AIMC Topic: Phase Separation

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Multi-omics and machine learning refine HCC molecular subtypes and prognosis based on liquid-liquid phase separation related genes.

Scientific reports
Accumulating evidence has demonstrated that biological processes associated with liquid-liquid phase separation (LLPS) play a critical role in cancer development. However, the effect of LLPS on hepatocellular carcinoma (HCC) remains largely unknown. ...

When is Not Enough: Evaluating Simple Metrics for Predicting Phase Separation of Intrinsically Disordered Proteins.

The journal of physical chemistry. B
Understanding and predicting the phase behavior of intrinsically disordered proteins (IDPs) is of significant interest due to their role in many biological processes. However, effectively characterizing phase behavior and its complex dependence on pr...

Comprehensive protein datasets and benchmarking for liquid-liquid phase separation studies.

Genome biology
BACKGROUND: Proteins self-organize in dynamic cellular environments by assembling into reversible biomolecular condensates through liquid-liquid phase separation (LLPS). These condensates can comprise single or multiple proteins, with different roles...

Machine learning-informed liquid-liquid phase separation for personalized breast cancer treatment assessment.

Frontiers in immunology
BACKGROUND: Breast cancer, characterized by its heterogeneity, is a leading cause of mortality among women. The study aims to develop a Machine Learning-Derived Liquid-Liquid Phase Separation (MDLS) model to enhance the prognostic accuracy and person...

Decoding Missense Variants by Incorporating Phase Separation via Machine Learning.

Nature communications
Computational models have made significant progress in predicting the effect of protein variants. However, deciphering numerous variants of uncertain significance (VUS) located within intrinsically disordered regions (IDRs) remains challenging. To ad...

Exploring liquid-liquid phase separation-related diagnostic biomarkers in osteoarthritis based on machine learning algorithms and experiment.

Immunobiology
BACKGROUND: Osteoarthritis (OA) is a prevalent joint disorder characterized by cartilage degeneration and joint inflammation. Liquid-liquid phase separation (LLPS), a biophysical process involved in cellular organization, has recently gained attentio...

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Proteomics
RNA-dependent liquid-liquid phase separation (LLPS) proteins play critical roles in cellular processes such as stress granule formation, DNA repair, RNA metabolism, germ cell development, and protein translation regulation. The abnormal behavior of t...

Mining phase separation-related diagnostic biomarkers for endometriosis through WGCNA and multiple machine learning techniques: a retrospective and nomogram study.

Journal of assisted reproduction and genetics
OBJECTIVE: The objective of this study was to investigate the role of phase separation-related genes in the development of endometriosis (EMs) and to identify potential characteristic genes associated with the condition.

Leveraging machine learning and single-cell RNA sequencing strategies to develop a risk prognosis scoring based on liquid-liquid phase separation feature genes in pediatric hepatoblastoma.

Computers in biology and medicine
BACKGROUND: Considerable evidence highlights the intricate association between liquid-liquid phase separation (LLPS) and tumorigenesis, progression, and therapy resistance. However, there has been limited exploration of the role of LLPS in hepatoblas...

MambaPhase: deep learning for liquid-liquid phase separation protein classification.

Briefings in bioinformatics
Liquid-liquid phase separation plays a critical role in cellular processes, including protein aggregation and RNA metabolism, by forming membraneless subcellular structures. Accurate identification of phase-separated proteins is essential for underst...