AIMC Topic: Regulatory Sequences, Nucleic Acid

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pDHS-SVM: A prediction method for plant DNase I hypersensitive sites based on support vector machine.

Journal of theoretical biology May 26, 2017
DNase I hypersensitive sites (DHSs) are accessible chromatin regions hypersensitive to cleavages by DNase I endonucleases. DHSs are indicative of cis-regulatory DNA elements (CREs), all of which play important roles in global gene expression regulati...
Support Vector Machine Oryza Binding Sites Algorithms Regulatory Sequences, Nucleic Acid Deoxyribonuclease I Dinucleotide Repeats Genome, Plant Arabidopsis
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The identification of cis-regulatory elements: A review from a machine learning perspective.

Bio Systems Oct 21, 2015
The majority of the human genome consists of non-coding regions that have been called junk DNA. However, recent studies have unveiled that these regions contain cis-regulatory elements, such as promoters, enhancers, silencers, insulators, etc. These ...
Regulatory Sequences, Nucleic Acid Pattern Recognition, Automated Base Sequence Sequence Alignment Chromosome Mapping Molecular Sequence Data Animals Sequence Analysis, DNA Humans Machine Learning
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CREATE: cell-type-specific cis-regulatory element identification via discrete embedding.

Nature communications May 17, 2025
Cis-regulatory elements (CREs), including enhancers, silencers, promoters and insulators, play pivotal roles in orchestrating gene regulatory mechanisms that drive complex biological traits. However, current approaches for CRE identification are pred...
Humans Deep Learning Computational Biology Enhancer Elements, Genetic Regulatory Sequences, Nucleic Acid Chromatin Gene Expression Regulation Promoter Regions, Genetic
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An Attention-Based Deep Neural Network Model to Detect Cis-Regulatory Elements at the Single-Cell Level From Multi-Omics Data.

Genes to cells : devoted to molecular & cellular mechanisms Mar 1, 2025
Cis-regulatory elements (cREs) play a crucial role in regulating gene expression and determining cell differentiation and state transitions. To capture the heterogeneous transitions of cell states associated with these processes, detecting cRE activi...
Humans Regulatory Elements, Transcriptional Regulatory Sequences, Nucleic Acid Multiomics Glioma Zinc Finger E-box-Binding Homeobox 1 SOXB1 Transcription Factors Epithelial-Mesenchymal Transition Single-Cell Analysis Genomics Neural Networks, Computer Leukocytes, Mononuclear
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Semi-supervised learning with pseudo-labeling compares favorably with large language models for regulatory sequence prediction.

Briefings in bioinformatics Sep 23, 2024
Predicting molecular processes using deep learning is a promising approach to provide biological insights for non-coding single nucleotide polymorphisms identified in genome-wide association studies. However, most deep learning methods rely on superv...
Deep Learning Genome-Wide Association Study Polymorphism, Single Nucleotide Humans Algorithms Genome, Human Regulatory Sequences, Nucleic Acid Computational Biology Supervised Machine Learning
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LegNet: a best-in-class deep learning model for short DNA regulatory regions.

Bioinformatics (Oxford, England) Aug 1, 2023
MOTIVATION: The increasing volume of data from high-throughput experiments including parallel reporter assays facilitates the development of complex deep-learning approaches for modeling DNA regulatory grammar.
Software Deep Learning Promoter Regions, Genetic Regulatory Sequences, Nucleic Acid DNA
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DeepPHiC: predicting promoter-centered chromatin interactions using a novel deep learning approach.

Bioinformatics (Oxford, England) Jan 1, 2023
MOTIVATION: Promoter-centered chromatin interactions, which include promoter-enhancer (PE) and promoter-promoter (PP) interactions, are important to decipher gene regulation and disease mechanisms. The development of next-generation sequencing techno...
Deep Learning Regulatory Sequences, Nucleic Acid Chromatin Promoter Regions, Genetic Chromosomes
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Deep learning-assisted genome-wide characterization of massively parallel reporter assays.

Nucleic acids research Nov 11, 2022
Massively parallel reporter assay (MPRA) is a high-throughput method that enables the study of the regulatory activities of tens of thousands of DNA oligonucleotides in a single experiment. While MPRA experiments have grown in popularity, their small...
Sequence Analysis, DNA DNA Regulatory Sequences, Nucleic Acid Genome, Human Humans Deep Learning
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Genome-wide cis-decoding for expression design in tomato using cistrome data and explainable deep learning.

The Plant cell May 24, 2022
In the evolutionary history of plants, variation in cis-regulatory elements (CREs) resulting in diversification of gene expression has played a central role in driving the evolution of lineage-specific traits. However, it is difficult to predict expr...
Deep Learning Solanum lycopersicum Fruit Transcription Factors Regulatory Sequences, Nucleic Acid Plant Proteins Gene Expression Regulation, Plant
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seqgra: principled selection of neural network architectures for genomics prediction tasks.

Bioinformatics (Oxford, England) Apr 28, 2022
MOTIVATION: Sequence models based on deep neural networks have achieved state-of-the-art performance on regulatory genomics prediction tasks, such as chromatin accessibility and transcription factor binding. But despite their high accuracy, their con...
Chromatin Genomics Regulatory Sequences, Nucleic Acid Neural Networks, Computer Software
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