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 …

Single cell RNA‐sequencing: A powerful yet still challenging technology to study cellular heterogeneity

M Ke, B Elshenawy, H Sheldon, A Arora, FM Buffa - Bioessays, 2022 - Wiley Online Library
Almost all biomedical research to date has relied upon mean measurements from cell
populations, however it is well established that what it is observed at this macroscopic level …

cGAS–STING drives ageing-related inflammation and neurodegeneration

MF Gulen, N Samson, A Keller, M Schwabenland… - Nature, 2023 - nature.com
Low-grade inflammation is a hallmark of old age and a central driver of ageing-associated
impairment and disease. Multiple factors can contribute to ageing-associated inflammation; …

DestVI identifies continuums of cell types in spatial transcriptomics data

R Lopez, B Li, H Keren-Shaul, P Boyeau… - Nature …, 2022 - nature.com
Most spatial transcriptomics technologies are limited by their resolution, with spot sizes
larger than that of a single cell. Although joint analysis with single-cell RNA sequencing can …

Unique functional responses differentially map onto genetic subtypes of dopamine neurons

M Azcorra, Z Gaertner, C Davidson, Q He, H Kim… - Nature …, 2023 - nature.com
Dopamine neurons are characterized by their response to unexpected rewards, but they
also fire during movement and aversive stimuli. Dopamine neuron diversity has been …

Slide-tags enables single-nucleus barcoding for multimodal spatial genomics

AJC Russell, JA Weir, NM Nadaf, M Shabet, V Kumar… - Nature, 2024 - nature.com
Recent technological innovations have enabled the high-throughput quantification of gene
expression and epigenetic regulation within individual cells, transforming our understanding …

Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation

Z Liu, X Kong, Y Long, S Liu, H Zhang, J Jia, W Cui… - Nature Plants, 2023 - nature.com
Legumes form symbiosis with rhizobium leading to the development of nitrogen-fixing
nodules. By integrating single-nucleus and spatial transcriptomics, we established a cell …

[HTML][HTML] The choroid plexus synergizes with immune cells during neuroinflammation

H Xu, P Lotfy, S Gelb, A Pragana, C Hehnly, LIJ Byer… - Cell, 2024 - cell.com
The choroid plexus (ChP) is a vital brain barrier and source of cerebrospinal fluid (CSF).
Here, we use longitudinal two-photon imaging in awake mice and single-cell transcriptomics …

IL-12 sensing in neurons induces neuroprotective CNS tissue adaptation and attenuates neuroinflammation in mice

M Andreadou, F Ingelfinger, D De Feo… - Nature …, 2023 - nature.com
Abstract Interleukin-12 (IL-12) is a potent driver of type 1 immunity. Paradoxically, in
autoimmune conditions, including of the CNS, IL-12 reduces inflammation. The underlying …

Multiplexed single-cell characterization of alternative polyadenylation regulators

MH Kowalski, HH Wessels, J Linder, C Dalgarno… - Cell, 2024 - cell.com
Most mammalian genes have multiple polyA sites, representing a substantial source of
transcript diversity regulated by the cleavage and polyadenylation (CPA) machinery. To …