Evidence map›Paper›PMID 39713350›Full record

ArticlebioRxiv : the preprint server for biology2024

Efficient High-Throughput DNA Breathing Features Generation Using Jax-EPBD.

Toki Tahmid Inan, Anowarul Kabir, Kim Rasmussen, Amarda Shehu, Anny Usheva, Alan Bishop, Boian Alexandrov, Manish Bhattarai

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. 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

8 authors.

Toki Tahmid InanTheoretical Division, Los Alamos National Laboratory, Los Alamos, NM.
Anowarul KabirTheoretical Division, Los Alamos National Laboratory, Los Alamos, NM.
Kim RasmussenTheoretical Division, Los Alamos National Laboratory, Los Alamos, NM.
Amarda ShehuDepartment of Computer Science, George Mason University, Fairfax, Va.ORCID 0000-0001-5230-4610
Anny UshevaDepartment of Surgery, Brown University, Providence, RI.
Alan BishopTheoretical Division, Los Alamos National Laboratory, Los Alamos, NM.
Boian AlexandrovTheoretical Division, Los Alamos National Laboratory, Los Alamos, NM.
Manish BhattaraiTheoretical Division, Los Alamos National Laboratory, Los Alamos, NM.

Funding

Vascular Dysfunction in Myocardial Ischemia and Metabolic SyndromeR01HL128831 · NHLBI · RHODE ISLAND HOSPITAL · PI SELLKE, FRANK W, USHEVA-SIMIDJIYSKA, ANNY · 2016 to 2025
$5.7M
Integrating epigenomics with DNA breathing dynamics for human non-coding disease variantsR01MH116281 · NIMH · ENDEAVOR HEALTH CLINICAL OPERATIONS · PI ALEXANDROV, BOIAN STOIANOV, DUAN, JUBAO · 2019 to 2023
$3.0M
NHLBI NIH HHS R01 HL128831NIMH NIH HHS R01 MH116281
6 · The paper itself

Abstract

DNA breathing dynamics-transient base-pair opening and closing due to thermal fluctuations-are vital for processes like transcription, replication, and repair. Traditional models, such as the Extended Peyrard-Bishop-Dauxois (EPBD), provide insights into these dynamics but are computationally limited for long sequences. We present

Identifiers

PMID39713350
PMCPMC11661089

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.