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Computational Biology

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Identification of lipid metabolism related immune markers in atherosclerosis through machine learning and experimental analysis.

Frontiers in immunology
BACKGROUND: Atherosclerosis is a significant contributor to cardiovascular disease, and conventional diagnostic methods frequently fall short in the timely and accurate detection of early-stage atherosclerosis. Abnormal lipid metabolism plays a criti...

DeepTree-AAPred: Binary tree-based deep learning model for anti-angiogenic peptides prediction.

Journal of molecular graphics & modelling
Anti-angiogenic peptides (AAPs) show important potential in tumor therapy by limiting the growth and metastasis of tumor cells. Accurate prediction of AAPs is of very positive significance for the therapeutic efficacy of tumors. The high cost of wet ...

A novel coarsened graph learning method for scalable single-cell data analysis.

Computers in biology and medicine
The emergence of single-cell technologies, including flow and mass cytometry, as well as single-cell RNA sequencing, has revolutionized the study of cellular heterogeneity, generating vast datasets rich in biological insights. Despite the effectivene...

Identification of Biomarkers for Response to Interferon in Chronic Hepatitis B Based on Bioinformatics Analysis and Machine Learning.

Viral immunology
Interferon (IFN) is a pivotal agent against hepatitis B virus (HBV) in clinic, but there is a lack of accurate biomarkers to predict the response to IFN therapy in patients with chronic hepatitis B (CHB). Our study aimed to investigate potential targ...

Atrial fibrillation risk model based on LASSO and SVM algorithms and immune infiltration of key mitochondrial energy metabolism genes.

Scientific reports
Atrial fibrillation (AF) is a predominant cardiac arrhythmia with unclear etiology. This study used bioinformatics and machine learning to explore the relationship between mitochondrial energy metabolism-related genes (MEMRGs) and immune infiltration...

Peptide classification landscape: An in-depth systematic literature review on peptide types, databases, datasets, predictors architectures and performance.

Computers in biology and medicine
Peptides are gaining significant attention in diverse fields such as the pharmaceutical market has seen a steady rise in peptide-based therapeutics over the past six decades. Peptides have been utilized in the development of distinct applications inc...

Machine learning-based characterization of PANoptosis-related biomarkers and immune infiltration in ulcerative colitis: A comprehensive bioinformatics analysis and experimental validation.

International immunopharmacology
Ulcerative colitis (UC) is a heterogeneous autoimmune condition. PANoptosis, a new form of programmed cell death, plays a role in inflammatory diseases. This study aimed to identify differentially expressed PANoptosis-related genes (PRGs) involved in...

Teaching AI to speak protein.

Current opinion in structural biology
Large Language Models for proteins, namely protein Language Models (pLMs), have begun to provide an important alternative to capturing the information encoded in a protein sequence in computers. Arguably, pLMs have advanced importantly to understandi...

EC2Vec: A Machine Learning Method to Embed Enzyme Commission (EC) Numbers into Vector Representations.

Journal of chemical information and modeling
Enzyme commission (EC) numbers play a vital role in classifying enzymes and understanding their functions in enzyme-related research. Although accurate and informative encoding of EC numbers is essential for enhancing the effectiveness of machine lea...

An ensemble deep learning framework for multi-class LncRNA subcellular localization with innovative encoding strategy.

BMC biology
BACKGROUND: Long non-coding RNA (LncRNA) play pivotal roles in various cellular processes, and elucidating their subcellular localization can offer crucial insights into their functional significance. Accurate prediction of lncRNA subcellular localiz...