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This is the best summary of my conversations with Sid while at Santa Fe Institute. I highly recommend his episode of the Complexity podcast (h/o Michael Garfield 🔮) to hear about his approach to choosing interesting problems. Link: open.spotify.com/episode/1Tq0Sh….

It's time for the 2022 application cycle! We are reopening our HMS_SysBio SSQBio application assistance program for the third year at the following link. Can't wait to meet the new applicants! forms.gle/DyshN9KfbAznQV…

We’re thrilled to share MrVI, a deep generative model for analyzing sample-level heterogeneity in single-cell RNA-seq datasets! This work with Pierre Boyeau and Adam Gayoso Yosef Lab was born out of a simple yet challenging question: what can we do with large-sample data? 1/

A very elegant approach to simulating cell state transitions based on inferring gene regulatory networks locally and then walking through the cell state manifold by propagating in silico TF perturbations. Excellent work by Kenji Kamimoto and Samantha Morris!

Neutrophils — the most common cell type in the immune system — play a key role in immunotherapy success hvrd.me/vv3X50Nw2xn

Shout out to Nico Gort-Freitas, Jeremy Gungabeesoon, Kiss Máté on our paper doi.org/10.1016/j.cell… on heterogeneity in tumor neutrophils and why it matters. A great summary by The Pittet Lab below:

Thrilled to share our latest work elucidating the critical role of neutrophils in successful cancer immunotherapy, featured in Cell. authors.elsevier.com/c/1gqieL7PXmbtw

Ahmad Jamal was someone who always left me completely starstruck. I’ve stood in a room with him numerous times and never had the guts to say hello. His vibe was just too regal. Thank you, Mr. Jamal for all the music you gave us. 🙏🏾❤️ RIP.

Congrats MariusMessemaker!

scRNA-seq is great for non-model organisms—with just a transcriptome you can discover new cell types. But for many marine organisms there's one big problem: SALT 🧂 A solution from our awesome student Tal Scully (1/7🧵) biorxiv.org/content/10.110…

This is the best video to introduce a computational biology course. There will never be a better one x.com/fan_of_gpu/sta…

🎉 Excited to share a big part of my PhD work in Allon Klein Lab that took many, many years and my blood, sweat, and tears! 😅 We ask - What’s the role of cell division in the formation of initial cell types during early development ?🧐 biorxiv.org/content/10.110… 🧵 (1/14)

Another outstanding study by Mikaël's group! @RubenBill5 et al. disentangled key axes of variation in the TME and their influence on cancer prognosis, showing that CXCL9:SPP1 polarization in macrophages is more predictive of patient survival than M1:M2 🤯.

"These methods can order a set of individual cells along a path, and assign a pseudotime value to each cell that represents where the cell is along that path. This can be a starting point for further analysis to determine gene expression programs driving cell phenotypes."

Our 🪐SATURN method is now out in Nature Methods! SATURN paves the way for universal cell embeddings, enabling integration of datasets across different species 🐒🐁🧍🐟🐸 Using protein language models, we encode biological meaning of genes in scRNA-seq datasets.

The most important unexpected lesson of my PhD.

This account endorses NICH as a valid pronunciation of niche.

Welcome!