6 years 646 patients 1193 samples 100 endoscopists 9 lab scientists 3 postdocs 2 PhD students 502 courier runs from Addenbrooke’s Hospital to @sangerinstitute.bsky.social IBDverse is the largest single-cell dataset of Inflammatory Bowel Disease (IBD)—and generating the data for it was no mean feat

"Patients know what it’s like to live with these conditions on a daily basis and the impact it has on our lives. By getting involved, we can help clinicians and researchers understand what really matters to us, so future research and treatments genuinely meet our needs." fg.bmj.com/content/earl...

Patient and public involvement and engagement in research: who, why, when and how to get it right

Patient and public involvement and engagement (PPIE) refers to the different ways those with lived experience, including patients, family, friends and carers, and the public engage with the design, de...

fg.bmj.com

“We hope our framework will help drive a conceptual shift in how MASLD is studied and understood.” A new study reframes Metabolic dysfunction-Associated Steatotic Liver Disease as a continuous process, better capturing the underlying disease biology www.nature.com/articles/s42...

A data-driven framework reconstructs the molecular continuum of human MASLD progression - Nature Metabolism

A trajectory-based molecular framework reveals coordinated temporal shifts in metabolic, inflammatory and fibrogenic mechanisms across the human MASLD spectrum.

nature.com

Our MASLD paper is finally out @naturemetabolism.bsky.social @ebi.embl.org @opentargets.org ! Fantastic collaboration with Toni Vidal-Puig's group in the IMS, UCam (co-led), Papatheodorou @earlhaminst.bsky.social and other coauthors, led by Ioannis Kamzolas and Thodoris Koutsandreas. Check it out!

Open Targets@opentargets.org · 3w ago

Out now in Nature Metabolism! 🖥️🧬 An Open Targets project has identified a set of plasma proteins that could be used to diagnose and monitor patients with Metabolic dysfunction-Associated Steatotic Liver Disease (MASLD) www.nature.com/articles/s42...

Out now in Nature Metabolism! 🖥️🧬 An Open Targets project has identified a set of plasma proteins that could be used to diagnose and monitor patients with Metabolic dysfunction-Associated Steatotic Liver Disease (MASLD) www.nature.com/articles/s42...

A data-driven framework reconstructs the molecular continuum of human MASLD progression - Nature Metabolism

A trajectory-based molecular framework reveals coordinated temporal shifts in metabolic, inflammatory and fibrogenic mechanisms across the human MASLD spectrum.

nature.com

VIDRA is out now on medRxiv! Variant-Informed Dose-Response Analysis (VIDRA) is a computational framework which infers genetic dose-response relationships by integrating trait-associated variants across a spectrum of allele frequencies and functional consequences. www.medrxiv.org/content/10.6...

Genetic dose-response modelling predicts drug mechanisms, dosing, and adverse events

Understanding how changes in gene function affect disease risk is central to drug development. Genetic variants are natural perturbations of gene activity and provide an opportunity to systematically ...

medrxiv.org

“The scale at which we’re doing things, and in such an unbiased way, means that anything could come out of it. You have to be open to a new theory or something completely out of the ordinary happening.” Lewis Evans is @sangerinstitute.bsky.social Senior Staff Scientist and Open Targets project lead

The Open Targets Platform 26.06 release is out now! ✋ 🔴 Find out about all the updates on the blog: blog.opentargets.org/open-targets...

“There isn’t anywhere else in the world where you’ve got genomics, computational, clinical, biological, and pharmaceutical expertise all in one group or consortium.” @mhaniffa.bsky.social discusses her experience working with partners across industry and academia as part of her Open Targets project

How do you ensure the stability of a platform with millions of data points updated every release? You start testing patterns In the last release of the Open Targets Platform, we implemented automated end-to-end testing into our development workflow 🧬🖥️ blog.opentargets.org/end-to-end-t...

