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Computational Biology

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GRL-PUL: predicting microbe-drug association based on graph representation learning and positive unlabeled learning.

Molecular omics
Extensive research has confirmed the widespread presence of microorganisms in the human body and their crucial impact on human health, with drugs being an effective method of regulation. Hence it is essential to identify potential microbe-drug associ...

Analysis and validation of serum biomarkers in brucellosis patients through proteomics and bioinformatics.

Frontiers in cellular and infection microbiology
INTRODUCTION: This study aims to utilize proteomics, bioinformatics, and machine learning algorithms to identify diagnostic biomarkers in the serum of patients with acute and chronic brucellosis.

UniAMP: enhancing AMP prediction using deep neural networks with inferred information of peptides.

BMC bioinformatics
Antimicrobial peptides (AMPs) have been widely recognized as a promising solution to combat antimicrobial resistance of microorganisms due to the increasing abuse of antibiotics in medicine and agriculture around the globe. In this study, we propose ...

Integrating CNN and Bi-LSTM for protein succinylation sites prediction based on Natural Language Processing technique.

Computers in biology and medicine
Protein succinylation, a post-translational modification wherein a succinyl group (-CO-CH₂-CH₂-CO-) attaches to lysine residues, plays a critical regulatory role in cellular processes. Dysregulated succinylation has been implicated in the onset and p...

AntiT2DMP-Pred: Leveraging feature fusion and optimization for superior machine learning prediction of type 2 diabetes mellitus.

Methods (San Diego, Calif.)
Pancreatic α-amylase breaks down starch into isomaltose and maltose, which are further hydrolyzed by α-glucosidase in the intestine into monosaccharides, rapidly raising blood sugar levels and contributing to type 2 diabetes mellitus (T2DM). Syntheti...

deep-AMPpred: A Deep Learning Method for Identifying Antimicrobial Peptides and Their Functional Activities.

Journal of chemical information and modeling
Antimicrobial peptides (AMPs) are small peptides that play an important role in disease defense. As the problem of pathogen resistance caused by the misuse of antibiotics intensifies, the identification of AMPs as alternatives to antibiotics has beco...

A novel machine learning-based immune prognostic signature for improving clinical outcomes and guiding therapy in colorectal cancer: an integrated bioinformatics and experimental study.

BMC cancer
Immune cells are pivotal components in the tumor microenvironment (TME), which can interact with tumor cells and significantly influence cancer progression and therapeutic outcomes. Therefore, classifying cancer patients based on the status of immune...

SMR-guided molecular subtyping and machine learning model reveals novel prognostic biomarkers and therapeutic targets in non-small cell lung adenocarcinoma.

Scientific reports
Non-small cell lung adenocarcinoma (LUAD) is a markedly heterogeneous disease, with its underlying molecular mechanisms and prognosis prediction presenting ongoing challenges. In this study, we integrated data from multiple public datasets, including...

A robust transfer learning approach for high-dimensional linear regression to support integration of multi-source gene expression data.

PLoS computational biology
Transfer learning aims to integrate useful information from multi-source datasets to improve the learning performance of target data. This can be effectively applied in genomics when we learn the gene associations in a target tissue, and data from ot...

The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models.

PLoS computational biology
Complex deep learning models trained on very large datasets have become key enabling tools for current research in natural language processing and computer vision. By providing pre-trained models that can be fine-tuned for specific applications, they...