Evidence map›Paper›PMID 37745370›Full record

ArticlebioRxiv : the preprint server for biology2023

Examining DNA Breathing with pyDNA-EPBD.

Anowarul Kabir, Manish Bhattarai, Kim Ø Rasmussen, Amarda Shehu, Anny Usheva, Alan R Bishop, Boian S Alexandrov

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. 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

7 authors.

Anowarul KabirTheoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102.
Manish BhattaraiTheoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102.
Kim Ø RasmussenTheoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102.
Amarda ShehuGeorge Mason University, 4400 University Dr, Fairfax, VA 22030.
Anny UshevaBrown University, 69 Brown St Box 1822, Providence, RI 02912.
Alan R BishopTheoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102.
Boian S AlexandrovTheoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102.

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

Motivation: The two strands of the DNA double helix locally and spontaneously separate and recombine in living cells due to the inherent thermal DNA motion.This dynamics results in transient openings in the double helix and is referred to as "DNA breathing" or "DNA bubbles." The propensity to form local transient openings is important in a wide range of biological processes, such as transcription, replication, and transcription factors binding. However, the modeling and computer simulation of these phenomena, have remained a challenge due to the complex interplay of numerous factors, such as, temperature, salt content, DNA sequence, hydrogen bonding, base stacking, and others. Results: We present pyDNA-EPBD, a parallel software implementation of the Extended Peyrard-Bishop- Dauxois (EPBD) nonlinear DNA model that allows us to describe some features of DNA dynamics in detail. The pyDNA-EPBD generates genomic scale profiles of average base-pair openings, base flipping probability, DNA bubble probability, and calculations of the characteristically dynamic length indicating the number of base pairs statistically significantly affected by a single point mutation using the Markov Chain Monte Carlo (MCMC) algorithm.

Indexed as

DNA breathingDNA bubblesDNA non-linear dynamicsEPBD

Identifiers

PMID37745370
PMCPMC10515784

What OpenQuestion holds

Textmetadata
LicenceCC0
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.