[HTML][HTML] Unravelling fibrosis using single-cell transcriptomics

R Dobie, NC Henderson - Current Opinion in Pharmacology, 2019 - Elsevier
Fibrosis, the excessive accumulation of extracellular matrix, is a major global healthcare
burden. Despite major advances in our understanding of the mechanisms regulating …

MultiCellDS: a community-developed standard for curating microenvironment-dependent multicellular data

SH Friedman, ARA Anderson, DM Bortz, AG Fletcher… - bioRxiv, 2016 - biorxiv.org
Exchanging and understanding scientific data and their context represents a significant
barrier to advancing research, especially with respect to information siloing. Maintaining …

Integrated spatial multiomics reveals fibroblast fate during tissue repair

DS Foster, M Januszyk, KE Yost… - Proceedings of the …, 2021 - National Acad Sciences
In the skin, tissue injury results in fibrosis in the form of scars composed of dense
extracellular matrix deposited by fibroblasts. The therapeutic goal of regenerative wound …

Inter-tissue coexpression network analysis reveals DPP4 as an important gene in heart to blood communication

Q Long, C Argmann, SM Houten, T Huang, S Peng… - Genome medicine, 2016 - Springer
Background Inter-tissue molecular interactions are critical to the function and behavior of
biological systems in multicellular organisms, but systematic studies of interactions between …

Multiomic signatures of body mass index identify heterogeneous health phenotypes and responses to a lifestyle intervention

K Watanabe, T Wilmanski, C Diener, JC Earls… - Nature medicine, 2023 - nature.com
Multiomic profiling can reveal population heterogeneity for both health and disease states.
Obesity drives a myriad of metabolic perturbations and is a risk factor for multiple chronic …

High-resolution mycobiota analysis reveals dynamic intestinal translocation preceding invasive candidiasis

B Zhai, M Ola, T Rolling, NL Tosini, S Joshowitz… - Nature medicine, 2020 - nature.com
The intestinal microbiota is a complex community of bacteria, archaea, viruses, protists and
fungi,. Although the composition of bacterial constituents has been linked to immune …

Comprehensive analysis of tissue-wide gene expression and phenotype data reveals tissues affected in rare genetic disorders

A Feiglin, BK Allen, IS Kohane, SW Kong - Cell systems, 2017 - cell.com
Linking putatively pathogenic variants to the tissues they affect is necessary for determining
the correct diagnostic workup and therapeutic regime in undiagnosed patients. Here, we …

Interrogating mechanisms of liver fibrosis with omics

F Oakley - Nature Reviews Gastroenterology & Hepatology, 2022 - nature.com
Important studies in 2021 demonstrated sophisticated developments in the study of liver
fibrosis through omics. Cell-specific mapping, single-cell sequencing and deep-learning …

Multimodal dynamic profiling of healthy and diseased states for future personalized health care

GI Mias, M Snyder - Clinical Pharmacology & Therapeutics, 2013 - Wiley Online Library
Personalized medicine is rapidly emerging as the future direction in the post–genome
sequencing era. Early applications have concentrated on variant‐based assessment of …

Resolving the fibrotic niche of human liver cirrhosis at single-cell level

P Ramachandran, R Dobie, JR Wilson-Kanamori… - Nature, 2019 - nature.com
Liver cirrhosis is a major cause of death worldwide and is characterized by extensive
fibrosis. There are currently no effective antifibrotic therapies available. To obtain a better …