Innate immunity

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A study of the systems biology of innate immunity

Web page: http://sysba.nl

Funding details:

no funding

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Alexey Kolodkin

Projects: SulfoSys, FAIRDOM user meeting, Service to Milano-Bicocca with respect to their ATP-ROS model (Active NOW), Make Me My Model, Service to University of Lisbon (Portugal) with respect to their CFTR maturation model (Active NOW), Service to LCSB (Luxembourg) with respect to ROS management in Parkinson’s disease and cancer model (Active NOW), Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), Service to Universidade Católica Portugues with respect to their Molecular Insight into Autism Spectrum Disorder (ASD) model (Active NOW), Service to Slovenia with respect to their Protease signaling network in neurodegeneration model (Active NOW), Service to University of Duisburg- Essen (Germany): with respect to their The Yin-Yang of Metabolism; Endometatoxicity (YYME) model (Active NOW), Service to Sheffield University (UK): with respect to Mitochondrial perfect adaptation model (Active NOW), Service to Sanquin (Amsterdam): with respect to Modelling of acute and chronic inflammation (Prospective), Service to Munich (Germany): with respect toCharged peptide to charged membrane binding model (Prospective), Training Hunfeld, EraCoBiotech 2 nd call proposal preparation, ROS detailed model for MSB manucript, Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population, COVID-19 Disease Map, Modelling COVID-19 epidemics, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation

Institutions: University of Amsterdam, VU University Amsterdam, Infrastructure Systems Biology Europe, Systems Biomedicine Center, University of Luxembourg, Luxembourg Centre for Systems Biomedicine (LCSB)

I have modelling expertise in precise kinetic models of metabolism and signal transduction; metabolic control analysis, hierarchical regulation analysis, non-equilibrium dynamics, statistical mechanics, enzyme kinetics, flux balance analysis. Energy and carbohydrate metabolism in Archaea, Bacteria and human; ammonium assimilation in Bacteria; differential network-based drug design; cancer metabolic rewiring; cell cycle; genome wide metabolic map and inborn errors of metabolism; epigenetics.

Hans V. Westerhoff

Expertise: Systems Biology, Thermodynamics, Biochemistry, Dynamic modelling, Mathematical modelling, Metabolic Engineering, Microbiology, Molecular Biology, standards

Tools: Computational Systems Biology, Dynamic modelling, Biochemistry

Systems Biologist at University of Amsterdam, Free University Amsterdam, University of Manchester, Infrastructure Systems Biology.NL (ISBE.NL), Systems Biology Amsterdam.

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Make Me My Model

This is the FAIRDOM hub for the Make Me My Model part of ISBE.NL. Various models for ISDBE.NL clients are stored here.

Programme: Innate immunity

Public web page: http://isbe.nl/

Organisms: Not specified

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VU University Amsterdam

ROR ID: Not specified

Department: Not specified

Country: Netherlands

City: Amsterdam

Web page: http://www.falw.vu.nl/en/index.asp

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ROS networks: designs, aging, Parkinson's disease and precision therapies

Service to Milano-Bicocca with respect to their ATP-ROS model (Active NOW), Make Me My Model, Service to LCSB (Luxembourg) with respect to ROS management in Parkinson’s disease and cancer model (Active NOW), ROS detailed model for MSB manucript

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Submitter: Alexey Kolodkin

Studies: ROS Models and Data for NPJ Systems Biology and Application (A. Kolodkin...

Assays: Comprehensive model of ROS management, Main Figure 1, Main Figure 2, Main Figure 3, Main Figure 4, Supplementary_Information_Data_Model_Archives

Snapshots: Snapshot 1, Snapshot 2, Snapshot 3, Snapshot 4

DOI: 10.15490/fairdomhub.1.investigation.399.4

Created: 10th Jul 2020 at 17:47, Last updated: 10th Jul 2020 at 18:03

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ROS Models and Data for NPJ Systems Biology and Application (A. Kolodkin, R.P. Sharma, A.M. Colangelo, H.V. Westerhoff et al, NPJ SBA 2020)

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Submitter: Alexey Kolodkin

Investigation: ROS networks: designs, aging, Parkinson's disea...

