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 …

scAnno: a deconvolution strategy-based automatic cell type annotation tool for single-cell RNA-sequencing data sets

H Liu, H Li, A Sharma, W Huang, D Pan… - Briefings in …, 2023 - academic.oup.com
Undoubtedly, single-cell RNA sequencing (scRNA-seq) has changed the research
landscape by providing insights into heterogeneous, complex and rare cell populations …

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 …

[HTML][HTML] Immune microenvironment heterogeneity reveals distinct subtypes in neuroblastoma: insights into prognosis and therapeutic targets

Y Yang, H Li, D Zheng, X Li, H Liu - Aging (Albany NY), 2023 - ncbi.nlm.nih.gov
Background: Neuroblastoma (NB) is a childhood cancer originating from immature nerve
cells in the sympathetic nervous system. Current clinical and molecular subtyping methods …

A transcriptomic based deconvolution framework for assessing differentiation stages and drug responses of AML

EO Karakaslar, JF Severens, E Sánchez-López… - npj Precision …, 2024 - nature.com
The diagnostic spectrum for AML patients is increasingly based on genetic abnormalities
due to their prognostic and predictive value. However, information on the AML blast …

From cellular infiltration assessment to a functional gene set-based prognostic model for breast cancer

H Li, Y Huang, A Sharma, W Ming, K Luo, Z Gu… - Frontiers in …, 2021 - frontiersin.org
Background Cancer heterogeneity is a major challenge in clinical practice, and to some
extent, the varying combinations of different cell types and their cross-talk with tumor cells …

Identification of the integrated prognostic signature associated with immuno-relevant genes and long non-coding RNAs in acute myeloid leukemia

C Zhao, Y Wang, A Sharma, Z Wang, C Zheng… - Cancer …, 2022 - Taylor & Francis
Background Like other cancers, considerable effort has been made in acute myeloid
leukemia (AML) to identify prognostic genes and long noncoding RNAs (lncRNAs) with their …

Cellular abundance-based prognostic model associated with deregulated gene expression of leukemic stem cells in acute myeloid leukemia

DJ Han, S Kim, SY Lee, SJ Kang, Y Moon… - Frontiers in Cell and …, 2024 - frontiersin.org
Background: Previous studies have reported that genes highly expressed in leukemic stem
cells (LSC) may dictate the survival probability of patients and expression-based cellular …

Global proteomic profiling of pediatric AML: a pilot study

NHK Nguyen, H Wu, H Tan, J Peng, JE Rubnitz, X Cao… - Cancers, 2021 - mdpi.com
Simple Summary The second most common childhood leukemia, acute myeloid leukemia
(AML), is a heterogeneous disease with a poor prognosis. In order to improve outcomes …

Computational analysis of heat shock proteins and ferroptosis-associated lncRNAs to predict prognosis in acute myeloid leukemia patients

F Ge, Y Wang, A Sharma, U Jaehde, M Essler… - Frontiers in …, 2023 - frontiersin.org
Owing to their functional diversity in many cancers, long noncoding RNAs (lncRNAs) are
receiving special attention. LncRNAs not only function as oncogenes or tumor suppressors …