@yosephbarash.bsky.social
📤 275
📥 36
📝 43
Opinions - own. Lab RNA+AI+Genetics
@upenn.edu
www.biociphers.org
Embracing Uncertainty in Life, Science It has been a long time since I wrote a non strictly scientific blog post. The holiday time, often a time of reflection and new resolutions, seems good for getting back to that. But don’t worry, there will be connections to science work as well… 😉 Today’s…
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Embracing Uncertainty in Life, Science
It has been a long time since I wrote a non strictly scientific blog post. The holiday time, often a time of reflection and new resolutions, seems good for getting back to that. But don’t worry, there will be connections to science work as well… 😉 Today’s blog is about uncertainty - in our science, in our lives, in the world.
https://biociphers.wordpress.com/2025/12/28/embracing-uncertainty-in-life-science/
2 days ago
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reposted by
Matthew Taliaferro
23 days ago
Announcing the 2026 edition of the EMBO workshop on RNA localization and local translation! This meeting will be held June 30 - July 4 near Porto, Portugal. Come for exciting updates in the field from both established investigators and trainees. See the link below for details!
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reposted by
Dr. Suzanne R Lee
23 days ago
@rnasociety.bsky.social
now offers an "undergraduate" category for membership!
rnasociety.memberclicks.net/membership
#RNA@PUI
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Membership
Membership
https://rnasociety.memberclicks.net/membership
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reposted by
Ted Morgan
22 days ago
The new Enabling Discovery through GEnomics (EDGE) Program page is posted. Please contact us at
[email protected]
if you have questions.
www.nsf.gov/funding/oppo...
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Enabling Discovery Through Genomics (EDGE)
https://www.nsf.gov/funding/opportunities/edge-enabling-discovery-through-genomics
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reposted by
Jeremy Berg
29 days ago
New York Times article on science funding with some depressing but familiar curves with interactive graphics.
www.nytimes.com/interactive/...
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The U.S. Is Funding Fewer Grants in Every Area of Science and Medicine (Gift Article)
A quiet policy change means the government is making fewer bets on long-term science.
https://www.nytimes.com/interactive/2025/12/02/upshot/trump-science-funding-cuts.html?unlocked_article_code=1.5k8.-Yuf._rLIqKb0F-aK&smid=url-share
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📣📣📣 (one for each new paper from the lab😀): Within ~1 week we had 3 papers published (two in the same day!), each took years... This calls for a quick tweetorial to explain why these may be interesting for you if you are into
#RNA
processing (
#Splicing
#APA
#UTR
#rG4
) with
#AI
#StatisticalGenetics
.
about 1 month ago
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1
reposted by
Joshua G. Schraiber
about 2 months ago
Really cool paper that changed the way I think about what GWAS and Burden tests are doing, and also basically made me pleiotropy-pilled
add a skeleton here at some point
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reposted by
Richard Sever
about 2 months ago
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...
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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...
https://openrxiv.org/enabling-review-options/
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reposted by
Ensembl
about 2 months ago
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
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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.
https://www.nature.com/articles/s41592-025-02850-9
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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...
about 2 months ago
1
4
3
reposted by
Danny IncaRNAto
3 months ago
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...
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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.
https://www.nature.com/articles/s41588-025-02347-3
0
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reposted by
Oded Rechavi
3 months ago
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 👇)
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📣 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...
3 months ago
0
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3
reposted by
Nicky Whiffin
3 months ago
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 🧬
0
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reposted by
Kurianlab
4 months ago
www.sciencedirect.com/science/arti...
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Rethinking RNA-binding proteins: Riboregulation challenges prevailing views
RNA-binding proteins (RBPs) are best known as effectors along the entire gene expression pathway and as constituents of RNA-protein machines such as t…
https://www.sciencedirect.com/science/article/pii/S0092867425006877
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reposted by
Christel Depienne
4 months ago
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...
