Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets

SK Maden, SH Kwon, LA Huuki-Myers… - Genome biology, 2023 - Springer
Deconvolution of cell mixtures in “bulk” transcriptomic samples from homogenate human
tissue is important for understanding disease pathologies. However, several experimental …

Single-cell genomics in AML: extending the frontiers of AML research

A Ediriwickrema, AJ Gentles, R Majeti - Blood, 2023 - ashpublications.org
The era of genomic medicine has allowed acute myeloid leukemia (AML) researchers to
improve disease characterization, optimize risk-stratification systems, and develop new …

Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes

FA Cobos, MJN Panah, J Epps, X Long, TK Man… - Genome biology, 2023 - Springer
Background RNA profiling technologies at single-cell resolutions, including single-cell and
single-nuclei RNA sequencing (scRNA-seq and snRNA-seq, scnRNA-seq for short), can …

Staphylococcus aureus proteases trigger eosinophil-mediated skin inflammation

SN Kline, NA Orlando, AJ Lee, MJ Wu… - Proceedings of the …, 2024 - National Acad Sciences
Staphylococcus aureus skin colonization and eosinophil infiltration are associated with
many inflammatory skin disorders, including atopic dermatitis, bullous pemphigoid …

MiXcan: a framework for cell-type-aware transcriptome-wide association studies with an application to breast cancer

X Song, J Ji, JH Rothstein, SE Alexeeff… - Nature …, 2023 - nature.com
Human bulk tissue samples comprise multiple cell types with diverse roles in disease
etiology. Conventional transcriptome-wide association study approaches predict genetically …

Challenges and perspectives in computational deconvolution of genomics data

LX Garmire, Y Li, Q Huang, C Xu, SA Teichmann… - Nature …, 2024 - nature.com
Deciphering cell-type heterogeneity is crucial for systematically understanding tissue
homeostasis and its dysregulation in diseases. Computational deconvolution is an efficient …

AraLeTA: An Arabidopsis leaf expression atlas across diurnal and developmental scales

GYW Vong, K McCarthy, W Claydon, SJ Davis… - Plant …, 2024 - academic.oup.com
Mature plant leaves are a composite of distinct cell types, including epidermal, mesophyll,
and vascular cells. Notably, the proportion of these cells and the relative transcript …

Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges

H Nguyen, H Nguyen, D Tran, S Draghici… - Nucleic Acids …, 2024 - academic.oup.com
Single-cell RNA sequencing (scRNA-Seq) is a recent technology that allows for the
measurement of the expression of all genes in each individual cell contained in a sample …

Transcriptomics of Human Brain Tissue in Parkinson's Disease: a Comparison of Bulk and Single-cell RNA Sequencing

MR Fiorini, AA Dilliott, RA Thomas, SMK Farhan - Molecular Neurobiology, 2024 - Springer
Parkinson's disease (PD) is a chronic and progressive neurodegenerative disease leading
to motor dysfunction and, in some cases, dementia. Transcriptome analysis is one promising …

Brain cell-type shifts in Alzheimer's disease, autism, and schizophrenia interrogated using methylomics and genetics

CX Yap, DD Vo, MG Heffel, A Bhattacharya, C Wen… - Science …, 2024 - science.org
Few neuropsychiatric disorders have replicable biomarkers, prompting high-resolution and
large-scale molecular studies. However, we still lack consensus on a more foundational …