AIMC Topic: Gene Expression Profiling

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sRNARFTarget: a fast machine-learning-based approach for transcriptome-wide sRNA target prediction.

RNA biology
Bacterial small regulatory RNAs (sRNAs) are key regulators of gene expression in many processes related to adaptive responses. A multitude of sRNAs have been identified in many bacterial species; however, their function has yet to be elucidated. A ke...

MFmap: A semi-supervised generative model matching cell lines to tumours and cancer subtypes.

PloS one
Translating in vitro results from experiments with cancer cell lines to clinical applications requires the selection of appropriate cell line models. Here we present MFmap (model fidelity map), a machine learning model to simultaneously predict the c...

A Convolutional Deep Clustering Framework for Gene Expression Time Series.

IEEE/ACM transactions on computational biology and bioinformatics
The functional or regulatory processes within the cell are explicitly governed by the expression levels of a subset of its genes. Gene expression time series captures activities of individual genes over time and aids revealing underlying cellular dyn...

Identifying Molecular Biomarkers for Diseases With Machine Learning Based on Integrative Omics.

IEEE/ACM transactions on computational biology and bioinformatics
Molecular biomarkers are certain molecules or set of molecules that can be of help for diagnosis or prognosis of diseases or disorders. In the past decades, thanks to the advances in high-throughput technologies, a huge amount of molecular 'omics' da...

Genes and regulatory mechanisms associated with experimentally-induced bovine respiratory disease identified using supervised machine learning methodology.

Scientific reports
Bovine respiratory disease (BRD) is a multifactorial disease involving complex host immune interactions shaped by pathogenic agents and environmental factors. Advancements in RNA sequencing and associated analytical methods are improving our understa...

Are we there yet? A machine learning architecture to predict organotropic metastases.

BMC medical genomics
BACKGROUND & AIMS: Cancer metastasis into distant organs is an evolutionarily selective process. A better understanding of the driving forces endowing proliferative plasticity of tumor seeds in distant soils is required to develop and adapt better tr...

Identification of Alzheimer associated differentially expressed gene through microarray data and transfer learning-based image analysis.

Neuroscience letters
Major factors contribute to mental stress and enhance the progression of late-onset Alzheimer's disease (AD). The factors that lead to neurodegeneration, such as tau protein hyperphosphorylation and increased amyloid-beta production, can be mimicked ...

Manifold learning analysis suggests strategies to align single-cell multimodal data of neuronal electrophysiology and transcriptomics.

Communications biology
Recent single-cell multimodal data reveal multi-scale characteristics of single cells, such as transcriptomics, morphology, and electrophysiology. However, integrating and analyzing such multimodal data to deeper understand functional genomics and ge...

Discriminating Neoplastic from Nonneoplastic Tissues Using an miRNA-Based Deep Cancer Classifier.

The American journal of pathology
Next-generation sequencing has enabled the collection of large biological data sets, allowing novel molecular-based classification methods to be developed for increased understanding of disease. miRNAs are small regulatory RNA molecules that can be q...