Evidence map›Paper›PMID 41951735›Full record

ArticleNature2026

Multiomics and deep learning dissect regulatory syntax in human development.

Betty B Liu, Selin Jessa, Samuel H Kim, Yan Ting Ng, Soon Il Higashino, Georgi K Marinov, Derek C Chen, Benjamin E Parks, Li Li, Tri C Nguyen and 11 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing 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

11 citing papers in PubMed.

  1. AlphaGenome Atlas:medRxiv : the preprint server for health sciences · 2026
    Article
  2. Review
  3. Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Deep learning-guided design of cell type-specific AAV promoters.bioRxiv : the preprint server for biology · 2026
    Article
  9. Article
  10. Article
  11. Article
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

21 authors.

Betty B Liu *Department of Bioengineering, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-1655-7164
Selin Jessa *Department of Genetics, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-4192-6523
Samuel H Kim *Cancer Biology Program, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-8353-6190
Yan Ting Ng *Illumina Artificial Intelligence Laboratory, Illumina, Foster City, CA, USA.ORCID http://orcid.org/0000-0001-8075-8791
Soon Il HigashinoDepartment of Genetics, Stanford University, Stanford, CA, USA.
Georgi K MarinovDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-1822-7273
Derek C ChenDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-9652-4885
Benjamin E ParksDepartment of Computer Science, Stanford University, Stanford, CA, USA.
Li LiDepartment of Pediatrics, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-7886-6056
Tri C NguyenDepartment of Genetics, Stanford University, Stanford, CA, USA.
Austin T WangDepartment of Computer Science, Stanford University, Stanford, CA, USA.
Sean K WangDepartment of Ophthalmology, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-1557-8510
Meng How TanSchool of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore.ORCID http://orcid.org/0000-0003-3627-5586
Serena Y TanDepartment of Pathology, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-5409-0695
Michael KosickiEnvironmental Genomics and System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0001-7173-8852
Len A PennacchioEnvironmental Genomics and System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-8748-3732
Eyal Ben-DavidIllumina Artificial Intelligence Laboratory, Illumina, Foster City, CA, USA.ORCID http://orcid.org/0000-0003-0514-0400
Anca M PascaDepartment of Pediatrics, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-0445-9009
Anshul KundajeDepartment of Genetics, Stanford University, Stanford, CA, USA. akundaje@stanford.edu.ORCID http://orcid.org/0000-0003-3084-2287
Kyle K H FarhIllumina Artificial Intelligence Laboratory, Illumina, Foster City, CA, USA. kfarh@illumina.com.ORCID http://orcid.org/0000-0001-6947-8537
William J GreenleafDepartment of Genetics, Stanford University, Stanford, CA, USA. wjg@stanford.edu.ORCID http://orcid.org/0000-0003-1409-3095

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Transcription factors establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility and regulating gene expression

Indexed as

Deep LearningGene Expression Regulation, DevelopmentalMultiomicsRegulatory Sequences, Nucleic AcidChromatinEnhancer Elements, GeneticFemaleHumansNucleotide MotifsOrgan SpecificitySingle-Cell AnalysisTranscription FactorsChromatinTranscription Factors

Identifiers

PMID41951735
PMCPMC13216069

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.