AIMC Topic: Proteome
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Functional annotation and biological interpretation of proteomics data.
Biochimica et biophysica acta
Oct 31, 2014
Proteomics experiments often generate a vast amount of data. However, the simple identification and quantification of proteins from a cell proteome or subproteome is not sufficient for the full understanding of complex mechanisms occurring in the bio...
TopCysteineDB: A Cysteinome-wide Database Integrating Structural and Chemoproteomics Data for Cysteine Ligandability Prediction.
Journal of molecular biology
Aug 1, 2025
Development of targeted covalent inhibitors and covalent ligand-first approaches have emerged as a powerful strategy in drug design, with cysteines being attractive targets due to their nucleophilicity and relative scarcity. While structural biology ...
Uncovering hepatic transcriptomic and circulating proteomic signatures in MASH: A meta-analysis and machine learning-based biomarker discovery.
Computers in biology and medicine
Jun 1, 2025
BACKGROUND: Metabolic-associated steatohepatitis (MASH), the progressive form of metabolic-associated steatotic liver disease (MASLD), poses significant risks for liver fibrosis and cardiovascular complications. Despite extensive research, reliable b...
[Serum proteomics and machine learning unveil new diagnostic biomarkers for tuberculosis in adolescents and young adults].
Sheng wu gong cheng xue bao = Chinese journal of biotechnology
Apr 25, 2025
Adolescents and young adults (AYAs) are one of the major populations susceptible to tuberculosis. However, little is known about the unique characteristics and diagnostic biomarkers of tuberculosis in this population. In this study, 81 AYAs were recr...
AtSubP-2.0: An integrated web server for the annotation of Arabidopsis proteome subcellular localization using deep learning.
The plant genome
Mar 1, 2025
The organization of subcellular components in a cell is critical for its function and studying cellular processes, protein-protein interactions, identifying potential drug targets, network analysis, and other systems biology mechanisms. Determining p...
UniProt: the Universal Protein Knowledgebase in 2025.
Nucleic acids research
Jan 6, 2025
The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/) is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication, we describe o...
OrgXenomics: an integrated proteomic knowledge base for patient-derived organoid and xenograft.
Nucleic acids research
Jan 6, 2025
Patient-derived models (PDMs, particularly organoids and xenografts) are irreplaceable tools for precision medicine, from target development to lead identification, then to preclinical evaluation, and finally to clinical decision-making. So far, PDM-...
Artificial intelligence and omics-based autoantibody profiling in dementia.
Frontiers in immunology
Jan 1, 2025
INTRODUCTION: Dementia is a neurodegenerative syndrome marked by the accumulation of disease-specific proteins and immune dysregulation, including autoimmune mechanisms involving autoantibodies. Current diagnostic methods are often invasive, time-con...
Sitetack: a deep learning model that improves PTM prediction by using known PTMs.
Bioinformatics (Oxford, England)
Nov 1, 2024
MOTIVATION: Post-translational modifications (PTMs) increase the diversity of the proteome and are vital to organismal life and therapeutic strategies. Deep learning has been used to predict PTM locations. Still, limitations in datasets and their ana...
Machine learning-based analysis identifies and validates serum exosomal proteomic signatures for the diagnosis of colorectal cancer.
Cell reports. Medicine
Aug 20, 2024
The potential of serum extracellular vesicles (EVs) as non-invasive biomarkers for diagnosing colorectal cancer (CRC) remains elusive. We employed an in-depth 4D-DIA proteomics and machine learning (ML) pipeline to identify key proteins, PF4 and AACT...
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