Newsroom and dissemination of results

SyMBioSys Final Symposium, Athens, 9 September 2018

Papers:

Oxidized alginate hydrogels with the GHK peptide enhance cord blood mesenchymal stem cell osteogenesis: A paradigm for metabolomics-based evaluation of biomaterial design, Michail E. Klontzas, Supachai Reakasame, Raquel Silva, Jose C.F. Morais, Spyros Vernardis, Robert J. MacFarlane, Manolis Heliotis, Eleftherios Tsiridis, Nicki Panoskaltsis, Aldo R. Boccaccini, Athanasios Mantalaris (2019), Acta Biomaterialia, February 2019.

Parameter estimation in models of biological oscillators: an automated regularised estimation approach, Pitt, J.A. and Banga, J.R. (2019), BMC Bioinformatics, 20:82. February 2019.

A guide to gene regulatory network inference for obtaining predictive solutions: Underlying assumptions and fundamental biological and data constraints, Sara Barbosa, Bastian Niebel, Sebastian Wolf, Klaus Mauch, Ralf Takors, Biosystems, December 2018.

High-dimensional single cell-analysis of lymphocytic activation in melanoma, Bosisio, F.M., Antoranz, A., Bolognesi, M.M., Chinello, C., Wouters, J., Magni, F., Alexopoulos, L., Cattoretti, G. and van den Oord, J., in bioRxiv, September 2018.

A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering, Osvaldo D. Kim, Miguel Rocha and Paulo Maia in Frontiers of Microbiology, July 2018, https://doi.org/10.3389/fmicb.2018.01690

Alterations of mTOR signaling impact metabolic stress resistance in colorectal carcinomas with BRAF and KRAS mutations, Raphaela Fritsche-Guenther, Christin Zasada, Guido Mastrobuoni, Nadine Royla, Roman Rainer, Florian Roßner, Matthias Pietzke, Edda Klipp, Christine Sers & Stefan Kempa, nature.com/Scientific Reports, June 2018, doi: 10.1038/s41598-018-27394-1

Critical Assessment of Parameter Estimation Methods in Models of Biological Oscillators, Jake Alan Pitt, Lucian Gomoescu, Constantinos C. Pantelides, Benoît Chachuat, Julio R. Banga, in IFAC-PapersOnLine, Volume 51, Issue 19, 2018, Pages 72-75

Optimality and identification of dynamic models in systems biology: an inverse optimal control framework, Nikolaos Tsiantis, Eva Balsa-Canto, Julio R. Banga, Bioinformatics, March 2018.

A functional landscape of chronic kidney disease entities from public transcriptomic data, Tajti, F., Antoranz, A., Ibrahim, M.M., Kim, H., Ceccarelli, F., Kuppe, C., Alexopoulos, L.G., Kramann, R. and Saez-Rodriguez, J., in bioRxiv, February 2018.

Phosphoprotein patterns predict trametinib responsiveness and optimal trametinib sensitisation strategies in melanoma, Rožanc, J., Sakellaropoulos, T., Antoranz, A., Gutta, C., Podder, B., Vetma, V., Rufo, N., Agostinis, P., Pliaka, V., Sauter, T. and Kulms, D., in Cell Death & Differentiation, March 2018.

Network-based technologies for early drug discovery, in Stem Cells and Development, Chris Fotis, Asier Antoranz, Dimitris Hatziavramidis, Theodore Sakellaropoulos and Leonidas G. Alexopoulos, Drug Discovery Today, December 2017.

Mechanism-based biomarker discovery, Asier Antoranz, Theodore Sakellaropoulos, Julio Saez-Rodriguez, Leonidas G. Alexopoulos, in Drug Discovery Today, August 2017.

Metabolomics Analysis of the Osteogenic Differentiation of Umbilical Cord Blood Mesenchymal Stem Cells REveals Differential Sensitivity to Osteogenic Agents, Michail E. Klontzas, Spyros I. Vernardis, Manolis Heliotis, Eleftherios Tsiridis, Athanasios Mantalaris, in Stem Cells and Development, Volume 26- Issue 10, May 2017.

Gli1+ Mesenchymal Stromal Cells Are a Key Driver of Bone Marrow Fibrosis and an Important Cellular Therapeutic Target, Rebekka K. Schneider, Ann Mullally, Aurelien Dugourd, Fabian Peisker, Remco Hoogenboezem, Paulina M.H. Van Strien, Eric M. Bindels, Dirk Heckl, Guntram Beusche, David Fleck, Gerhard Muller-Newen, Janewit Wongboonsin, Monica Ventura Ferreira, Victor G. Puelles, Julio Saez-Rodriguez, Benjamin L. Ebert, Benjamin D. Humphreys, and Rafael Kramann, in Cell Stem Cell, April 2017, DOI: 10.1016/j.stem.2017.03.008

SyMBiosys Webinars and Seminars

SyMBioSys webinar on Networks Visualisation, speaker Paulo Maia:

SyMBioSys webinar on Bayesian Parameter Estimations , speaker: Costas Pantelides

SyMBioSys webinar on Cell Signalling, speakers: Julio Saez-Rodriguez, Aurelien Dugourd and Enio Gjerga.

