Another Claude project: a static site that pulls in GWAS SNP data from ensemble, multiple public biobanks, open targets, gtex, eqtl catalog, and OMIM.
sashagusev.github.io/gwas_lookup/
sashagusev.github.io/gwas_lookup/
February 9, 2026 at 6:50 PM
Another Claude project: a static site that pulls in GWAS SNP data from ensemble, multiple public biobanks, open targets, gtex, eqtl catalog, and OMIM.
sashagusev.github.io/gwas_lookup/
sashagusev.github.io/gwas_lookup/
Just saw gtexr, related package for GTEx data
docs.ropensci.org/gtexr/articl...
H/t @jeremymsimon.bsky.social
docs.ropensci.org/gtexr/articl...
H/t @jeremymsimon.bsky.social
April 28, 2025 at 4:42 PM
Just saw gtexr, related package for GTEx data
docs.ropensci.org/gtexr/articl...
H/t @jeremymsimon.bsky.social
docs.ropensci.org/gtexr/articl...
H/t @jeremymsimon.bsky.social
I know many of you have been awaiting us launching transcript expression data in gnomAD. We were waiting for the GTEx v10 release which is now out so we are finally able to launch this. Enjoy!!
Proportion expressed across transcripts (pext), using GTEx v10, is now available on #gnomAD v4!
November 22, 2024 at 2:44 PM
I know many of you have been awaiting us launching transcript expression data in gnomAD. We were waiting for the GTEx v10 release which is now out so we are finally able to launch this. Enjoy!!
I’ve never announced grant funding before, not sure why! I love celebrating others’ news, but for some reason, I kept quiet about mine. This time, though, I want to share: our Baboon GTEx R01 grant has been funded! 🐒🎉
January 5, 2025 at 7:00 PM
I’ve never announced grant funding before, not sure why! I love celebrating others’ news, but for some reason, I kept quiet about mine. This time, though, I want to share: our Baboon GTEx R01 grant has been funded! 🐒🎉
gtexr: R interface to the GTEx Portal API docs.ropensci.org/gtexr/ #rstats
Query the GTEx Portal API
A convenient R interface to the Genotype-Tissue Expression (GTEx) Portal API. The GTEx project is a comprehensive public resource for studying tissue-specific gene expression and regulation in human…
docs.ropensci.org
April 28, 2025 at 3:30 PM
gtexr: R interface to the GTEx Portal API docs.ropensci.org/gtexr/ #rstats
People always stop me in the street to ask: "Yoav, where are the disease-associated eQLTs? We found a lot in GTEx but we can't find anymore. Do you know where they are?"
(For the record, no one has ever asked me this, but it is a really good question!)
I think we know where they are.
(For the record, no one has ever asked me this, but it is a really good question!)
I think we know where they are.
June 10, 2025 at 2:20 PM
People always stop me in the street to ask: "Yoav, where are the disease-associated eQLTs? We found a lot in GTEx but we can't find anymore. Do you know where they are?"
(For the record, no one has ever asked me this, but it is a really good question!)
I think we know where they are.
(For the record, no one has ever asked me this, but it is a really good question!)
I think we know where they are.
weisen im Vergleich zur Allgemeinbevölkerung erhebliche genetische Unterschiede in ihrer DNA auf. Diese liegen an vielen Stellen im Genom und betreffen nicht nur ein einzelnes Gen.
• Acht genetische Signale wurden identifiziert. Da sich die DNA bei Ausbruch von ME/CFS nicht
• Acht genetische Signale wurden identifiziert. Da sich die DNA bei Ausbruch von ME/CFS nicht
August 6, 2025 at 11:03 PM
weisen im Vergleich zur Allgemeinbevölkerung erhebliche genetische Unterschiede in ihrer DNA auf. Diese liegen an vielen Stellen im Genom und betreffen nicht nur ein einzelnes Gen.
