Talk||11th International Conference on Systems Biology||2010||Edinburgh, UK|
|Modeling without Borders: Building Models and Annotations using Web Resources||Talk||TCNP All Hands Meeting||2010||Bethesda, MD|
|Computational Biology: Virtual Cell||Talk||SC10 International Conference for High Performance Computing||2010||New Orleans, LA|
|Systems Biology Pathway Exchange - Bridging pathway Data and Quantitative Models||Poster||54th Annual Meeting of the Biophysical Society||2010||San Francisco, CA|
|Merged Biochemical and Electrophysiological Modeling in Complex Neuronal Morphologies||Poster||11th International Conference on Systems Biology||2010||Edinburgh, UK|
|Advanced Modeling, Simulation, and Data Analysis using Virtual Cell and Virtual Microscopy||Talk||10th International Conference for Systems Biology||2009||Stanford, CA|
|The VCell Database: Sharing, Publishing, Reusing Models||Talk||CellML, SBGN, SBO, BioPAX, and MIASE Super Workshop||2009||Auckland, New Zealand|