AIMC Topic: Phosphoproteins
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A deep learning based approach for prediction of Chlamydomonas reinhardtii phosphorylation sites.
Scientific reports
Jun 15, 2021
Protein phosphorylation, which is one of the most important post-translational modifications (PTMs), is involved in regulating myriad cellular processes. Herein, we present a novel deep learning based approach for organism-specific protein phosphoryl...
Deep Transfer Learning Approach for Automatic Recognition of Drug Toxicity and Inhibition of SARS-CoV-2.
Viruses
Apr 2, 2021
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes COVID-19 and is responsible for the ongoing pandemic. Screening of potential antiviral drugs against SARS-CoV-2 depend on in vitro experiments, which are based on the quantification ...
Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics.
Cell systems
Jul 24, 2020
Cancer is driven by genomic alterations, but the processes causing this disease are largely performed by proteins. However, proteins are harder and more expensive to measure than genes and transcripts. To catalyze developments of methods to infer pro...
GPS-PBS: A Deep Learning Framework to Predict Phosphorylation Sites that Specifically Interact with Phosphoprotein-Binding Domains.
Cells
May 20, 2020
Protein phosphorylation is essential for regulating cellular activities by modifying substrates at specific residues, which frequently interact with proteins containing phosphoprotein-binding domains (PPBDs) to propagate the phosphorylation signaling...
Prediction of tumor location in prostate cancer tissue using a machine learning system on gene expression data.
BMC bioinformatics
Mar 11, 2020
BACKGROUND: Finding the tumor location in the prostate is an essential pathological step for prostate cancer diagnosis and treatment. The location of the tumor - the laterality - can be unilateral (the tumor is affecting one side of the prostate), or...
Deconvolution of subcellular protrusion heterogeneity and the underlying actin regulator dynamics from live cell imaging.
Nature communications
Apr 27, 2018
Cell protrusion is morphodynamically heterogeneous at the subcellular level. However, the mechanism of cell protrusion has been understood based on the ensemble average of actin regulator dynamics. Here, we establish a computational framework called ...
Humans
Machine Learning
Software
Animals
Cell Adhesion Molecules
Actin Cytoskeleton
Intravital Microscopy
Actin-Related Protein 2-3 Complex
Microfilament Proteins
Potoroidae
Pseudopodia
Vasodilator-Stimulated Phosphoprotein
Models, Biological
Phosphoproteins
Cell Line, Tumor
Indoles
Cell Movement
Actins
Cluster Analysis
Cell Line
AdaSampling for Positive-Unlabeled and Label Noise Learning With Bioinformatics Applications.
IEEE transactions on cybernetics
Apr 2, 2018
Class labels are required for supervised learning but may be corrupted or missing in various applications. In binary classification, for example, when only a subset of positive instances is labeled whereas the remaining are unlabeled, positive-unlabe...
Melatonin stimulates the secretion of progesterone along with the expression of cholesterol side-chain cleavage enzyme (P450scc) and steroidogenic acute regulatory protein (StAR) in corpus luteum of pregnant sows.
Theriogenology
Dec 16, 2017
The direct effect of melatonin on porcine luteal function during the pregnancy remains unknown. The objective of the study was to analyse the molecular mechanism(s) by which melatonin directly affects progesterone (P4) production in the corpus luteum...
Machine Learning of Global Phosphoproteomic Profiles Enables Discrimination of Direct versus Indirect Kinase Substrates.
Molecular & cellular proteomics : MCP
Mar 6, 2017
Mass spectrometry allows quantification of tens of thousands of phosphorylation sites from minute amounts of cellular material. Despite this wealth of information, our understanding of phosphorylation-based signaling is limited, in part because it is...
Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data.
PLoS computational biology
Aug 7, 2015
Cell signaling underlies transcription/epigenetic control of a vast majority of cell-fate decisions. A key goal in cell signaling studies is to identify the set of kinases that underlie key signaling events. In a typical phosphoproteomics study, phos...
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