AIMC Topic: Computational Biology

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SARS-CoV-2: lessons in virus mutation prediction and pandemic preparedness.

Current opinion in immunology
The COVID-19 pandemic has prompted an unprecedented global response. In particular, extraordinary efforts have been dedicated toward monitoring and predicting variant emergence due to its huge impact, particularly for vaccine escape. Broadly, we clas...

A Bayesian Optimization-Based Hybrid Deep Prediction Method for Zinc-Binding Protein Interaction Sites.

Journal of chemical information and modeling
The binding of zinc ions to proteins plays a crucial role in normal physiological functions and life activities of organisms. To enhance the prediction accuracy of zinc-binding protein interaction sites, the paper proposes a novel hybrid deep predict...

Predicting Biological Activity from Biosynthetic Gene Clusters Using Neural Networks.

Journal of chemical information and modeling
Microorganisms such as bacteria and fungi have been used for natural products that translate to drugs. However, assessing the bioactivity of extract from culture to identify novel natural molecules remains a strenuous process due to the cumbersome or...

InDeepNet: a web platform for predicting functional binding sites in proteins using InDeep.

Nucleic acids research
Predicting functional binding sites in proteins is crucial for understanding protein-protein interactions (PPIs) and identifying drug targets. While various computational approaches exist, many fail to assess PPI ligandability, which often involves c...

HawkDock version 2: an updated web server to predict and analyze the structures of protein-protein complexes.

Nucleic acids research
Protein-protein interactions (PPIs) are fundamental to cellular functions, yet predicting and analyzing their 3D structures remains a critical and computationally demanding challenge. To address this, the HawkDock web server was developed as an integ...

OntoTiger: a platform of ontology-based application tools for integrative biomedical exploration.

Nucleic acids research
Biomedical ontologies, such as Gene Ontology (GO), Disease Ontology (DO), and the Human Phenotype Ontology (HPO), have been extensively applied to characterize molecular roles and their semantic relationships in biomedical research and clinical pract...

VBayesMM: variational Bayesian neural network to prioritize important relationships of high-dimensional microbiome multiomics data.

Briefings in bioinformatics
The analysis of high-dimensional microbiome multiomics datasets is crucial for understanding the complex interactions between microbial communities and host physiological states across health and disease conditions. Despite their importance, current ...

spaLLM: enhancing spatial domain analysis in multi-omics data through large language model integration.

Briefings in bioinformatics
Spatial multi-omics technologies provide valuable data on gene expression from various omics in the same tissue section while preserving spatial information. However, deciphering spatial domains within spatial omics data remains challenging due to th...

Iterative clustering algorithm G-DESC-E and pan-cancer key gene analysis based on single-cell sequencing data.

Briefings in bioinformatics
Single-cell sequencing technology has profoundly revolutionized the field of cancer genomics, enabling researchers to explore gene expression profiles at the resolution of individual cells. Despite its extensive applications in the study of cancer ge...

Genomic language models (gLMs) decode bacterial genomes for improved gene prediction and translation initiation site identification.

Briefings in bioinformatics
Accurate bacterial gene prediction is essential for understanding microbial functions and advancing biotechnology. Traditional methods based on sequence homology and statistical models often struggle with complex genetic variations and novel sequence...