Evidence map›Paper›PMID 41279701›Full record

ArticlebioRxiv : the preprint server for biology2025

Deep learning the dynamic regulatory sequence code of cardiac organoid differentiation.

Eyal Metzl-Raz, Ryan Zhao, Salil Deshpande, Jackson Powell, Elizabeth G Porter, Yassine Zouaghi, Betty B Liu, Samuel H Kim, Immanuel Abdi, Ivy Evergreen and 9 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 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

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

19 authors.

Eyal Metzl-RazDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID 0000-0002-7111-2822
Ryan ZhaoDepartment of Computer Science, Stanford University, Stanford, CA, USA.ORCID 0009-0009-0204-9370
Salil DeshpandeDepartment of Bioengineering, Stanford University, Stanford, CA, USA.ORCID 0009-0009-5776-8428
Jackson PowellDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID 0000-0003-4302-1306
Elizabeth G PorterDepartment of Genetics, Stanford University, Stanford, CA, USA.
Yassine ZouaghiDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID 0000-0001-9864-4979
Betty B LiuDepartment of Bioengineering, Stanford University, Stanford, CA, USA.ORCID 0000-0003-1655-7164
Samuel H KimDepartment of Biomedical Sciences, Stanford University, Stanford, CA, USA.ORCID 0000-0002-0419-3351
Immanuel AbdiDepartment of Genetics, Stanford University, Stanford, CA, USA.
Ivy EvergreenDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID 0009-0004-6737-889X
Megha AgarwalDepartment of Genetics, Stanford University, Stanford, CA, USA.
Maya U ShethDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID 0000-0003-1466-8899
Joshua RicoDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID 0009-0004-3779-0963
Matthew MiyamotoDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID 0000-0002-2140-6769
Julie M SanchezDepartment of Genetics, Stanford University, Stanford, CA, USA.
Jesse M EngreitzDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID 0000-0002-5754-1719
Anshul KundajeDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID 0000-0003-3084-2287
William J GreenleafDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID 0000-0003-1409-3095
Casey A GiffordDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID 0000-0002-7757-573X

Funding

Center for Personal Dynamic RegulomesRM1HG007735 · NHGRI · STANFORD UNIVERSITY · PI CHANG, HOWARD Y · 2019 to 2023
$13.8M
Stanford Center for Connecting DNA Variants to Function and PhenotypeUM1HG011972 · NHGRI · STANFORD UNIVERSITY · PI JESSE M ENGREITZ, THOMAS QUERTERMOUS · 2021 to 2026
$10.5M
Spatial multiomic mapping of gene function with CRISPRoffUM1HG012660 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Luke Gilbert · 2022 to 2026
$8.2M
Combinatorial Cell State EngineeringDP1HG013599 · NHGRI · STANFORD UNIVERSITY · PI William James Greenleaf · 2023 to 2026
$5.4M
Training in Myocardial Biology at Stanford (TIMBS)T32HL094274 · NHLBI · STANFORD UNIVERSITY · PI Euan A Ashley, Daniel Bernstein · 2010 to 2026
$5.0M
Mapping, modeling, and manipulating 3D contacts in vascular cells to connect risk variants to disease genesR01HL159176 · NHLBI · STANFORD UNIVERSITY · PI ENGREITZ, JESSE M · 2022 to 2025
$2.8M
Defining and perturbing gene regulatory dynamics in the developing human brainR01NS128028 · NINDS · STANFORD UNIVERSITY · PI William James Greenleaf · 2023 to 2026
$2.4M
Defining and perturbing gene regulatory dynamics in the developing human heart to understand mechanisms of congenital heart defectsR01HL171611 · NHLBI · STANFORD UNIVERSITY · PI William James Greenleaf · 2024 to 2026
$2.1M
Fast, powerful, scalable, usable, and distributable methods for multi-modal single cell analysesR01HG013317 · NHGRI · STANFORD UNIVERSITY · PI William James Greenleaf · 2024 to 2026
$2.1M
NHGRI NIH HHS DP1 HG013599NHGRI NIH HHS R01 HG013317NHGRI NIH HHS RM1 HG007735NHGRI NIH HHS UM1 HG011972NHGRI NIH HHS UM1 HG012660NHLBI NIH HHS R01 HL159176NHLBI NIH HHS R01 HL171611NHLBI NIH HHS T32 HL094274NINDS NIH HHS R01 NS128028
6 · The paper itself

Abstract

Defining the temporal gene regulatory programs that drive human organogenesis is essential for understanding the origins of congenital disease. We combined a time-resolved, single-cell multi-omic atlas of human iPSC-derived cardiac organoids with deep learning models that predict chromatin accessibility from DNA sequence, enabling the discovery of the regulatory syntax underlying early heart development. This framework uncovered cell-state-specific rules of cardiogenesis, including context-dependent activities of TEAD, HAND, and TBX transcription factor families, and linked these motifs to their target genes. We identified distinct programs guiding lineage divergence, such as ventricular versus pacemaker cardiomyocytes, and validated predictions by perturbing Myocardin (

Identifiers

PMID41279701
PMCPMC12632746

What Socratic 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 Socratic graph.