AIMC Topic: Transcriptome

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KanCell: dissecting cellular heterogeneity in biological tissues through integrated single-cell and spatial transcriptomics.

Journal of genetics and genomics = Yi chuan xue bao
KanCell is a deep learning model based on Kolmogorov-Arnold networks (KAN) designed to enhance cellular heterogeneity analysis by integrating single-cell RNA sequencing and spatial transcriptomics (ST) data. ST technologies provide insights into gene...

Mapping the topography of spatial gene expression with interpretable deep learning.

Nature methods
Spatially resolved transcriptomics technologies provide high-throughput measurements of gene expression in a tissue slice, but the sparsity of these data complicates analysis of spatial gene expression patterns. We address this issue by deriving a to...

Identification of potential biomarkers for 2022 Mpox virus infection: a transcriptomic network analysis and machine learning approach.

Scientific reports
Monkeypox virus (MPXV), a zoonotic pathogen, re-emerged in 2022 with the Clade IIb variant, raising global health concerns due to its unprecedented spread in non-endemic regions. Recent studies have shown that Clade IIb (2022 MPXV) is marked by uniqu...

Identification and validation of immune and diagnostic biomarkers for interstitial cystitis/painful bladder syndrome by integrating bioinformatics and machine-learning.

Frontiers in immunology
BACKGROUND: The etiology of interstitial cystitis/painful bladder syndrome (IC/BPS) remains elusive, presenting significant challenges in both diagnosis and treatment. To address these challenges, we employed a comprehensive approach aimed at identif...

Identification and validation of glycolysis-related diagnostic signatures in diabetic nephropathy: a study based on integrative machine learning and single-cell sequence.

Frontiers in immunology
BACKGROUND: Diabetic nephropathy (DN) is a complication of systemic microvascular disease in diabetes mellitus. Abnormal glycolysis has emerged as a potential factor for chronic renal dysfunction in DN. The current lack of reliable predictive biomark...

Inferring disease progression stages in single-cell transcriptomics using a weakly supervised deep learning approach.

Genome research
Application of single-cell/nucleus genomic sequencing to patient-derived tissues offers potential solutions to delineate disease mechanisms in humans. However, individual cells in patient-derived tissues are in different pathological stages, and henc...

Analyzing the relationship between gene expression and phenotype in space-flown mice using a causal inference machine learning ensemble.

Scientific reports
Spaceflight has several detrimental effects on human and rodent health. For example, liver dysfunction is a common phenotype observed in space-flown rodents, and this dysfunction is partially reflected in transcriptomic changes. Studies linking trans...

Biologically relevant integration of transcriptomics profiles from cancer cell lines, patient-derived xenografts, and clinical tumors using deep learning.

Science advances
Cell lines and patient-derived xenografts are essential to cancer research; however, the results derived from such models often lack clinical translatability, as they do not fully recapitulate the complex cancer biology. Identifying preclinical model...

SenPred: a single-cell RNA sequencing-based machine learning pipeline to classify deeply senescent dermal fibroblast cells for the detection of an in vivo senescent cell burden.

Genome medicine
BACKGROUND: Senescence classification is an acknowledged challenge within the field, as markers are cell-type and context dependent. Currently, multiple morphological and immunofluorescence markers are required. However, emerging scRNA-seq datasets h...

Epigenetic profiling for prognostic stratification and personalized therapy in breast cancer.

Frontiers in immunology
BACKGROUND: The rising incidence of breast cancer and its heterogeneity necessitate precise tools for predicting patient prognosis and tailoring personalized treatments. Epigenetic changes play a critical role in breast cancer progression and therapy...