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🚨 Excited to share our latest paper in Cell identifying how under-replicated chromosomes in micronuclei become shattered by the Fanconi anemia pathway during mitosis. This work was led by UTSW Graduate School of Biomedical Sciences student Justin Engel. 🧵 (1/13): cell.com/cell/fulltext/…

As we look to optimize more of Minimap2 on the GPUs in mm2-gb, we are looking for feedbacks from our user community. Please feel free to reach out to us. github.com/Minimap2onGPU/… Joy Dong , Gina Sitaraman , AMD , University of Michigan Oxford Nanopore

We’re excited to announce new long-read #sequencing chemistry for #Revio that will increase the system’s output & enable customers to reduce their sequencing cost per genome by up to 50%. Discover more enhancements here: bit.ly/4for8D2 #PacBio #ASHG24

New de-novo TCR design preprint from dhuv.io just dropped: TCR-TRANSLATE: Conditional Generation of Real Antigen Specific T-cell Receptor Sequences biorxiv.org/content/10.110…

Some high level slides so you can imagine how Illumina constellation technology works presented by Nadia_Sedl . I still think it’s cool. They had me at “no library prep”😂

SPECIAL ISSUE! This month Genome Research publishes a diverse collection of research and review articles in a special issue highlighting advances in long-read sequencing applications in biology and medicine. tinyurl.com/Genome-Res-34-….

Here's our latest, led by Drs. Riaz Gillani & Ryan Collins - we studied a type of inherited genetic event (structural variants) + risk of developing certain cancers in kids: Dana-Farber News Dana-Farber Division of Population Sciences Boston Children's Broad Institute Science Magazine science.org/doi/10.1126/sc…

QUICHE reveals structural definitions of anti-tumor responses in triple negative breast cancer biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

We're thrilled to present ESM3 in Science Magazine. ESM3 is a generative language model that reasons over the three fundamental properties of proteins: sequence, structure, and function. Today we're making ESM3 available free to researchers worldwide via the public beta of an API

This UMAP plot was generated from data simulated without inherent clusters, meaning the observed clusters are artifacts. It highlights how default Seurat clustering and UMAP settings can sometimes produce misleading patterns in data visualization.

Scalable co-sequencing of RNA and DNA from individual nuclei nature.com/articles/s4159…

Extremely excited re: IMA203 - PRAME TCR T cells Ph 1 study published in Nature Medicine! This is a transformative Rx in #melanoma for HLA-A201+ & PD1 refractory pts. Compared to TIL, easier to make, less toxic & so far ~2x response rate in heavily pre-Rx. nature.com/articles/s4159…

New paper by Dr. Amy Pomeroy! A model of intratumor and interpatient heterogeneity explains clinical trials of curative combination therapy for lymphoma Out now in Blood Cancer Discovery Blood Cancer Discovery doi.org/10.1158/2643-3… #mathonc #lymsm #BloodCancer 1/n

🚨Today in Cell, we show that RNA splicing factor mutations in myeloid cancers generate splicing-derived public neoantigens targetable by #TCR tx. Amazing collaboration co-led by Abdel-Wahab Lab, Robert K. Bradley, and Klebanoff_Lab. #Tcellpower cell.com/cell/fulltext/…

Took a year but today marks a very special day for Jin Seok (Andy) Lee and I. ACE may be used as a *teenie* part of a clinical trial. Confronted with the slim possibility of actually making a fraction of a difference and suddenly the months of sleepless nights don’t seem all that bad 🥲

After next round of the bake-off, going to pivot to tumor antigens (once we get some mass spec validation of which ones are real). For now, read the blog post by Benjamin Vincent: pirlblog.substack.com/p/an-experimen…

Update to our software for predicting tumor antigens using genomics data (LENS v1.7), done by Steven Vensko II - Now with native package support for HLApollo, pepsickle, and RNA-only analysis (+ fixes and improvements) pirlblog.substack.com/p/announcing-l… alex rubinsteyn Jin Seok (Andy) Lee dhuv.io

Have you ever wondered how a somatic inversion is detected? In this Tenet-inspired blog post, I break down the telltale signs: head-to-head (5' to 5') and tail-to-tail (3' to 3') inversion breakpoints. pirlblog.substack.com/p/inversion

Alcohol use reduces the efficacy of anti-PD1 immunotherapy by disrupting anti-tumor immunity Paper starts from an interesting observation