[HTML][HTML] Computational single cell oncology: state of the art
E Paas-Oliveros, E Hernández-Lemus… - Frontiers in …, 2023 - frontiersin.org
Single cell computational analysis has emerged as a powerful tool in the field of oncology,
enabling researchers to decipher the complex cellular heterogeneity that characterizes …
enabling researchers to decipher the complex cellular heterogeneity that characterizes …
[HTML][HTML] Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters
Abstract Two-dimensional (2D) embedding methods are crucial for single-cell data
visualization. Popular methods such as t-distributed stochastic neighbor embedding (t-SNE) …
visualization. Popular methods such as t-distributed stochastic neighbor embedding (t-SNE) …
Mapping cells through time and space with moscot
Single-cell genomics technologies enable multimodal profiling of millions of cells across
temporal and spatial dimensions. Experimental limitations prevent the measurement of all …
temporal and spatial dimensions. Experimental limitations prevent the measurement of all …
Multiparametric single-vesicle flow cytometry resolves extracellular vesicle heterogeneity and reveals selective regulation of biogenesis and cargo distribution
AK von Lersner, F Fernandes, PMM Ozawa… - ACS …, 2024 - ACS Publications
Mammalian cells release a heterogeneous array of extracellular vesicles (EVs) that
contribute to intercellular communication by means of the cargo that they carry. To resolve …
contribute to intercellular communication by means of the cargo that they carry. To resolve …
Single‐cell transcriptomics stratifies organoid models of metabolic dysfunction‐associated steatotic liver disease
A Hess, SD Gentile, A Ben Saad, RU Rahman… - The EMBO …, 2023 - embopress.org
Metabolic dysfunction‐associated steatotic liver disease (MASLD) is a growing cause of
morbidity with limited treatment options. Thus, accurate in vitro systems to test new therapies …
morbidity with limited treatment options. Thus, accurate in vitro systems to test new therapies …
[HTML][HTML] Comparative analysis of dimension reduction methods for cytometry by time-of-flight data
While experimental and informatic techniques around single cell sequencing (scRNA-seq)
are advanced, research around mass cytometry (CyTOF) data analysis has severely lagged …
are advanced, research around mass cytometry (CyTOF) data analysis has severely lagged …
[HTML][HTML] Visualizing metagenomic and metatranscriptomic data: A comprehensive review
E Aplakidou, N Vergoulidis, M Chasapi… - Computational and …, 2024 - Elsevier
The fields of Metagenomics and Metatranscriptomics involve the examination of complete
nucleotide sequences, gene identification, and analysis of potential biological functions …
nucleotide sequences, gene identification, and analysis of potential biological functions …
[HTML][HTML] Improving Dimensionality Reduction Projections for Data Visualization
B Rafieian, P Hermosilla, PP Vázquez - Applied Sciences, 2023 - mdpi.com
In data science and visualization, dimensionality reduction techniques have been
extensively employed for exploring large datasets. These techniques involve the …
extensively employed for exploring large datasets. These techniques involve the …
[HTML][HTML] Atypical and non-classical CD45RBlo memory B cells are the majority of circulating SARS-CoV-2 specific B cells following mRNA vaccination or COVID-19
Resting memory B cells can be divided into classical or atypical groups, but the
heterogenous marker expression on activated memory B cells makes similar classification …
heterogenous marker expression on activated memory B cells makes similar classification …
Tree visualizations of protein sequence embedding space enable improved functional clustering of diverse protein superfamilies
Protein language models, trained on millions of biologically observed sequences, generate
feature-rich numerical representations of protein sequences. These representations, called …
feature-rich numerical representations of protein sequences. These representations, called …