Challenges and best practices in omics benchmarking

TG Brooks, NF Lahens, A Mrčela, GR Grant - Nature Reviews Genetics, 2024 - nature.com
Technological advances enabling massively parallel measurement of biological features—
such as microarrays, high-throughput sequencing and mass spectrometry—have ushered in …

scGPT: toward building a foundation model for single-cell multi-omics using generative AI

H Cui, C Wang, H Maan, K Pang, F Luo, N Duan… - Nature …, 2024 - nature.com
Generative pretrained models have achieved remarkable success in various domains such
as language and computer vision. Specifically, the combination of large-scale diverse …

[HTML][HTML] Decentralised, collaborative, and privacy-preserving machine learning for multi-hospital data

C Fang, A Dziedzic, L Zhang, L Oliva, A Verma… - …, 2024 - thelancet.com
Summary Background Machine Learning (ML) has demonstrated its great potential on
medical data analysis. Large datasets collected from diverse sources and settings are …

Single-cell omics: experimental workflow, data analyses and applications

F Sun, H Li, D Sun, S Fu, L Gu, X Shao, Q Wang… - Science China Life …, 2024 - Springer
Cells are the fundamental units of biological systems and exhibit unique development
trajectories and molecular features. Our exploration of how the genomes orchestrate the …

Single-cell profiling of healthy human kidney reveals features of sex-based transcriptional programs and tissue-specific immunity

CM McEvoy, JM Murphy, L Zhang… - Nature …, 2022 - nature.com
Abstract Knowledge of the transcriptional programs underpinning the functions of human
kidney cell populations at homeostasis is limited. We present a single-cell perspective of …

Beaconet: A Reference‐Free Method for Integrating Multiple Batches of Single‐Cell Transcriptomic Data in Original Molecular Space

H Xu, Y Ye, R Duan, Y Gao, Y Hu, L Gao - Advanced Science, 2024 - Wiley Online Library
Integrating multiple single‐cell datasets is essential for the comprehensive understanding of
cell heterogeneity. Batch effect is the undesired systematic variations among technologies or …

Dynamic immune status analysis of peripheral blood mononuclear cells in patients with Klebsiella pneumoniae bloodstream infection sepsis using single-cell RNA …

S Zhang, N Zhang, J Han, Z Sun, H Jiang… - Frontiers in …, 2024 - frontiersin.org
Background Klebsiella pneumoniae is a common Gram-negative bacterium. Blood infection
caused by K. pneumoniae is one of the most common causes of human sepsis, which …

scFormer: a universal representation learning approach for single-cell data using transformers

H Cui, C Wang, H Maan, N Duan, B Wang - bioRxiv, 2022 - biorxiv.org
Single-cell sequencing has emerged as a promising technique to decode cellular
heterogeneity and analyze gene functions. With the high throughput of modern techniques …

Regulatory Role of RNA N6‐Methyladenosine Modification in Plants

S Tayier, E Tian, G Jia - Israel Journal of Chemistry, 2024 - Wiley Online Library
Abstract N6‐methyladenosine (m6A), as the most abundant and well‐studied RNA
modification, can be reversibly added or removed by m6A methyltransferase and …

Identification of a human hematopoietic stem cell subset that retains memory of inflammatory stress

AGX Zeng, MS Nagree, NA Jakobsen, S Shah… - bioRxiv, 2023 - biorxiv.org
Inflammation activates many blood cell types, driving aging and malignancy. Yet,
hematopoietic stem cells (HSCs) survive a lifetime of infection to sustain life-long blood …