iiinova — where your digital self keeps evolving

Reposted by Armita Nourmohammad

Harmit Singh Malik @harmitmalik.bsky.social · 06/08/2026

Come be our colleague. I have been in this Division for 27 years (4 as a postdoc and 23 as a PI). It is an amazing place to work, collaborate, and be inspired. If you are applying to be an Assistant or Associate Professor this Fall, don't miss this deadline.

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Reposted by Armita Nourmohammad

John Tsang @tsanglab.bsky.social · 09/06/2026

6th iteration of the Physics & Computation in Immunology meeting will be at Yale CSEI @yalecsei.bsky.social Sep 28–30. With Arup Chakraborty, Michael Lässig, @thearmita.bsky.social & Alex Walczak. Speakers from Princeton, Cambridge, Harvard, MSK, UCSF & more. Free. 120 spots. Deadline Sep 6.

sites.google.com

PCI VI

6th Workshop and Symposium Physics and Computation in Immunology 28 – 30 September, 2026 | Yale University

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Reposted by Armita Nourmohammad

William DeWitt @wsdewitt.github.io · 05/06/2026

This started in 2019 as daydreamy PhD student musings with Tatsuya Araki. We're as excited as ever about germinal centers as a platform for experimental evolution. Many thanks to PIs @victora.bsky.social @matsen.bsky.social, co-1st authors Ashni Vora and Tatsuya, and many other key collaborators!

cell.com

Replaying germinal center evolution on a quantified affinity landscape

Antibody affinity maturation results from a somatic evolutionary process that takes place in the germinal center. A “parallel replay” experiment on germinal center B cells reveals the evolutionary for...

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Armita Nourmohammad @thearmita.bsky.social · 26/04/2026

check out our new work on the design principles underlying cytotoxic T-cell responses. how do trade-offs and cell economics shape immune decision making? led by Obinna Ukogu and in collaboration with Grégoire Altan-Bonnet. www.pnas.org/doi/10.1073/...

pnas.org

Design principles of the cytotoxic CD8+ T cell response | PNAS

Cytotoxic T lymphocytes eliminate infected or malignant cells, safeguarding surrounding tissues. Although experimental and systems-immunology studi...

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Armita Nourmohammad @thearmita.bsky.social · 27/10/2025

excited to announce that this January we are relocating to Yale to start a theory initiative at the Center for Systems and Engineering Immunology (CSEI): @yalecsei.bsky.social looking to hire 2 postdocs to join us in this endeavor. more details can be found here: sites.google.com/uw.edu/statp...

sites.google.com

SPE - join us

Postdoctoral position: In January 2026, we are relocating to Yale university to start a theory initiative at the Center for Systems and Engineering Immunology (CSEI). We are looking for talented postd...

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Reposted by Armita Nourmohammad

Frederick "Erick" Matsen @matsen.bsky.social · 19/10/2025

The Mahan postdoctoral fellowship offers 21 months of support to develop your own research with Fred Hutch computational biology faculty-- lots of excellent labs to choose from! Apply: apply.interfolio.com/172697 Faculty: www.fredhutch.org/en/research...

fredhutch.org

Herbold Computational Biology Faculty & Labs

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Armita Nourmohammad @thearmita.bsky.social · 06/10/2025

check out our manuscript (led by Obinna Ukogu) on Design principles of cytotoxic T-cell response: www.biorxiv.org/content/10.1...

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Reposted by Armita Nourmohammad

Gabriel Victora @victora.bsky.social · 05/06/2025

Wanted to highlight our latest preprint--a huge effort by multiple people and labs, but led primarily by @wsdewitt.github.io, Tatsuya Araki, and Ashni Vora, in a very close wet-dry collaboration with @matsen.bsky.social’s lab at the Hutch www.biorxiv.org/content/10.1...

biorxiv.org

Replaying germinal center evolution on a quantified affinity landscape

Darwinian evolution of immunoglobulin genes within germinal centers (GC) underlies the progressive increase in antibody affinity following antigen exposure. Whereas the mechanics of how competition be...

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Reposted by Armita Nourmohammad

William DeWitt @wsdewitt.github.io · 21/05/2025

Recasting the perils of phylodynamic non-identifiability as a feature not a bug, we show that a unique forward-equivalent process enables exact and efficient simulation from arbitrarily large populations. With M Celentano, S Prillo, @yun-s-song.bsky.social www.pnas.org/doi/10.1073/pnas.2412978122

A full lineage tree and it's corresponding ascertained tree

Tree conditioned on survival is equal in law to an unconditioned tree with modified parameters

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Armita Nourmohammad @thearmita.bsky.social · 04/03/2025

check out our new manuscript (led by Gian Marco Visani): structure-based machine learning model for TCR-pMHC complexes, predicting T-cell affinity to peptide-MHC complexes, quantifying T-cell receptor specificity, and designing de-novo immunogenic peptides: arxiv.org/abs/2503.00648

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