References

Key papers for this project, organized by topic.

SC-islet differentiation and characterization

Augsornworawat et al. (2023) "Single-nucleus multi-omics of human stem cell-derived islets identifies deficiencies in lineage specification" Nature Cell Biology https://www.nature.com/articles/s41556-023-01150-8
Zhu et al. (2023) "Understanding cell fate acquisition in stem-cell-derived pancreatic islets using single-cell multiome-inferred regulomes" Developmental Cell https://www.sciencedirect.com/science/article/pii/S1534580723001077
Veres et al. (2019) "Charting cellular identity during human in vitro β-cell differentiation" Nature https://www.nature.com/articles/s41586-019-1168-5
- Note: describes an enterochromaffin-like endocrine cell type expressing CHGA, TPH1, LMX1A, SLC18A1; also cells expressing TPH1, NKX6-1 and low insulin but lacking G6PC2, NPTX2, ISL1, PDX1
Balboa et al. (2022) "Functional, metabolic and transcriptional maturation of human pancreatic islets derived from stem cells" Nature Biotechnology https://www.nature.com/articles/s41587-022-01219-z

Chiou et al. (2021) "Interpreting type 1 diabetes risk with genetics and single-cell epigenomics" Nature https://www.nature.com/articles/s41586-021-03552-w
Chiou et al. (2019) "Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk" Nature Genetics https://www.nature.com/articles/s41588-019-0457-0
Thurner et al. (2018) "Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci" eLife https://elifesciences.org/articles/31977
Varshney et al. (2017) "Genetic regulatory signatures underlying islet gene expression and type 2 diabetes" PNAS https://www.nature.com/articles/s41588-018-0241-6

Wesolowska-Andersen et al. (2020) "Deep learning models predict regulatory variants in pancreatic islets and refine type 2 diabetes association signals" eLife https://elifesciences.org/articles/51503
Linder et al. (2023) "Modeling islet enhancers using deep learning identifies candidate causal variants at loci associated with T2D and glycemic traits" PNAS https://www.pnas.org/doi/abs/10.1073/pnas.2206612120
Muttillo et al. (2022) "Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures" Diabetes & Metabolism https://linkinghub.elsevier.com/retrieve/pii/S2212877819309573

Chiou et al. (2021) "Interpreting type 1 diabetes risk with genetics and single-cell epigenomics" Nature https://www.nature.com/articles/s41586-021-03552-w
Vujkovic et al. (2020) "Discovery of 318 new risk loci for type 2 diabetes and related vascular outcomes among 1.4 million participants in a multi-ancestry meta-analysis" Nature Genetics https://www.nature.com/articles/s41588-020-0637-y
Aylward et al. (2021) "Mutations and variants of ONECUT1 in diabetes" Nature Medicine https://www.nature.com/articles/s41591-021-01502-7

Yuan et al. (2024) "Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina" bioRxiv https://www.biorxiv.org/content/10.1101/2024.12.28.630634v1
Lee et al. (2023) "Simultaneous profiling of 3D genome structure and DNA methylation in single human cells" Nature Methods https://www.nature.com/articles/s41586-023-06819-6