AIMC Topic: Proteomics

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Machine Learning-Based Radiomics in Malignancy Prediction of Pancreatic Cystic Lesions: Evidence from Cyst Fluid Multi-Omics.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)
The malignant potential of pancreatic cystic lesions (PCLs) varies dramatically, leading to difficulties when making clinical decisions. This study aimed to develop noninvasive clinical-radiomic models using preoperative CT images to predict the mali...

Mapping the rapid growth of multi-omics in tumor immunotherapy: Bibliometric evidence of technology convergence and paradigm shifts.

Human vaccines & immunotherapeutics
This study aims to fill the knowledge gap in systematically mapping the evolution of omics-driven tumor immunotherapy research through a bibliometric lens. While omics technologies (genomics, transcriptomics, proteomics, metabolomics)provide multidim...

Identification of pivotal genes and regulatory networks associated with SAH based on multi-omics analysis and machine learning.

Scientific reports
Subarachnoid hemorrhage (SAH) is a disease with high mortality and morbidity, and its pathophysiology is complex but poorly understood. To investigate the potential therapeutic targets post-SAH, the SAH-related feature genes were screened by the comb...

Deconvolution of cell types and states in spatial multiomics utilizing TACIT.

Nature communications
Identifying cell types and states remains a time-consuming, error-prone challenge for spatial biology. While deep learning increasingly plays a role, it is difficult to generalize due to variability at the level of cells, neighborhoods, and niches in...

Deep Learning-Based Prediction of Decoy Spectra for False Discovery Rate Estimation in Spectral Library Searching.

Journal of proteome research
With the advantage of extensive coverage, predicted spectral libraries are becoming an attractive alternative in proteomic data analysis. As a popular false discovery rate estimation method, target decoy search has been adopted in library search work...

Deep Visual Proteomics maps proteotoxicity in a genetic liver disease.

Nature
Protein misfolding diseases, including α1-antitrypsin deficiency (AATD), pose substantial health challenges, with their cellular progression still poorly understood. We use spatial proteomics by mass spectrometry and machine learning to map AATD in h...

A strategy for multimodal integration of transcriptomics, proteomics, and radiomics data for the prediction of recurrence in patients with IDH-mutant gliomas.

International journal of cancer
Isocitrate dehydrogenase-mutant gliomas are lethal brain cancers that impair quality of life in young adults. Although less aggressive than glioblastomas, IDH-mutant gliomas invariably progress to incurable disease with unpredictable recurrence. A be...

Peptide Property Prediction for Mass Spectrometry Using AI: An Introduction to State of the Art Models.

Proteomics
This review explores state of the art machine learning and deep learning models for peptide property prediction in mass spectrometry-based proteomics, including, but not limited to, models for predicting digestibility, retention time, charge state di...

How did we get there? AI applications to biological networks and sequences.

Computers in biology and medicine
The rapidly advancing field of artificial intelligence (AI) has transformed numerous scientific domains, including biology, where a vast and complex volume of data is available for analysis. This paper provides a comprehensive overview of the current...

Pancreatic Cancer Detection and Differentiation from Chronic Pancreatitis: Potential Biomarkers Identified through a High-Throughput Multiplex Proteomic Assay and Machine Learning-Based Analysis.

Annals of laboratory medicine
BACKGROUND: Pancreatic cancer (PC)-screening methods have limited accuracy despite their high clinical demand. Differential diagnosis of chronic pancreatitis (CP) poses another challenge for PC diagnosis. Therefore, we aimed to identify blood protein...