AIMC Topic: Cell Line, Tumor

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Spatial and temporal dynamics of RhoA activities of single breast tumor cells in a 3D environment revealed by a machine learning-assisted FRET technique.

Experimental cell research
One of the hallmarks of cancer cells is their exceptional ability to migrate within the extracellular matrix (ECM) for gaining access to the circulatory system, a critical step of cancer metastasis. RhoA, a small GTPase, is known to be a key molecula...

DeepPhospho accelerates DIA phosphoproteome profiling through in silico library generation.

Nature communications
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...

Cell-morphodynamic phenotype classification with application to cancer metastasis using cell magnetorotation and machine-learning.

PloS one
We define cell morphodynamics as the cell's time dependent morphology. It could be called the cell's shape shifting ability. To measure it we use a biomarker free, dynamic histology method, which is based on multiplexed Cell Magneto-Rotation and Mach...

Establishment of a 13 genes-based molecular prediction score model to discriminate the neurotoxic potential of food relevant-chemicals.

Toxicology letters
Although many neurotoxicity prediction studies of food additives have been developed, they are applicable in a qualitative way. We aimed to develop a novel prediction score that is described quantitatively and precisely. We examined cell viability, r...

Deep learning-based classification of preclinical breast cancer tumor models using chemical exchange saturation transfer magnetic resonance imaging.

NMR in biomedicine
Chemical exchange saturation transfer (CEST) magnetic resonance imaging has shown promise for classifying tumors based on their aggressiveness, but CEST contrast is complicated by multiple signal sources and thus prolonged acquisition times are often...

Rapid, label-free classification of tumor-reactive T cell killing with quantitative phase microscopy and machine learning.

Scientific reports
Quantitative phase microscopy (QPM) enables studies of living biological systems without exogenous labels. To increase the utility of QPM, machine-learning methods have been adapted to extract additional information from the quantitative phase data. ...

Machine Learning Assisted Classification of Cell Lines and Cell States on Quantitative Phase Images.

Cells
In this report, we present implementation and validation of machine-learning classifiers for distinguishing between cell types (HeLa, A549, 3T3 cell lines) and states (live, necrosis, apoptosis) based on the analysis of optical parameters derived fro...

Time-resolved in vivo ubiquitinome profiling by DIA-MS reveals USP7 targets on a proteome-wide scale.

Nature communications
Mass spectrometry (MS)-based ubiquitinomics provides system-level understanding of ubiquitin signaling. Here we present a scalable workflow for deep and precise in vivo ubiquitinome profiling, coupling an improved sample preparation protocol with dat...

Predicting drug sensitivity of cancer cells based on DNA methylation levels.

PloS one
Cancer cell lines, which are cell cultures derived from tumor samples, represent one of the least expensive and most studied preclinical models for drug development. Accurately predicting drug responses for a given cell line based on molecular featur...

Uncovering cancer vulnerabilities by machine learning prediction of synthetic lethality.

Molecular cancer
BACKGROUND: Synthetic lethality describes a genetic interaction between two perturbations, leading to cell death, whereas neither event alone has a significant effect on cell viability. This concept can be exploited to specifically target tumor cells...