Systems Biology in Cancer Diagnosis Integrating Omics Technologies and Artificial Intelligence to Support Physician Decision Making

A Fawaz, A Ferraresi, C Isidoro - Journal of Personalized Medicine, 2023 - mdpi.com
Cancer is the second major cause of disease-related death worldwide, and its accurate
early diagnosis and therapeutic intervention are fundamental for saving the patient's life …

Identifying tumor cells at the single-cell level using machine learning

J Dohmen, A Baranovskii, J Ronen, B Uyar, V Franke… - Genome Biology, 2022 - Springer
Tumors are complex tissues of cancerous cells surrounded by a heterogeneous cellular
microenvironment with which they interact. Single-cell sequencing enables molecular …

Single-cell analysis for whole-organism datasets

AO Pisco, B Tojo, A McGeever - Annual Review of Biomedical …, 2021 - annualreviews.org
Cell atlases are essential companions to the genome as they elucidate how genes are used
in a cell type–specific manner or how the usage of genes changes over the lifetime of an …

Nested Stochastic Block Models applied to the analysis of single cell data

L Morelli, V Giansanti, D Cittaro - BMC bioinformatics, 2021 - Springer
Single cell profiling has been proven to be a powerful tool in molecular biology to
understand the complex behaviours of heterogeneous system. The definition of the …

Marker-free characterization of full-length transcriptomes of single live circulating tumor cells

S Poonia, A Goel, S Chawla, N Bhattacharya… - Genome …, 2023 - genome.cshlp.org
The identification and characterization of circulating tumor cells (CTCs) are important for
gaining insights into the biology of metastatic cancers, monitoring disease progression, and …

CASSL: A cell-type annotation method for single cell transcriptomics data using semi-supervised learning

DB Seal, V Das, RK De - Applied Intelligence, 2023 - Springer
Single cell RNA sequencing (scRNA-seq) allows global transcriptomic profiling at a cellular
resolution, thus, identifying underlying cell types and corresponding lineages. Such cell type …

Improving replicability in single-cell RNA-Seq cell type discovery with Dune

H Roux de Bézieux, K Street, S Fischer… - BMC …, 2024 - Springer
Background Single-cell transcriptome sequencing (scRNA-Seq) has allowed new types of
investigations at unprecedented levels of resolution. Among the primary goals of scRNA …

Cell-type annotation with accurate unseen cell-type identification using multiple references

YX Xiong, MG Wang, L Chen… - PLOS Computational …, 2023 - journals.plos.org
The recent advances in single-cell RNA sequencing (scRNA-seq) techniques have
stimulated efforts to identify and characterize the cellular composition of complex tissues …

Quantitative assessment of single-cell RNA-seq clustering with CONCORDEX

K Jackson, AS Booeshaghi, Á Gálvez-Merchán… - bioRxiv, 2023 - biorxiv.org
Many single cell RNA-sequencing (scRNA-seq) data analysis workflows rely on methods
that embed and visualize the properties of a k-nearest neighbor (kNN) graph in two …

Microglia and infiltrating T-cells adopt long-term, age-specific, transcriptional changes after traumatic brain injury in mice

Z Chen, MBAR Islam, KP Ford, G Zhao, SY Chen… - Shock, 2023 - journals.lww.com
Aged traumatic brain injury (TBI) patients suffer increased mortality and long-term
neurocognitive and neuropsychiatric morbidity compared with younger patients. Microglia …