Best practices for single-cell analysis across modalities

L Heumos, AC Schaar, C Lance, A Litinetskaya… - Nature Reviews …, 2023 - nature.com
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …

Using clusterProfiler to characterize multiomics data

S Xu, E Hu, Y Cai, Z Xie, 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 …

A TREM2-activating antibody with a blood–brain barrier transport vehicle enhances microglial metabolism in Alzheimer's disease models

B van Lengerich, L Zhan, D Xia, D Chan, D Joy… - Nature …, 2023 - nature.com
Loss-of-function variants of TREM2 are associated with increased risk of Alzheimer's
disease (AD), suggesting that activation of this innate immune receptor may be a useful …

Persistent complement dysregulation with signs of thromboinflammation in active Long Covid

C Cervia-Hasler, SC Brüningk, T Hoch, B Fan, G Muzio… - Science, 2024 - science.org
Long Covid is a debilitating condition of unknown etiology. We performed multimodal
proteomics analyses of blood serum from COVID-19 patients followed up to 12 months after …

Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson's disease

T Kamath, A Abdulraouf, SJ Burris, J Langlieb… - Nature …, 2022 - nature.com
The loss of dopamine (DA) neurons within the substantia nigra pars compacta (SNpc) is a
defining pathological hallmark of Parkinson's disease (PD). Nevertheless, the molecular …

A multi-organ chip with matured tissue niches linked by vascular flow

K Ronaldson-Bouchard, D Teles, K Yeager… - Nature Biomedical …, 2022 - nature.com
Engineered tissues can be used to model human pathophysiology and test the efficacy and
safety of drugs. Yet, to model whole-body physiology and systemic diseases, engineered …

Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy

M Chaffin, I Papangeli, B Simonson, AD Akkad, MC Hill… - Nature, 2022 - nature.com
Heart failure encompasses a heterogeneous set of clinical features that converge on
impaired cardiac contractile function, and presents a growing public health concern …

Acute inflammatory response via neutrophil activation protects against the development of chronic pain

M Parisien, LV Lima, C Dagostino… - Science translational …, 2022 - science.org
The transition from acute to chronic pain is critically important but not well understood. Here,
we investigated the pathophysiological mechanisms underlying the transition from acute to …

Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology

T Chu, Z Wang, D Pe'er, CG Danko - Nature Cancer, 2022 - nature.com
Inferring single-cell compositions and their contributions to global gene expression changes
from bulk RNA sequencing (RNA-seq) datasets is a major challenge in oncology. Here we …

Vorasidenib and ivosidenib in IDH1-mutant low-grade glioma: a randomized, perioperative phase 1 trial

IK Mellinghoff, M Lu, PY Wen, JW Taylor, EA Maher… - Nature medicine, 2023 - nature.com
Vorasidenib and ivosidenib inhibit mutant forms of isocitrate dehydrogenase (mIDH) and
have shown preliminary clinical activity against m IDH glioma. We evaluated both agents in …