AIMC Topic: Proteomics
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Peptide Property Prediction for Mass Spectrometry Using AI: An Introduction to State of the Art Models.
Proteomics
Apr 10, 2025
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
Apr 3, 2025
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
Apr 2, 2025
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...
Amogel: a multi-omics classification framework using associative graph neural networks with prior knowledge for biomarker identification.
BMC bioinformatics
Mar 28, 2025
The advent of high-throughput sequencing technologies, such as DNA microarray and DNA sequencing, has enabled effective analysis of cancer subtypes and targeted treatment. Furthermore, numerous studies have highlighted the capability of graph neural ...
Imaging and spatially resolved mass spectrometry applications in nephrology.
Nature reviews. Nephrology
Mar 27, 2025
The application of spatially resolved mass spectrometry (MS) and MS imaging approaches for studying biomolecular processes in the kidney is rapidly growing. These powerful methods, which enable label-free and multiplexed detection of many molecular c...
Systems biology of Haemonchus contortus - Advancing biotechnology for parasitic nematode control.
Biotechnology advances
Mar 22, 2025
Parasitic nematodes represent a substantial global burden, impacting animal health, agriculture and economies worldwide. Of these worms, Haemonchus contortus - a blood-feeding nematode of ruminants - is a major pathogen and a model for molecular and ...
Plasma Proteomic Profiles Predict Individual Future Osteoarthritis Risk.
Arthritis & rheumatology (Hoboken, N.J.)
Mar 20, 2025
OBJECTIVE: Osteoarthritis (OA) is a widespread degenerative joint disease that causes a considerable socioeconomic burden. Despite progress in genetic and environmental insights, early diagnosis is still limited by the lack of evident symptoms during...
Deciphering the dark cancer phosphoproteome using machine-learned co-regulation of phosphosites.
Nature communications
Mar 20, 2025
Mass spectrometry-based phosphoproteomics offers a comprehensive view of protein phosphorylation, yet our limited knowledge about the regulation and function of most phosphosites hampers the extraction of meaningful biological insights. To address th...
The IBEX Knowledge-Base: A central resource for multiplexed imaging techniques.
PLoS biology
Mar 19, 2025
Multiplexed imaging is a powerful approach in spatial biology, although it is complex, expensive and labor-intensive. Here, we present the IBEX Knowledge-Base, a central resource for reagents, protocols and more, to enhance knowledge sharing, optimiz...
Proteomics and Machine Learning-Based Approach to Decipher Subcellular Proteome of Mouse Heart.
Molecular & cellular proteomics : MCP
Mar 18, 2025
Protein compartmentalization to distinctive subcellular niches is critical for cardiac function and homeostasis. Here, we employed a rapid and robust workflow based on differential centrifugal-based fractionation with mass spectrometry-based proteomi...
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