Computational principles and challenges in single-cell data integration

R Argelaguet, ASE Cuomo, O Stegle… - Nature biotechnology, 2021 - nature.com
The development of single-cell multimodal assays provides a powerful tool for investigating
multiple dimensions of cellular heterogeneity, enabling new insights into development …

Macrophage phenotypes in tissue repair and the foreign body response: Implications for biomaterial-based regenerative medicine strategies

KE Martin, AJ García - Acta biomaterialia, 2021 - Elsevier
Macrophages are a highly heterogeneous and plastic population of cells that are crucial for
tissue repair and regeneration. This has made macrophages a particularly attractive target …

A pan-grass transcriptome reveals patterns of cellular divergence in crops

B Guillotin, R Rahni, M Passalacqua, MA Mohammed… - Nature, 2023 - nature.com
Different plant species within the grasses were parallel targets of domestication, giving rise
to crops with distinct evolutionary histories and traits. Key traits that distinguish these species …

An atlas of rabbit development as a model for single-cell comparative genomics

MLN Ton, D Keitley, B Theeuwes, C Guibentif… - Nature Cell …, 2023 - nature.com
Traditionally, the mouse has been the favoured vertebrate model for biomedical research,
due to its experimental and genetic tractability. However, non-rodent embryological studies …

Mapping single-cell atlases throughout Metazoa unravels cell type evolution

AJ Tarashansky, JM Musser, M Khariton, P Li, D Arendt… - Elife, 2021 - elifesciences.org
Comparing single-cell transcriptomic atlases from diverse organisms can elucidate the
origins of cellular diversity and assist the annotation of new cell atlases. Yet, comparison …

Integrated single-cell analysis-based classification of vascular mononuclear phagocytes in mouse and human atherosclerosis

A Zernecke, F Erhard, T Weinberger… - Cardiovascular …, 2023 - academic.oup.com
Aims Accumulation of mononuclear phagocytes [monocytes, macrophages, and dendritic
cells (DCs)] in the vessel wall is a hallmark of atherosclerosis. Using integrated single-cell …

Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application

M Wang, W Song, C Ming, Q Wang, X Zhou… - Molecular …, 2022 - Springer
Alzheimer's disease (AD) is the most common form of dementia, characterized by
progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic …

Deep learning of cross-species single-cell landscapes identifies conserved regulatory programs underlying cell types

J Li, J Wang, P Zhang, R Wang, Y Mei, Z Sun, L Fei… - Nature Genetics, 2022 - nature.com
Despite extensive efforts to generate and analyze reference genomes, genetic models to
predict gene regulation and cell fate decisions are lacking for most species. Here, we …

Detecting signatures of selection on gene expression

PD Price, DH Palmer Droguett, JA Taylor… - Nature Ecology & …, 2022 - nature.com
A substantial amount of phenotypic diversity results from changes in gene expression levels
and patterns. Understanding how the transcriptome evolves is therefore a key priority in …

Current advances in primate genomics: novel approaches for understanding evolution and disease

D Juan, G Santpere, JL Kelley, OE Cornejo… - Nature reviews …, 2023 - nature.com
Primate genomics holds the key to understanding fundamental aspects of human evolution
and disease. However, genetic diversity and functional genomics data sets are currently …