@yosephbarash.bsky.social
Opinions - own. Lab RNA+AI+Genetics @upenn.edu
www.biociphers.org
www.biociphers.org
Reposted
Really cool paper that changed the way I think about what GWAS and Burden tests are doing, and also basically made me pleiotropy-pilled
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:17 AM
Really cool paper that changed the way I think about what GWAS and Burden tests are doing, and also basically made me pleiotropy-pilled
Reposted
Excited to launch an openRxiv partnership with the scientist-run AI review service qed (@qedscience.bsky.social), the brainchild of @odedrechavi.bsky.social 1/n
openrxiv.org/enabling-rev...
openrxiv.org/enabling-rev...
Enabling options for review: from training and transparency to author-centered AI tools - openRxiv
Peer review is widely viewed as a critical aspect of biomedical communication. Ideally, it provides authors with feedback so they can improve manuscripts and gives readers, particularly nonspecialists...
openrxiv.org
November 6, 2025 at 2:32 PM
Excited to launch an openRxiv partnership with the scientist-run AI review service qed (@qedscience.bsky.social), the brainchild of @odedrechavi.bsky.social 1/n
openrxiv.org/enabling-rev...
openrxiv.org/enabling-rev...
Reposted
As new human assemblies become available on beta.ensembl.org - which human reference genome will you choose? This article explores the question with insights from Ensembl’s own Fergal Martin - www.nature.com/articles/s41...
#HumanGenomics #Pangenomes #ReferenceGenomes
#HumanGenomics #Pangenomes #ReferenceGenomes
Choose your human genome reference wisely - Nature Methods
Scientists can choose between multiple human genome references, and a pangenome reference is coming. Deciding what to use when is not quite straightforward.
www.nature.com
November 4, 2025 at 12:28 PM
As new human assemblies become available on beta.ensembl.org - which human reference genome will you choose? This article explores the question with insights from Ensembl’s own Fergal Martin - www.nature.com/articles/s41...
#HumanGenomics #Pangenomes #ReferenceGenomes
#HumanGenomics #Pangenomes #ReferenceGenomes
And it's a wrap! We just finished a fantastic #RNA #Theraputics meeting in Palermo 🇮🇹😀 And yes, the location was beautiful and the food was 😋 but l want to share a little from the cool things I learned about this week, as they may be interesting for you too...
November 1, 2025 at 11:58 PM
And it's a wrap! We just finished a fantastic #RNA #Theraputics meeting in Palermo 🇮🇹😀 And yes, the location was beautiful and the food was 😋 but l want to share a little from the cool things I learned about this week, as they may be interesting for you too...
Reposted
So excited to see this out in @natgenet.nature.com! An amazing collaboration with @gagneurlab.bsky.social, I am happy I was (a small) part of. Nucleotide dependencies can capture regulatory elements, including #RNA structures! Congrats to the whole team! Check it out: www.nature.com/articles/s41...
Nucleotide dependency analysis of genomic language models detects functional elements - Nature Genetics
Mapping pairwise nucleotide dependencies by leveraging genomic language models highlights functional genomic elements and predicts deleterious genetic variants more effectively than alignment-based conservation metrics.
www.nature.com
October 11, 2025 at 2:00 PM
So excited to see this out in @natgenet.nature.com! An amazing collaboration with @gagneurlab.bsky.social, I am happy I was (a small) part of. Nucleotide dependencies can capture regulatory elements, including #RNA structures! Congrats to the whole team! Check it out: www.nature.com/articles/s41...
Reposted
BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)
October 15, 2025 at 12:22 PM
BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)
📣 Attention #RNA #Splicing lovers! How is splicing of exons coordinated??🤔 ➡️ Exon Junction Complex (EJC) coordinates inclusion of blocks of neighboring exons!😯 Cool work by Alexandra Bergfort @karlaneugebauer.bsky.social lab - check it out! (we got to help a bit 😊) genesdev.cshlp.org/content/earl...
October 17, 2025 at 2:12 AM
📣 Attention #RNA #Splicing lovers! How is splicing of exons coordinated??🤔 ➡️ Exon Junction Complex (EJC) coordinates inclusion of blocks of neighboring exons!😯 Cool work by Alexandra Bergfort @karlaneugebauer.bsky.social lab - check it out! (we got to help a bit 😊) genesdev.cshlp.org/content/earl...
