Media & Publications

Publications

Peer-reviewed journal articles from the DarkMatter consortium. Our research spans immunology, the microbiome, and autoimmune and infectious disease.
Browse the latest publications below.

Untargeted faecal metabolomics for the discovery of biomarkers and treatment targets for inflammatory bowel diseases

Gut

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Systemic antibody responses against gut microbiota flagellins implicate shared and divergent immune reactivity in Crohn's disease and chronic fatigue syndrome

Microbiome

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Prior Anti-TNF Exposure Is Associated with an Increased Risk of Short- and Long-Term Colectomy in Acute Severe Ulcerative Colitis

Digestive Diseases and Sciences

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Molecular mimicry in the pathogenesis of autoimmune rheumatic diseases

Journal of Translational Autoimmunity

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Modulator of VRAC Current 1 Is a Potential Target Antigen in Multiple Sclerosis

Neurology Neuroimmunology & Neuroinflammation

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Five dominant amino acid substitution signatures shape tumour immunity

Molecular Systems Biology

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Elevated serum glutathione reflects endoscopic disease activity in inflammatory bowel disease

Free Radical Biology and Medicine

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Das Mikrobiom bei rheumatoider Arthritis und systemischem Lupus erythematodes

rheuma plus

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Associations between HLA-II variation and antibody specificity are predicted by antigen properties

Genome Medicine

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A reconceptualized framework for human microbiome transmission in early life

Nature Communications

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A journey to your self: The vague definition of immune self and its practical implications

Proceedings of the National Academy of Sciences

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Public Deliverables

Deliverables are updated regularly and include downloadable reports, protocols, and datasets. Our Data Management Plan ensures compliance with FAIR principles and GDPR. Visit our repository for the latest files.

We publish key outputs as open-access deliverables, including:

D7.3 Ethics and Governance Framework

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This deliverable establishes the ethical and governance framework guiding all research activities within the ID-DarkMatter-NCD project. Building on the work of the Ethics and Governance Committee and existing ethical approvals, it outlines the principles, procedures, and compliance measures that ensure research is conducted responsibly, transparently, and in accordance with applicable ethical, legal, and data protection requirements across the consortium.

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D7.1 Data Management Plan (DMP)

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This deliverable provides the project's Data Management Plan, outlining how research data will be collected, stored, managed, shared, and preserved throughout the project lifecycle. Developed in line with Horizon Europe requirements, it ensures that data management practices support transparency, accessibility, legal compliance, and the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles.

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D2.1 Genetic Data — Curation and Harmonisation of HLA and Whole Genome Sequencing Datasets

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This deliverable establishes a harmonised and interoperable repository of existing HLA and whole genome sequencing (WGS) datasets from the participating project cohorts. It defines common data standards and analysis pipelines to enable consistent cross-cohort comparisons, facilitate data sharing, and support downstream analyses such as HLA promiscuity and clustering studies.

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Communication Materials

We create content for various audiences:scientific peers, healthcare providers, patients, and the public. All visuals and downloadable content are designed for sharing and reuse. Subscribe to our newsletter, follow us on Social Media for updates.

Unmasking the Triggers of Chronic Immune-Related Diseases

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Unraveling the Dark Matter of infectious diseases, environmental and genetic factors tipping the balance towards NCDs

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A Deep-Dive into Infection-Linked Immune Diseases

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This project has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement no. 101136582 as well as the Swiss State Secretariat forEducation, Research and lnnovation (SERI).

Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of theEuropean Union, the European Health and Digital Executive Agency (HaDEA) orSERI. Neither the European Union, HaDEA nor SERI can be held responsible for them.

https://cordis.europa.eu/project/id/101136582
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