Evidence map›Paper›PMID 42182479›Full record

ArticlebioRxiv : the preprint server for biology2026

Biological foundation models illuminate annotation blind spots in evolutionarily divergent genomes.

Toby B Lanser, Sydney K Caldwell, Gaspar A Pacheco, Jessica W Chen, Shahab Saghaei, Mariah Hassan, Meydan Kronrod, Duane R Wesemann, H Robert Frost

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. 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

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Toby B LanserProgram in Quantitative Biomedical Sciences, Geisel School of Medicine, Dartmouth College, Hanover, NH, 03755, USA.ORCID 0000-0002-2250-6075
Sydney K CaldwellDepartment of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Gaspar A PachecoDepartment of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Jessica W ChenDepartment of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Shahab SaghaeiDepartment of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Mariah HassanDepartment of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Meydan KronrodDepartment of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Duane R WesemannDepartment of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
H Robert FrostProgram in Quantitative Biomedical Sciences, Geisel School of Medicine, Dartmouth College, Hanover, NH, 03755, USA.

Funding

Translational Engineering in Cancer (TEC)P30CA023108 · NCI · DARTMOUTH COLLEGE · PI Steven D Leach · 1985 to 2026
$91.3M
Technology and Computational CoreP01AI165072 · NIAID · BRIGHAM AND WOMEN'S HOSPITAL · PI SAPHIRE, ERICA OLLMANN · 2021 to 2023
$19.6M
Flipped Germinal CentersR01AI169619 · NIAID · BRIGHAM AND WOMEN'S HOSPITAL · PI WESEMANN, DUANE R. · 2021 to 2025
$3.7M
Antibody Durability DynamicsR01AI170715 · NIAID · BRIGHAM AND WOMEN'S HOSPITAL · PI Duane R. Wesemann · 2022 to 2026
$3.4M
Understanding IgE BiologyR01AI158811 · NIAID · BRIGHAM AND WOMEN'S HOSPITAL · PI WESEMANN, DUANE R. · 2022 to 2025
$3.0M
Elucidating Germinal Center-Mediated Antibody EvolutionR01AI139538 · NIAID · BRIGHAM AND WOMEN'S HOSPITAL · PI WESEMANN, DUANE R. · 2019 to 2022
$2.4M
Gene set analysis of single cell genomicsR35GM146586 · NIGMS · DARTMOUTH COLLEGE · PI Hildreth Frost · 2022 to 2026
$2.0M
Understanding IgE BiologyR56AI158811 · NIAID · BRIGHAM AND WOMEN'S HOSPITAL · PI WESEMANN, DUANE R. · 2021 to 2021
$300k
Structural and functional integrity of antigen receptorsF31AI186232 · NIAID · HARVARD MEDICAL SCHOOL · PI Jessica WT Chen · 2024 to 2026
$119k
NCI NIH HHS P30 CA023108NIAID NIH HHS F31 AI186232NIAID NIH HHS P01 AI165072NIAID NIH HHS R01 AI139538NIAID NIH HHS R01 AI158811NIAID NIH HHS R01 AI169619NIAID NIH HHS R01 AI170715NIAID NIH HHS R56 AI158811NIGMS NIH HHS R35 GM146586
6 · The paper itself

Abstract

Chromosome-scale assemblies are increasingly available for non-model organisms, but functional annotation remains limited when deep evolutionary divergence erodes primary amino-acid sequence identity even though protein structural similarity can remain conserved. We present a hybrid annotation framework that decouples gene-model discovery from cross-species similarity assignment by combining Evo2-based

Indexed as

foundation modelsgenome annotationprotein language modelssea lampreysingle-cell RNA-seq

Identifiers

PMID42182479
PMCPMC13193013

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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.