Projects

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 ...

Multi-level mathematical modeling of erythropoiesis for optimized expansion of erythroid progenitor cells and improved treatment regimes

Hypoglycaemia and lactic acidosis are key diagnostics for poor chances of survival in malaria patients. In this project we aim to test to what extent the metabolic activity of Plasmodium falciparum contributes to a changed glucose metabolism in malaria patients. The approach is to start with detailed bottom up models for the parasite and then merge these with more coarse grained models at the whole body level.

Translating Systems Virology data into broad-spectrum antiviral Drugs

We used the Neo4j graph database approach to integrate the content of the COVID-19 Disease Map diagrams to efficiently access, query and manage the content of these diagrams and enable communication with external resources, such as Reactome and Recon, that already provide support via a similar environment. This work complements the efforts on exploring COVID-19 disease mechanisms within the COVID-19 Disease Map Project.

Rationale: Individuals with a cancer predisposition due to a mutation in the paradigm tumor suppressor gene RB1, have a high risk to develop the childhood cancer retinoblastoma (Rb). Biopsies are not possible in Rb, before treatment selection. Heritable Rb patients have also a high risk to develop other types of second primary, either childhood or adult, malignancies (SPMs), notably sarcomas and melanomas. Remarkably, SPMs are now the leading cause of death in heritable-Rb-survivors. Unfortunately, ...

Here we share resources and best practices to develop a disease map for COVID-19. The project is progressing as a broad community-driven effort. We aim to establish a knowledge repository on virus-host interaction mechanisms specific to the SARS-CoV-2. The COVID-19 Disease Map is an assembly of molecular interaction diagrams established based on literature evidence.

By intelligent use of existing registries and health data, DeCipher aims to develop a data-driven framework to provide a personalized time-varying risk assessment for cancer initiation and identify subgroups of individuals and factors leading to similar disease progression. By unveiling structure hidden in the data, we will develop novel theoretically grounded machine learning methods for the analysis of large-scale registry and health data.DeCipher consists of an excellent multidisciplinary ...

Standard ASO design is based on the sequence complementarity of the oligo to its target. However, the degree of target knockdown that ASOs can achieve varies strongly between different ASOs having full complementarity to the target. To determine which factors affect the ASOs’ activity, Secarna has used a novel approach: the Company has designed and screened 51 multi-specific ASOs with a common target (IDO1, a gene involved in tryptophan metabolism), and varying numbers of diverse other targets ...

The project addresses the generation and establishment of programmed pacemaker cells for an in vitro drug testing possibility to perform predictive tests. This may lead to an improved treatment of cardiac arrhythmias or an accurate identification of potential drug molecules at a very early stage of development. Important benefits will arise in verifying the safety of a wide variety of medicines while reducing animal testing. For more information you may visit our project website at ...

The Integrated Platform for Endocrine Disruptor Risk Assessment (SNAPPER) project will propose solutions based around three core philosophies: Integrated Science: Integration of knowledge from a complete pipeline of systems biology into a holistic yet mechanistic framework that enhances the understanding both of endocrine biology and of adverse effects due to externally induced disruption of the body’s endocrine system. The pipeline includes in vivo, in vitro, and in silico data resulting both ...

Most biological processes require energy and are tightly regulated. Energy is extracted from food supplies and eventually transformed into ATP, the universal energy carrier of the cell. These pathways consist of many reactions which involve NAD or NADP, small molecules which serve as intermediate energy transmitters. Vitamin B3 is essential for the synthesis of these nucleotides. Interestingly, the key molecules in energy transduction also have important roles in the regulation of all vital ...

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In the CoVIDD project, we aim at unravelling interactions of viral proteins with the cellular factors and the host pathways involved in SARS-CoV-2 infection by a combination of modern technologies, genomics, proteomics, structural biology, chemoinformatics and drug discovery. To effectively search for drugs that could modify viral replication we need to know what human proteins and viral proteins interact. Thus, a comprehensive virus-host protein interaction network will help us to identify the ...

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Aim of HUMET Startup Project is to make an inventory of expertise, research goals, resources etc. of the HUMET Coaliytion of the Willing.

In this project, we integrate COVID19 Disease Maps curated regulatory information in a macrophage logical model. This allows logical simulations of the effects of acute inflammation caused by the SARS-CoV-2 virus, both in general and in a cell-specific perspective. Moreover, understanding the regulatory network behavior of macrophages following infection opens new ways to test and predict drug and drug combination effects, as a first step towards the development of new treatments.

Data and experimental methods to support the work in the following paper:

Establishing Consensus Annotation for the Hallmarks of Cancer, 2020, Yi Chen, F.J.Verbeek and K.Wolstencroft, in submission

Collaboration with Miltos Tsiantis for reconstructing RCO transcriptional regulation

This project gathers all biomics projects submitted to biomics.pasteur.fr

generation of a toggle switch based on a non-cooperative network