• Acht genetische Signale wurden identifiziert. Da sich die DNA bei Ausbruch von ME/CFS nicht
• Acht genetische Signale wurden identifiziert. Da sich die DNA bei Ausbruch von ME/CFS nicht
Why do so many disease risk variants show no regulatory effects in GTEx and/or other standard eQTL studies?
What do we mean when we say a regulatory effect is "context-specific" and how do we define the context?
We explored these questions using brain organoids and oxygen stress.
What do we mean when we say a regulatory effect is "context-specific" and how do we define the context?
We explored these questions using brain organoids and oxygen stress.
June 9, 2025 at 12:03 AM
Why do so many disease risk variants show no regulatory effects in GTEx and/or other standard eQTL studies?
What do we mean when we say a regulatory effect is "context-specific" and how do we define the context?
We explored these questions using brain organoids and oxygen stress.
What do we mean when we say a regulatory effect is "context-specific" and how do we define the context?
We explored these questions using brain organoids and oxygen stress.
Our new perspective article describing the human and non-human primate developmental GTEx projects is now out in
@nature.com! We outline the scope, vision, opportunities and challenges of these projects here:
www.nature.com/articles/s41...
The human and non-human primate developmental GTEx projects - Nature
The developmental Genotype-Tissue Expression (dGTEx) projects will catalogue and integrate gene expression, regulation and genetics data across 120 human donors from birth to adulthood with developmen...
www.nature.com
January 15, 2025 at 4:40 PM
Our new perspective article describing the human and non-human primate developmental GTEx projects is now out in
@nature.com! We outline the scope, vision, opportunities and challenges of these projects here:
www.nature.com/articles/s41...
In this collaboration with the Gokcumen lab, @alberaqil.bsky.social developed a method based on interchromosomal linkage disequilibrium to detect false positive trans-eQTLs, showcased on GTEx and MAGE. The approach could be used to filter other trans molecular QTLs, which may be similarly impacted.
New paper with @rajivmccoy.bsky.social @ajhgnews.bsky.social.
Bottom line: Polymorphic gene duplications absent in the reference genome can produce spurious trans-eQTLs, and we propose a method to identify these false positives.
authors.elsevier.com/c/1nWChgeXHnOF
Bottom line: Polymorphic gene duplications absent in the reference genome can produce spurious trans-eQTLs, and we propose a method to identify these false positives.
authors.elsevier.com/c/1nWChgeXHnOF
July 29, 2026 at 3:52 PM
In this collaboration with the Gokcumen lab, @alberaqil.bsky.social developed a method based on interchromosomal linkage disequilibrium to detect false positive trans-eQTLs, showcased on GTEx and MAGE. The approach could be used to filter other trans molecular QTLs, which may be similarly impacted.
Network analysis of TCGA and GTEx gene expression datasets for identification of trait-associated biomarkers in human cancer - PMC
pmc.ncbi.nlm.nih.gov/articles/PM...
pmc.ncbi.nlm.nih.gov/articles/PM...
December 22, 2024 at 2:45 PM
Network analysis of TCGA and GTEx gene expression datasets for identification of trait-associated biomarkers in human cancer - PMC
pmc.ncbi.nlm.nih.gov/articles/PM...
pmc.ncbi.nlm.nih.gov/articles/PM...
Thanks to the large consortia like ENCODE, FANTOM5, GTEx, 4DNucleome for generating key training data. And finally, thanks to numerous researchers developing inspiring DNA sequence-to-function models, informative evaluations, and interpretation tools.
June 25, 2025 at 2:29 PM
Thanks to the large consortia like ENCODE, FANTOM5, GTEx, 4DNucleome for generating key training data. And finally, thanks to numerous researchers developing inspiring DNA sequence-to-function models, informative evaluations, and interpretation tools.