Ensuring stability of the Open Targets Platform: the case for automated end-to-end testing

As a platform grows in complexity, maintaining stability becomes increasingly difficult. The Open Targets Frontend Team has introduced automated end-to-end testing to ensure that core user journeys an...

blog.opentargets.org

New study into Crohn’s disease helps explain why gut inflammation persists, and could help unlock more targeted treatments for patients. Researchers analysed millions of gut cells, uncovering lasting molecular changes and key inflammatory immune cells. 👇 www.sanger.ac.uk/news_item/ce...

Cellular study maps gene activity changes across more than 50 gut cell types in Crohn’s disease

The latest IBDverse study identifies the genes expressed in Crohn's disease, revealing a lasting 'molecular scar' in the gut lining.

sanger.ac.uk

Out now in Nature Genetics! The largest single-cell RNA sequencing dataset of terminal ileal biopsies profiles 1.1 million cells from over 100 Crohn’s disease patients and over 200 healthy controls. Crohn’s disease is a type of inflammatory bowel disease (IBD) www.nature.com/articles/s41...

Single-cell RNA sequencing of terminal ileal biopsies identifies signatures of Crohn’s disease pathogenesis - Nature Genetics

IBDverse is a single-cell RNA atlas of terminal ileal biopsies comprising 1.1 million cells from 111 patients with Crohn’s disease and 232 healthy participants. Analysis of the data identifies genes, ...

nature.com

“Open Targets has had the single biggest impact in integrating the @sangerinstitute.bsky.social and @ebi.embl.org science, above and beyond any other initiative I’ve seen in that time." 🤝

Out now in Nature! Genetic analysis of the largest single-cell dataset of Inflammatory Bowel Disease (IBD)-relevant tissues nominates effector genes and cell types at over half of known IBD loci, including 74 for which this is the first candidate effector gene 🖥️🧬 www.nature.com/articles/s41...

Cell-type-resolved genetic variation shapes inflammatory bowel disease risk - Nature

Single-cell mapping of cis-expression quantitative trait loci in inflammatory bowel disease revealed distal, enhancer-enriched variants detected at the cell-type level more frequently co-loc...

nature.com

We're at #ESHG2026! Come say hello and find out about current Open Targets projects. See you there!

Excited to release #OpenSplice - the impact of >500,000 mutations on the alternative splicing of 600 human exons www.biorxiv.org/content/10.6... Led by @gioia-quarantani.bsky.social + funded by @opentargets.org ‬ @sangerinstitute.bsky.social @crg.eu #cshlsymp26 #RNA2026 @rnasociety.bsky.social

Introducing OpenSplice, an atlas of splice-altering variants and the largest systematic analysis of splicing regulatory variants OpenSplice quantifies the impact of 590,000+ variants on the splicing of 608 alternatively spliced exons, and is out now on bioRxiv 🧬🖥️ www.biorxiv.org/content/10.6...

1\ Excited to finally share some of my PhD work: OpenSplice! We measured how >590,000 mutations affect exon inclusion across 600 human exons, creating a resource to study splicing regulation, benchmark variant effect predictors, and support variant interpretation.

bioRxiv Genomics@biorxiv-genomic.bsky.social · 2mo ago

OpenSplice: the impact of half a million mutations on the alternative splicing of 600 human exons https://www.biorxiv.org/content/10.64898/2026.05.22.727141v1

Design is a team sport. Galabina Yordanova and Adedoyin Okunade share how they crafted an intuitive experience for the Perturbation Catalogue through user research and iterative design. blog.opentargets.org/designing-th...

Designing the Perturbation Catalogue—a UX journey through perturbation data

The Perturbation Catalogue brings genetic perturbation data into one curated, harmonised, and discoverable platform. Once the data is in, how do you ensure it's useful and structured in a way that ans...

blog.opentargets.org

GWAS discovery is far from saturation. We need more GWAS, and more diverse GWAS 🧬🖥️

How do you present complex information in an easily understandable and visually appealing way? Our web developer Graham McNeill walks you through our design process for visualising locus-to-gene scores in the Platform: blog.opentargets.org/design-proce...

