Yoseph Barash
@YosephBarash
@[email protected] Opinions - own. Lab @PennGenetics , @CIS_Penn , @UPennIBI
Our work on "Evaluating the representational power of pre-trained DNA language models for regulatory genomics" led by @AmberZqt with help from @NiraliSomia & @stevenyuyy is finally published in Genome Biology! Check it out! genomebiology.biomedcentral.com/articles/10.11…
Do current genomic language models (pre-trained on whole genomes) learn a foundational understanding of biology in the non-coding region of human genomes? A new evaluation led by @AmberZqt suggests not yet! 1/N paper: biorxiv.org/content/10.110…
I worry the pendulum has swung too far towards generalists over specialists, sacrificing wisdom for speed. Resulting in either boring consensus or unserious hype. There is such a thing as deep technical craft, but I’m not sure you can understand if you’ve never done it yourself
Join us for our next Kipoi Seminar with Yoseph Barash,University of Pennsylvania @PennGenetics @CIS_Penn @UPennIBI @YosephBarash 👉From identifying UTR regulatory elements to potential RNA therapeutic targets 📅Wed Jul 2,5:30pmCET 🧬kipoi.org/seminar 🦋@kipoizoo.bsky.social
📣We are happy to announce the release of MAJIQ V3 😊🎉 check out details here #RNA #Splicing #RNASeq biociphers.wordpress.com/2025/06/20/maj…
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/tis…
Excited to share our latest work! We asked if and how TDP-43 regulates RNA transport in neurons and if this is misregulated in ALS. We found that it works to keep RNAs *out* of neurites, and that loss of TDP-43 activity results in specific RNAs aberrantly accumulating there.
We are excited to report the discovery of TIGRs, a widely-occurring RNA-guided system found in bacteria and their viruses. TIGRs consist of a peculiar repeat region which is transcribed into RNA and processed into multiple guide RNAs to direct TIGR-associated proteins to their…
🚀 New Paper Alert! 🚀 𝐑𝟐𝐃𝐓: a comprehensive platform for visualising RNA secondary structure Check it out in @NAR_Open: academic.oup.com/nar/article/53… Here’s why you should give it a try 🧵👇
📣 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-d…
An #RNA #splicing project 3 yrs in the making finally sees the light of day. Microexons, meet macroglia… cancerous macroglia, meet engineered T cells (at your own peril). Jointly with @aanaqvi @hagentilgner @YosephBarash et al @CHOP_Research @PennMedicine biorxiv.org/content/10.110…
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
I'm hiring: 1. PhD-level Research associate to generate perturbation data 2. ML postdoc to build multimodal generative AI for DNA (eg diffusion and LLM) 3. Bioinformatician (any level) to harmonize functional genomics data for training foundation models DM me if interested!
Where RNA Science Meets AI, May 4–8, 2025, Ascona. Invited speakers: @OliverStegle @fabian_theis @fiddle @EvaMariaNovoa @BTreutlein @satijalab @RivasElenaRivas @RouskinLab @YosephBarash @gagneurlab, Rhiju Das, Karla Neugebauer, Jernej Ule Registration open,…
G4mer: RNA language model identifies G-quadruplexes and disease variants across transcriptome. AI analyses population-scale genetic data, advancing RNA structure and disease understanding.@FaricaZhuang @YosephBarash biorxiv.org/content/10.110…
💥💥💥New preprint 💥💥💥on the EuPRI resource. Where we reconstruct the motifs for 34,736 RBPs and study their function and evolution. Joint work with @ProfTimHughes (Toronto), Matt Weirauch, @LXandR_, Deb Ray, Kaitlin Laverty and many more. More details to come
Reconstructing the sequence specificities of RNA-binding proteins across eukaryotes biorxiv.org/cgi/content/sh… #biorxiv_genomic
Yet more ways alt #RNA #splicing drives #cancer chemoresistance. Take-home messages: a) some drugs targeting purine metabolism are more equal than others; b) you need to sequence mRNA (not DNA) to choose the right one! @adolfo_ferrando @YosephBarash et al aacrjournals.org/cancerres/arti…
Are you a wet lab biologist ready to shape the future of AI in genomics? CSHL is hiring a PhD-level Research Associate to join a collaborative team of genomic scientists and AI researchers. Help build the next generation of AI models for genomics! plz RT jobrxiv.org/job/cold-sprin…