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.

A walkthrough of using GitHub's spec-kit for spec-driven development on a bioinformatics pipeline.

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

YouTube video by Erick Matsen

YouTube video by Erick Matsen

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.

Primary Work Address: 19700 Helix Drive, Ashburn, VA, 20147 Current HHMI Employees, click here to apply via your Workday account. Intro: AI@HHMI: HHMI is investing $500 million over the next 10 years ...

Convolutional embedding models efficiently capture wide sequence context in antibody somatic hypermutation, avoiding exponential k-mer parameter scaling and eliminating the need for per-site modeling.

Contribute to matsengrp/preflight development by creating an account on GitHub.

Let's have fun, work hard, and feel lucky that our job is to expand the boundary of knowledge.

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

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...

Comprehensive MCP server for PDF reading, navigation, and text search - matsengrp/pdf-navigator-mcp

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...

Biology is composed of many small interacting processes. We can use AI to develop models accordingly.

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.

The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability. It has long bee...

We study the optimization landscape of maximum likelihood estimation for a binary latent tree model with hidden variables at internal nodes and observed variables at the leaves. This model, known as t...

RNA viruses like SARS-CoV-2 have a high mutation rate, which contributes to their rapid evolution. The rate of mutations depends on the mutation type (e.g., A→C, A→G, etc.) and can vary between sites ...

Amino acid substitution rate matrices are fundamental to statistical phylogenetics and evolutionary biology. Estimating them typically requires reconstructed trees for massive amounts of aligned...