Evidence map›Paper›PMID 38293094›Full record

ArticlebioRxiv : the preprint server for biology2024

Advancing Transcription Factor Binding Site Prediction Using DNA Breathing Dynamics and Sequence Transformers via Cross Attention.

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

Open access · greenAbstract 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. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed, 4 citations in OpenAlex.

  1. Review
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

7 authors at 3 institutions in 1 country.

Anowarul KabirTheoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, USA.ORCID 0000-0001-8060-2084
Manish BhattaraiTheoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, USA.ORCID 0000-0002-1421-3643
Kim Ø RasmussenTheoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, USA.ORCID 0000-0002-4029-4723
Amarda ShehuDepartment of Computer Science, George Mason University, 4400 University Dr, 22030, VA, USA.ORCID 0000-0001-5230-4610
Alan R BishopTheoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, USA.
Boian AlexandrovTheoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, USA.ORCID 0000-0001-8636-4603
Anny UshevaDepartment of Surgery, Brown University, 69 Brown St Box 1822, 02912, RI, USA.ORCID 0000-0003-3788-2425
Los Alamos National Laboratory · USGeorge Mason University · USJohn Brown University · US

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

Understanding the impact of genomic variants on transcription factor binding and gene regulation remains a key area of research, with implications for unraveling the complex mechanisms underlying various functional effects. Our study delves into the role of DNA's biophysical properties, including thermodynamic stability, shape, and flexibility in transcription factor (TF) binding. We developed a multi-modal deep learning model integrating these properties with DNA sequence data. Trained on ChIP-Seq (chromatin immunoprecipitation sequencing) data

Indexed as

attention mechanismDNA breathingDNA non-linear dynamicsEPBDTransformers

Identifiers

PMID38293094
PMCPMC10827174
OpenAlexW4391044474

What Socratic 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 Socratic graph.