AIMC Topic: DNA

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BertSNR: an interpretable deep learning framework for single-nucleotide resolution identification of transcription factor binding sites based on DNA language model.

Bioinformatics (Oxford, England) Aug 2, 2024
MOTIVATION: Transcription factors are pivotal in the regulation of gene expression, and accurate identification of transcription factor binding sites (TFBSs) at high resolution is crucial for understanding the mechanisms underlying gene regulation. T...
Software Algorithms Deep Learning Sequence Analysis, DNA DNA Binding Sites Computational Biology Transcription Factors
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iM-Seeker: a webserver for DNA i-motifs prediction and scoring via automated machine learning.

Nucleic acids research Jul 5, 2024
DNA, beyond its canonical B-form double helix, adopts various alternative conformations, among which the i-motif, emerging in cytosine-rich sequences under acidic conditions, holds significant biological implications in transcription modulation and t...
Internet Machine Learning Sequence Analysis, DNA Nucleotide Motifs Algorithms DNA Humans Software
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EGPDI: identifying protein-DNA binding sites based on multi-view graph embedding fusion.

Briefings in bioinformatics May 23, 2024
Mechanisms of protein-DNA interactions are involved in a wide range of biological activities and processes. Accurately identifying binding sites between proteins and DNA is crucial for analyzing genetic material, exploring protein functions, and desi...
Algorithms Protein Binding Computational Biology Neural Networks, Computer Binding Sites DNA DNA-Binding Proteins
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Prediction of DNA i-motifs via machine learning.

Nucleic acids research Mar 21, 2024
i-Motifs (iMs), are secondary structures formed in cytosine-rich DNA sequences and are involved in multiple functions in the genome. Although putative iM forming sequences are widely distributed in the human genome, the folding status and strength of...
DNA Base Sequence Nucleotide Motifs Humans Machine Learning Cytosine
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Multiple sequence alignment-based RNA language model and its application to structural inference.

Nucleic acids research Jan 11, 2024
Compared with proteins, DNA and RNA are more difficult languages to interpret because four-letter coded DNA/RNA sequences have less information content than 20-letter coded protein sequences. While BERT (Bidirectional Encoder Representations from Tra...
Proteins DNA Solvents Sequence Alignment RNA Machine Learning
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Simulations of Sequence Evolution: How (Un)realistic They Are and Why.

Molecular biology and evolution Jan 3, 2024
MOTIVATION: Simulating multiple sequence alignments (MSAs) using probabilistic models of sequence evolution plays an important role in the evaluation of phylogenetic inference tools and is crucial to the development of novel learning-based approaches...
Sequence Alignment Proteins DNA Software Phylogeny Neural Networks, Computer
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Peptidic Compound as DNA Binding Agent: Fragment-based Design, Machine Learning, Molecular Modeling, Synthesis, and DNA Binding Evaluation.

Protein and peptide letters Jan 1, 2024
BACKGROUND: Cancer remains a global burden, with increasing mortality rates. Current cancer treatments involve controlling the transcription of malignant DNA genes, either directly or indirectly. DNA exhibits various structural forms, including the G...
DNA Molecular Dynamics Simulation Binding Sites G-Quadruplexes Antineoplastic Agents Machine Learning Protein Binding Computer Simulation Molecular Docking Simulation Peptides Drug Design Humans
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Classification of DNA Sequence Based on a Non-gradient Algorithm: Pseudoinverse Learners.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2024
This chapter proposes a prototype-based classification approach for analyzing DNA barcodes that uses a spectral representation of DNA sequences and a non-gradient neural network. Biological sequences can be viewed as data components with higher non-f...
Humans DNA DNA Barcoding, Taxonomic Deep Learning Neural Networks, Computer Algorithms Computational Biology Sequence Analysis, DNA
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Design and deep learning of synthetic B-cell-specific promoters.

Nucleic acids research Nov 27, 2023
Synthetic biology and deep learning synergistically revolutionize our ability for decoding and recoding DNA regulatory grammar. The B-cell-specific transcriptional regulation is intricate, and unlock the potential of B-cell-specific promoters as synt...
Gene Expression Regulation Promoter Regions, Genetic Animals Humans Mice Deep Learning Immunoglobulin Variable Region DNA
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Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures.

Briefings in bioinformatics Sep 22, 2023
The interactions between nucleic acids and proteins are important in diverse biological processes. The high-quality prediction of nucleic-acid-binding sites continues to pose a significant challenge. Presently, the predictive efficacy of sequence-bas...
RNA Binding Sites Proteins Neural Networks, Computer DNA Language
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