[HTML][HTML] Comparison and evaluation of statistical error models for scRNA-seq

S Choudhary, R Satija - Genome biology, 2022 - Springer
Background Heterogeneity in single-cell RNA-seq (scRNA-seq) data is driven by multiple
sources, including biological variation in cellular state as well as technical variation …

Goals and approaches for each processing step for single-cell RNA sequencing data

Z Zhang, F Cui, C Wang, L Zhao… - Briefings in …, 2021 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) has enabled researchers to study gene
expression at the cellular level. However, due to the extremely low levels of transcripts in a …

[HTML][HTML] Ref-1 redox activity alters cancer cell metabolism in pancreatic cancer: exploiting this novel finding as a potential target

S Gampala, F Shah, X Lu, H Moon, O Babb… - Journal of Experimental …, 2021 - Springer
Background Pancreatic cancer is a complex disease with a desmoplastic stroma, extreme
hypoxia, and inherent resistance to therapy. Understanding the signaling and adaptive …

Identification of differentially distributed gene expression and distinct sets of cancer-related genes identified by changes in mean and variability

AGK Roberts, DR Catchpoole… - NAR Genomics and …, 2022 - academic.oup.com
There is increasing evidence that changes in the variability or overall distribution of gene
expression are important both in normal biology and in diseases, particularly cancer. Genes …

scShapes: a statistical framework for identifying distribution shapes in single-cell RNA-sequencing data

M Dharmaratne, AS Kulkarni, A Taherian Fard… - …, 2023 - academic.oup.com
Background Single-cell RNA sequencing (scRNA-seq) methods have been advantageous
for quantifying cell-to-cell variation by profiling the transcriptomes of individual cells. For …

SSMD: a semi-supervised approach for a robust cell type identification and deconvolution of mouse transcriptomics data

X Lu, SW Tu, W Chang, C Wan, J Wang… - Briefings in …, 2021 - academic.oup.com
Deconvolution of mouse transcriptomic data is challenged by the fact that mouse models
carry various genetic and physiological perturbations, making it questionable to assume …

[HTML][HTML] Leveraging novel integrated single-cell analyses to define HIV-1 latency reversal

S Zhao, A Tsibris - Viruses, 2021 - mdpi.com
While suppressive antiretroviral therapy can effectively limit HIV-1 replication and evolution,
it leaves behind a residual pool of integrated viral genomes that persist in a state of …

[HTML][HTML] The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases

Z Zhao, Y Dai, C Zhang, E Mathé, L Wei, K Wang - BMC bioinformatics, 2019 - Springer
Abstract Between June 9–11, 2019, the International Conference on Intelligent Biology and
Medicine (ICIBM 2019) was held in Columbus, Ohio, USA. The conference included 12 …

A data denoising approach to optimize functional clustering of single cell RNA-sequencing data

C Wan, D Jia, Y Zhao, W Chang, S Cao… - 2020 IEEE …, 2020 - ieeexplore.ieee.org
Single cell RNA-sequencing (scRNA-seq) technology enables comprehensive
transcriptomic profiling of thousands of cells with distinct phenotypic and physiological states …

[图书][B] Discovery and Interpretation of Subspace Structures in Omics Data by Low-Rank Representation

X Lu - 2022 - search.proquest.com
Biological functions in cells are highly complicated and heterogenous, and can be reflected
by omics data, such as gene expression levels. Detecting subspace structures in omics data …