AIMC Topic: Computational Biology

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Utilizing a deep learning model based on BERT for identifying enhancers and their strength.

PloS one Apr 9, 2025
An enhancer is a specific DNA sequence typically located within a gene at upstream or downstream position and serves as a pivotal element in the regulation of eukaryotic gene transcription. Therefore, the recognition of enhancers is highly significan...
Algorithms Humans Deep Learning Neural Networks, Computer Computational Biology Enhancer Elements, Genetic
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A comprehensive review of computational methods for Protein-DNA binding site prediction.

Analytical biochemistry Apr 8, 2025
Accurately identifying protein-DNA binding sites is essential for understanding the molecular mechanisms underlying biological processes, which in turn facilitates advancements in drug discovery and design. While biochemical experiments provide the m...
Machine Learning Deep Learning Humans DNA DNA-Binding Proteins Binding Sites Protein Binding Computational Biology
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Unified Deep Learning of Molecular and Protein Language Representations with T5ProtChem.

Journal of chemical information and modeling Apr 8, 2025
Deep learning has revolutionized difficult tasks in chemistry and biology, yet existing language models often treat these domains separately, relying on concatenated architectures and independently pretrained weights. These approaches fail to fully e...
Models, Molecular Drug Discovery Computational Biology Proteins Deep Learning
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MIDAA: deep archetypal analysis for interpretable multi-omic data integration based on biological principles.

Genome biology Apr 8, 2025
High-throughput multi-omic molecular profiling allows the probing of biological systems at unprecedented resolution. However, integrating and interpreting high-dimensional, sparse, and noisy multimodal datasets remains challenging. Deriving new biolo...
Computational Biology Multiomics Deep Learning Genomics Humans Software
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DeepMethyGene: a deep-learning model to predict gene expression using DNA methylations.

BMC bioinformatics Apr 8, 2025
Gene expression is the basis for cells to achieve various functions, while DNA methylation constitutes a critical epigenetic mechanism governing gene expression regulation. Here we propose DeepMethyGene, an adaptive recursive convolutional neural net...
Transcription Initiation Site Software Humans Deep Learning Epigenesis, Genetic Neural Networks, Computer Computational Biology DNA Methylation
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Subtractive genomics approach: A guide to unveiling therapeutic targets across pathogens.

Journal of microbiological methods Apr 7, 2025
Subtractive genomics is an adaptable bioinformatics technique that is used to identify potential therapeutic targets by differentiating essential genes in pathogens and non-pathogenic genes. Since, identification of therapeutic targets and understand...
Genome, Bacterial Software Drug Discovery Bacteria Computational Biology Humans Genomics
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An integrated AI knowledge graph framework of bacterial enzymology and metabolism.

Proceedings of the National Academy of Sciences of the United States of America Apr 7, 2025
The study of bacterial metabolism holds immense significance for improving human health and advancing agricultural practices. The prospective applications of genomically encoded bacterial metabolism present a compelling opportunity, particularly in t...
Computational Biology Metabolic Networks and Pathways Bacterial Proteins Deep Learning Bacteria Artificial Intelligence
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scAMZI: attention-based deep autoencoder with zero-inflated layer for clustering scRNA-seq data.

BMC genomics Apr 7, 2025
BACKGROUND: Clustering scRNA-seq data plays a vital role in scRNA-seq data analysis and downstream analyses. Many computational methods have been proposed and achieved remarkable results. However, there are several limitations of these methods. First...
Software Algorithms Single-Cell Analysis RNA-Seq Deep Learning Humans Autoencoder Sequence Analysis, RNA Single-Cell Gene Expression Analysis Cluster Analysis Computational Biology
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Machine learning-based in-silico analysis identifies signatures of lysyl oxidases for prognostic and therapeutic response prediction in cancer.

Cell communication and signaling : CCS Apr 5, 2025
BACKGROUND: Lysyl oxidases (LOX/LOXL1-4) are crucial for cancer progression, yet their transcriptional regulation, potential therapeutic targeting, prognostic value and involvement in immune regulation remain poorly understood. This study comprehensi...
Neoplasms Computational Biology Computer Simulation Prognosis Gene Expression Regulation, Neoplastic Protein-Lysine 6-Oxidase Humans Machine Learning
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CGLoop: a neural network framework for chromatin loop prediction.

BMC genomics Apr 5, 2025
BACKGROUND: Chromosomes of species exhibit a variety of high-dimensional organizational features, and chromatin loops, which are fundamental structures in the three-dimensional (3D) structure of the genome. Chromatin loops are visible speckled patter...
Humans Neural Networks, Computer Software Chromatin Deep Learning Computational Biology
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