Single-cell sequencing reveals novel proliferative cell type: a key player in renal cell carcinoma prognosis and therapeutic response

B Ye, H Ji, M Zhu, A Wang, J Tang, Y Liang… - Clinical and …, 2024‏ - Springer
Renal cell carcinoma (RCC) is characterized by a variety of subtypes, each defined by
unique genetic and morphological features. This study utilizes single-cell RNA sequencing …

Bulk and single-nucleus transcriptomics highlight intra-telencephalic and somatostatin neurons in Alzheimer's disease

ME Consens, Y Chen, V Menon, Y Wang… - Frontiers in Molecular …, 2022‏ - frontiersin.org
Cortical neuron loss is a pathological hallmark of late-onset Alzheimer's disease (AD).
However, it remains unclear which neuronal subtypes beyond broad excitatory and …

Heterogeneous pseudobulk simulation enables realistic benchmarking of cell-type deconvolution methods

M Hu, M Chikina - Genome Biology, 2024‏ - Springer
Background Computational cell type deconvolution enables the estimation of cell type
abundance from bulk tissues and is important for understanding tissue microenviroment …

BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk

NR Davidson, F Zhang, CS Greene - PLOS Computational Biology, 2025‏ - journals.plos.org
While single-cell experiments provide deep cellular resolution within a single sample, some
single-cell experiments are inherently more challenging than bulk experiments due to …

Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors

AA Hippen, DK Omran, LM Weber, E Jung, R Drapkin… - Genome biology, 2023‏ - Springer
Background Single-cell gene expression profiling provides unique opportunities to
understand tumor heterogeneity and the tumor microenvironment. Because of cost and …

IL-33, a neutrophil extracellular trap-related gene involved in the progression of diabetic kidney disease

Y Ye, A Huang, X Huang, Q **, H Gu, LL Liu, B Yu… - Inflammation …, 2025‏ - Springer
Background Chronic inflammation is well recognized as a key factor related to renal function
deterioration in patients with diabetic kidney disease (DKD). Neutrophil extracellular traps …

Differences in gene expression profiles in early and late stage rhodesiense HAT individuals in Malawi

P Nambala, J Mulindwa, H Noyes… - PLoS neglected …, 2023‏ - journals.plos.org
T. b. rhodesiense is the causative agent of Rhodesian human African trypanosomiasis (r-
HAT) in Malawi. Clinical presentation of r-HAT in Malawi varies between foci and differs from …

Single Cell Transcriptomics

Y Muto, H Li, BD Humphreys - Innovations in Nephrology: Breakthrough …, 2022‏ - Springer
Kidney is a highly complex organ comprised of diverse cell types and subpopulations. This
cellular complexity complicates efforts to understand both physiology and disease …

Extending the capabilities of deconvolution to provide cell type specific pathway analysis of bulk RNA-seq data for idiopathic pulmonary fibrosis

MR Calvero, SH Meghadri, A Carleo, A Prasse… - bioRxiv, 2024‏ - biorxiv.org
Motivation Transcriptome data are confounded by differences in cell type proportions.
Differentiating between regulated changes in gene expression and changes due to differing …

Methods for ChIP-seq Normalization and Their Application for the Analysis of Regulatory Elements in Brain Cells

FE Gusev, TV Andreeva, EI Rogaev - Russian Journal of Genetics, 2023‏ - Springer
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become one of the
major tools to elucidate gene-expression regulation. Similar to other molecular profiling …