Evidence map›Paper›PMID 41993329›Full record

ArticlebioRxiv : the preprint server for biology2026

Evolutionary transfer learning enables organism-wide inference of mammalian enhancer landscapes.

Chengxiang Qiu, Riza M Daza, Ian C Welsh, Rupali P Patwardhan, Beth K Martin, Tony Li, Shizhao Yang, Camiel C A Mannens, Seppe De Winter, Niklas Kempynck and 10 more

Abstract readPreprint
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

20 authors.

Chengxiang QiuDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0002-6346-8669
Riza M DazaDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0003-1635-8675
Ian C WelshThe Jackson Laboratory, Bar Harbor, ME, USA.ORCID 0000-0002-5685-3235
Rupali P PatwardhanDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Beth K MartinDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Tony LiDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0003-3546-123X
Shizhao YangDepartment of Molecular and Systems Biology, Dartmouth College, Hanover, NH, USA.
Camiel C A MannensLaboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium.ORCID 0000-0002-1318-2603
Seppe De WinterLaboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium.ORCID 0000-0001-7907-1247
Niklas KempynckLaboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium.ORCID 0000-0002-0104-4844
Megan L TaylorDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0009-0002-2511-1498
Olivia FultonDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Truc-Mai LeBrotman Baty Institute for Precision Medicine, Seattle, WA, USA.
Diana R O'DayBrotman Baty Institute for Precision Medicine, Seattle, WA, USA.
Jean-Benoît LalanneDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0001-8753-0669
Silvia DomckeDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0002-4102-7774
Stephen A MurrayThe Jackson Laboratory, Bar Harbor, ME, USA.ORCID 0000-0002-0594-1702
Stein AertsLaboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium.ORCID 0000-0002-8006-0315
Cole TrapnellDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0002-8105-4347
Jay ShendureDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.ORCID 0000-0002-1516-1865

Funding

The Jackson Laboratory Knockout Mouse Production and Phenotyping Project (JAX KOMP2)UM1OD023222 · OD · JACKSON LABORATORY · PI ROBERT E BRAUN, Stephen A Murray · 2016 to 2026
$47.2M
Zhao - Proj 2P20GM130454 · NIGMS · DARTMOUTH COLLEGE · PI MICHAEL L WHITFIELD · 2019 to 2026
$27.2M
Versatile, exponentially scalable methods for single cell molecular profilingR01HG010632 · NHGRI · UNIVERSITY OF WASHINGTON · PI Jay Ashok Shendure, Bruce Colston Trapnell · 2019 to 2026
$5.9M
Genomic Risk Variants in Orofacial Clefting: Discovery and Functional ValidationR01DE032319 · NIDCR · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Mary L. Marazita, Stephen A Murray · 2023 to 2026
$2.8M
NHGRI NIH HHS R01 HG010632NIDCR NIH HHS R01 DE032319NIGMS NIH HHS P20 GM130454NIH HHS UM1 OD023222
6 · The paper itself

Abstract

Understanding and modeling how a single human genome concurrently encodes gene regulatory programs for thousands of cell types remains a central challenge in genomics and machine learning. Most human cell types emerge during embryonic, fetal, and pediatric development which are inaccessible to comprehensive molecular profiling. To circumvent this, we hypothesized that the mismatch in evolutionary rates between

Identifiers

PMID41993329
PMCPMC13081831

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.