Peter Winter

Excited to share our latest preprint, introducing the hierarchical cross-entropy (HCE) loss — a simple change that consistently improves performance in atlas-scale cell type annotation models. doi.org/10.1101/2025.0…

Current methods in the field are trained on atlases ranging from 1 to 100 million cells. In our newest preprint, we show that these same approaches tend to plateau in performance with pre-training datasets that are only a fraction of the size.

This work is a huge collaborative effort led by co-first authors @IvyNuoLiu, @kattan_walaa, Ben Mead, @cskummerlowe, co-supervised by @peterswinter, @SriRaghavanMD, @shaleklab, with contributions from our colleagues at CDoT @broadinstitute, @ragoninstitute & @MSFTResearch! (10/n)

This one has been a long time coming! Very excited to get this highly collaborative work out. More evidence that considering cell states in conjunction with driver oncogenes needs a close look!

Excited to share our lab’s latest preprint exploring how mutations and transcriptional cell states cooperate to drive therapeutic resistance in Ph+ B cell acute lymphoblastic leukemia (Ph+ ALL)! (1/14) biorxiv.org/content/10.110…

Happening now 9AM- 12:30PM! “Dissecting acquired resistance to KRASG12D inhibition in a mouse model of pancreatic ductal adenocarcinoma” #AACR2024 authored by our TeamLab members @Julien__Dilly, @shaleklab, S. Chugh,S. Dougan, B. Wolpin, @jonathan_nowak, @peterswinter, A. Aguirre

1/5🚨 New preprint alert! Excited to share NCLUSION: a Bayesian nonparametric framework using a sparse hierarchical Dirichlet process mixture model to jointly cluster and select marker genes! 📄biorxiv.org/content/10.110… 💻github.com/microsoft/Nclu… 🌐 microsoft.github.io/Nclusion.jl/ 🧵👇

Don’t miss the @CellCellPress research of #FacesOfCell Andrew Navia, “Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer” cell.com/cell/fulltext/…

1/ Our paper that looks at cells in human breast over the course of lactation was published in PNAS this week! A press release from MIT covers this, but read on for more details! Paper: pnas.org/doi/10.1073/pn… MIT News: news.mit.edu/2022/study-rev…

So excited that our longitudinal study of the cells in human breast milk is out this week!

I am thrilled to officially announce that The Jaeger Lab is open for business at Moffitt Cancer Center in Tampa, FL! @MoffittResearch @MoffittNews Excited for this next chapter, and ready for the opportunities and challenges ahead. Come join our team! alex.jaeger@moffitt.org

We want to send a warm welcome to Dr. Alex Jaeger. The newest faculty member of @MoffittNews Department of Molecular Oncology. moffitt.org/research-scien…

.@valarlabs is a new startup out of @Stanford on the application of #AI to #pathology (with an early focus on treatment decisions in #PancreaticCancer). Eric Collisson from @UCSFCancer has a great quote in this story: valarlabs.medium.com/valar-labs-rei…

@lorin_crawford Couldn’t have happened to a nicer Lakers fan. Congrats Lorin!

I guess I can comment on this now that it’s out in the public. Tenure… Wow. They say it takes a village and it’s so true. I’m just incredibly thankful for my community. No way this happens without them. Looking forward to this next season 🙏🏾

1/10 Our new paper is out today in @natBME! Read the details here!nature.com/articles/s4155…

Read this week's Cancer Discovery #ResearchWatch Tumor Microenvironment Influences Cancer Cell Transcriptional State. bit.ly/3FlWysb @shaleklab @peterswinter @MIT @broadinstitute @harvardmed

Congratulations to Carly Zeigler, a physician–scientist in training who gave a brilliant and inspiring lecture after receiving the inaugural 2021 Stuart L. Schreiber Award in Scientific Excellence for Graduate Students!

Outstanding story just published in Cell @CellCellPress from Aguirre lab @DanaFarber_Hale and Shalek lab @shaleklab about microenvironmental modulation of pancreatic cancer cell states at single cell level. A must read! doi.org/10.1016/j.cell…

Now online @CellCellPress Microenvironment drives cell state, plasticity, and drug response in #PancreaticCancer cell.com/cell/fulltext/… Fantastic paper from Srivatsan Raghavan @shaleklab @andrewaguirremd @DanaFarber_Hale