Droplet-based microfluidics

T Moragues, D Arguijo, T Beneyton, C Modavi… - Nature Reviews …, 2023 - nature.com
Droplet-based microfluidic systems generate, manipulate and control sub-microlitre droplets
enclosed within an immiscible carrier fluid. Owing to a number of remarkable features, such …

[HTML][HTML] Macrophage diversity in cancer revisited in the era of single-cell omics

RY Ma, A Black, BZ Qian - Trends in immunology, 2022 - cell.com
Tumor-associated macrophages (TAMs) have multiple potent functions in cancer and, thus,
represent important therapeutic targets. These diverse functions highlight the heterogenous …

Dictionary learning for integrative, multimodal and scalable single-cell analysis

Y Hao, T Stuart, MH Kowalski, S Choudhary… - Nature …, 2024 - nature.com
Map** single-cell sequencing profiles to comprehensive reference datasets provides a
powerful alternative to unsupervised analysis. However, most reference datasets are …

Single-cell chromatin state analysis with Signac

T Stuart, A Srivastava, S Madad, CA Lareau, R Satija - Nature methods, 2021 - nature.com
The recent development of experimental methods for measuring chromatin state at single-
cell resolution has created a need for computational tools capable of analyzing these …

Characterizing cis-regulatory elements using single-cell epigenomics

S Preissl, KJ Gaulton, B Ren - Nature Reviews Genetics, 2023 - nature.com
Cell type-specific gene expression patterns and dynamics during development or in disease
are controlled by cis-regulatory elements (CREs), such as promoters and enhancers …

A single-cell atlas of chromatin accessibility in the human genome

K Zhang, JD Hocker, M Miller, X Hou, J Chiou… - Cell, 2021 - cell.com
Current catalogs of regulatory sequences in the human genome are still incomplete and lack
cell type resolution. To profile the activity of gene regulatory elements in diverse cell types …

Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex

A Uzquiano, AJ Kedaigle, M Pigoni, B Paulsen… - Cell, 2022 - cell.com
Realizing the full utility of brain organoids to study human development requires
understanding whether organoids precisely replicate endogenous cellular and molecular …

Immune ageing at single-cell resolution

DA Mogilenko, I Shchukina, MN Artyomov - Nature Reviews …, 2022 - nature.com
Ageing leads to profound alterations in the immune system and increases susceptibility to
some chronic, infectious and autoimmune diseases. In recent years, widespread application …

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

EP Mimitou, CA Lareau, KY Chen… - Nature …, 2021 - nature.com
Recent technological advances have enabled massively parallel chromatin profiling with
scATAC-seq (single-cell assay for transposase accessible chromatin by sequencing). Here …

[HTML][HTML] Chromatin potential identified by shared single-cell profiling of RNA and chromatin

S Ma, B Zhang, LM LaFave, AS Earl, Z Chiang, Y Hu… - Cell, 2020 - cell.com
Cell differentiation and function are regulated across multiple layers of gene regulation,
including modulation of gene expression by changes in chromatin accessibility. However …