[HTML][HTML] Massively parallel base editing to map variant effects in human hematopoiesis

JD Martin-Rufino, N Castano, M Pang, EI Grody… - Cell, 2023 - cell.com
Systematic evaluation of the impact of genetic variants is critical for the study and treatment
of human physiology and disease. While specific mutations can be introduced by genome …

[HTML][HTML] Deciphering cell states and genealogies of human haematopoiesis

C Weng, F Yu, D Yang, M Poeschla, LA Liggett… - Nature, 2024 - nature.com
The human blood system is maintained through the differentiation and massive amplification
of a limited number of long-lived haematopoietic stem cells (HSCs). Perturbations to this …

Revealing gene function with statistical inference at single-cell resolution

C Trapnell - Nature Reviews Genetics, 2024 - nature.com
Single-cell and spatial molecular profiling assays have shown large gains in sensitivity,
resolution and throughput. Applying these technologies to specimens from human and …

[HTML][HTML] Polygenic regression uncovers trait-relevant cellular contexts through pathway activation transformation of single-cell RNA sequencing data

Y Ma, C Deng, Y Zhou, Y Zhang, F Qiu, D Jiang… - Cell Genomics, 2023 - cell.com
Advances in single-cell RNA sequencing (scRNA-seq) techniques have accelerated
functional interpretation of disease-associated variants discovered from genome-wide …

[HTML][HTML] A systems biology approach uncovers novel disease mechanisms in age-related macular degeneration

LD Orozco, LA Owen, J Hofmann, AD Stockwell, J Tao… - Cell genomics, 2023 - cell.com
Age-related macular degeneration (AMD) is a leading cause of blindness, affecting 200
million people worldwide. To identify genes that could be targeted for treatment, we created …

[HTML][HTML] Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types

SS Kim, B Truong, K Jagadeesh, KK Dey… - Nature …, 2024 - nature.com
Prioritizing disease-critical cell types by integrating genome-wide association studies
(GWAS) with functional data is a fundamental goal. Single-cell chromatin accessibility …

[HTML][HTML] Single-cell characterization of macrophages in uveal melanoma uncovers transcriptionally heterogeneous subsets conferring poor prognosis and aggressive …

K Li, L Sun, Y Wang, Y Cen, J Zhao, Q Liao… - … & Molecular Medicine, 2023 - nature.com
Uveal melanoma (UM) is the most frequent primary intraocular malignancy with high
metastatic potential and poor prognosis. Macrophages represent one of the most abundant …

[HTML][HTML] Pathway centric analysis for single-cell RNA-seq and spatial transcriptomics data with GSDensity

Q Liang, Y Huang, S He, K Chen - Nature communications, 2023 - nature.com
Advances in single-cell technology have enabled molecular dissection of heterogeneous
biospecimens at unprecedented scales and resolutions. Cluster-centric approaches are …

Chromatin accessibility analysis and architectural profiling of human kidneys reveal key cell types and a regulator of diabetic kidney disease

M Eun, D Kim, SI Shin, HO Yang, KD Kim, SY Choi… - Kidney International, 2024 - Elsevier
Diabetes is the leading cause of kidney disease that progresses to kidney failure. However,
the key molecular and cellular pathways involved in diabetic kidney disease (DKD) …

[HTML][HTML] DNA methylation predicts the outcome of COVID-19 patients with acute respiratory distress syndrome

M Bradic, S Taleb, B Thomas, O Chidiac… - Journal of Translational …, 2022 - Springer
Background COVID-19 infections could be complicated by acute respiratory distress
syndrome (ARDS), increasing mortality risk. We sought to assess the methylome of …