Biological sequence classification: A review on data and general methods

C Ao, S Jiao, Y Wang, L Yu, Q Zou - Research, 2022 - spj.science.org
With the rapid development of biotechnology, the number of biological sequences has
grown exponentially. The continuous expansion of biological sequence data promotes the …

[PDF][PDF] Revealing the molecular landscape of human placenta: a systematic review and meta-analysis of single-cell RNA sequencing studies

E Derisoud, H Jiang, A Zhao… - Human …, 2024 - academic.oup.com
BACKGROUND With increasing significance of developmental programming effects
associated with placental dysfunction, more investigations are devoted to improving the …

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 …

Dimensionality reduction and visualization of single-cell RNA-seq data with an improved deep variational autoencoder

J Jiang, J Xu, Y Liu, B Song, X Guo… - Briefings in …, 2023 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) is a revolutionary breakthrough that determines
the precise gene expressions on individual cells and deciphers cell heterogeneity and …

Machine learning-based prediction model for distant metastasis of breast cancer

H Duan, Y Zhang, H Qiu, X Fu, C Liu, X Zang… - Computers in Biology …, 2024 - Elsevier
Background Breast cancer is the most prevalent malignancy in women. Advanced breast
cancer can develop distant metastases, posing a severe threat to the life of patients …

Research progress of single-cell transcriptome sequencing in autoimmune diseases and autoinflammatory disease: A review

L Zeng, K Yang, T Zhang, X Zhu, W Hao, H Chen… - Journal of …, 2022 - Elsevier
Autoimmunity refers to the phenomenon that the body's immune system produces antibodies
or sensitized lymphocytes to its own tissues to cause an immune response. Immune …

Critical downstream analysis steps for single-cell RNA sequencing data

Z Zhang, F Cui, C Lin, L Zhao, C Wang… - Briefings in …, 2021 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) has enabled us to study biological questions at
the single-cell level. Currently, many analysis tools are available to better utilize these …

A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data

Y Sun, L Kong, J Huang, H Deng, X Bian… - Briefings in …, 2024 - academic.oup.com
In recent years, the application of single-cell transcriptomics and spatial transcriptomics
analysis techniques has become increasingly widespread. Whether dealing with single-cell …

[HTML][HTML] T cell-related prognostic risk model and tumor immune environment modulation in lung adenocarcinoma based on single-cell and bulk RNA sequencing

J Zhang, X Liu, Z Huang, C Wu, F Zhang, A Han… - Computers in biology …, 2023 - Elsevier
Background T cells are present in all stages of tumor formation and play an important role in
the tumor microenvironment. We aimed to explore the expression profile of T cell marker …

Integration of computational analysis and spatial transcriptomics in single-cell studies

R Wang, G Peng, PPL Tam… - Genomics, Proteomics & …, 2023 - academic.oup.com
Recent advances of single-cell transcriptomics technologies and allied computational
methodologies have revolutionized molecular cell biology. Meanwhile, pioneering …