We view science as hypothesis testing, but where do hypotheses originate? From observing associations in systems we study—whether to fill known gaps or reveal the unexpected. SEAHORSE engineers serendipity—finding unexpected associations, beginning with GTEx and TCGA.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
SEAHORSE: A Serendipity Engine Assaying Heterogeneous Omics-Related Sampling Experiments
Large-scale, open-access data sets such as the Genotype Tissue Expression Project (GTEx) and The Cancer Genome Atlas (TCGA) include multi-omic data on large numbers of samples along with extensive cli...
www.biorxiv.org
August 25, 2025 at 2:55 PM
We view science as hypothesis testing, but where do hypotheses originate? From observing associations in systems we study—whether to fill known gaps or reveal the unexpected. SEAHORSE engineers serendipity—finding unexpected associations, beginning with GTEx and TCGA.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
A massive genomic exploration of drug targets 🧬💊
👉phenotypic data from UK Biobank, FinnGen, MVP (N>1M) for 2,000 diagnoses
👉gene expression data from GTEx & eQTLGen
👉proteomic data from deCODE, ARIC & Fenland
👉phenotypic data from UK Biobank, FinnGen, MVP (N>1M) for 2,000 diagnoses
👉gene expression data from GTEx & eQTLGen
👉proteomic data from deCODE, ARIC & Fenland
February 15, 2025 at 8:53 PM
A massive genomic exploration of drug targets 🧬💊
👉phenotypic data from UK Biobank, FinnGen, MVP (N>1M) for 2,000 diagnoses
👉gene expression data from GTEx & eQTLGen
👉proteomic data from deCODE, ARIC & Fenland
👉phenotypic data from UK Biobank, FinnGen, MVP (N>1M) for 2,000 diagnoses
👉gene expression data from GTEx & eQTLGen
👉proteomic data from deCODE, ARIC & Fenland
At my instruction, codex developed a fast variance component test for HxH + additive effects. I ran it on GTEx v8 using the phased data. What did I find? Bupkis. I'm bummed it didnt pan out, but this is a win imo. I used a little spare time I had to investigate my long held idea and can move on.
September 29, 2026 at 5:51 PM
At my instruction, codex developed a fast variance component test for HxH + additive effects. I ran it on GTEx v8 using the phased data. What did I find? Bupkis. I'm bummed it didnt pan out, but this is a win imo. I used a little spare time I had to investigate my long held idea and can move on.
SigCom Library of Integrated Network-based Cellular Signatures/LINCS: data & metadata search engine for a million gene expression signatures
Just fill your DEG list to explore the signatures😆
downloadable processed data L1000 GEO/CREEDS GTEx
#NucAcidRes 2022
maayanlab.cloud/sigcom-lincs...
Just fill your DEG list to explore the signatures😆
downloadable processed data L1000 GEO/CREEDS GTEx
#NucAcidRes 2022
maayanlab.cloud/sigcom-lincs...
April 6, 2025 at 7:58 PM
SigCom Library of Integrated Network-based Cellular Signatures/LINCS: data & metadata search engine for a million gene expression signatures
Just fill your DEG list to explore the signatures😆
downloadable processed data L1000 GEO/CREEDS GTEx
#NucAcidRes 2022
maayanlab.cloud/sigcom-lincs...
Just fill your DEG list to explore the signatures😆
downloadable processed data L1000 GEO/CREEDS GTEx
#NucAcidRes 2022
maayanlab.cloud/sigcom-lincs...
🚀 Expression Atlas Release 43 is live!
🧬 New Marker Gene View for all baseline (RNA & protein) experiments - instantly spot tissue- or condition-specific expression patterns.
🔎 Plus, a new technology filter for faster dataset discovery.
🔗ebi.ac.uk/gxa
@ebi.embl.org
🧬 New Marker Gene View for all baseline (RNA & protein) experiments - instantly spot tissue- or condition-specific expression patterns.
🔎 Plus, a new technology filter for faster dataset discovery.
🔗ebi.ac.uk/gxa
@ebi.embl.org
October 17, 2025 at 1:32 PM
🚀 Expression Atlas Release 43 is live!
