The diversification of methods for studying cell–cell interactions and communication
No cell lives in a vacuum, and the molecular interactions between cells define most
phenotypes. Transcriptomics provides rich information to infer cell–cell interactions and …
phenotypes. Transcriptomics provides rich information to infer cell–cell interactions and …
Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system
PSL Schäfer, D Dimitrov, EJ Villablanca… - Nature …, 2024 - nature.com
The immune system comprises diverse specialized cell types that cooperate to defend the
host against a wide range of pathogenic threats. Recent advancements in single-cell and …
host against a wide range of pathogenic threats. Recent advancements in single-cell and …
[HTML][HTML] Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists
A Abedini, A Sánchez-Navaro, J Wu… - The Journal of …, 2024 - Am Soc Clin Investig
Mineralocorticoid excess commonly leads to hypertension (HTN) and kidney disease. In our
study, we used single-cell expression and chromatin accessibility tools to characterize the …
study, we used single-cell expression and chromatin accessibility tools to characterize the …
Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease
Biomedical single-cell atlases describe disease at the cellular level. However, analysis of
this data commonly focuses on cell-type-centric pairwise cross-condition comparisons …
this data commonly focuses on cell-type-centric pairwise cross-condition comparisons …
[HTML][HTML] Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics
From single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics (ST), one can
extract high-dimensional gene expression patterns that can be described by intercellular …
extract high-dimensional gene expression patterns that can be described by intercellular …
LIANA+: an all-in-one cell-cell communication framework
D Dimitrov, PSL Schäfer, E Farr, P Rodriguez Mier… - BioRxiv, 2023 - biorxiv.org
The growing availability of single-cell and spatially-resolved transcriptomics has led to the
rapidly growing popularity of methods to infer cell-cell communication. Many approaches …
rapidly growing popularity of methods to infer cell-cell communication. Many approaches …
Deep generative modeling of sample-level heterogeneity in single-cell genomics
The field of single-cell genomics is now observing a marked increase in the prevalence of
cohort-level studies that include hundreds of samples and feature complex designs. These …
cohort-level studies that include hundreds of samples and feature complex designs. These …
Resource allocation in mammalian systems
HM Baghdassarian, NE Lewis - Biotechnology Advances, 2024 - Elsevier
Cells execute biological functions to support phenotypes such as growth, migration, and
secretion. Complementarily, each function of a cell has resource costs that constrain …
secretion. Complementarily, each function of a cell has resource costs that constrain …
[HTML][HTML] Treatment effects of soluble guanylate cyclase modulation on diabetic kidney disease at single-cell resolution
Diabetic kidney disease (DKD) is the most common cause of renal failure. Therapeutics
development is hampered by our incomplete understanding of animal models on a cellular …
development is hampered by our incomplete understanding of animal models on a cellular …
Single nuclei RNAseq stratifies multiple sclerosis patients into distinct white matter glial responses
The lack of understanding of the cellular and molecular basis of clinical and genetic
heterogeneity in progressive multiple sclerosis (MS) has hindered the search for new …
heterogeneity in progressive multiple sclerosis (MS) has hindered the search for new …