AIMC Topic: Protein Processing, Post-Translational

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Predicting the effect of CRISPR-Cas9-based epigenome editing.

eLife
Epigenetic regulation orchestrates mammalian transcription, but functional links between them remain elusive. To tackle this problem, we use epigenomic and transcriptomic data from 13 ENCODE cell types to train machine learning models to predict gene...

The Clinical Prognostic Value of Lactylation-Regulated Proteins in Gastric Cancer.

Journal of proteome research
Gastric cancer (GC) is a leading cause of cancer-related mortality globally. Histone lactylation, an emerging post-translational modification, holds promise as a therapeutic target and prognostic biomarker, though its expression patterns and clinical...

IGFBP7 and CCT2 are novel lactylation-driven mediators of endothelial-to-mesenchymal transition in idiopathic pulmonary fibrosis.

Functional & integrative genomics
Lactylation is a post-translational modification that can influence the onset and progression of various diseases.However, its role in Idiopathic Pulmonary Fibrosis (IPF) has not been systematically investigated. Single-cell sequencing and bulk RNA s...

Integrating machine learning and experimental validation identifies a post-translational modification gene signature for prognosis and treatment response in breast cancer.

Scientific reports
Breast cancer (BC) is the most prevalent malignancy among women, and the steadily increasing disease burden has garnered considerable global attention. Post-translational modifications (PTMs) are critical in the initiation and progression of BC. This...

A deep learning framework for lysine 2-hydroxyisobutyrylation site prediction using evolutionary feature representation.

Scientific reports
Lysine 2-hydroxyisobutyrylation (Khib) has emerged as a crucial Post-Translational Modification (PTM) with significant roles in diverse biological processes ranging from gene expression to metabolic regulation. Despite its importance, computational a...

AIPred: comprehensive prediction and analysis of non-histone acetylation via protein language model and interpretable machine learning.

BMC biology
BACKGROUND: Non-histone lysine acetylation is a widespread protein post-translational modification that regulates almost all key cellular processes, and its dysregulation is closely associated with various human diseases. Precise identification of no...

Rising Stars: Bioinformatics of Post-translational Modifications.

Journal of molecular biology
Yu Xue is a professor in the College of Life Science and Technology at Huazhong University of Science and Technology, and hold a joint position in the Hubei Hongshan Laboratory at Huazhong Agricultural University. He received two B.E. degrees in poly...

Single-cell and spatial transcriptomics reveal post-translational modifications in osteosarcoma progression and tumor microenvironment.

PloS one
Emerging evidence suggests that post-translational modifications (PTMs) contribute to osteosarcoma pathogenesis, yet their exact molecular roles require further elucidation. Using the AddModuleScore method, we classified tumor cells on the basis of P...

Predicting the structural impact of human alternative splicing.

Genome biology
BACKGROUND: Protein structure prediction with neural networks is a powerful new method for linking protein sequence, structure, and function, but structures have generally been predicted for only a single isoform of each gene, neglecting splice varia...

Lactylation associated biomarkers and immune infiltration in aortic dissection.

Scientific reports
Protein lactylation, a novel post-translational modification (PTM), has emerged as a critical factor in disease processes related to glycolysis and immune responses. However, its role in aortic dissection (AD) has yet to be thoroughly investigated. T...