Wound healing, fibroblast heterogeneity, and fibrosis

HE Talbott, S Mascharak, M Griffin, DC Wan… - Cell stem cell, 2022 - cell.com
Fibroblasts are highly dynamic cells that play a central role in tissue repair and fibrosis.
However, the mechanisms by which they contribute to both physiologic and pathologic …

Tumour heterogeneity and metastasis at single-cell resolution

DA Lawson, K Kessenbrock, RT Davis… - Nature cell …, 2018 - nature.com
Tumours comprise a heterogeneous collection of cells with distinct genetic and phenotypic
properties that can differentially promote progression, metastasis and drug resistance …

CellMarker: a manually curated resource of cell markers in human and mouse

X Zhang, Y Lan, J Xu, F Quan, E Zhao… - Nucleic acids …, 2019 - academic.oup.com
One of the most fundamental questions in biology is what types of cells form different tissues
and organs in a functionally coordinated fashion. Larger-scale single-cell sequencing and …

Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities

M Zitnik, F Nguyen, B Wang, J Leskovec… - Information …, 2019 - Elsevier
New technologies have enabled the investigation of biology and human health at an
unprecedented scale and in multiple dimensions. These dimensions include a myriad of …

Single-cell transcriptomics in cancer: computational challenges and opportunities

J Fan, K Slowikowski, F Zhang - Experimental & Molecular Medicine, 2020 - nature.com
Intratumor heterogeneity is a common characteristic across diverse cancer types and
presents challenges to current standards of treatment. Advancements in high-throughput …

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications

A Haque, J Engel, SA Teichmann, T Lönnberg - Genome medicine, 2017 - Springer
RNA sequencing (RNA-seq) is a genomic approach for the detection and quantitative
analysis of messenger RNA molecules in a biological sample and is useful for studying …

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

L Zappia, B Phipson, A Oshlack - PLoS computational biology, 2018 - journals.plos.org
As single-cell RNA-sequencing (scRNA-seq) datasets have become more widespread the
number of tools designed to analyse these data has dramatically increased. Navigating the …

Transcriptome profiling in human diseases: new advances and perspectives

A Casamassimi, A Federico, M Rienzo… - International journal of …, 2017 - mdpi.com
In the last decades, transcriptome profiling has been one of the most utilized approaches to
investigate human diseases at the molecular level. Through expression studies, many …

DEsingle for detecting three types of differential expression in single-cell RNA-seq data

Z Miao, K Deng, X Wang, X Zhang - Bioinformatics, 2018 - academic.oup.com
The excessive amount of zeros in single-cell RNA-seq (scRNA-seq) data includes 'real'zeros
due to the on-off nature of gene transcription in single cells and 'dropout'zeros due to …

Understanding tumor ecosystems by single-cell sequencing: promises and limitations

X Ren, B Kang, Z Zhang - Genome biology, 2018 - Springer
Cellular heterogeneity within and across tumors has been a major obstacle in
understanding and treating cancer, and the complex heterogeneity is masked if bulk tumor …