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David Ochoa

@d0choa.bsky.social
334 followers 352 following 32 posts

Target discovery | Computational Biology | Human Disease Genetics | ML | Cloud computing - @opentargets.org - @ebi.embl.org

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David Ochoa @d0choa.bsky.social · 01/05/2026
Combining strong variant effects (e.g. protein-altering variation) with intermediate pleiotropy (2–5 TAs) nearly doubles the predictive power: OR 10.3, 4.8× clinical success. Led by Yakov Tsepilov + @opentargets.org www.biorxiv.org/content/10.6...
biorxiv.org
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David Ochoa @d0choa.bsky.social · 01/05/2026
🧬 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.
The Human Pleiotropic Map of GWAS Associations and Therapeutic Implications
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David Ochoa @d0choa.bsky.social · 23/03/2026
Thank you to all our data providers, partners, and the Open Targets core team who make this possible. 🙏
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David Ochoa @d0choa.bsky.social · 23/03/2026
Other highlights: 🧬 ENCODE-rE2G scores now in L2G → 5% gain in selectivity 📊 710 new GWAS Catalog studies → 5,000+ new credible sets (incl. Rand et al., Nat Genet 2025) ⚡ ClickHouse migration complete → ~2x query speed ☁️ Platform data now on AWS Open Data Program
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David Ochoa @d0choa.bsky.social · 23/03/2026
This is the first in a series of updates aimed at maximising what we can learn from clinical reports about the intended and unintended consequences of target modulation. More to come.
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David Ochoa @d0choa.bsky.social · 23/03/2026
The headline: a revamped clinical mining pipeline pulling from 6 sources (ClinicalTrials.gov, ChEMBL, TTD, EMA, PMDA Japan) → 285,213 clinical reports across 13 stages, feeding directly into target-disease evidence.
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David Ochoa @d0choa.bsky.social · 23/03/2026
The Open Targets Platform spring 🌼 release is out — and this one marks the beginning of something we've been building towards for a while.
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David Ochoa @d0choa.bsky.social · 23/01/2026
The needle in the haystack problem: spotting novel drug targets among redundant evidence. Our solution? A time-series novelty metric for Open Targets Platform associations. Thanks to Coté Falaguera & @opentargets.org partners for making this happen.
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David Ochoa @d0choa.bsky.social · 12/01/2026
🚀 Announcing the Official @opentargets.org MCP! We've partnered with @anthropic.com to give AI seamless access to high-quality genetic and target-discovery data. Open for the entire community to accelerate therapeutic development. Read more at blog.opentargets.org/official-ope...
blog.opentargets.org
Introducing the official Open Targets Platform Model Context Protocol
We have released the first iteration of a dedicated MCP server to bring our systematic target discovery capabilities to Large Language Model (LLM)-based workflows.
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David Ochoa @d0choa.bsky.social · 08/12/2025
What a ride so far… 🎂
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Konrad @konradjk.bsky.social · 18/09/2025
A project many years in the process, we’re pleased to present our work on multi-ancestry meta-analysis across a boatload of traits in the UK Biobank: www.nature.com/articles/s41...
nature.com
Pan-UK Biobank genome-wide association analyses enhance discovery and resolution of ancestry-enriched effects - Nature Genetics
Genome-wide analyses for 7,266 traits leveraging data from several genetic ancestry groups in UK Biobank identify new associations and enhance resources for interpreting risk variants across diverse p...
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David Ochoa @d0choa.bsky.social · 18/09/2025
If you care about regulatory variants don’t miss the E2G extension of the @opentargets.org Platform. There are synergies that only a fully open science allows and this is a good one!
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Tobi Alegbe @tobioinformatics.bsky.social · 08/07/2025
🚨New preprint just dropped 🚨 medrxiv.org/content/10.1101/2025.06.24.25330216 The main output from my PhD is finally public and we’re SUPER excited about the findings! If you’re interested in what we learnt about IBD with a massive 700+ sample sc-eQTL dataset of the gut, read on!
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David Ochoa @d0choa.bsky.social · 18/06/2025
📅 Join our Q&A drop-in on June 19 at 3pm BST to explore the new features and ask questions: 🔗 www.linkedin.com/events/25-06... 📰 Read more on our blog: 🔗 blog.opentargets.org/open-targets... Thanks @helenacornu.bsky.social for the infographic!
linkedin.com
25.06 Platform Release Q&A | LinkedIn
Join our Q&A session about the Open Targets Platform June release. The team will run through the main points of the release, after which they will open the floor to questions. The walkthrough will b...
