Evidence map›Paper›PMID 39282372›Full record

ArticlebioRxiv : the preprint server for biology2025

Enhancer activation from transposable elements in extrachromosomal DNA.

Katerina Kraft, Sedona E Murphy, Matthew G Jones, Quanming Shi, Aarohi Bhargava-Shah, Christy Luong, King L Hung, Britney J He, Rui Li, Seung Kuk Park 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

5 · Who and what money

Authors and funding

19 authors.

Katerina KraftCenter for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA.ORCID 0000-0002-2011-6946
Sedona E MurphyPresent affiliation: Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA.
Matthew G JonesCenter for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA.
Quanming ShiCenter for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA.
Aarohi Bhargava-ShahCenter for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA.
Christy LuongCenter for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA.
King L HungCenter for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA.ORCID 0000-0002-3662-4662
Britney J HeCenter for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA.
Rui LiCenter for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA.
Seung Kuk ParkStanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
Michael T MontgomeryDepartment of Genetics, Stanford University, Stanford, CA 94305, USA.
Natasha E WeiserSarafan ChEM-H Institute and Department of Pathology, Stanford University, Stanford, CA, 94305 USA.
Yanbo WangSarafan ChEM-H Institute and Department of Pathology, Stanford University, Stanford, CA, 94305 USA.
Jens LuebeckDepartment of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA.
Vineet BafnaDepartment of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA.ORCID 0000-0002-5810-6241
Jef D BoekeInstitute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA.ORCID 0000-0001-5322-4946
Paul S MischelSarafan ChEM-H Institute and Department of Pathology, Stanford University, Stanford, CA, 94305 USA.
Alistair N BoettigerDepartment of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
Howard Y ChangCenter for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA.

Funding

Live-cell multiplex super-resolution imaging of chromatin state transitionsU01DK127419 · NIDDK · STANFORD UNIVERSITY · PI BINTU, LACRAMIOARA, BOETTIGER, ALISTAIR N. · 2020 to 2024
$5.3M
Software and algorithms for elucidating the structure, function, and evolution of extrachromosomal DNAU24CA264379 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BAFNA, VINEET, MESIROV, JILL P. · 2021 to 2025
$3.5M
Computational methods for detecting patterns of complex genomic variationR01GM114362 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Vineet Bafna · 2016 to 2026
$3.1M
eDyNAmiC - UCSDOT2CA278635 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Vineet Bafna · 2022 to 2026
$1.8M
Spatial Regulation of Epigenetic MemoryDP5OD037361 · OD · YALE UNIVERSITY · PI MURPHY, SEDONA · 2024 to 2025
$419k
Quantitative modeling of extrachromosomal DNA (ecDNA) evolution in tumorsK99CA286968 · NCI · STANFORD UNIVERSITY · PI JONES, MATTHEW GREGORY · 2024 to 2025
$335k
Amplifications and signaling of oncoproteins in cancerK00CA274692 · NCI · SCRIPPS RESEARCH INSTITUTE, THE · PI HUNG, KING L. · 2025 to 2025
$96k
Regulation and retention of extrachromosomal oncogene amplifications in cancerF99CA274692 · NCI · STANFORD UNIVERSITY · PI HUNG, KING L. · 2022 to 2023
$82k
NCI NIH HHS F99 CA274692NCI NIH HHS K00 CA274692NCI NIH HHS K99 CA286968NCI NIH HHS OT2 CA278635NCI NIH HHS U24 CA264379NIDDK NIH HHS U01 DK127419NIGMS NIH HHS R01 GM114362NIH HHS DP5 OD037361
6 · The paper itself

Abstract

Extrachromosomal DNA (ecDNA) drives oncogene amplification and intratumoral heterogeneity in aggressive cancers. While transposable element (TE) reactivation is common in cancer, its role on ecDNA remains unexplored. Here, we map the 3D architecture of

Identifiers

PMID39282372
PMCPMC11398463

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.