Mason

We are hiring! Please consider joining our team, focused on uncovering molecular mechanisms of cardiac arrhythmia, with a focus on atrial fibrillation. Internal Job Posting: utsw.taleo.net/careersection/…

TimeVault provides a general strategy for storing and recovering past transcriptomes in living mammalian cells, directly linking earlier gene expression states to later outcomes @ScienceMagazine @insitubiology @BroadInstitute science.org/doi/10.1126/sc…

The Lu lab at UIowa combines high-resolution live imaging with a multidisciplinary approach to study cell-cell fusion in muscle. AND we are looking for motivated and energetic graduate students and postdocs to join our team. Contact me yue-lu@uiowa.edu #CellBiology #Myogenesis

@GuonHuang @NicolasAvilaJA @XiaoxinChen2024 @PNASNews Great work! Congratulations!

Our new paper led by @XiaoxinChen2024 is out @PNASNews! bit.ly/4785aCD We built a tissue atlas of ~2K transcription regulators ➔ identified Tox3 as a long-sought Atoh1 amplifer in cerebellar development, tumorigenesis & evolution. 1/10 📢 We're recruiting postdocs!

I felt like Twitter's algorithm was still terrible when I made this post! Let's hope that it picks up some views now 🤞

Can't wait to release a 10-year-old birthday version for SeqKit! - 10 years - 2 papers, 3500 citations - 20 contributors - 40 subcommands - 880 commits - 500 issues - 685.5K Bioconda total downloads Thank you all, dear contributors and users! github.com/shenwei356/seq…

Excited to share new finetuning scripts for AlphaGenome in JAX! This was in collaboration with @anshulkundaje group. As part of the initial release, we provide lightweight wrapper to finetune AlphaGenome on functional genomics (i.e. bigwig) tracks.

1/ RNA‑seq batch effects are one of the easiest ways to fool yourself in genomics. They can create beautiful, completely wrong biology if you’re not careful.

Dr. James Martin and colleagues discovered that an active form of YAP, named YAP6SA, which is not inhibited by the Hippo signaling pathway and does not interact with TEADs, induces #cardiomyocyte cell cycle reentry. | @bcmhouston 📚 Read the article: bit.ly/4q9DS5p

Both chambers of Congress have now passed the FY26 minibus with NIH provisions. The President will sign. (1) $48.7 billion for NIH (2) Full IDC recovery (3) No more multi-year funding (4) No NIH reorganization, maintaining the current IC structure.

Zhang & colleagues demonstrated base editing correction of a #MYBPC3 splice-site mutation in humanized mice ameliorates #HCM. Learn more at ahajrnls.org/4bN1Ekj

@AmandaTong2013 @UTSWMedCenter @utswheart Congratulations!! Great presentation!

So proud of Sarah who successfully defended her thesis today! Congrats, Dr. Ware!!! First Ph.D. coming from the Tong lab @UTSWMedCenter @utswheart

“Show me the mechanism of action.” “Uh. from the p-p-perturb seq? right here. Knocks down Gene X, and the cells shift into Cluster 7." “You used fkn UMAP again. FUCK. Zoom in.” “Sorry?” “Zoom. The fuck. In.” “…Okay.” “Do you see it?” “…See what?” “He doesn’t see it. The cell biology postdoc from Stanford does not know how to see a cell. He stares at a two-million-cell embedding and doesn’t see the conflations he just planted in my S3 bucket. WHERE is the temporal resolution?” “The… what?” “Where is the time? You hit the cell with a perturbation and you measured it once. Once. That’s not a mechanism. That’s a fucking POSTCARD!” “We sequenced at 72 hours. That’s standard.” “Standard is not the same as correct. You are aliasing causality. You compressed a dynamic process into a static endpoint and you’re think you will cure metastatic cancer.” “But the differential expression is significant.” “WOW! DIFFEWENTIAL EXPRESSION IS SIGNIFICANT! WOW! WHEN THE FUCK IS IT NOT. Yes, because statistics is Mario Kart. A fantasy land where causality is optional and variance disappears if you collect enough cells. Real biology has inertia. Feedback. Competing pathways. Do you understand the difference between correlation and mechanism? Or did you flunk out of STAT 101?” “…I mean, we saw Gene X regulate Pathway Y.” “No. You saw Pathway Y exist in the same cell after you kicked it down the stairs and waited three days. That’s not even a crime scene, you dimwit. That is a post-mortem autopsy.” “The model inferred a trajectory--” “STOP the buffoonery. Do not blame the model. The model is a mirror. In this particular case, you can see it mirrors the clusterfuck you just created in my biosafety cabinet. If the reflection is warped, it’s because your measurement is warped.” “Pull up the raw counts.” “…Okay.” “Scroll. Cell 14,982. Read it to me. What does it say?” “Uh… mitochondrial genes up, ribosomal genes down-” “And?” “…And stress response markers?” “Yes. Because you poisoned the cell and waited long enough for it to panic. Where is the early signaling? Where is the metabolic inflection? Where is the first irreversible decision?” “We don’t capture that.” “Exactly. You built a platform that cannot see the mechanism. YOUR PLATFORM IS FUCKING BLIND.” “The virtual cell...showed the perturbation effect cleanly.” “Yes. because your VIRTUAL CELL IS VIRTUAL. it assumes the cell is a bag of transcripts. Do you think metabolites show up? OR AN ISOFORM? AN ISOFORM, THAT WILL DEGRADE IN THE CELL BEFORE YOU EVER REACH YOUR SENSOR? THAT ONE? YOU THINK THAT'S HOW CELLS WORK?” “So what do you want me to do?” “Delete the atlas.” “What?” “Delete it. The whole thing.” “But that’s the core result.” “It’s three weeks of garbage narrative built on a blind instrument. Delete it.” “…Now what?” “Now you rebuild the measurement. You observe the cell while the perturbation propagates. You track chemistry, not just transcripts. You capture the first divergence, not the final corpse.” “That’s… not perturb-seq anymore.” “Exactly.” door slams

A research team led by Amanda Tong, M.D., Ph.D., mapped the heart’s lymphatic vessels in unprecedented detail, revealing new cellular subtypes and showing common markers are not fully specific. Read more: bit.ly/45ipS1t

Findings may move science closer to growing organs in other species: Newsroom - UT Southwestern, Dallas, Texas utsouthwestern.edu/newsroom/artic…

A perfect model for coming together this season: mouse skeletal muscles undergoing fusion, obviously. In this mesmerizing confocal microscopy video, nuclei are labeled in green & cell bodies are labeled in red. Credit: Yue Lu, Elizabeth Chen Lab, @UTSWMedCenter

First Sweat Lab conference, AHA Scientific Sessions! It’s been a great opportunity to catch up with dear friends, meet new collaborators, and learn about some amazing science!

#ICYMI: CHD4 and TBX5 control aCM gene expression @MasonSweatPhD, @williampu66 @yiwang_tim

Our latest paper is in print today @CircAHA (second one in under a year). Huge thanks to Jinxi @jinxi_wang22 for leading this exciting and unexpected discovery of Junctophilin-2 in fibroblasts. @CircAHA @AHAScience @IntMedIowa @IowaMed