Visualising complex data in the Open Targets Platform: our design process for Locus-to-Gene scoring representation

Our Shapley value-based explanations for Locus-to-Gene scores presented a design challenge of providing a diverse range of users with an intuitive ‘explanation’ of the score but also ensuring enough d...

blog.opentargets.org

"Beyond the technical aspects of large-scale data analysis, the internship gave me a clearer view of how deep biological knowledge and genetic evidence can be combined to support target discovery and safety assessment." 🖥️🧬 blog.opentargets.org/from-genetic...

From genetic perturbation to drug safety: Sam Moix’s internship at Open Targets

Working with a team at the forefront of large-scale biomedical data integration, I learned a great deal about large-scale data processing, reproducible research, human genetics, and the challenges of ...

blog.opentargets.org

Want to maximise your chance of clinical success? Gene-disease associations with: 1️⃣ Genetic support from protein-altering variants 2️⃣ Intermediate pleiotropy are 10 times more likely to result in approved medicines, balancing impactful genetic variation with genetically informed safety liability

How can you compare cells across conditions? We chat to Marie Moullet about Tripso, a self-supervised transformer model she co-developed for single cell data analyses going beyond canonical cell type markers and annotations to understand cell states blog.opentargets.org/how-the-lotf...

How the Lotfollahi lab created Tripso to interpret single cell data

Marie Moullet describes Tripso—Transformers for learning Representations of Interpretable gene Programs in Single-cell transcriptOmics—a method for single cell data analyses that goes beyond canonical...

blog.opentargets.org

Our findings from the largest systematic analysis of complex trait associations is out now on bioRxiv! 🧬🖥️ www.biorxiv.org/content/10.6...

🧬 New preprint: "The Human Pleiotropic Map of GWAS Associations and Therapeutic Implications" Why do some genetically supported drug targets succeed in the clinic while others fail? Across 100,526 GWAS, the same evidence flags constrained gene functions rarely safe to modulate.

What a conversation! 🙌 Thank you to everyone who joined "Closed Licences, Closed Doors" with @knowledgerights21.org Do restrictive licences protect your research from AI, or just limit its impact? Couldn't make it? Watch the recording 👇 youtu.be/BprlLw6CRyI #OpenScience #AcademicSky 🧪

Closed licences closed doors: Open licensing, AI, and the future of research impact

YouTube video by EuropePMC

youtu.be

📣Tomorrow: Closed Licences, Closed Doors webinar! Join us and @knowledgerights21.org to find out about open licensing, AI, and the future of research impact! 🗓️ 14 April | ⏰ 10:00 BST/11:00 CEST There's still time to register 👉 embl-org.zoom.us/meeting/regi... #OpenScience #AcademicSky 🧪

EMBL-EBI@ebi.embl.org · 4mo ago

How does open licensing shape scientific research in the age of AI? Do restrictive licences protect your work, or limit collaboration? Join @europepmc.org & @knowledgerights21.org to explore these questions in the webinar. 🗓️ 14 April, 10:00 BST Register: embl-org.zoom.us/meeting/regi...

🧬🖥️ Introducing TRIPSO: a transformer network to help interpret single cell data analyses by learning multiple predefined or data-driven gene programme-specific embeddings Tripso was developed by a team across the Lotfollahi, Haniffa, Gottgens and Vento labs www.biorxiv.org/content/10.6...

The reveal is here! Meet your experts: 🎤 Presentations: Dr. David Hulcoop @opentargets.org Dr. Benjamin White @knowledgerights21.org Dr. Summer Rosonovski #EuropePMC 💬 Panel: Melissa Harrison #EuropePMC @ebi.embl.org Dr. Kiera McNeice Research Transparency Manager* Dr. Bastian Drees @embl.org

Europe PMC@europepmc.org · 5mo ago

Closed licences, closed doors. We're hosting a webinar with @kr21.bsky.social exploring how licensing shapes real-world research impact, from @opentargets.org to pandemic response. Speaker panel reveal soon 👀 🗓️ 14 April ⏰ 10:00 BST 🔗 embl-org.zoom.us/meeting/regi... #OpenScience #AcademicSky 🧪