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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...
https://www.medrxiv.org/content/10.1101/2025.09.02.25334923v1
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reposted by
Kurianlab
4 months ago
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...
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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, ...
https://www.biorxiv.org/content/10.1101/2025.09.04.674271v1
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📣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...
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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...
https://rnahorizons.com/abstract-submission/
4 months ago
0
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0
reposted by
Vikram Agarwal
5 months ago
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
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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.
https://url.de.m.mimecastprotect.com/s/4OWmC36zDVFg1G2rvTgfliQx9_J?domain=rdcu.be
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reposted by
Yoav Gilad
7 months ago
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...
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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...
https://www.biorxiv.org/content/10.1101/2025.04.30.651602v1
1
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reposted by
Markus Landthaler
5 months ago
www.cell.com/cell/fulltex...
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SPIDR enables multiplexed mapping of RNA-protein interactions and uncovers a mechanism for selective translational suppression upon cell stress
SPIDR, a massively multiplexed method that simultaneously maps dozens of RNA-binding proteins to their RNA targets at single-nucleotide resolution, uncovers new RNA-protein interactions and provides c...
https://www.cell.com/cell/fulltext/S0092-8674(25)00743-3
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reposted by
John Murray
6 months ago
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/...
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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 ...
https://www.science.org/doi/10.1126/science.adu8249
5
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reposted by
Arjun Raj
6 months ago
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...
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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...
https://www.biorxiv.org/content/10.1101/2025.07.14.664617v1
2
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reposted by
6 months ago
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 🧵
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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...
https://doi.org/10.1101/2025.07.05.662870
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📣We are happy to announce the release of MAJIQ V3 😊🎉 check out details here
#RNA
#Splicing
#RNASeq
biociphers.wordpress.com/2025/06/20/m...
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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…
https://biociphers.wordpress.com/2025/06/20/majiq-v3-release/
6 months ago
0
2
1
reposted by
Ted Pavlic (he/him/his)
7 months ago
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...
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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.
https://www.richmondscientific.com/how-a-discovery-in-yellowstone-national-park-led-to-the-renowned-technique-of-dna-amplification-pcr
22
1229
547
reposted by
D2R | DNA to RNA
7 months ago
🔊 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
0
3
2
reposted by
Kurianlab
8 months ago
www.biorxiv.org/content/10.1...
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Integrative analysis of RNA binding proteins identifies DDX55 as a novel regulator of 3′UTR isoform diversity
The 3′ untranslated regions (3′UTRs) of mRNAs play a critical role in controlling gene expression and function because they contain binding sites for microRNAs and RNA binding proteins (RBPs) that alt...
https://www.biorxiv.org/content/10.1101/2025.05.06.652471v1
0
9
7
reposted by
Sri Kosuri
8 months ago
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...
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Our Helpline for American Scientists
https://www.luxcapital.com/news/our-helpline-for-american-scientists
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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...
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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…
https://biociphers.wordpress.com/2025/04/09/tissue-specific-splicing-prediction-whats-in-a-name-whats-in-a-claim-and-are-target-functions-all-the-same/
9 months ago
0
2
0
reposted by
Satan’s Niece
9 months ago
This is high art
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26479
8608
reposted by
Maxim Raginsky
9 months ago
To say that I am shocked at this tragic news is an understatement. I got to know Sayan well during my time at Duke; he was deeply knowledgeable about all sorts of things and had a great sense of humor. He was the one and only Bayesian anarchist.
www.mis.mpg.de/news/loss-sa...
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We Mourn the Loss of Sayan Mukherjee
We are shocked and saddened by the news that our colleague and Max Planck Fellow Sayan Mukherjee passed away. He was a dear colleague in Leipzig who formed a vital connection between mathematics, comp...
https://www.mis.mpg.de/news/loss-sayan-mukherjee
2
37
5
reposted by
Einstein Foundation Berlin
10 months ago
🏆 Research integrity consultant and image forensics expert
@elisabethbik.bsky.social
has uncovered fraudulent data in over 7,600 scientific papers and exposed the practices of ‘paper mills’ that produce counterfeit scientific articles. She is honoured with the €200K Individual Award. Congrats!
