David Ochoa
@d0choa.bsky.social
Target discovery | Computational Biology | Human Disease Genetics | ML | Cloud computing - @opentargets.org
- @ebi.embl.org
- @ebi.embl.org
Reposted by David Ochoa
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...
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...
www.nature.com
September 18, 2025 at 5:25 PM
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...
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!
Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome:
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
September 18, 2025 at 5:06 PM
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!
Reposted by David Ochoa
🚨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!
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!
July 8, 2025 at 8:52 AM
🚨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!
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!
🚀 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 👇
If you thought the last update was big… just wait till you see what’s inside.
A quick thread on the highlights 👇
June 18, 2025 at 5:55 PM
🚀 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 👇
If you thought the last update was big… just wait till you see what’s inside.
A quick thread on the highlights 👇
Reposted by David Ochoa
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...
www.biorxiv.org/content/10.1...
May 6, 2025 at 5:01 PM
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...
www.biorxiv.org/content/10.1...
Reposted by David Ochoa
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?
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?
April 13, 2025 at 6:36 PM
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?
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?
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 🧬🖥️
March 28, 2025 at 11:18 AM
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 🧬🖥️
Reposted by David Ochoa
🚀 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
Get ahead of the curve—check them out & start your submissions! 👇
🔗 github.com/PRIDE-Archiv...
#Proteomics #Olink #SomaScan
github.com
March 28, 2025 at 7:20 AM
🚀 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
Get ahead of the curve—check them out & start your submissions! 👇
🔗 github.com/PRIDE-Archiv...
#Proteomics #Olink #SomaScan
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-chang...
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 ...
blog.opentargets.org
March 20, 2025 at 12:28 PM
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-chang...
From next spring, the Open Targets Platform will incorporate the best of Open Targets Genetics into an integrated drug discovery platform 🧵
December 17, 2024 at 5:06 PM
From next spring, the Open Targets Platform will incorporate the best of Open Targets Genetics into an integrated drug discovery platform 🧵
Reposted by David Ochoa
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...
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...
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...
www.biorxiv.org
December 17, 2024 at 7:05 AM
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...
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...
Reposted by David Ochoa
Specificity, length, and luck: How genes are prioritized by rare and common variant association studies https://www.biorxiv.org/content/10.1101/2024.12.12.628073v1
December 16, 2024 at 10:33 AM
Specificity, length, and luck: How genes are prioritized by rare and common variant association studies https://www.biorxiv.org/content/10.1101/2024.12.12.628073v1
Reposted by David Ochoa
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...
We've focused on adding data and analyses to help build therapeutic hypotheses, from expanding our associations page...
December 10, 2024 at 10:59 AM
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...
We've focused on adding data and analyses to help build therapeutic hypotheses, from expanding our associations page...
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-...
December 6, 2024 at 5:06 PM
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-...
Reposted by David Ochoa
Instarted making a list the other day, with the help of others adding their own faves: github.com/MichelNivard...
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
github.com
December 2, 2024 at 8:57 PM
Instarted making a list the other day, with the help of others adding their own faves: github.com/MichelNivard...
crispy morning in the genome campus…
November 28, 2024 at 1:27 PM
crispy morning in the genome campus…
plain and simple 👌
"Integration, integration, integration"!
Dame Janet Thornton describes how she came up with the idea for the Open Targets Platform
The full Open Targets founders panel is available to watch on YouTube: youtu.be/an2fer-dxXU
#OpenTargetsAt10
Dame Janet Thornton describes how she came up with the idea for the Open Targets Platform
The full Open Targets founders panel is available to watch on YouTube: youtu.be/an2fer-dxXU
#OpenTargetsAt10
November 22, 2024 at 9:34 AM
plain and simple 👌
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
November 21, 2024 at 8:01 PM
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
Reposted by David Ochoa
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.
November 20, 2024 at 4:15 PM
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.
Reposted by David Ochoa
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...
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...
www.medrxiv.org
November 20, 2024 at 2:28 PM
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...
To complete the healing it would be good to start thinking who are we missing here 🦋
November 20, 2024 at 8:57 AM
To complete the healing it would be good to start thinking who are we missing here 🦋
Reposted by David Ochoa
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
November 19, 2024 at 6:54 AM
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...
Reposted by David Ochoa
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 🧵
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 🧵
Therapeutic Genomics Centre, DPhil Programme
www.paediatrics.ox.ac.uk
November 18, 2024 at 1:57 PM
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 🧵
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 🧵
Reposted by David Ochoa
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
Pivotal study started, top-line data could come early 2026. FDA accelerated approval filing to follow.
www.statnews.com/2024/11/18/d... $SRPT
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.
www.statnews.com
November 18, 2024 at 12:19 PM
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
Pivotal study started, top-line data could come early 2026. FDA accelerated approval filing to follow.
www.statnews.com/2024/11/18/d... $SRPT
First day on bsky. A fresh start. A chance to do better, to be kind, to listen other voices. 👋 Hello everyone
November 16, 2024 at 8:48 PM
First day on bsky. A fresh start. A chance to do better, to be kind, to listen other voices. 👋 Hello everyone