Using clusterProfiler to characterize multiomics data

S Xu, E Hu, Y Cai, Z **e, X Luo, L Zhan, W Tang… - Nature protocols, 2024 - nature.com
With the advent of multiomics, software capable of multidimensional enrichment analysis
has become increasingly crucial for uncovering gene set variations in biological processes …

RNA sequencing: the teenage years

R Stark, M Grzelak, J Hadfield - Nature Reviews Genetics, 2019 - nature.com
Over the past decade, RNA sequencing (RNA-seq) has become an indispensable tool for
transcriptome-wide analysis of differential gene expression and differential splicing of …

[HTML][HTML] Inflammasome activation in infected macrophages drives COVID-19 pathology

E Sefik, R Qu, C Junqueira, E Kaffe, H Mirza, J Zhao… - Nature, 2022 - nature.com
Severe COVID-19 is characterized by persistent lung inflammation, inflammatory cytokine
production, viral RNA and a sustained interferon (IFN) response, all of which are …

B cells and tertiary lymphoid structures promote immunotherapy response

BA Helmink, SM Reddy, J Gao, S Zhang, R Basar… - Nature, 2020 - nature.com
Abstract Treatment with immune checkpoint blockade (ICB) has revolutionized cancer
therapy. Until now, predictive biomarkers,,,,,,,,–and strategies to augment clinical response …

Analysing high-throughput sequencing data in Python with HTSeq 2.0

GH Putri, S Anders, PT Pyl, JE Pimanda… - Bioinformatics, 2022 - academic.oup.com
HTSeq 2.0 provides a more extensive application programming interface including a new
representation for sparse genomic data, enhancements for htseq-count to suit single-cell …

Negative feedback control of neuronal activity by microglia

A Badimon, HJ Strasburger, P Ayata, X Chen, A Nair… - Nature, 2020 - nature.com
Microglia, the brain's resident macrophages, help to regulate brain function by removing
dying neurons, pruning non-functional synapses, and producing ligands that support …

Disruption of mitochondrial complex I induces progressive parkinsonism

P González-Rodríguez, E Zampese, KA Stout… - Nature, 2021 - nature.com
Loss of functional mitochondrial complex I (MCI) in the dopaminergic neurons of the
substantia nigra is a hallmark of Parkinson's disease. Yet, whether this change contributes to …

Multi-omic machine learning predictor of breast cancer therapy response

SJ Sammut, M Crispin-Ortuzar, SF Chin, E Provenzano… - Nature, 2022 - nature.com
Breast cancers are complex ecosystems of malignant cells and the tumour
microenvironment. The composition of these tumour ecosystems and interactions within …

Genetics of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and therapeutic targets

JH Zhao, D Stacey, N Eriksson… - Nature …, 2023 - nature.com
Circulating proteins have important functions in inflammation and a broad range of diseases.
To identify genetic influences on inflammation-related proteins, we conducted a genome …

A pathology atlas of the human cancer transcriptome

M Uhlen, C Zhang, S Lee, E Sjöstedt, L Fagerberg… - Science, 2017 - science.org
INTRODUCTION Cancer is a leading cause of death worldwide, and there is great need to
define the molecular mechanisms driving the development and progression of individual …