The triumphs and limitations of computational methods for scRNA-seq
PV Kharchenko - Nature methods, 2021 - nature.com
The rapid progress of protocols for sequencing single-cell transcriptomes over the past
decade has been accompanied by equally impressive advances in the computational …
decade has been accompanied by equally impressive advances in the computational …
Functional and biomimetic materials for engineering of the three-dimensional cell microenvironment
The cell microenvironment has emerged as a key determinant of cell behavior and function
in development, physiology, and pathophysiology. The extracellular matrix (ECM) within the …
in development, physiology, and pathophysiology. The extracellular matrix (ECM) within the …
Increased glucose metabolism in TAMs fuels O-GlcNAcylation of lysosomal Cathepsin B to promote cancer metastasis and chemoresistance
Q Shi, Q Shen, Y Liu, Y Shi, W Huang, X Wang, Z Li… - Cancer cell, 2022 - cell.com
How glucose metabolism remodels pro-tumor functions of tumor-associated macrophages
(TAMs) needs further investigation. Here we show that M2-like TAMs bear the highest …
(TAMs) needs further investigation. Here we show that M2-like TAMs bear the highest …
T cell characteristics associated with toxicity to immune checkpoint blockade in patients with melanoma
Severe immune-related adverse events (irAEs) occur in up to 60% of patients with
melanoma treated with immune checkpoint inhibitors (ICIs). However, it is unknown whether …
melanoma treated with immune checkpoint inhibitors (ICIs). However, it is unknown whether …
[HTML][HTML] Complete map** of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition
Antibodies targeting the SARS-CoV-2 spike receptor-binding domain (RBD) are being
developed as therapeutics and are a major contributor to neutralizing antibody responses …
developed as therapeutics and are a major contributor to neutralizing antibody responses …
Galectin-9 interacts with PD-1 and TIM-3 to regulate T cell death and is a target for cancer immunotherapy
The two T cell inhibitory receptors PD-1 and TIM-3 are co-expressed during exhausted T cell
differentiation, and recent evidence suggests that their crosstalk regulates T cell exhaustion …
differentiation, and recent evidence suggests that their crosstalk regulates T cell exhaustion …
CellRank for directed single-cell fate map**
Computational trajectory inference enables the reconstruction of cell state dynamics from
single-cell RNA sequencing experiments. However, trajectory inference requires that the …
single-cell RNA sequencing experiments. However, trajectory inference requires that the …
Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients
Coronavirus disease 2019 (COVID-19) is characterized by distinct patterns of disease
progression that suggest diverse host immune responses. We performed an integrated …
progression that suggest diverse host immune responses. We performed an integrated …
[HTML][HTML] Comprehensive profiling of an aging immune system reveals clonal GZMK+ CD8+ T cells as conserved hallmark of inflammaging
Systematic understanding of immune aging on a whole-body scale is currently lacking. We
characterized age-associated alterations in immune cells across multiple mouse organs …
characterized age-associated alterations in immune cells across multiple mouse organs …
Understanding how dimension reduction tools work: an empirical approach to deciphering t-SNE, UMAP, TriMAP, and PaCMAP for data visualization
Dimension reduction (DR) techniques such as t-SNE, UMAP, and TriMap have
demonstrated impressive visualization performance on many real-world datasets. One …
demonstrated impressive visualization performance on many real-world datasets. One …