AIMC Topic: Cell Line, Tumor

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Machine-Learning Provides Patient-Specific Prediction of Metastatic Risk Based on Innovative, Mechanobiology Assay.

Annals of biomedical engineering
Cancer mortality is mostly related to metastasis. Metastasis is currently prognosed via histopathology, disease-statistics, or genetics; those are potentially inaccurate, not rapidly available and require known markers. We had developed a rapid (~ 2 ...

MethylationToActivity: a deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors.

Genome biology
Although genome-wide DNA methylomes have demonstrated their clinical value as reliable biomarkers for tumor detection, subtyping, and classification, their direct biological impacts at the individual gene level remain elusive. Here we present Methyla...

Phytochemical, antibacterial, antioxidant and cytoxicity investigation of .

Zeitschrift fur Naturforschung. C, Journal of biosciences
The phytochemical investigation of led to the isolation of 18 known compounds of which were four flavones, three anthraquinones, one phenyl propanoic derivative, five triterpenoids, four steroids and a mixture of glucose. Luteolin () and soranjidiol...

Phase imaging with computational specificity (PICS) for measuring dry mass changes in sub-cellular compartments.

Nature communications
Due to its specificity, fluorescence microscopy has become a quintessential imaging tool in cell biology. However, photobleaching, phototoxicity, and related artifacts continue to limit fluorescence microscopy's utility. Recently, it has been shown t...

Super resolution microscopy and deep learning identify Zika virus reorganization of the endoplasmic reticulum.

Scientific reports
The endoplasmic reticulum (ER) is a complex subcellular organelle composed of diverse structures such as tubules, sheets and tubular matrices. Flaviviruses such as Zika virus (ZIKV) induce reorganization of ER membranes to facilitate viral replicatio...

Leveraging multi-way interactions for systematic prediction of pre-clinical drug combination effects.

Nature communications
We present comboFM, a machine learning framework for predicting the responses of drug combinations in pre-clinical studies, such as those based on cell lines or patient-derived cells. comboFM models the cell context-specific drug interactions through...

Image-based phenotyping of disaggregated cells using deep learning.

Communications biology
The ability to phenotype cells is fundamentally important in biological research and medicine. Current methods rely primarily on fluorescence labeling of specific markers. However, there are many situations where this approach is unavailable or undes...

DeepciRGO: functional prediction of circular RNAs through hierarchical deep neural networks using heterogeneous network features.

BMC bioinformatics
BACKGROUND: Circular RNAs (circRNAs) are special noncoding RNA molecules with closed loop structures. Compared with the traditional linear RNA, circRNA is more stable and not easily degraded. Many studies have shown that circRNAs are involved in the ...

Quantitative Structure-Mutation-Activity Relationship Tests (QSMART) model for protein kinase inhibitor response prediction.

BMC bioinformatics
BACKGROUND: Protein kinases are a large family of druggable proteins that are genomically and proteomically altered in many human cancers. Kinase-targeted drugs are emerging as promising avenues for personalized medicine because of the differential r...

H-RACS: a handy tool to rank anti-cancer synergistic drugs.

Aging
Though promising, identifying synergistic combinations from a large pool of candidate drugs remains challenging for cancer treatment. Due to unclear mechanism and limited confirmed cases, only a few computational algorithms are able to predict drug s...