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 …

Rapid and sensitive detection of genome contamination at scale with FCS-GX

A Astashyn, ES Tvedte, D Sweeney, V Sapojnikov… - Genome biology, 2024 - Springer
Assembled genome sequences are being generated at an exponential rate. Here we
present FCS-GX, part of NCBI's Foreign Contamination Screen (FCS) tool suite, optimized to …

[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 …

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 …

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 …

[HTML][HTML] Airborne environmental DNA for terrestrial vertebrate community monitoring

C Lynggaard, MF Bertelsen, CV Jensen, MS Johnson… - Current Biology, 2022 - cell.com
Biodiversity monitoring at the community scale is a critical element of assessing and
studying species distributions, ecology, diversity, and movements, and it is key to …

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 …

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 …

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 …