Evidence map›Paper›PMID 40670076›Full record

ArticleGenome research2025

Genetic variation in recalcitrant repetitive regions of the

Harsh G Shukla, Mahul Chakraborty, J J Emerson

Abstract read
In one paragraph

Article in Genome research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing 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

14 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Polymorphic 3D genome architecture mediated by transposable elements.bioRxiv : the preprint server for biology · 2026
    Article
  6. Article
  7. The histone gene family inmicroPublication biology · 2026
    Article
  8. Heterochromatin-based silencing of a foreign tandem repeat inbioRxiv : the preprint server for biology · 2025
    Article
  9. Article
  10. Cell-cycle-regulated transcriptional pausing ofMolecular biology of the cell · 2025
    Article
  11. Article
  12. Cell cycle-regulated transcriptional pausing ofbioRxiv : the preprint server for biology · 2024
    Article
  13. Article
  14. bioRxiv : the preprint server for biology · 2024
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

3 authors.

Harsh G ShuklaDepartment of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA.
Mahul ChakrabortyDepartment of Biology, Texas A&M University, College Station, Texas 77843, USA; mahul@tamu.edu jje@uci.edu.ORCID 0000-0003-2414-9187
J J EmersonDepartment of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA; mahul@tamu.edu jje@uci.edu.ORCID 0000-0001-9474-0891

Funding

Univ.of Calif., Irvine Cancer Center Support GrantP30CA062203 · NCI · UNIVERSITY OF CALIFORNIA-IRVINE · PI Melanie Funes · 1994 to 2026
$57.9M
UCI P30 Skin Center Systems Biology CoreP30AR075047 · NIAMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI LANDER, ARTHUR D · 2019 to 2025
$5.1M
Structural variation population size and the evolution of genome complexityR01GM123303 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI EMERSON, JAMES JORDAN · 2017 to 2021
$1.5M
The origin, maintenance, and adaptive consequences of variation in genome structureR35GM153327 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI James Jordan Emerson · 2024 to 2026
$1.1M
Evolutionary and functional consequences of structural genetic variation in DrosophilaR00GM129411 · NIGMS · TEXAS A&M UNIVERSITY · PI CHAKRABORTY, MAHUL · 2023 to 2025
$735k
High-Throughput DNA SequencerS10OD021718 · OD · UNIVERSITY OF CALIFORNIA-IRVINE · PI SANDMEYER, SUZANNE · 2016 to 2016
$600k
PacBio RS Single Molecule, Real-Time (SMRT) DNA SequencerS10OD010794 · OD · UNIVERSITY OF CALIFORNIA-IRVINE · PI SANDMEYER, SUZANNE · 2012 to 2012
$600k
Evolutionary and functional consequences of structural genetic variation in DrosophilaK99GM129411 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI CHAKRABORTY, MAHUL · 2019 to 2021
$145k
NCI NIH HHS P30 CA062203NIAMS NIH HHS P30 AR075047NIGMS NIH HHS K99 GM129411NIGMS NIH HHS R00 GM129411NIGMS NIH HHS R01 GM123303NIGMS NIH HHS R35 GM153327NIH HHS S10 OD010794NIH HHS S10 OD021718
6 · The paper itself

Abstract

Many essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure chromosome integrity, piRNA clusters encoding host defenses against selfish elements, and virtually the entire Y Chromosome. These regions, formed by highly similar tandem arrays, pose significant challenges for experimental and computational studies, impeding sequence-level descriptions essential for understanding genetic variation. Here, we report the assembly and variation analysis of such repetitive regions in

Indexed as

Drosophila melanogasterGenetic VariationGenome, InsectRepetitive Sequences, Nucleic AcidAnimalsHeterochromatinHistonesX ChromosomeHeterochromatinHistones

Identifiers

PMID40670076
PMCPMC12400953

What Socratic 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 Socratic graph.