Episode 17 - perhaps my favorite yet. How do you write a forum.image.sc post that will get you the answers you need without revealing information you don't want to tell? @erinweisbart.bsky.social and I go through what the experts need to know to help you. Post your sci q's today on forum.image.sc !

👏 @broadinstitute.org "in mice AND humans"

gReLU advances deep learning based modeling and analysis of DNA sequences with comprehensive toolsets and versatile applications. @avantikalal.bsky.social @gokcen.bsky.social www.nature.com/articles/s41...

तमसो मा ज्योतिर्गमय From darkness, lead me to the light. Focus on the good and let the year be an act of random kindness. Happy Diwali 🪔

podcasts.apple.com/us/podcast/l... @florisbarthel.bsky.social and team on liquid biopsy for brain tumors 💪

This 7-year journey has reached a first milestone! 🥳 Excited to share our preprint (3rd of 2025) on the 3D telomeric interactome, a project that started with a K99 in 2018. Thanks to Yi-An Chen, first postdoc in our lab and first author who worked tirelessly to realize this dream. bit.ly/3W3wuMk

Characterising cancer-stroma interactions through high-content phenotyping from microscopy time-lapses https://www.biorxiv.org/content/10.1101/2025.10.02.680037v1

Halfway to I2K is BACK, friends of all kinds! Last year, 650 people attended 30+ TOTALLY FREE image analysis workshops of all kinds, across many timezones. If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.

Studying cancer evolution needs multi-region or single cell seq for phylogenetics, right? Amazingly (I think!) we found single-sample bulk methylation suffices, via analysis of "fluctuating methylation". In @nature.com today led by brilliant @calumgabbutt.bsky.social www.nature.com/articles/s41...

@jeffgenome.bsky.social from ❤️ @jacksonlab.bsky.social at YaleMed grand rounds

Episode 11 - In which @erinweisbart.bsky.social and I talk about just how much we love ilastik (@ilastik-team.bsky.social) and how it's great for so many problems! Also, that you should use a small brush.

New research, published today in @natureportfolio.nature.com, decodes the most elusive, difficult-to-sequence regions of the genome from populations around the world, rewriting knowledge of human biology and setting a new benchmark for precision medicine. 🧪🧬🔬

👏 "...lineage tracing and conditional p53 mouse models to dissect how genetic alterations, cell state transitions, and microenvironmental remodeling converge to drive early PDAC progression."

❤️

New post: On the failure of rescoring in virtual screening. Or why automated virtual screening and docking remains hard and why expertise remains essential. medchemash.substack.com/p/on-the-fai...

Excited to share our latest manuscript www.biorxiv.org/content/10.1... This was a great collaboration with Drs. Huse, Lang, @jesserdixon.bsky.social

@s-j-aitken.bsky.social on how genetic background shapes cancer evolution. 💎

The story of Python 😍 www.youtube.com/watch?v=pqBq...

landscape of CRISPR-Cas9 genome-wide double-standed breaks and underlying determinants of cut & repair process. www.nature.com/articles/s41...

Estimating de novo mutation rate over four generations from total 28 individuals. 👏

Is cancer suppression in and of itself an adaptation? The full version of our The Elephant & the Spandrel is now online. academic.oup.com/emph/article...

A dream come true: the first expansion microscopy images of C. flexa 🤩 Generated by Mylan & Uzuki who learned from the best (@hiralshah.bsky.social @gautamdey.bsky.social @dudinlab.bsky.social). We will learn so much from these!

a tale of phage-bacteria co-evolution 💎 by Bonnie Bassler

Targeting PDGFRA in pediatric high-grade glioma 👏 www.cell.com/cancer-cell/...

From PCAWG resource to validation 👏: Cancer cells undo amplification of BRD4 region by introducing (and selecting for cells with) recurrent breakpoints in BRD4 locus to maintain goldilocks non-toxic state of BRD4 expression.

🧩DNA Lesions Piece Together Impossible Trees🧩 This was a fun piece to write (and illustrate!) with Dr Claudia Arnedo Pac about @mikespencerchapman.bsky.social and co’s recent @nature.com paper. Thank you for the invitation, Maria @cp-trendsgenetics.bsky.social authors.elsevier.com/sd/article/S...

