Wound healing: a cellular perspective

M Rodrigues, N Kosaric, CA Bonham… - Physiological …, 2019 - journals.physiology.org
Wound healing is one of the most complex processes in the human body. It involves the
spatial and temporal synchronization of a variety of cell types with distinct roles in the …

Clinical metagenomic next-generation sequencing for pathogen detection

W Gu, S Miller, CY Chiu - Annual Review of Pathology …, 2019 - annualreviews.org
Nearly all infectious agents contain DNA or RNA genomes, making sequencing an attractive
approach for pathogen detection. The cost of high-throughput or next-generation …

Unicycler: resolving bacterial genome assemblies from short and long sequencing reads

RR Wick, LM Judd, CL Gorrie… - PLoS computational …, 2017 - journals.plos.org
The Illumina DNA sequencing platform generates accurate but short reads, which can be
used to produce accurate but fragmented genome assemblies. Pacific Biosciences and …

Shotgun metagenomics, from sampling to analysis

C Quince, AW Walker, JT Simpson, NJ Loman… - Nature …, 2017 - nature.com
Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes
have crucial roles in the environment and in human health. However, microbes are …

[HTML][HTML] The short chain fatty acid butyrate imprints an antimicrobial program in macrophages

J Schulthess, S Pandey, M Capitani, KC Rue-Albrecht… - Immunity, 2019 - cell.com
Host microbial cross-talk is essential to maintain intestinal homeostasis. However,
maladaptation of this response through microbial dysbiosis or defective host defense toward …

Distinct fibroblast subsets drive inflammation and damage in arthritis

AP Croft, J Campos, K Jansen, JD Turner, J Marshall… - Nature, 2019 - nature.com
The identification of lymphocyte subsets with non-overlap** effector functions has been
pivotal to the development of targeted therapies in immune-mediated inflammatory diseases …

Identification of the human skeletal stem cell

CKF Chan, GS Gulati, R Sinha, JV Tompkins, M Lopez… - Cell, 2018 - cell.com
Stem cell regulation and hierarchical organization of human skeletal progenitors remain
largely unexplored. Here, we report the isolation of a self-renewing and multipotent human …

Profiling cell type abundance and expression in bulk tissues with CIBERSORTx

CB Steen, CL Liu, AA Alizadeh… - Stem Cell Transcriptional …, 2020 - Springer
CIBERSORTx is a suite of machine learning tools for the assessment of cellular abundance
and cell type-specific gene expression patterns from bulk tissue transcriptome profiles. With …

Benchmarking metagenomics tools for taxonomic classification

HY Simon, KJ Siddle, DJ Park, PC Sabeti - Cell, 2019 - cell.com
Metagenomic sequencing is revolutionizing the detection and characterization of microbial
species, and a wide variety of software tools are available to perform taxonomic …

Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations

JJ Salk, MW Schmitt, LA Loeb - Nature Reviews Genetics, 2018 - nature.com
Mutations, the fuel of evolution, are first manifested as rare DNA changes within a population
of cells. Although next-generation sequencing (NGS) technologies have revolutionized the …