AIMC Topic: Computational Biology

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Promoter Prediction in Agrobacterium tumefaciens Strain C58 by Using Artificial Intelligence Strategies.

Methods in molecular biology (Clifton, N.J.)
Promoters are the genomic regions upstream of genes that RNA polymerase binds in order to initiate gene transcription. Understanding the regulation of gene expression depends on being able to identify promoters, because they are the most important co...

An effective deep learning-based approach for splice site identification in gene expression.

Science progress
A crucial stage in eukaryote gene expression involves mRNA splicing by a protein assembly known as the spliceosome. This step significantly contributes to generating and properly operating the ultimate gene product. Since non-coding introns disrupt e...

Interpreting Gene Ontology Annotations Derived from Sequence Homology Methods.

Methods in molecular biology (Clifton, N.J.)
The Gene Ontology (GO) project describes the functions of the gene products of organisms from all kingdoms of life in a standardized way, enabling powerful analyses of experiments involving genome-wide analysis. The scientific literature is used to c...

AI-Assisted Processing Pipeline to Boost Protein Isoform Detection.

Methods in molecular biology (Clifton, N.J.)
Proteomics, the study of proteins within biological systems, has seen remarkable advancements in recent years, with protein isoform detection emerging as one of the next major frontiers. One of the primary challenges is achieving the necessary peptid...

Assessment of Protein-Protein Docking Models Using Deep Learning.

Methods in molecular biology (Clifton, N.J.)
Protein-protein interactions are involved in almost all processes in a living cell and determine the biological functions of proteins. To obtain mechanistic understandings of protein-protein interactions, the tertiary structures of protein complexes ...

Machine Learning Methods in Protein-Protein Docking.

Methods in molecular biology (Clifton, N.J.)
An exponential increase in the number of publications that address artificial intelligence (AI) usage in life sciences has been noticed in recent years, while new modeling techniques are constantly being reported. The potential of these methods is va...

DeepHLApan: A Deep Learning Approach for the Prediction of Peptide-HLA Binding and Immunogenicity.

Methods in molecular biology (Clifton, N.J.)
Neoantigens are crucial in distinguishing cancer cells from normal ones and play a significant role in cancer immunotherapy. The field of bioinformatics prediction for tumor neoantigens has rapidly developed, focusing on the prediction of peptide-HLA...

Deep Learning-Based HLA Allele Imputation Applicable to GWAS.

Methods in molecular biology (Clifton, N.J.)
Human leukocyte antigen (HLA) imputation is an essential step following genome-wide association study, particularly when putative associations in HLA genes are identified, to fully understand the genetic basis of human traits. Different HLA imputatio...

hdWGCNA and Cellular Communication Identify Active NK Cell Subtypes in Alzheimer's Disease and Screen for Diagnostic Markers through Machine Learning.

Current Alzheimer research
BACKGROUND: Alzheimer's disease (AD) is a recognized complex and severe neurodegenerative disorder, presenting a significant challenge to global health. Its hallmark pathological features include the deposition of β-amyloid plaques and the formation ...

Classification of DNA Sequence Based on a Non-gradient Algorithm: Pseudoinverse Learners.

Methods in molecular biology (Clifton, N.J.)
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...