scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses

J Wang, A Ma, Y Chang, J Gong, Y Jiang, R Qi… - Nature …, 2021 - nature.com
Single-cell RNA-sequencing (scRNA-Seq) is widely used to reveal the heterogeneity and
dynamics of tissues, organisms, and complex diseases, but its analyses still suffer from …

Single-cell RNA analysis reveals the potential risk of organ-specific cell types vulnerable to SARS-CoV-2 infections

Z Zhang, F Cui, C Cao, Q Wang, Q Zou - Computers in biology and …, 2022 - Elsevier
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global
pandemic of coronavirus disease 2019 (COVID-19) since December 2019 that has led to …

Biclustering data analysis: a comprehensive survey

EN Castanho, H Aidos, SC Madeira - Briefings in Bioinformatics, 2024 - academic.oup.com
Biclustering, the simultaneous clustering of rows and columns of a data matrix, has proved
its effectiveness in bioinformatics due to its capacity to produce local instead of global …

scREAD: a single-cell RNA-Seq database for Alzheimer's disease

J Jiang, C Wang, R Qi, H Fu, Q Ma - Iscience, 2020 - cell.com
Alzheimer's disease (AD) is a progressive neurodegenerative disorder of the brain and the
most common form of dementia among the elderly. The single-cell RNA-sequencing (scRNA …

BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both alignment-based and alignment-free quantification …

S Sun, L Xu, Q Zou, G Wang - Bioinformatics, 2021 - academic.oup.com
Processing raw reads of RNA-sequencing (RNA-seq) data, no matter public or newly
sequenced data, involves a lot of specialized tools and technical configurations that are …

A Comprehensive Survey on Biclustering-based Collaborative Filtering

M G. Silva, S C. Madeira, R Henriques - ACM Computing Surveys, 2024 - dl.acm.org
Collaborative Filtering (CF) is achieving a plateau of high popularity. Still, recommendation
success is challenged by the diversity of user preferences, structural sparsity of user-item …

[Retracted] Healthcare Biclustering‐Based Prediction on Gene Expression Dataset

M Ramkumar, N Basker, D Pradeep… - BioMed Research …, 2022 - Wiley Online Library
In this paper, we develop a healthcare biclustering model in the field of healthcare to reduce
the inconveniences linked to the data clustering on gene expression. The present study …

Biclustering fMRI time series: a comparative study

EN Castanho, H Aidos, SC Madeira - BMC bioinformatics, 2022 - Springer
Background The effectiveness of biclustering, simultaneous clustering of rows and columns
in a data matrix, was shown in gene expression data analysis. Several researchers …

A spectral clustering with self-weighted multiple kernel learning method for single-cell RNA-seq data

R Qi, J Wu, F Guo, L Xu, Q Zou - Briefings in Bioinformatics, 2021 - academic.oup.com
Single-cell RNA-sequencing (scRNA-seq) data widely exist in bioinformatics. It is crucial to
devise a distance metric for scRNA-seq data. Almost all existing clustering methods based …

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 …