Billy Palmer

Excited to finally see our paper on KIR3DL3 out now in @SciImmunology. An answer to the question, “where is this receptor hiding?” science.org/doi/10.1126/sc…

Don't like p-values? We're presenting a completely new interpretation in the context of clinical trials. With Andrew Gelman, Sander Greenland, @guido_imbens Simon Schwab and Steve Goodman. @Lester_Domes @goodmanmetrics @NEJMEvidence evidence.nejm.org/stoken/default…

50-color phenotyping of the human immune system with in-depth assessment of T cells and dendritic cells biorxiv.org/cgi/content/sh… #biorxiv_immuno

Thymic eviction explains CD8 T cell tolerance and why autoreactive CD8 T cells appear in the periphery but not the thymus @ScienceMagazine Badr Singer science.org/doi/epdf/10.11…

🔥🚨@TargetALS funded TDP-43 RNA aptamer preprint🚨🔥 Using deeply phenotyped #ALS post-mortem tissue cohorts we show nuclear TDP-43 pathology is an early event, co-incident with STMN-2 cryptic splicing, preceding cytoplasmic aggreg. & symptom onset 🧵1/4 biorxiv.org/content/10.110…

What gets erased when you integrate #singlecell data across samples/studies, and can you get it back? When samples are from e.g. healthy & disease, should you simply massage cells together? FINALLY, I feel we can answer this question: doi.org/10.1101/2023.0…

A mass screening of immune activating receptors on natural killer cells shows how different peptide variants can affect innate immunity. @mjwsim @NIAIDNews Check out the study: scim.ag/43l

I’m excited to share some work I co-lead with @i_rodcast and spanned the labs of @PardisSabeti, @ReillyLikesIt, and @r_tewhey to design and validate synthetic cis-regulatory elements with cell type-specific activity. biorxiv.org/content/10.110… 1/n

Absolutely delighted to share our paper detailing an HLA association with asymptomatic SARS-CoV-2 infection, out today in @Nature @UCSF with @GrasLab @dan_gard @jsabatino37 @martinmaiers @spellman_s @LawtonMurdolo @DimitraChatzil1 nature.com/articles/s4158…

Researchers @BillyHPalmer and @PN0rmski from @CUBiomedInfo report their investigation of a potential new immune checkpoint target (KIR3DL3/HHLA2) - work which could inform new approaches cancer treatment. news.cuanschutz.edu/news-stories/c…

Are you or do you know an evolutionary biologist working non-in-academia? See below, and please retweet! Link to survey: liverpool.onlinesurveys.ac.uk/non-academic-c….

Congratulations @popgen_oumie ! What viruses do lab flies commonly have, and what might this do to gene expression? biorxiv.org/content/10.110…

🎉Exciting Update of scGPT 🎉: After receiving significant attention from the community since our April release, we're thrilled to announce the first major update for scGPT - a foundation model for single-cell multi-omic data. This update integrates community feedback and leverages the latest data release from @cellxgene. It boasts larger pretraining data, and more robust models, and expands the range of application tasks. Pre-print (V2) available: biorxiv.org/content/10.110… Access our open-source code and models here: github.com/bowang-lab/scG… Detailed tutorials: scgpt.readthedocs.io/en/latest/ Highlights of this update include: 🔬 Introducing the first GPT-style foundation model for single-cell multi-omic data, pretrained on over 33M human cell atlas data. 💡 Our generalist approach enables one model to accomplish multiple tasks in single-cell analysis, including multi-omic integrative analysis and perturbation prediction. 🧬 Discovering gene-gene interactions specific to various conditions using learned attention weights and gene embeddings. 🚀 Uncovered a scaling law showcasing continuous model performance enhancement as data volume increases. 🐾 scGPT model zoo (see github) now offers multiple pre-trained foundation models for various solid organs and a comprehensive pan-cancer model. Begin exploring your data with the most fitting foundation model. We welcome your thoughts on specialist vs generalist approaches in single-cell studies. Many thanks for the following technical analyses of scGPT: 1. Excellent twittorial by @simocristea: x.com/simocristea/st… 2. Comprehensive review on LLM in cell biology by @s_batzoglou: towardsdatascience.com/large-language… 3. Insightful blog by @SalvatoreRaieli: levelup.gitconnected.com/scgpt-when-tra… Kudos to Haotian (@HAOTIANCUI1) & Chloe (@chloexwang1) for their exemplary work on this project. @VectorInst @pmcc_ai @UHNAIHUB @bradwouters @drbarryrubin @UofT_TCAIREM @UofT_LMP @UofTCompSci @uoftmedicine

Such a fun project to work on with contributions from so many. Special shout out to Norman lab members who worked on this @laleaton @anaacodo Liyen Loh @PN0rmski

HHLA2 has already garnered interest as a therapeutic target. Our results suggest that KIR3DL3 is an interesting candidate for immune checkpoint blockade due to its tissue-specificity, its association with a unique set of TCRs, and its role as an inhibitory receptor.

Excited to finally see our paper on KIR3DL3 out now in @SciImmunology. An answer to the question, “where is this receptor hiding?” science.org/doi/10.1126/sc…

🐓 Key gene that blocks the spillover of #AvianFlu to humans discovered. @RuteMPinto, @WilsonLabCVR & colleagues have identified that the BTN3A3 gene is vital to protecting humans against avian flu. 📄 Paper: nature.com/articles/s4158… 🗞️ News article: gla.ac.uk/news/headline_…