Analyzing high-dimensional cytometry data using FlowSOM

K Quintelier, A Couckuyt, A Emmaneel, J Aerts… - Nature protocols, 2021 - nature.com
The dimensionality of cytometry data has strongly increased in the last decade, and in many
situations the traditional manual downstream analysis becomes insufficient. The field is …

Application of machine learning for cytometry data

Z Hu, S Bhattacharya, AJ Butte - Frontiers in immunology, 2022 - frontiersin.org
Modern cytometry technologies present opportunities to profile the immune system at a
single-cell resolution with more than 50 protein markers, and have been widely used in both …

An atlas of the protein-coding genes in the human, pig, and mouse brain

E Sjöstedt, W Zhong, L Fagerberg, M Karlsson… - Science, 2020 - science.org
INTRODUCTION The brain is the most complex organ of the mammalian body, boasting a
diverse physiology combined with intricate cellular organization. In an effort to expand our …

Pan-cancer characterization of immune-related lncRNAs identifies potential oncogenic biomarkers

Y Li, T Jiang, W Zhou, J Li, X Li, Q Wang, X **… - Nature …, 2020 - nature.com
Long noncoding RNAs (lncRNAs) are emerging as critical regulators of gene expression
and they play fundamental roles in immune regulation. Here we introduce an integrated …

A genome-wide transcriptomic analysis of protein-coding genes in human blood cells

M Uhlen, MJ Karlsson, W Zhong, A Tebani, C Pou… - Science, 2019 - science.org
INTRODUCTION Blood is the predominant source for molecular analyses in humans, both in
clinical and research settings, and is the target for many therapeutic strategies, emphasizing …

Association of intratumoral microbiota with prognosis in patients with nasopharyngeal carcinoma from 2 hospitals in China

H Qiao, XR Tan, H Li, JY Li, XZ Chen, YQ Li… - JAMA …, 2022 - jamanetwork.com
Importance Microbiota-tumor interactions have qualified microbiota as a promising
prognostic biomarker in various types of cancers. Although the nasopharynx acts as a …

Bioinformatics-led discovery of osteoarthritis biomarkers and inflammatory infiltrates

X Hu, S Ni, K Zhao, J Qian, Y Duan - Frontiers in immunology, 2022 - frontiersin.org
The molecular mechanisms of osteoarthritis, the most common chronic disease, remain
unexplained. This study aimed to use bioinformatic methods to identify the key biomarkers …

[HTML][HTML] Prolonged sleep deprivation induces a cytokine-storm-like syndrome in mammals

D Sang, K Lin, Y Yang, G Ran, B Li, C Chen, Q Li, Y Ma… - Cell, 2023 - cell.com
Most animals require sleep, and sleep loss induces serious pathophysiological
consequences, including death. Previous experimental approaches for investigating sleep …

Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq

B Li, J Gould, Y Yang, S Sarkizova, M Tabaka… - Nature …, 2020 - nature.com
Massively parallel single-cell and single-nucleus RNA sequencing has opened the way to
systematic tissue atlases in health and disease, but as the scale of data generation is …

Prototype of running clinical trials in an untrustworthy environment using blockchain

DR Wong, S Bhattacharya, AJ Butte - Nature communications, 2019 - nature.com
Monitoring and ensuring the integrity of data within the clinical trial process is currently not
always feasible with the current research system. We propose a blockchain-based system to …