Evidence map›Paper›PMID 40832049›Full record

ArticleArXiv2025

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

Duncan K Ralph, Athanasios G Bakis, Jared Galloway, Ashni A Vora, Tatsuya Araki, Gabriel D Victora, Yun S Song, William S DeWitt, Frederick A Matsen

Abstract readPreprint
PubMed Full text at PMC
In one paragraph

Article in ArXiv, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors.

Duncan K RalphFred Hutchinson Cancer Research Center, Seattle, Washington, USA.
Athanasios G BakisDepartment of Statistics, University of California, Irvine, CA.
Jared GallowayFred Hutchinson Cancer Research Center, Seattle, Washington, USA.
Ashni A VoraLaboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY.
Tatsuya ArakiLaboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY.
Gabriel D VictoraLaboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY.
Yun S SongDepartment of Statistics, University of California, Berkeley, CA.
William S DeWittDepartment of Genome Sciences, University of Washington, Seattle, WA.
Frederick A MatsenFred Hutchinson Cancer Research Center, Seattle, Washington, USA.

Funding

DYNAMICS AND EVOLUTION OF IMMUNE RESPONSES TO INFLUENZA VIRUSESU01AI150747 · NIAID · EMORY UNIVERSITY · PI AHMED, RAFI, ANTIA, RUSTOM NOSHIR · 2020 to 2024
$5.9M
Blending deep learning with probabilistic mechanistic models to predict and understand the evolution and function of adaptive immune receptorsR01AI146028 · NIAID · FRED HUTCHINSON CANCER RESEARCH CENTER · PI MATSEN, FREDERICK ALBERT · 2019 to 2024
$3.4M
High-Performance Compute Cluster for Comprehensive Cancer and Infectious Diseases ResearchS10OD028685 · OD · FRED HUTCHINSON CANCER RESEARCH CENTER · PI BRADLEY, PHILIP · 2020 to 2020
$2.0M
Scalable Computational Methods for Genealogical Inference: from species level to single cellsR01HG013117 · NHGRI · UNIVERSITY OF CALIFORNIA BERKELEY · PI Ian H Holmes, RASMUS NIELSEN · 2024 to 2026
$1.7M
Scalable Computational Methods for Genealogical Inference: from species level to single cellsR56HG013117 · NHGRI · UNIVERSITY OF CALIFORNIA BERKELEY · PI HOLMES, IAN H, NIELSEN, RASMUS · 2023 to 2023
$315k
NHGRI NIH HHS R01 HG013117NHGRI NIH HHS R56 HG013117NIAID NIH HHS R01 AI146028NIAID NIH HHS U01 AI150747NIH HHS S10 OD028685
6 · The paper itself

Abstract

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 (GCs) from which mature B cells arise. It is known that B cells with higher affinity for their cognate antigen (Ag) will, on average, tend to have more offspring. However the exact form of this relationship between affinity and fecundity, which we call the "affinity-fitness response function", is not known. Here we use deep learning and simulation-based inference to learn this function from a unique experiment that replays a particular combination of GC conditions many times. All code is freely available at https://github.com/matsengrp/gcdyn, while datasets and inference results can be found at https://doi.org/10.5281/zenodo.15022130.

Identifiers

PMID40832049
PMCPMC12364052

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.