Evidence map›Paper›PMID 42523210›Full record

ArticlebioRxiv : the preprint server for biology2026

Direct detection of alternative DNA conformations with long-read sequencing and machine learning approaches.

Jacob P Sieg, Huqing Zeng, Lauren Heaverly, Kateryna D Makova

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. 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

4 authors.

Jacob P SiegDepartment of Biology, Penn State University, University Park, PA, United States.ORCID 0000-0001-5414-1667
Huqing ZengDepartment of Biology, Penn State University, University Park, PA, United States.
Lauren HeaverlyDepartment of Biology, Penn State University, University Park, PA, United States.
Kateryna D MakovaDepartment of Biology, Penn State University, University Park, PA, United States.ORCID 0000-0002-6212-9526

Funding

Non-B DNA and Genome EvolutionR35GM151945 · NIGMS · PENNSYLVANIA STATE UNIVERSITY, THE · PI KATERYNA MAKOVA · 2024 to 2026
$2.6M
NIGMS NIH HHS R35 GM151945
6 · The paper itself

Abstract

Progress has been made in identifying G-quadruplexes (G4s) and other non-canonical (non-B) DNA structures in live cells. However, these experiments have been limited by methodological constraints, including low resolution and specificity, and GC-sequencing bias inherent to the short-read sequencing technologies. Direct, single-molecule, and long-read technologies have the potential to address these shortcomings. Here, we investigated the use of long-read DNA sequencing with Oxford Nanopore Technologies (ONT) to detect G4 and other non-B DNA structures. We applied ONT sequencing to oligos known to form G4s

Identifiers

PMID42523210
PMCPMC13404671

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.