AIMC Topic: RNA-Seq

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Machine-learning and scRNA-Seq-based diagnostic and prognostic models illustrating survival and therapy response of lung adenocarcinoma.

Genes and immunity
Lung cancer is a major cause accounting for cancer-related mortalities, with lung adenocarcinoma (LUAD) being the most prevalent subtype. Given the high clinical and cellular heterogeneities of LUAD, accurate diagnosis and prognosis are crucial to av...

Robust evaluation of deep learning-based representation methods for survival and gene essentiality prediction on bulk RNA-seq data.

Scientific reports
Deep learning (DL) has shown potential to provide powerful representations of bulk RNA-seq data in cancer research. However, there is no consensus regarding the impact of design choices of DL approaches on the performance of the learned representatio...

TabDEG: Classifying differentially expressed genes from RNA-seq data based on feature extraction and deep learning framework.

PloS one
Traditional differential expression genes (DEGs) identification models have limitations in small sample size datasets because they require meeting distribution assumptions, otherwise resulting high false positive/negative rates due to sample variatio...

NNICE: a deep quantile neural network algorithm for expression deconvolution.

Scientific reports
The composition of cell-type is a key indicator of health. Advancements in bulk gene expression data curation, single cell RNA-sequencing technologies, and computational deconvolution approaches offer a new perspective to learn about the composition ...

DCRELM: dual correlation reduction network-based extreme learning machine for single-cell RNA-seq data clustering.

Scientific reports
Single-cell ribonucleic acid sequencing (scRNA-seq) is a high-throughput genomic technique that is utilized to investigate single-cell transcriptomes. Cluster analysis can effectively reveal the heterogeneity and diversity of cells in scRNA-seq data,...

Identification of Marker Genes in Infectious Diseases from ScRNA-seq Data Using Interpretable Machine Learning.

International journal of molecular sciences
A common result of infection is an abnormal immune response, which may be detrimental to the host. To control the infection, the immune system might undergo regulation, therefore producing an excess of either pro-inflammatory or anti-inflammatory pat...

A deep learning framework for denoising and ordering scRNA-seq data using adversarial autoencoder with dynamic batching.

STAR protocols
Single-cell RNA sequencing (scRNA-seq) provides high resolution of cell-to-cell variation in gene expression and offers insights into cell heterogeneity, differentiating dynamics, and disease mechanisms. However, technical challenges such as low capt...

Unveiling the molecular complexity of proliferative diabetic retinopathy through scRNA-seq, AlphaFold 2, and machine learning.

Frontiers in endocrinology
BACKGROUND: Proliferative diabetic retinopathy (PDR), a major cause of blindness, is characterized by complex pathogenesis. This study integrates single-cell RNA sequencing (scRNA-seq), Non-negative Matrix Factorization (NMF), machine learning, and A...

A comparison of RNA-Seq data preprocessing pipelines for transcriptomic predictions across independent studies.

BMC bioinformatics
BACKGROUND: RNA sequencing combined with machine learning techniques has provided a modern approach to the molecular classification of cancer. Class predictors, reflecting the disease class, can be constructed for known tissue types using the gene ex...

Analysis of Bladder Cancer Staging Prediction Using Deep Residual Neural Network, Radiomics, and RNA-Seq from High-Definition CT Images.

Genetics research
Bladder cancer has recently seen an alarming increase in global diagnoses, ascending as a predominant cause of cancer-related mortalities. Given this pressing scenario, there is a burgeoning need to identify effective biomarkers for both the diagnosi...