🧬 New Marker Gene View for all baseline (RNA & protein) experiments - instantly spot tissue- or condition-specific expression patterns.
🔎 Plus, a new technology filter for faster dataset discovery.
🔗ebi.ac.uk/gxa
@ebi.embl.org
🧬 New Marker Gene View for all baseline (RNA & protein) experiments - instantly spot tissue- or condition-specific expression patterns.
🔎 Plus, a new technology filter for faster dataset discovery.
🔗ebi.ac.uk/gxa
@ebi.embl.org
Excited to share our MPAC preprint, a scalable ensemble of ML models for genome-wide non-coding variant effect prediction and our findings from 575M predictions across databases including @ukbiobank.bsky.social, GTEx, ClinVar, COSMIC, and @gnomad-project.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
| bioRxiv
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
https://www.biorxiv.org/content/10.1101/2025.04.16.648420v1\
April 23, 2025 at 5:28 PM
Excited to share our MPAC preprint, a scalable ensemble of ML models for genome-wide non-coding variant effect prediction and our findings from 575M predictions across databases including @ukbiobank.bsky.social, GTEx, ClinVar, COSMIC, and @gnomad-project.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Cool paper (and great resource). I’m especially keen the disconnect between mRNA and protein levels in adult tissues! Pay attention #devbiol, it’ll be the same in embryonic tissues.
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
January 8, 2025 at 1:06 PM
Cool paper (and great resource). I’m especially keen the disconnect between mRNA and protein levels in adult tissues! Pay attention #devbiol, it’ll be the same in embryonic tissues.
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
The human and non-human primate developmental GTEx projects www.nature.com/articles/s41...
The human and non-human primate developmental GTEx projects - Nature
The developmental Genotype-Tissue Expression (dGTEx) projects will catalogue and integrate gene expression, regulation and genetics data across 120 human donors from birth to adulthood with developmen...
www.nature.com
January 16, 2025 at 9:03 PM
The human and non-human primate developmental GTEx projects www.nature.com/articles/s41...
Are there dog equivalents to GTEx and the Human Protein Atlas?
January 7, 2026 at 10:57 PM
Are there dog equivalents to GTEx and the Human Protein Atlas?
Another reminder that RNA content does not necessarily correspond with protein content.
RNA-Seq is useful, but cannot be interpreted as describing protein concentrations
🦠🧪🧫🔬🧬 #MicroSky
www.cell.com/cell/fulltex...
RNA-Seq is useful, but cannot be interpreted as describing protein concentrations
🦠🧪🧫🔬🧬 #MicroSky
www.cell.com/cell/fulltex...
A Quantitative Proteome Map of the Human Body
Proteomics analysis across human tissues from the GTeX resource reveals insight into tissue-specific pathways and phenotypes arising from genetic diseases.
www.cell.com
January 8, 2025 at 1:28 PM
Another reminder that RNA content does not necessarily correspond with protein content.
RNA-Seq is useful, but cannot be interpreted as describing protein concentrations
🦠🧪🧫🔬🧬 #MicroSky
www.cell.com/cell/fulltex...
RNA-Seq is useful, but cannot be interpreted as describing protein concentrations
🦠🧪🧫🔬🧬 #MicroSky
www.cell.com/cell/fulltex...
Very happy to share *two* new projects from my group now on @biorxivpreprint.bsky.social on mtDNA variation effects on tissue-specific gene expression conducted using RNAseq data in 49 tissues in the GTEx project! 🧵
1/n
1/n
December 19, 2024 at 9:11 AM
Very happy to share *two* new projects from my group now on @biorxivpreprint.bsky.social on mtDNA variation effects on tissue-specific gene expression conducted using RNAseq data in 49 tissues in the GTEx project! 🧵
1/n
1/n
Would love to know how much data engineering was required to turn GTEx, ENCODE etc into usable training data 👀
Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind
June 25, 2025 at 4:49 PM
Would love to know how much data engineering was required to turn GTEx, ENCODE etc into usable training data 👀