The diversification of methods for studying cell–cell interactions and communication

E Armingol, HM Baghdassarian, NE Lewis - Nature Reviews Genetics, 2024 - nature.com
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 …

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 …

[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 …

Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease

ROR Flores, JD Lanzer, D Dimitrov, B Velten… - Elife, 2023 - elifesciences.org
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 …

[HTML][HTML] Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics

AA Almet, YC Tsai, M Watanabe, Q Nie - Nature Methods, 2024 - nature.com
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 …

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 …

Deep generative modeling of sample-level heterogeneity in single-cell genomics

P Boyeau, J Hong, A Gayoso, M Kim… - BioRxiv, 2022 - biorxiv.org
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 …

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 …

[HTML][HTML] Treatment effects of soluble guanylate cyclase modulation on diabetic kidney disease at single-cell resolution

MS Balzer, M Pavkovic, J Frederick, A Abedini… - Cell Reports …, 2023 - cell.com
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 …

Single nuclei RNAseq stratifies multiple sclerosis patients into distinct white matter glial responses

W Macnair, D Calini, E Agirre, J Bryois, S Jäkel… - BioRxiv, 2022 - biorxiv.org
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 …