AIMC Topic: Phosphoproteins
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Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model.
Cell genomics
Apr 1, 2025
Signaling pathway components are well studied, but how they mediate cell-type-specific transcription responses is an unresolved problem. Using the Hippo pathway in mouse trophoblast stem cells as a model, we show that the DNA binding of signaling eff...
Mice
Signal Transduction
Transcription Factors
Protein Serine-Threonine Kinases
Adaptor Proteins, Signal Transducing
Animals
Deep Learning
Protein Binding
Enhancer Elements, Genetic
Muscle Proteins
Hippo Signaling Pathway
YAP-Signaling Proteins
TEA Domain Transcription Factors
DNA-Binding Proteins
Molecular Dynamics Simulation
Phosphoproteins
Trophoblasts
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...
Empirical Comparison and Analysis of Artificial Intelligence-Based Methods for Identifying Phosphorylation Sites of SARS-CoV-2 Infection.
International journal of molecular sciences
Dec 21, 2024
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a member of the large coronavirus family with high infectivity and pathogenicity and is the primary pathogen causing the global pandemic of coronavirus disease 2019 (COVID-19). Phosphory...
DeepPhoPred: Accurate Deep Learning Model to Predict Microbial Phosphorylation.
Proteins
Sep 6, 2024
Phosphorylation is a substantial posttranslational modification of proteins that refers to adding a phosphate group to the amino acid side chain after translation process in the ribosome. It is vital to coordinate cellular functions, such as regulati...
Prediction of molecular subclasses of uveal melanoma by deep learning using routine haematoxylin-eosin-stained tissue slides.
Histopathology
Jul 1, 2024
AIMS: Uveal melanoma has a high propensity to metastasize. Prognosis is associated with specific driver mutations and copy number variations, and these can only be obtained after genetic testing. In this study we evaluated the efficacy of patient out...
Eukaryotic Initiation Factor-1
RNA Splicing Factors
Uveal Neoplasms
Ubiquitin Thiolesterase
Uveal Melanoma
Male
Middle Aged
Deep Learning
Staining and Labeling
Tumor Suppressor Proteins
Eosine Yellowish-(YS)
Hematoxylin
Mutation
Phosphoproteins
Melanoma
Aged
Aged, 80 and over
Adult
Humans
Prognosis
Retrospective Studies
Female
Effects of exogenous energy on synthesis of steroid hormones and expression characteristics of the CREB/StAR signaling pathway in theca cells of laying hen.
Poultry science
Dec 30, 2023
Energy and the cAMP-response element binding protein (CREB)/steroidogenic acute regulatory protein (StAR) signaling pathway play important roles in steroid hormone production and follicular development in hens. This present study aimed to investigate...
A Transfer-Learning-Based Deep Convolutional Neural Network for Predicting Leukemia-Related Phosphorylation Sites from Protein Primary Sequences.
International journal of molecular sciences
Feb 3, 2022
As one of the most important post-translational modifications (PTMs), phosphorylation refers to the binding of a phosphate group with amino acid residues like Ser (S), Thr (T) and Tyr (Y) thus resulting in diverse functions at the molecular level. Ab...
A novel strategy to uncover specific GO terms/phosphorylation pathways in phosphoproteomic data in Arabidopsis thaliana.
BMC plant biology
Dec 14, 2021
BACKGROUND: Proteins are the workforce of the cell and their phosphorylation status tailors specific responses efficiently. One of the main challenges of phosphoproteomic approaches is to deconvolute biological processes that specifically respond to ...
DeepPhospho accelerates DIA phosphoproteome profiling through in silico library generation.
Nature communications
Nov 18, 2021
Phosphoproteomics integrating data-independent acquisition (DIA) enables deep phosphoproteome profiling with improved quantification reproducibility and accuracy compared to data-dependent acquisition (DDA)-based phosphoproteomics. DIA data mining he...
NIgPred: Class-Specific Antibody Prediction for Linear B-Cell Epitopes Based on Heterogeneous Features and Machine-Learning Approaches.
Viruses
Aug 3, 2021
Upon invasion by foreign pathogens, specific antibodies can identify specific foreign antigens and disable them. As a result of this ability, antibodies can help with vaccine production and food allergen detection in patients. Many studies have focus...
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