16
499
129
reposted by
Manny Ares 👀
10 months ago
Hey all! The RNA Society meeting in San Diego features a new session for sharing results on new ways to bring RNA into the curriculum. Get your abstracts in ASAP!
1
7
5
reposted by
Eric Van Nostrand Lab @ BCM
10 months ago
Happy to say our paper with the Whipple lab on snoRNA target profiling with chimeric eCLIP is now out! Great work by co-first authors Joey & Min with the help of a bunch of other folks!
genomebiology.biomedcentral.com/articles/10....
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Mapping snoRNA-target RNA interactions in an RNA-binding protein-dependent manner with chimeric eCLIP - Genome Biology
Background Small nucleolar RNAs (snoRNAs) are non-coding RNAs that function in ribosome and spliceosome biogenesis, primarily by guiding modifying enzymes to specific sites on ribosomal RNA (rRNA) and...
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-025-03508-7
2
22
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reposted by
Putrino Lab
10 months ago
A tumultuous 24-ish hours since our preprint was released yesterday. I mentioned that this was a fraught issue and I genuinely do understand that people have mixed feelings about the work. I wanted to take some time to respond to some of the concerns and comments that have 1/
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reposted by
Nikolai Slavov
11 months ago
The success of LLMs has inspired their extension to genomics data. A preprints reports that such models lack understanding of genomics and provide minimal utility, even for basic tasks such as sequence classification.
www.biorxiv.org/content/10.1...
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Genomic Foundationless Models: Pretraining Does Not Promise Performance
The success of Large Language Models has inspired the development of Genomic Foundation Models (GFMs) through similar pretraining techniques. However, the relationship between pretraining performance ...
https://www.biorxiv.org/content/10.1101/2024.12.18.628606v1
4
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21
reposted by
Nadav Ahituv
12 months ago
Massively parallel reporter assays (MPRAs) testing >680,000 sequences combined with machine learning to improve regulatory element & variant effect prediction. Amazing work by
@vagar.bsky.social
, Fumitaka Inoue,
@jshendure.bsky.social
and many others as part of ENCODE.
www.nature.com/articles/s41...
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Massively parallel characterization of transcriptional regulatory elements - Nature
Lentivirus-based reporter assays for 680,000 regulatory sequences from three cell lines coupled to machine-learning models lead to insights into the grammar of cis-regulatory elements.
https://www.nature.com/articles/s41586-024-08430-9
1
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42
reposted by
Abdul Muntakim Rafi
11 months ago
0/ Essential reading for anyone training or using sequence-function models trained on genomic sequences! 🚨 In our new preprint, we explore the ways homology within genomes can cause leakage when training sequence-based models and ways to prevent it
1
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reposted by
Gunnar Rätsch
11 months ago
I'm excited about a meeting on RNA + AI together with
@quaidmorris.bsky.social
and
@hagentilgner.bsky.social
in Ascona, Ticino on May 4-8. We have a great line-up of speakers and room for you to present your work. Please join us if you are into RNA & AI. Registration open www.rna-ai.org.
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11
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📣 Our 2nd Blog post on improving
#sQTL
modeling and why it matters
#RNASplicing
#Genetics
#Statistics
#QTL
biociphers.wordpress.com/2025/01/28/a...
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A Deep Dive into sQTL Modeling – Part 2
In my previous post, I described how, in our recent sQTL preprint, we broke current sQTL pipelines into their basic elements. This led to identifying potential issues/areas we may be able to improv…
https://biociphers.wordpress.com/2025/01/28/a-deep-dive-into-sqtl-modeling-part-2/
11 months ago
1
5
1
📣 New post re our recent findings/methods dev for
#sQTL
#RNA
#Splicing
#RNA-Seq
. We think this will be highly useful/impactful for (s)QTL detection/quantification. Hope to get (constructive 😉) feedback and much usage from the community! 😀
biociphers.wordpress.com/2025/01/20/a...