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David Ochoa @d0choa.bsky.social · 18/06/2025
Every update helps complete the puzzle 🧩 of target discovery. Huge thanks to our data providers, partners, and the entire Open Targets team for their tireless work 🙏
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David Ochoa @d0choa.bsky.social · 18/06/2025
🥐 We’ve also redesigned the data downloads section — now built on the ML Commons Croissant standard. Better documentation + improved AI-readiness = easier use for researchers and developers alike.
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David Ochoa @d0choa.bsky.social · 18/06/2025
More highlights from the release: 🧬 New gene burden studies 💊 Expanded pharmacogenetics annotations 🧠 Interacting protein evidence from IntAct, Reactome, SIGNOR, STRING 🔬 First look at our molecular structure viewers!
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David Ochoa @d0choa.bsky.social · 18/06/2025
Over the past 3 months, we’ve added GWAS from: VA Million Veteran Program 210+ publications Including the Nature meta-analysis of osteoarthritis (April 2024) 🧠 All integrated + contextualised with existing data + functional genomics.
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David Ochoa @d0choa.bsky.social · 18/06/2025
🧬 One of our big promises with bringing Open Targets Genetics to the Platform was keeping post-GWAS analysis fresh and integrated. This release brings a 36% increase in GWAS credible sets, thanks to collaboration with the @gwascatalog.bsky.social and enhanced pipelines.
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David Ochoa @d0choa.bsky.social · 18/06/2025
🚀 The Summer ☀️ @opentargets.org Platform release is here! If you thought the last update was big… just wait till you see what’s inside. A quick thread on the highlights 👇
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Tuuli Lappalainen @tuuliel.bsky.social · 06/05/2025
Our new contribution to the quest to find causal GWAS genes! Sam Ghatan from my lab at @nygenome.org led a systematic comparison of eQTLs and CRISPRi+scRNA-seq screens. TL;DR: they provide highly complementary insights, with ortogonal pros and cons. 🧵👇 www.biorxiv.org/content/10.1...
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Eric Fauman (he/him) @ericfauman.bsky.social · 13/04/2025
The most famous heuristic in mapping gwas snps to genes is "it's usually the closest gene". But only slightly less well-known is this: consider the colocalized phenotypes. That is, a genetic variant seldom disrupts exactly one phenotype. What else does tugging on that thread do?
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David Ochoa @d0choa.bsky.social · 28/03/2025
Big thanks to the community for the great feedback we are receiving on the spring @opentargets.org Platform release. There are many positive and new ideas for improving our scientific interpretation and products. Feedback is a critical aspect of an open project's lifecycle. Please keep it coming 🧬🖥️
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Yasset Perez-Riverol @ypriverol.bsky.social · 28/03/2025
🚀 Big news! We've just published the official guidelines for submitting affinity proteomics data to PRIDE @pride-ebi.bsky.social (supported technologies Olink & SomaScan)! Get ahead of the curve—check them out & start your submissions! 👇 🔗 github.com/PRIDE-Archiv... #Proteomics #Olink #SomaScan
github.com
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David Ochoa @d0choa.bsky.social · 20/03/2025
The @opentargets.org Platform Spring 🌼 release brings a step-change in how we address common disease genetics. We included the results of a large-scale analysis on GWAS and functional genomics studies to inform target selection further 🧬 👩‍💻 blog.opentargets.org/a-step-chang...
blog.opentargets.org
A step-change in common disease genetics in the Open Targets Platform
We identified an opportunity to create a unified resource to seamlessly access human genetic and target discovery information. The Platform now integrates and evaluates gene-disease associations from ...
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David Ochoa @d0choa.bsky.social · 17/12/2024
We might not get everything right from the first shot. Still, we hope that by providing an open framework and the community's help, we could consolidate our collective understanding of disease-causing genetics. Stay tuned!
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David Ochoa @d0choa.bsky.social · 17/12/2024
The merged product will bring the best of both worlds in a single web application, covering all journeys from identifying the likely causal signals to the prioritising factors relevant to target progression
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David Ochoa @d0choa.bsky.social · 17/12/2024
This update will power our current target identification coverage, as well as the mechanistic interpretation and biological context
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David Ochoa @d0choa.bsky.social · 17/12/2024
The update will include a refreshed post-GWAS analysis covering state-of-the-art data and methodologies, resulting on 2.5M GWAS and molQTL credible sets, colocalisation analysis and L2G predictions
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David Ochoa @d0choa.bsky.social · 17/12/2024
From next spring, the Open Targets Platform will incorporate the best of Open Targets Genetics into an integrated drug discovery platform 🧵
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Jeff Spence @jeffspence.github.io · 17/12/2024
What do GWAS and rare variant burden tests discover, and why? Do these studies find the most IMPORTANT genes? If not, how DO they rank genes? Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬) www.biorxiv.org/content/10.1...
biorxiv.org
Specificity, length, and luck: How genes are prioritized by rare and common variant association studies
Standard genome-wide association studies (GWAS) and rare variant burden tests are essential tools for identifying trait-relevant genes. Although these methods are conceptually similar, we show by anal...
