Evidence map›Paper›PMID 39443793›Full record

ArticleNature2024

Machine-guided design of cell-type-targeting cis-regulatory elements.

Sager J Gosai, Rodrigo I Castro, Natalia Fuentes, John C Butts, Kousuke Mouri, Michael Alasoadura, Susan Kales, Thanh Thanh L Nguyen, Ramil R Noche, Arya S Rao and 4 more

Abstract readValidation Study
In one paragraph

Article in Nature, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.

0numbers the graph read from it
0cells of the map it votes in
92citing 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

92 citing papers in PubMed.

  1. Article
  2. Article
  3. UnlockingNAR genomics and bioinformatics · 2026
    Article
  4. Article
  5. Article
  6. Review
  7. Review
  8. Article
  9. Article
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  11. Review
  12. Article
  13. Article
  14. Article
  15. Article
  16. Article
  17. Article
  18. Article
  19. Article
  20. Learning genes deeply.Nature methods · 2026
    Article

32 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

14 authors.

Sager J Gosai *Broad Institute of MIT and Harvard, Cambridge, MA, USA. sgosai@broadinstitute.org.ORCID 0000-0003-4494-7362
Rodrigo I Castro *The Jackson Laboratory, Bar Harbor, ME, USA. rodrigo.castro@jax.org.ORCID 0000-0002-9833-4169
Natalia FuentesThe Jackson Laboratory, Bar Harbor, ME, USA.
John C ButtsThe Jackson Laboratory, Bar Harbor, ME, USA.
Kousuke MouriThe Jackson Laboratory, Bar Harbor, ME, USA.ORCID 0000-0003-1712-6833
Michael AlasoaduraThe Jackson Laboratory, Bar Harbor, ME, USA.ORCID 0000-0001-7103-8063
Susan KalesThe Jackson Laboratory, Bar Harbor, ME, USA.
Thanh Thanh L NguyenDepartment of Genetics, Yale School of Medicine, New Haven, CT, USA.ORCID 0000-0002-2281-6540
Ramil R NocheDepartment of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA.ORCID 0000-0002-4894-5682
Arya S RaoBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Mary T JoyThe Jackson Laboratory, Bar Harbor, ME, USA.
Pardis C SabetiBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-9843-1890
Steven K ReillyDepartment of Genetics, Yale School of Medicine, New Haven, CT, USA. steven.k.reilly@yale.edu.ORCID 0000-0003-3140-1483
Ryan TewheyThe Jackson Laboratory, Bar Harbor, ME, USA. ryan.tewhey@jax.org.ORCID 0000-0002-4607-8001

Funding

Medical Scientist Training ProgramT32GM144273 · NIGMS · HARVARD MEDICAL SCHOOL · PI David Shumway Jones, Jacqueline A. Lees · 2022 to 2026
$14.7M
RESEARCH TRAINING - BIOLOGICAL SCIENCEST32MH014276 · NIMH · YALE UNIVERSITY · PI Marina R Picciotto · 1985 to 2026
$7.2M
Comprehensive functional characterization and dissection of noncoding regulatory elements and human genetic variationUM1HG009435 · NHGRI · BROAD INSTITUTE, INC. · PI SABETI, PARDIS CHRISTINE · 2017 to 2021
$6.6M
Multi-scale functional dissection and modeling of regulatory variation associated with human traitsR01HG012872 · NHGRI · YALE UNIVERSITY · PI Steven K. Reilly · 2023 to 2026
$3.1M
Functional Mapping of Enhancer Conservation Between Species to Enable Mechanistic Insights into Polygenic DiseaseR35HG011329 · NHGRI · JACKSON LABORATORY · PI TEWHEY, RYAN · 2021 to 2025
$2.6M
Comprehensive Characterization of Adaptive Regulatory Variation Linked to Human DiseaseR00HG010669 · NHGRI · YALE UNIVERSITY · PI REILLY, STEVEN K. · 2021 to 2023
$737k
NHGRI NIH HHS R00 HG010669NHGRI NIH HHS R01 HG012872NHGRI NIH HHS R35 HG011329NHGRI NIH HHS UM1 HG009435NIGMS NIH HHS T32 GM144273NIMH NIH HHS T32 MH014276
6 · The paper itself

Abstract

Cis-regulatory elements (CREs) control gene expression, orchestrating tissue identity, developmental timing and stimulus responses, which collectively define the thousands of unique cell types in the body

Indexed as

CellsGene Expression RegulationGenetic EngineeringMachine LearningRegulatory Sequences, Nucleic AcidAnimalsCell LineComputer SimulationDeep LearningFemaleGenes, ReporterGenome, HumanHumansMaleMiceNeural Networks, Computer

Identifiers

PMID39443793
PMCPMC11525185

What OpenQuestion holds

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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.