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A Deep Dive into sQTL Modeling – Part 1
The next few blog posts will be dedicated to a high level overview of our preprint on splicing QTL (sQTL) modeling: “A Deep Dive into Statistical Modeling of RNA Splicing QTLs Reveals New Variants …
https://biociphers.wordpress.com/2025/01/20/a-deep-dive-into-sqtl-modeling-part-1/
11 months ago
0
4
1
reposted by
Hani Goodarzi
12 months ago
The first preprint of 2025! Together with Matvei,
@halfacrocodile.bsky.social
, & our amazing team, we are excited to share PARADE: an AI framework for designing mRNA UTRs with enhanced cell-type specificity & stability.
www.biorxiv.org/content/10.1...
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A generative framework for enhanced cell-type specificity in rationally designed mRNAs
mRNA delivery offers new opportunities for disease treatment by directing cells to produce therapeutic proteins. However, designing highly stable mRNAs with programmable cell type-specificity remains ...
https://www.biorxiv.org/content/10.1101/2024.12.31.630783v1
1
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43
reposted by
Shweta Ramdas
12 months ago
Our mentor Casey Brown, apart from being an extraordinary scientist, was a brilliant teacher who loved everything genetics. In his honor, some of the world's leading experts came together to create the 'Casey Brown Lecture Series' on human genetics 1/
shorturl.at/eCm7S
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Casey Brown Lecture Series - YouTube
https://shorturl.at/eCm7S
1
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35
reposted by
Astronomer Royal for Scotland | Catherine Heymans
12 months ago
Happy New Year everyone. I having pleasing maths to share (courtesy of my 18yo who saw it on insta). 2025 is the only square this century! 🤓
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reposted by
Elena Rivas
about 1 year ago
Inaugural post "All-at-one RNA folding with 3D motif prediction framed by evolutionary information"
www.biorxiv.org/content/10.1...
Introducing CaCoFold-R3D by
@aakaran31.bsky.social
and myself
@rivaselenarivas.bsky.social
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All-at-once RNA folding with 3D motif prediction framed by evolutionary information
Structural RNAs exhibit a vast array of recurrent short 3D elements involving non-Watson-Crick interactions that help arrange canonical double helices into tertiary structures. We present CaCoFold-R3D...
https://www.biorxiv.org/content/10.1101/2024.12.17.628809v1
1
25
9
reposted by
Cell Chemical Biology
about 1 year ago
Check out the latest Reviews and Perspectives from experts in RNA biology in this joint collection from @CellChemBiol and @MolecularCell
http://dlvr.it/TGwFkr
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Molecular mechanisms in RNA biology: Cell Press
http://dlvr.it/TGwFkr
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21
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reposted by
Atul Butte
about 1 year ago
Great! @UCSD Biomedical Informatics is recruiting new tenure-track faculty! Assistant Professor
https://buff.ly/49LX6rf
; Associate or Full Professor
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Associate or Full Professor (Ladder/In-Residence) Biomedical Informatics Research
University of California, San Diego is hiring. Apply now!
https://buff.ly/4iKBAap
0
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reposted by
Molly Przeworski
about 1 year ago
Most of the talks from our Oct meeting are now online, with a few more to come:
www.precisionmedicine.columbia.edu/videos
add a skeleton here at some point
0
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40
reposted by
Gunnar Rätsch
about 1 year ago
Where RNA Science Meets AI, May 4–8, 2025, Ascona. Invited speakers:
@evamarianovoa.bsky.social
@fabiantheis.bsky.social
@rivaselenarivas.bsky.social
, Sterling Churchman, Barbara Treutlein, Rahul Satijia, Registration open
www.rna-ai.org
@hagentilgner.bsky.social
@quaidmorris.bsky.social
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RNA-AI 2025
https://www.rna-ai.org
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