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Bipartite is an agent orchestration system built around a simple idea: the manuscript is the source of truth, so understanding a project should mean reading its paper.

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...

Generations of “sociobiologists” have tried and failed to argue that genetic analysis offers the key to understanding social inequality. A new book fares no better.

Arc Institute’s “MULTI-evolve” learns a classical additive model, not epistasis.

Nature - Polyclonal selection of immune checkpoint mutations in thyroid autoimmunity

Employing a minimal but biochemically relevant model of trigger waves, this study obtained an analytic expression for wave ignition thresholds in cell signaling in 1D and numerical solutions in 2D and...

The ability to predict rapid evolutionary processes within our bodies would advance both medical science and evolutionary biology. We discuss technologies that move us towards intrahost evolutionary p...

Antibodies generated by prior immune responses regulate B cell responses upon recall immunization. Barbulescu et al. examine whether antibodies produced by an ongoing immune response influence the out...

This post explores mathematical aspects of recovering mutation rate histories from an ancestral recombination graph (ARG) Vs a sample frequency spectrum (SFS), expanding on a recent collaborative pape...

A five year collaboration with the Victora lab is bearing fruit for evolutionary biology.

A four-part series on using coding agents like Claude Code for scientific programming, covering fundamentals, workflows, best practices, and the human side of AI-assisted development.

Serum antibodies from prior immune responses regulate B cell activation and germinal center (GC) access upon recall immunization. However, how antibodies produced by an ongoing immune response influen...

T cells play a key role in adaptive immunity by mounting specific responses against diverse pathogens. Effective bindings between T cell receptors ...

ICMU supports top-level research in mathematics, with special emphasis on training younger generations of scientists and the development of mathematics in Ukraine.

Preprint: BH Schlomann, WS DeWitt, Y Zhang, K Shah. Ignition criteria for trigger waves in cell signaling. arXiv:2508.16810 [q-bio.CB]

Three recent papers quantify how nucleotide-level mutation processes drive antibody evolution.

When our immune system encounters foreign antigens (i.e., from pathogens), the B cells that produce our antibodies undergo a cyclic process of proliferation, mutation, and selection, improving their a...

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...

B cells and the antibodies they produce are vital to health and survival, motivating research on the details of the mutational and evolutionary processes in the germinal centers (GC) from which mature...

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...

We try to learn about SHM mechanism and do so by directly using mechanistic models, and by exploring deep architectures.

My return to blogging, and why I hope to read your blog too.

NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: 2024 NIH Public Access Policy NOT-OD-25-047. OD