Gene regulatory network inference in the era of single-cell multi-omics

P Badia-i-Mompel, L Wessels, S Müller-Dott… - Nature Reviews …, 2023 - nature.com
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …

Deep learning in cancer diagnosis, prognosis and treatment selection

KA Tran, O Kondrashova, A Bradley, ED Williams… - Genome Medicine, 2021 - Springer
Deep learning is a subdiscipline of artificial intelligence that uses a machine learning
technique called artificial neural networks to extract patterns and make predictions from …

TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining

C Chen, Y Wu, J Li, X Wang, Z Zeng, J Xu, Y Liu… - Molecular plant, 2023 - cell.com
Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020, its
superior functionality in data analysis has been demonstrated by its widespread adoption by …

Sangerbox: A comprehensive, interaction‐friendly clinical bioinformatics analysis platform

W Shen, Z Song, X Zhong, M Huang, D Shen, P Gao… - Imeta, 2022 - Wiley Online Library
In recent decades, with the continuous development of high‐throughput sequencing
technology, data volume in medical research has increased, at the same time, almost all …

[HTML][HTML] A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

Z Yao, CTJ van Velthoven, M Kunst, M Zhang… - Nature, 2023 - nature.com
The mammalian brain consists of millions to billions of cells that are organized into many cell
types with specific spatial distribution patterns and structural and functional properties …

Graph pangenome captures missing heritability and empowers tomato breeding

Y Zhou, Z Zhang, Z Bao, H Li, Y Lyu, Y Zan, Y Wu… - Nature, 2022 - nature.com
Missing heritability in genome-wide association studies defines a major problem in genetic
analyses of complex biological traits,. The solution to this problem is to identify all causal …

Identification of antimicrobial peptides from the human gut microbiome using deep learning

Y Ma, Z Guo, B Xia, Y Zhang, X Liu, Y Yu, N Tang… - Nature …, 2022 - nature.com
The human gut microbiome encodes a large variety of antimicrobial peptides (AMPs), but
the short lengths of AMPs pose a challenge for computational prediction. Here we combined …

Majorbio Cloud: A one‐stop, comprehensive bioinformatic platform for multiomics analyses

Y Ren, G Yu, C Shi, L Liu, Q Guo, C Han, D Zhang… - IMeta, 2022 - Wiley Online Library
The rapid developments of high‐throughput sequencing technology in the last decade
allowed the emergence of multiomics analyses. Analytic platforms for high‐throughput omics …

Molecular basis of astrocyte diversity and morphology across the CNS in health and disease

F Endo, A Kasai, JS Soto, X Yu, Z Qu, H Hashimoto… - Science, 2022 - science.org
Astrocytes, a type of glia, are abundant and morphologically complex cells. Here, we report
astrocyte molecular profiles, diversity, and morphology across the mouse central nervous …

[HTML][HTML] Cholesterol and matrisome pathways dysregulated in astrocytes and microglia

TCW Julia, L Qian, NH Pipalia, MJ Chao, SA Liang… - Cell, 2022 - cell.com
The impact of apolipoprotein E ε4 (APOE4), the strongest genetic risk factor for Alzheimer's
disease (AD), on human brain cellular function remains unclear. Here, we investigated the …