Assays: Comprehensive model of ROS management, Main Figure 1, Main Figure 2, Main Figure 3, Main Figure 4, Supplementary_Information_Data_Model_Archives

Snapshots: No snapshots

Created: 10th Jul 2020 at 18:05, Last updated: 10th Jul 2020 at 18:28

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Comprehensive model of ROS management

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Submitter: Alexey Kolodkin

Biological problem addressed: Model Analysis Type

Investigation: ROS networks: designs, aging, Parkinson's disea...

Study: ROS Models and Data for NPJ Systems Biology and...

Organisms: Homo sapiens

Models: Calibrated comprehensive model of ROS management, Calibrated comprehensive model of ROS managemen..., Detailed model of ROS management

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 10th Jul 2020 at 18:17, Last updated: 12th Jul 2020 at 19:01

Main Figure 1

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Submitter: Alexey Kolodkin

Biological problem addressed: Model Analysis Type

Investigation: ROS networks: designs, aging, Parkinson's disea...

Study: ROS Models and Data for NPJ Systems Biology and...

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: Main Figure 1

Snapshots: No snapshots

Created: 10th Jul 2020 at 18:31, Last updated: 10th Jul 2020 at 19:09

Main Figure 2

To obtain each of the figure 2A - 2E please download "Main Figure Copasi" and open the sub-directory with the name of the sub-figure, run the Copasi files and the time dependence simulation. This will reproduce the figure in this paper.

Submitter: Alexey Kolodkin

Biological problem addressed: Model Analysis Type

Investigation: ROS networks: designs, aging, Parkinson's disea...

Study: ROS Models and Data for NPJ Systems Biology and...

Organisms: No organisms

Models: Main Figure 2 COPASI

SOPs: No SOPs

Data files: Main Figure 2 Excel files

Snapshots: No snapshots

Created: 10th Jul 2020 at 19:10, Last updated: 20th Jul 2020 at 16:10

Main Figure 3

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No description specified

Submitter: Alexey Kolodkin

Biological problem addressed: Model Analysis Type

Investigation: ROS networks: designs, aging, Parkinson's disea...

Study: ROS Models and Data for NPJ Systems Biology and...

Organisms: No organisms

Models: Figure-3_Detailed Model Diagram

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 10th Jul 2020 at 19:35, Last updated: 16th Jul 2020 at 11:38

Main Figure 4

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To obtain each of the figure 4A - 4D please download "Main Figure 4 Copasi" and open the sub-directory with the name of the sub-figure, run the Copasi files and the time dependence simulation. This will reproduce the figure in this paper.

Submitter: Alexey Kolodkin

Biological problem addressed: Model Analysis Type

Investigation: ROS networks: designs, aging, Parkinson's disea...

Study: ROS Models and Data for NPJ Systems Biology and...

Organisms: No organisms

Models: Main Figure 4 Models_Copasi

SOPs: No SOPs

Data files: Data-Model_Menadione, Data_Models_ATP_mRNA

Snapshots: No snapshots

Created: 10th Jul 2020 at 19:45, Last updated: 20th Jul 2020 at 16:12

Supplementary_Information_Data_Model_Archives

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No description specified

Submitter: Alexey Kolodkin

Biological problem addressed: Model Analysis Type

Investigation: ROS networks: designs, aging, Parkinson's disea...

Study: ROS Models and Data for NPJ Systems Biology and...

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: Section B2A, Section A, Section B1, Section B2B, Section B3, Section B4, Section B5, Section C, Section D, Section E, Section F, Section G, Section H, Section I

Snapshots: No snapshots

Created: 12th Jul 2020 at 23:37, Last updated: 13th Jul 2020 at 00:08

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Design principles of ROS dynamic networks relevant to precision therapies for age-related diseases

Make Me My Model

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Abstract (Expand)

The eminently complex regulatory network protecting the cell against oxidative stress, surfaces in several disease maps, including that of Parkinson’s disease (PD). How this molecular networking achieves …

Authors: Alexey Kolodkin, Raju Prasad Sharma, Anna Maria Colangelo, Andrew Ignatenko, Francesca Martorana, Danyel Jennen, Jacco J. Briede, Nathan Brady, Matteo Barberis, Thierry D.G.A. Mondeel, Michele Papa, Vikas Kumar, Bernhard Peters, Alexander Skupin, Lilia Alberghina, Rudi Balling, Hans V. Westerhoff