Reposted
Planning your afternoon poster session at #ashg25? Come say hello!
This is an amalgamation of our two recent preprints - working with @gregfindlay.bsky.social , @cassimons.bsky.social , @dgmacarthur.bsky.social and many others to study variation across RNU4-2 and describe a new recessive NDD 🧬
This is an amalgamation of our two recent preprints - working with @gregfindlay.bsky.social , @cassimons.bsky.social , @dgmacarthur.bsky.social and many others to study variation across RNU4-2 and describe a new recessive NDD 🧬
October 16, 2025 at 2:55 PM
Planning your afternoon poster session at #ashg25? Come say hello!
This is an amalgamation of our two recent preprints - working with @gregfindlay.bsky.social , @cassimons.bsky.social , @dgmacarthur.bsky.social and many others to study variation across RNU4-2 and describe a new recessive NDD 🧬
This is an amalgamation of our two recent preprints - working with @gregfindlay.bsky.social , @cassimons.bsky.social , @dgmacarthur.bsky.social and many others to study variation across RNU4-2 and describe a new recessive NDD 🧬
Reposted
After our study on RNU4-2 and RNU5B-1 published in May (Nava et al, Nature Genetics 2025), I am excited to share our new preprint reporting dominant and recessive variants in RNU2-2 as a frequent cause of developmental and epileptic encephalopathy (DEE).
📄 www.medrxiv.org/content/10.1...
📄 www.medrxiv.org/content/10.1...
Systematic analysis of snRNA genes reveals frequent RNU2-2 variants in dominant and recessive developmental and epileptic encephalopathies
Variants in spliceosomal small nuclear RNA (snRNA) genes RNU4-2 (ReNU syndrome), RNU5B-1 , and RNU2-2 have recently been linked to dominant neurodevelopmental disorders (NDDs), revealing a major, prev...
www.medrxiv.org
September 5, 2025 at 3:32 PM
After our study on RNU4-2 and RNU5B-1 published in May (Nava et al, Nature Genetics 2025), I am excited to share our new preprint reporting dominant and recessive variants in RNU2-2 as a frequent cause of developmental and epileptic encephalopathy (DEE).
📄 www.medrxiv.org/content/10.1...
📄 www.medrxiv.org/content/10.1...
Reposted
Many conserved exons in the heart and brain utilize weak 5 ′ splice sites, yet they are accurately spliced. But how? We show that splicing fidelity is actively enforced through a QKI-U6 checkpoint at the U1→U6 handover in essential cardiac genes during organogenesis.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5ʹ splice sites
During organogenesis, precise pre-mRNA splicing is essential to assemble tissue architecture. Many developmentally essential exons bear weak 5'splice sites (5'SS) yet are spliced with high precision, ...
www.biorxiv.org
September 8, 2025 at 6:12 AM
Many conserved exons in the heart and brain utilize weak 5 ′ splice sites, yet they are accurately spliced. But how? We show that splicing fidelity is actively enforced through a QKI-U6 checkpoint at the U1→U6 handover in essential cardiac genes during organogenesis.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
📣Abstract deadline is *tomorrow* ! The list of speakers from academia & industry, + dates in Sicily ➡️ you should be on your way to submitting your abstract....
#RNA #therapeutics rnahorizons.com/abstract-sub...
#RNA #therapeutics rnahorizons.com/abstract-sub...
Abstract Submission - RNA 2025 Therapeutics Symposium
Abstract Submission Click Here to Submit Your Abstract Abstract Submission Deadline: September 1, 2025 Participants are encouraged to submit an abstract for oral or poster presentation. GUIDELINES FOR...
rnahorizons.com
September 1, 2025 at 4:41 AM
📣Abstract deadline is *tomorrow* ! The list of speakers from academia & industry, + dates in Sicily ➡️ you should be on your way to submitting your abstract....
#RNA #therapeutics rnahorizons.com/abstract-sub...
#RNA #therapeutics rnahorizons.com/abstract-sub...
