The how and why of lncRNA function: an innate immune perspective
Next-generation sequencing has provided a more complete picture of the composition of the
human transcriptome indicating that much of the “blueprint” is a vastness of poorly …
human transcriptome indicating that much of the “blueprint” is a vastness of poorly …
Quantifying tumor-infiltrating immune cells from transcriptomics data
By exerting pro-and anti-tumorigenic actions, tumor-infiltrating immune cells can profoundly
influence tumor progression, as well as the success of anti-cancer therapies. Therefore, the …
influence tumor progression, as well as the success of anti-cancer therapies. Therefore, the …
Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage
Tissue fibrosis is a major cause of mortality that results from the deposition of matrix proteins
by an activated mesenchyme. Macrophages accumulate in fibrosis, but the role of specific …
by an activated mesenchyme. Macrophages accumulate in fibrosis, but the role of specific …
Benchmarking of cell type deconvolution pipelines for transcriptomics data
Many computational methods have been developed to infer cell type proportions from bulk
transcriptomics data. However, an evaluation of the impact of data transformation, pre …
transcriptomics data. However, an evaluation of the impact of data transformation, pre …
A multifunctional AAV–CRISPR–Cas9 and its host response
CRISPR–Cas9 delivery by adeno-associated virus (AAV) holds promise for gene therapy
but faces critical barriers on account of its potential immunogenicity and limited payload …
but faces critical barriers on account of its potential immunogenicity and limited payload …
Computational deconvolution of transcriptomics data from mixed cell populations
Gene expression analyses of bulk tissues often ignore cell type composition as an important
confounding factor, resulting in a loss of signal from lowly abundant cell types. In this review …
confounding factor, resulting in a loss of signal from lowly abundant cell types. In this review …
Dissection of influenza infection in vivo by single-cell RNA sequencing
The influenza virus is a major cause of morbidity and mortality worldwide. Yet, both the
impact of intracellular viral replication and the variation in host response across different cell …
impact of intracellular viral replication and the variation in host response across different cell …
Understanding virus–host interactions in tissues
E Speranza - Nature Microbiology, 2023 - nature.com
Although virus–host interactions are usually studied in a single cell type using in vitro assays
in immortalized cell lines or isolated cell populations, it is important to remember that what is …
in immortalized cell lines or isolated cell populations, it is important to remember that what is …
Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets
Deconvolution of cell mixtures in “bulk” transcriptomic samples from homogenate human
tissue is important for understanding disease pathologies. However, several experimental …
tissue is important for understanding disease pathologies. However, several experimental …
Multicellular communities are perturbed in the aging human brain and Alzheimer's disease
The role of different cell types and their interactions in Alzheimer's disease (AD) is a complex
and open question. Here, we pursued this question by assembling a high-resolution cellular …
and open question. Here, we pursued this question by assembling a high-resolution cellular …