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 16/12/2024
Specificity, length, and luck: How genes are prioritized by rare and common variant association studies www.biorxiv.org/content/10.1101/202…
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Open Targets @opentargets.org · 10/12/2024
Out now! A look back at all the changes to the Open Targets Platform in the past two years 🖥️🧬 We've focused on adding data and analyses to help build therapeutic hypotheses, from expanding our associations page...
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David Ochoa @d0choa.bsky.social · 06/12/2024
In the upcoming NAR issue, we summarise the last 2 years of updates in the @opentargets.org Platform. One step at a time... academic.oup.com/nar/advance-...
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Michel Nivard @michelnivard.bsky.social · 02/12/2024
Instarted making a list the other day, with the help of others adding their own faves: github.com/MichelNivard...
github.com
GitHub - MichelNivard/awesome-complex-trait-genetics: A list of awesome tools for complex trait genetics.
A list of awesome tools for complex trait genetics. - MichelNivard/awesome-complex-trait-genetics
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David Ochoa @d0choa.bsky.social · 28/11/2024
crispy morning in the genome campus…
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David Ochoa @d0choa.bsky.social · 22/11/2024
plain and simple 👌
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David Ochoa @d0choa.bsky.social · 21/11/2024
Moving day at @opentargets.org It always amazed me the UK ability to appreciate remarkable scientists. The new @ebi.embl.org building couldn’t be named after a more inspirational figure
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Hilary Martin @hilarycmartin.bsky.social · 20/11/2024
My group's work dissecting the contribution of common variants to rare neurodevelopmental conditions is now out at nature.com/articles/s41..., led by co-first authors Qinqin Huang (not yet on blue sky) and @emiliewigdor.bsky.social . See below for Emilie's tweetorial.
nature.com
Examining the role of common variants in rare neurodevelopmental conditions - Nature
Patients with neurodevelopmental conditions without a monogenic diagnosis have a higher polygenic burden than those with a monogenic diagnosis. Non-transmitted common all...
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Inigo Martincorena @imartincorena.bsky.social · 20/11/2024
Resharing here a recent X post. In this preprint, we introduce an improved version of NanoSeq, a duplex sequencing protocol with <5 errors per billion bp in single DNA molecules, and use it to study the somatic mutation landscape of oral epithelium in >1000 people. 1/ www.medrxiv.org/content/10.1...
medrxiv.org
Somatic mutation and selection at epidemiological scale
As we age, many tissues become colonised by microscopic clones carrying somatic driver mutations ([1][1]–[10][2]. Some of these clones represent a first step towards cancer whereas others may contribu...
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David Ochoa @d0choa.bsky.social · 20/11/2024
To complete the healing it would be good to start thinking who are we missing here 🦋
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Jonathan Frazer @jonnyfrazer.bsky.social · 19/11/2024
Models for predicting the effect of genetic variation have come a long way in the last few years. When it comes to diagnosis and preventative care, how can we make safe and yet efficient use of them? Here are some of our thoughts authors.elsevier.com/c/1k7J9_4GsX...
authors.elsevier.com
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Nicky Whiffin @nickywhiffin.bsky.social · 18/11/2024
Finally, a newly minted program in Therapeutic Genomics: www.paediatrics.ox.ac.uk/Study/therap... Combining expertise across Oxford with global collaborators to harness genomic approaches and technologies to accelerate the development of effective and safe genome-targeted therapies. End 🧵
paediatrics.ox.ac.uk
Therapeutic Genomics Centre, DPhil Programme
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David Ochoa @d0choa.bsky.social · 18/11/2024
some *.rxiv have subjects that can be used for domain-splitting. An LLM-based summarisation might work well here as well
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Adam Feuerstein✡️ @adamfeuerstein.bsky.social · 18/11/2024
Regenxbio $RGNX says gene therapy strengthened boys with Duchenne muscular dystrophy Pivotal study started, top-line data could come early 2026. FDA accelerated approval filing to follow. www.statnews.com/2024/11/18/d... $SRPT
statnews.com
Regenxbio says gene therapy strengthened boys with Duchenne muscular dystrophy
Based on a small trial with positive muscle performance data, Regenxbio is expected to pursue approval of its gene therapy for Duchenne muscular dystrophy.
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David Ochoa @d0choa.bsky.social · 16/11/2024
First day on bsky. A fresh start. A chance to do better, to be kind, to listen other voices. 👋 Hello everyone
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