SyMBioSys webinar on Global Sensitivity Analysis, speaker: Sergei Kucherenko.

 SyMBioSys seminar by Dr. Alex Kyparissides on “Parameters in Mathematical models and how to treat them: Estimation, Uncertainty and Sensitivity” (27 September, 10am, Imperial College London, Chemical Engineering department, RODH C615)

Conference posters and oral presentations:

“Methods for training signalling networks to data by using multiple logic formalisms” (Enio Gjerga), at BIOMS Symposium 2018

“Inferring dynamics in metabolic networks via optimality principles: the interplay of constraints and trade-offs” (Nikos Tsiantis), at ICSB 2018

“Tracking Carbons in the CCM of Neuron Cells”, (Roman Rainer, Edda Klipp) at INCOME October 2018, Bernried, Germany

 “Tracking Carbons in the CCM of Neuron Cells” (Roman Rainer, Edda Klipp) at ICSB October 2018, Lyon, France

Logical Modelling of Cellular Networks Workshop 6 – Advances in computational methods for the modelling of signalling networks by Enio Gjerga, at ECCB 2018, Workshop 6 “Modelling signalling networks from mass spectrometry phopshoproteomics using Integer Linear Programming” (Enio Gjerga), at ECCB 2018

“Reduction of logic-based differential equation models improving identifiability” (Jake Pitt), at ECCB 2018

“Inferring metabolic dynamics using optimal control: the role of constraints and trade-offs” (Nikos Tsiantis), at ECCB 2018

“Critical Assessment of Parameter Estimation Methods in Models of Biological Oscillators” (Jake Pitt and Lucian Gomoescu) at FOSBE 2018

“Exploring Metabolic Differences of Neuron Cells by Tracking 13C” (Roman Rainer, Edda Klipp, at FOSBE August 2018, Chicago, US

“Parameter estimation in models of biological oscillators: dealing with multimodality and overfitting” (Jake Pitt and Julio Banga) at ECMTB 2018

“Modelling the Central Carbon Metabolism of three Cancer Cell Lines using 13C Data” (Roman Rainer, Edda Klipp) at SYSBIO February 2018, Innsbruck, Austria

“Modeling signaling networks from mass spectrometry phosphoproteomics data using Integer Linear Programming” (Enio Gjerga ) at the HUPO Conference 2017  – 16th Human Proteome Organisation World Congress 2017.

“Toward the identification of new cancer therapy targets using metabolic modeling in a human genome scale model” (Maria Masid Barcon) at the Biochemical and Molecular Engineering xx 2017.

“Integrated experimental-modelling approach for the osteogenic differentiation of umbilical cord blood mesenchymal stem cells for bone tissue engineering applications” (Michail Klontzas and Romuald Gyorgy) at TERMIS 2017

“Metabolomics as a sensitive tool to assess the efficiency of umbilical cord blood mesenchymal stem cell osteogenic differentiation” (Michail Klontzas) at ISSCR 2017

“Biological oscillators: handling model calibration issues” (Jake Pitt) and “Understanding dynamics in biochemical pathways via optimality principles” (Nikos Tsiantis) at ICSB 2016.

“Using optimal control to understand complex metabolic pathways” (Nikos Tsiantis) and “Parameter estimation in models of biological oscillators: pitfalls and solutions” (Jake Pitt) at IFAC FOSBE 2016.

“Development of trans-omic data trained hybrid models” (Aurelien Dugourd) at ByteMal 2016

Other dissemination activities

Michail Klontzas is Featured Scientist (Sept-Oct 2017) – Stem Cell Regenerative Medicine Network

“Bayesian parameter estimation using gPROMS” (Lucian Gomoescu) at PSE @ ResearchDay UK , 27 June 2017.

SymBioSys research will be presented at the Advanced Process Modeling Forum 2017, 25 April 2017.

SyMBiOSys Article on the front page of Stem cell Development

SymBioSys research will be disseminated at the CPSE Industrial Consortium Meeting, 1-2 December 2016.

SymBioSys research will be disseminated in the event “School of Engineering at Aristotle University of Thessaloniki – 70 years” that will take place in Thessaloniki, Greece, on 15-16 October 2016.

 

Software:

GEARS: a toolbox for Global parameter Estimation with Automated Regularisation via Sampling.
Pitt, J. A. and Banga J. R. (2018) – https://japitt.github.io/GEARS/
doi: 10.5281/zenodo.1420464