AIMC Topic: Computational Biology

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Identification of hub genes for the diagnosis associated with heart failure using multiple cell death patterns.

ESC heart failure
AIMS: Heart failure (HF) is an important public health problem worldwide, and programmed cell death (PCD) plays a crucial role in its pathologic process. This study aims to identify the hub genes associated with HF through PCD in order to better unde...

Predicting viral host codon fitness and path shifting through tree-based learning on codon usage biases and genomic characteristics.

Scientific reports
Viral codon fitness (VCF) of the host and the VCF shifting has seldom been studied under quantitative measurements, although they could be concepts vital to understand pathogen epidemiology. This study demonstrates that the relative synonymous codon ...

Analysis and validation of hub genes for atherosclerosis and AIDS and immune infiltration characteristics based on bioinformatics and machine learning.

Scientific reports
Atherosclerosis is the major cause of cardiovascular diseases worldwide, and AIDS linked with chronic inflammation and immune activation, increases atherosclerosis risk. The application of bioinformatics and machine learning to identify hub genes for...

Integrative Multi-Omics Analysis Reveals Molecular Subtypes of Ovarian Cancer and Constructs Prognostic Models.

Journal of immunotherapy (Hagerstown, Md. : 1997)
Ovarian cancer (OV) remains the most lethal gynecological malignancy. The aim of this study was to identify molecular subtypes of OV through integrative multi-omics analysis and construct machine learning-based prognostic models for predicting the ef...

Integration of graph neural networks and transcriptomics analysis identify key pathways and gene signature for immunotherapy response and prognosis of skin melanoma.

BMC cancer
OBJECTIVE: The assessment of immunotherapy plays a pivotal role in the clinical management of skin melanoma. Graph neural networks (GNNs), alongside other deep learning algorithms and bioinformatics approaches, have demonstrated substantial promise i...

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

PloS one
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...

A comprehensive review of computational methods for Protein-DNA binding site prediction.

Analytical biochemistry
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...

Unified Deep Learning of Molecular and Protein Language Representations with T5ProtChem.

Journal of chemical information and modeling
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...

MIDAA: deep archetypal analysis for interpretable multi-omic data integration based on biological principles.

Genome biology
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...