[HTML][HTML] MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data

R Argelaguet, D Arnol, D Bredikhin, Y Deloro, B Velten… - Genome biology, 2020 - Springer
Technological advances have enabled the profiling of multiple molecular layers at single-
cell resolution, assaying cells from multiple samples or conditions. Consequently, there is a …

[HTML][HTML] scapGNN: A graph neural network–based framework for active pathway and gene module inference from single-cell multi-omics data

X Han, B Wang, C Situ, Y Qi, H Zhu, Y Li, X Guo - Plos Biology, 2023 - journals.plos.org
Although advances in single-cell technologies have enabled the characterization of multiple
omics profiles in individual cells, extracting functional and mechanistic insights from such …

[HTML][HTML] Multidimensional integrative genomics approaches to dissecting cardiovascular disease

D Arneson, L Shu, B Tsai, R Barrere-Cain… - Frontiers in …, 2017 - frontiersin.org
Elucidating the mechanisms of complex diseases such as cardiovascular disease (CVD)
remains a significant challenge due to multidimensional alterations at molecular, cellular …

[HTML][HTML] Advances in single-cell multi-omics and application in cardiovascular research

X Zhang, H Qiu, F Zhang, S Ding - Frontiers in Cell and …, 2022 - frontiersin.org
With the development of ever more powerful and versatile high-throughput sequencing
techniques and innovative ways to capture single cells, mapping the multicellular tissues at …

[HTML][HTML] Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space

L Xiong, K Tian, Y Li, W Ning, X Gao… - Nature …, 2022 - nature.com
Computational tools for integrative analyses of diverse single-cell experiments are facing
formidable new challenges including dramatic increases in data scale, sample …

Single cell analyses of development in the modern era

AM Klein, B Treutlein - Development, 2019 - journals.biologists.com
Single cell analyses encompass multiple approaches that, we suggest, can be summarized
by two unifying goals: to explain the cellular composition of tissues; and to characterize the …

Identifying disease-critical cell types and cellular processes across the human body by integration of single-cell profiles and human genetics

KA Jagadeesh, KK Dey, DT Montoro, R Mohan… - bioRxiv, 2021 - biorxiv.org
Genome-wide association studies (GWAS) provide a powerful means to identify loci and
genes contributing to disease, but in many cases the related cell types/states through which …

[HTML][HTML] Multi-omics single-cell data integration and regulatory inference with graph-linked embedding

ZJ Cao, G Gao - Nature Biotechnology, 2022 - nature.com
Despite the emergence of experimental methods for simultaneous measurement of multiple
omics modalities in single cells, most single-cell datasets include only one modality. A major …

[HTML][HTML] Integration of spatial and single-cell data across modalities with weakly linked features

S Chen, B Zhu, S Huang, JW Hickey, KZ Lin… - Nature …, 2023 - nature.com
Although single-cell and spatial sequencing methods enable simultaneous measurement of
more than one biological modality, no technology can capture all modalities within the same …

Cell type classification and discovery across diseases, technologies and tissues reveals conserved gene signatures and enables standardized single-cell readouts

M Chamberlain, R Hanamsagar, FO Nestle… - Biorxiv, 2021 - biorxiv.org
Autoimmune diseases are a major cause of mortality,. Current treatments often yield severe
insult to host tissue. It is hypothesized that improved “precision medicine” therapies will …