Reposted
Very excited that our most significant work, a collaboration w/ Dr. Can Cenik at UT Austin on translational gene regulation, was finally published in Nature Biotechnology in a dual set of studies:
Paper 1 -- an AI model trained to predict translation rates from mRNA sequences: rdcu.be/exN1l
Paper 1 -- an AI model trained to predict translation rates from mRNA sequences: rdcu.be/exN1l
Predicting the translation efficiency of messenger RNA in mammalian cells
Nature Biotechnology - A deep convolutional neural network model predicts the influence of the full-length mRNA sequence on translation efficiency.
url.de.m.mimecastprotect.com
July 25, 2025 at 1:37 PM
Very excited that our most significant work, a collaboration w/ Dr. Can Cenik at UT Austin on translational gene regulation, was finally published in Nature Biotechnology in a dual set of studies:
Paper 1 -- an AI model trained to predict translation rates from mRNA sequences: rdcu.be/exN1l
Paper 1 -- an AI model trained to predict translation rates from mRNA sequences: rdcu.be/exN1l
Reposted
If we want to connect genetic variation to disease, we need to move beyond baseline conditions. Our study shows that dynamic, context-specific regulation holds the key to understanding many unexplained GWAS signals. The preprint again:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Disease-associated loci share properties with response eQTLs under common environmental exposures
Many of the genetic loci associated with disease are expected to have context-dependent regulatory effects that are underrepresented in the transcriptomes of healthy, steady-state adult tissues. To un...
www.biorxiv.org
June 10, 2025 at 2:20 PM
If we want to connect genetic variation to disease, we need to move beyond baseline conditions. Our study shows that dynamic, context-specific regulation holds the key to understanding many unexplained GWAS signals. The preprint again:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted
Happy to announce our paper comparing embryonic gene expression between C. elegans and C. briggsae, work led by Christopher Large with Rupa Khanal and in collaboration with Junhyong Kim and Bob Waterston. www.science.org/doi/10.1126/...
Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae
The constraints that govern the evolution of gene expression patterns across development remain unclear. Single-cell RNA sequencing can detail these constraints by systematically profiling homologous ...
www.science.org
June 20, 2025 at 8:25 PM
Happy to announce our paper comparing embryonic gene expression between C. elegans and C. briggsae, work led by Christopher Large with Rupa Khanal and in collaboration with Junhyong Kim and Bob Waterston. www.science.org/doi/10.1126/...
Reposted
Very excited to share our new work on gastruloids by the incredible Cat Triandafillou! We mapped gene expression across 26 individual gastruloids at single-cell resolution and discovered some pretty amazing patterns about how these "mini-embryos" organize themselves.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Single-cell spatial mapping reveals reproducible cell type organization and spatially-dependent gene expression in gastruloids
Gastruloids are three-dimensional stem-cell-based models that recapitulate key aspects of mammalian gastrulation, including formation of an anterior-posterior (AP) axis. However, we do not have detail...
www.biorxiv.org
July 15, 2025 at 3:43 PM
Very excited to share our new work on gastruloids by the incredible Cat Triandafillou! We mapped gene expression across 26 individual gastruloids at single-cell resolution and discovered some pretty amazing patterns about how these "mini-embryos" organize themselves.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted
We are excited to introduce mRNABench, a comprehensive benchmarking suite that we used to evaluate the representational capabilities of 18 families of nucleotide foundation models on mature mRNA specific tasks.
Paper: doi.org/10.1101/2025...
Code: github.com/morrislab/mR...
A 🧵
Paper: doi.org/10.1101/2025...
Code: github.com/morrislab/mR...
A 🧵
mRNABench: A curated benchmark for mature mRNA property and function prediction
Messenger RNA (mRNA) is central in gene expression, and its half-life, localization, and translation efficiency drive phenotypic diversity in eukaryotic cells. While supervised learning has widely bee...
doi.org
July 15, 2025 at 7:09 PM
We are excited to introduce mRNABench, a comprehensive benchmarking suite that we used to evaluate the representational capabilities of 18 families of nucleotide foundation models on mature mRNA specific tasks.
Paper: doi.org/10.1101/2025...
Code: github.com/morrislab/mR...
A 🧵
Paper: doi.org/10.1101/2025...
