Projects

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

Understanding the molecular basis of diseases can shed light into new methods to manage and cure diseases. Exploring the common or unique molecular mechanisms among a group of diseases may enhance our understanding of each disease or uncover therapeutic approaches that can be effective in multiple diseases. In this project we develop methods that use biological networks and known gene-disease associations to identify common molecular mechanisms associated across multiple diseases.

This research discusses what is the status of fisheries provisioning services in Jatigede Reservoir and what anthropogenic pressures in the form of community activities affect the status of fisheries provisioning services.

Using standard systems biology methodologies a 14-compartment dynamic model was developed for the Corona virus epidemic. The model predicts that: (i) it will be impossible to limit lockdown intensity such that sufficient herd immunity develops for this epidemic to die down, (ii) the death toll from the SARS-CoV-2 virus decreases very strongly with increasing intensity of the lockdown, but (iii) the duration of the epidemic increases at first with that intensity and then decreases again, such that ...

MESI-Review 2024

MESI-STRAT: Systems Medicine of Metabolic-Signaling Networks -A New Concept for Breast Cancer Patient Stratification. Breast cancer is a complex disease with high prevalence in the European Union and world-wide. 75%-80 of the patients have estrogen receptor-positive (ER)-positive tumors and are treated with endocrine therapies. Endocrine therapies, which block ER-driven tumor growth, show high efficacy. Yet, a significant proportion of the patients will eventually relapse with metastatic breast ...

MESI-STRAT Review

Systems biology of bacterial methylotrophy for biotechnological

experimental data; middle ear transfer functions

Andrew Millar's research group, University of Edinburgh

This project aims to characterise the mechanisms through which microRNAs and small non-coding RNAs act to regulate cellular processes focusing on Naïve CD4 T cell activation and viral replication - namely HIV - and to explore their potential use as a therapeutic co-adjuvant agents or targets.

The main idea of MIX-UP (MIXed plastics biodegradation and UPcycling using microbial communities) is to showcase a novel approach for plastic recycling and therefore addresses one of the greatest challenges of our time: the establishment of a circular (bio)-economy for plastics. The continuing demand for plastic products, the lack of appropriate recycling and the ubiquitous pollution of the environment with plastic waste pose a global challenge. An ambitious vision and considerable efforts are ...

Time series response of potato cv. Désirée, which is tolerant to PVY infection, was analysed in both inoculated as well as upper non-inoculated leaves. Additionally, transgenic plants deficient in accumulation of salicylic acid (NahG- Désirée) were studied in the same setting.

This investigation is published under the CC BY 4.0 license.

Modulation of light, temperature and time networks using prime editing and mathematical modelling

Modelling COVID-19 epidemics : the training course organized by ISBE-NL, ELIXIR-LU, and EOSC-Life

tba

The Molecular Systems Biology project holds information for reproducing simulation figures in the journal. This can include experimental data files, model files and manuscript information.

MOSES (Micro Organism Systems biology: Energy and Saccharomyces cerevisiae) develops a new Systems Biology approach, which is called 'domino systems biology'. It uses this to unravel the role of cellular free energy ('ATP') in the control and regulation of cell function. MOSES operates though continuous iterations between partner groups through a new systems-biology driven data-management workflow. MOSES also tries to serve as a substrate for three or more other SYSMO programs.

Valorization of mussel processing water into bioplastics

We will contribute to the LiSyM Research Network an open source, freely available and reproducible multiscale model of the human liver from single cell metabolism to whole liver function. The model will be available in existing standards of systems biology, provide standardized interfaces for data integration and be fully annotated to available biological, medical and computational ontologies. All data, models and source code will be shared within the LiSyM Research Network and made available to ...

BBSRC sLoLa grantThe spread of antimicrobial resistance (AMR) is a slow-moving pandemic that has been identified by the WHO as one of the top 10 threats facing humanity. Plasmids and other MGEs play a key role in the dissemination of AMR, but we have only a rudimentary understanding of the factors that determine if and how MGEs spread through microbial communities. It is generally assumed that bacterial immune systems are a major determinant, but existing studies are limited to only a few stand-alone ...

Short-chain fatty-acids (SCFA) are produced from dietary fibres by the intestinal microbiota. They protect humans against obesity. The fate of SCFA and their impact on human fat metabolism is complex and dynamic. To optimally apply prebiotic (fibre) and probiotic (microbial) supplements, a better understanding of their mode of action is required. Our aim is to construct, infer, and analyse a dynamic, multiscale computational model predicting how dietary fibres affect the balance between fat intake ...

The MycoSynVac project AIMS at using cutting-edge synthetic biology methodologies to engineer Mycoplasma pneumoniae as a universal chassis for vaccination. Designing a universal Mycoplasma chassis that can be deployed as single- or multi-vaccine in a range of animal hosts. Annually, infections caused by Mycoplasma species in poultry, cows, and pigs result in multimillion Euro losses in the USA and Europe. There is no effective vaccination against many Mycoplasmas that infect pets, humans and farm ...