AIMC Topic: Computational Biology

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m5c-iDeep: 5-Methylcytosine sites identification through deep learning.

Methods (San Diego, Calif.) Jul 31, 2024
5-Methylcytosine (m5c) is a modified cytosine base which is formed as the result of addition of methyl group added at position 5 of carbon. This modification is one of the most common PTM that used to occur in almost all types of RNA. The conventiona...
5-Methylcytosine Deep Learning Humans Computational Biology Computer Simulation RNA
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DGCPPISP: a PPI site prediction model based on dynamic graph convolutional network and two-stage transfer learning.

BMC bioinformatics Jul 31, 2024
BACKGROUND: Proteins play a pivotal role in the diverse array of biological processes, making the precise prediction of protein-protein interaction (PPI) sites critical to numerous disciplines including biology, medicine and pharmacy. While deep lear...
Databases, Protein Protein Interaction Mapping Neural Networks, Computer Deep Learning Machine Learning Computational Biology Proteins
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scHiCyclePred: a deep learning framework for predicting cell cycle phases from single-cell Hi-C data using multi-scale interaction information.

Communications biology Jul 31, 2024
The emergence of single-cell Hi-C (scHi-C) technology has provided unprecedented opportunities for investigating the intricate relationship between cell cycle phases and the three-dimensional (3D) structure of chromatin. However, accurately predictin...
Deep Learning Single-Cell Analysis Computational Biology Cell Cycle Humans Chromatin
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Multitask learning of a biophysically-detailed neuron model.

PLoS computational biology Jul 31, 2024
The human brain operates at multiple levels, from molecules to circuits, and understanding these complex processes requires integrated research efforts. Simulating biophysically-detailed neuron models is a computationally expensive but effective meth...
Neurons Neural Networks, Computer Machine Learning Magnetoencephalography Brain Membrane Potentials Humans Models, Neurological Computer Simulation Action Potentials Computational Biology Electroencephalography
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pyRBDome: a comprehensive computational platform for enhancing RNA-binding proteome data.

Life science alliance Jul 30, 2024
High-throughput proteomics approaches have revolutionised the identification of RNA-binding proteins (RBPome) and RNA-binding sequences (RBDome) across organisms. Yet, the extent of noise, including false positives, associated with these methodologie...
Databases, Protein RNA Binding Sites Proteomics Proteome Humans Machine Learning Software Protein Binding Computational Biology RNA-Binding Proteins
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Cross-Species Prediction of Transcription Factor Binding by Adversarial Training of a Novel Nucleotide-Level Deep Neural Network.

Advanced science (Weinheim, Baden-Wurttemberg, Germany) Jul 30, 2024
Cross-species prediction of TF binding remains a major challenge due to the rapid evolutionary turnover of individual TF binding sites, resulting in cross-species predictive performance being consistently worse than within-species performance. In thi...
Binding Sites Neural Networks, Computer Animals Transcription Factors Deep Learning Nucleotides Mice Species Specificity Humans Polymorphism, Single Nucleotide Computational Biology
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Identification and immune landscape of sarcopenia-related molecular clusters in inflammatory bowel disease by machine learning and integrated bioinformatics.

Scientific reports Jul 30, 2024
Sarcopenia, a prevalent comorbidity of inflammatory bowel disease (IBD), is characterized by diminished skeletal muscle mass and strength. Nevertheless, the underlying interconnected mechanisms remain elusive. This study identified distinct expressio...
Humans Machine Learning Inflammatory Bowel Diseases Gene Regulatory Networks Computational Biology Male Sarcopenia Gene Expression Profiling Transcriptome
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Using deep learning to decipher the impact of telomerase promoter mutations on the dynamic metastatic morpholome.

PLoS computational biology Jul 30, 2024
Melanoma showcases a complex interplay of genetic alterations and intra- and inter-cellular morphological changes during metastatic transformation. While pivotal, the role of specific mutations in dictating these changes still needs to be fully eluci...
Humans Promoter Regions, Genetic Telomerase Deep Learning Mutation Phenotype Cell Line, Tumor Neoplasm Metastasis Melanoma Computational Biology Skin Neoplasms
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Utilizing machine learning and bioinformatics analysis to identify drought-responsive genes affecting yield in foxtail millet.

International journal of biological macromolecules Jul 29, 2024
Drought stress is a major constraint on crop development, potentially causing huge yield losses and threatening global food security. Improving Crop's stress tolerance is usually associated with a yield penalty. One way to balance yield and stress to...
Droughts Genes, Plant Plant Proteins Stress, Physiological Gene Expression Regulation, Plant Machine Learning Gene Expression Profiling Transcriptome Computational Biology Setaria Plant Haplotypes
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Extended dipeptide composition framework for accurate identification of anticancer peptides.

Scientific reports Jul 29, 2024
The identification of anticancer peptides (ACPs) is crucial, especially in the development of peptide-based cancer therapy. The classical models such as Split Amino Acid Composition (SAAC) and Pseudo Amino Acid Composition (PseAAC) lack the incorpora...
Humans Machine Learning Computational Biology Algorithms Support Vector Machine Reproducibility of Results Dipeptides Antineoplastic Agents
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