Code: github.com/morrislab/mR...
A 🧵
📣We are happy to announce the release of MAJIQ V3 😊🎉 check out details here #RNA #Splicing #RNASeq biociphers.wordpress.com/2025/06/20/m...
MAJIQ V3 Release
Ever since MAJIQ V2 was released we have been working on V3. It only took us a couple of years, but…. We are (finally!) pleased to announce the release of MAJIQ V3, a major update to our soft…
biociphers.wordpress.com
June 20, 2025 at 9:39 PM
📣We are happy to announce the release of MAJIQ V3 😊🎉 check out details here #RNA #Splicing #RNASeq biociphers.wordpress.com/2025/06/20/m...
Reposted
Reminder: Nobel-prize winning PCR (1983), used in basically all genetic tech today, was only possible because of extremophile bacterium discovered in 1964 in Yellowstone funded by a small ~$80k NSF grant with no obvious application at the time. #science 🧪
www.richmondscientific.com/how-a-discov...
www.richmondscientific.com/how-a-discov...
How a discovery in Yellowstone National Park led to the development of PCR - Richmond Scientific
A discovery in Yellowstone National Park led to the development of PCR, the gold-standard COVID-19 tests used to fight the global pandemic.
www.richmondscientific.com
June 8, 2025 at 9:09 PM
Reminder: Nobel-prize winning PCR (1983), used in basically all genetic tech today, was only possible because of extremophile bacterium discovered in 1964 in Yellowstone funded by a small ~$80k NSF grant with no obvious application at the time. #science 🧪
www.richmondscientific.com/how-a-discov...
www.richmondscientific.com/how-a-discov...
Reposted
🔊 Meet Mathieu Quesnel Vallières @rna-ken.bsky.social : Using transcriptomic analyses to find cancer immunotherapy targets, he’s bringing his expertise to @usherbrooke.bsky.social , supported by D2R’s New Faculty Start-Up program
🔗Learn more: buff.ly/laJgUJ3
#ResearcherSpotlight #RNAResearch
🔗Learn more: buff.ly/laJgUJ3
#ResearcherSpotlight #RNAResearch
May 27, 2025 at 1:15 PM
🔊 Meet Mathieu Quesnel Vallières @rna-ken.bsky.social : Using transcriptomic analyses to find cancer immunotherapy targets, he’s bringing his expertise to @usherbrooke.bsky.social , supported by D2R’s New Faculty Start-Up program
🔗Learn more: buff.ly/laJgUJ3
#ResearcherSpotlight #RNAResearch
🔗Learn more: buff.ly/laJgUJ3
#ResearcherSpotlight #RNAResearch
Reposted
Lux Capital & @wolfejosh.bsky.social are launching the Lux Science Helpline - a $100M commitment to support American scientists whose research is threatened by funding cuts, bureaucratic hurdles, and career roadblocks - that expands our Lux Labs program.
www.luxcapital.com/news/our-hel...
www.luxcapital.com/news/our-hel...
Our Helpline for American Scientists
www.luxcapital.com
May 9, 2025 at 10:10 PM
Lux Capital & @wolfejosh.bsky.social are launching the Lux Science Helpline - a $100M commitment to support American scientists whose research is threatened by funding cuts, bureaucratic hurdles, and career roadblocks - that expands our Lux Labs program.
www.luxcapital.com/news/our-hel...
www.luxcapital.com/news/our-hel...
Given some recent publications regarding #RNA #Splicing prediction using #DeepLearning we decided to assess some of those claims with surprising findings that have to do more with the target function you chose… biociphers.wordpress.com/2025/04/09/t...
Tissue-specific splicing prediction – What’s in a name, what’s in a claim, and are target functions all the same?
In today’s blog post, I want to discuss some work/claims related to a topic that has been one of my lab’s focus areas – predicting tissue-specific alternative splicing (AS) of RNA. Some backg…
biociphers.wordpress.com
April 9, 2025 at 7:25 PM
Given some recent publications regarding #RNA #Splicing prediction using #DeepLearning we decided to assess some of those claims with surprising findings that have to do more with the target function you chose… biociphers.wordpress.com/2025/04/09/t...
Reposted