Primer on blood brain barrier and CSF flow through ventricles: www.quantamagazine.org/how-the-brai...

APOBEC drives genetic variation in lung tumors, especially in response to tyrosine kinase inhibitor therapy 🧪. Inhibition of APOBEC during use of tyrosine kinase inhibitors could improve outcomes. In a paper just out in Lung Cancer, we show how much. www.sciencedirect.com/science/arti...

1/46 Hey folks, we have a new paper out on the MuLTEE. Strap in and I’ll tell you the story of how this “little paper on polyploidy” turned into the most data rich paper our lab has produced, largely thanks to the leadership and work ethic of @kaitong25.bsky.social. www.nature.com/articles/s41...

1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬 But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯 Our new study reveals how retrotransposons invade the germline directly from somatic cells. www.biorxiv.org/content/10.1... A short thread 🧵👇

Thrilled to share our work with Mariella Filbin, Johannes Gojo and Carl Koschmann, now published in @cp-cancercell.bsky.social We present a translational approach identifying the PDGFRA inhibitor avapritinib as a novel targeted treatment for pHGG with PDGFRA alterations www.cell.com/cancer-cell/...

Delighted to share a major update on our work investigating age-related deceleration in clonal haematopoiesis. Takehome: Widespread and substantial deceleration in fitness with age! Amazing effort by PhD student Hamish MacGregor 💪 www.biorxiv.org/content/10.1...

👏 @kcakdemir.bsky.social doi.org/10.1101/2025...

New preprint from the lab - Selective depletion of cancer cells with extrachromosomal DNA via lentiviral infection www.biorxiv.org/content/10.1...

📣 Open computational PhD & Postdoc positions! Excited about the open positions as part of our newly funded Emmy Noether Group are online now under kocakavuklab.vercel.app/joinus 📢 Please RT (what's the bsky equivalent here?) and distribute ! 👇A quick instruction on how to apply

This is part of my effort of rewriting all materials for my UT Austin dataviz class in Quarto. It's going very well. Most importantly, I now have live exercises integrated into the site, thanks to Quarto live. Check it out here: wilkelab.org/SDS366/

It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.

@carlzimmer.com on telling the stories of science

Inferring cell divisons by tracing indels in poly-G repeats. 👏 🧵 x.com/naxerova/sta... <> github.com/mblohmer/cel...

💎 ☑️ Check if mtDNA mutations are similar in cancer vs T-cells. ☑️ Monitor mtDNA exchange b/w cancer and T-cells with GFP tags. ☑️ Test T-cell function pre and post transfer of cancer mtDNA. Preface: www.nature.com/articles/d41... Article: www.nature.com/articles/s41...

Targeting tumor micro environment: "Multiplex universal combinatorial immunotherapy via gene silencing (MUCIG), which uses CRISPR–Cas13d to silence multiple endogenous immunosuppressive genes in the TME, promoting TME remodeling and enhancing antitumor immunity." news.yale.edu/2025/01/16/m...

💎 a base editor therapy that results in 50% reduction of PrP in the mouse brain and 52% extension of lifespan in transgenic human PRNP mice inoculated with pathogenic human prion isolates representing the most common sporadic and genetic subtypes of prion disease. @broadinstitute.org

Taking pictures of cells with a microscope, then extracting thousands of features from them is uncannily effective for quantifying cell state, esp. for genes and chemicals (e.g., Cell Painting). But we often average the rich single-cell data to simplify analysis. Can we do better? #bioML 🧪 1/n

Schrödinger's cat on 🚀 today - With 105 physical qubits, that's 2^105 computable binary states in parallel 🙀 Related on power of #qubit, www.smbc-comics.com/comic/the-ta...

www.nature.com/articles/s41... #hcs #cellpainting #review

Now on biorxiv! The JUMP-Cell Painting Consortium’s paper: “Morphological map of under- and over-expression of genes in human cells” This is the genetic perturbation portion of the JUMP’s dataset; our chemical perturbation paper will come in a few months www.biorxiv.org/content/10.1...

Look he is going to be on campus @jaxeducation.bsky.social 👍

💎 hypothesis and approach