F. A. Matsen

Career Trajectory

Research Cluster Map

Direct collaborators. Node size = influence, colour = community, dashed = past collaboration.

• Entrenchment of germline amino-acid differences in antibody affinity maturation

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-23

• Nucleotide context models outperform protein language models for predicting antibody affinity maturation

  PLoS Computational Biology · 2025-12-01 · 1 citations

• Objective Ignorance: A Flaw in Our Ability to Predict Patient Outcomes

  Journal of Bone and Joint Surgery · 2025-11-19

• Avoiding overstuffing: the kinematic total shoulder arthroplasty

  International Orthopaedics · 2025-11-05

• Inference of germinal center evolutionary dynamics via simulation-based deep learning

  eLife · 2025-11-03

• Inference of germinal center evolutionary dynamics via simulation-based deep learning

  eLife · 2025-11-03

• larch: mapping the parsimony-optimal landscape of trees for directed explorationPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-31 · 2 citations

• Separating selection from mutation in antibody language modelsPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-22

• Author response: Thrifty wide-context models of B cell receptor somatic hypermutation

  2025-08-29

• Inference of germinal center evolutionary dynamics via simulation-based deep learningPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-15

• Learning antibody sequence constraints from allelic inclusion

  Cell Systems · 2025-08-13 · 1 citations

• The Structure of Deviations From Maximum Parsimony for Densely-Sampled Data and Applications for Clade Support EstimationPreprint

  IEEE Transactions on Computational Biology and Bioinformatics · 2025-08-04

• Thrifty wide-context models of B cell receptor somatic hypermutation

  eLife · 2025-08-01

• A Sitewise Model of Natural Selection on Individual Antibodies via a Transformer–Encoder

  Molecular Biology and Evolution · 2025-07-30 · 7 citations

• Author Response: Thrifty wide-context models of B cell receptor somatic hypermutation

  2025-07-16

• Thrifty wide-context models of B cell receptor somatic hypermutationPreprint

  eLife · 2025-07-16

• <tt>torchtree</tt> : Flexible Phylogenetic Model Development and Inference Using PyTorch

  Systematic Biology · 2025-07-03 · 1 citations

• Nucleotide context models outperform protein language models for predicting antibody affinity maturationPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-18 · 7 citations

• Biological causes and impacts of rugged tree landscapes in phylodynamic inferencePreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-12 · 4 citations

• Replaying germinal center evolution on a quantified affinity landscapePreprint

  Cell · 2025-06-05 · 24 citations