Best practices for single-cell analysis across modalities

L Heumos, AC Schaar, C Lance, A Litinetskaya… - Nature Reviews …, 2023 - nature.com
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …

Doublet identification in single-cell sequencing data using scDblFinder

PL Germain, A Lun, CG Meixide, W Macnair… - …, 2022 - pmc.ncbi.nlm.nih.gov
Doublets are prevalent in single-cell sequencing data and can lead to artifactual findings. A
number of strategies have therefore been proposed to detect them. Building on the strengths …

Integrating population genetics, stem cell biology and cellular genomics to study complex human diseases

N Farbehi, DR Neavin, ASE Cuomo, L Studer… - Nature Genetics, 2024 - nature.com
Human pluripotent stem (hPS) cells can, in theory, be differentiated into any cell type,
making them a powerful in vitro model for human biology. Recent technological advances …

MitoSort: Robust Demultiplexing of Pooled Single-cell Genomic Data Using Endogenous Mitochondrial Variants

Z Tang, W Zhang, P Shi, S Li, X Li, Y Li… - Genomics …, 2024 - academic.oup.com
Multiplexing across donors has emerged as a popular strategy to increase throughput,
reduce costs, overcome technical batch effects, and improve doublet detection in single-cell …

Spatial multiomic landscape of the human placenta at molecular resolution

JR Ounadjela, K Zhang, KJ Kobayashi-Kirschvink… - Nature Medicine, 2024 - nature.com
Successful pregnancy relies directly on the placenta's complex, dynamic, gene-regulatory
networks. Disruption of this vast collection of intercellular and intracellular programs leads to …

Benchmarking single-cell hashtag oligo demultiplexing methods

G Howitt, Y Feng, L Tobar, D Vassiliadis… - NAR Genomics and …, 2023 - academic.oup.com
Sample multiplexing is often used to reduce cost and limit batch effects in single-cell RNA
sequencing (scRNA-seq) experiments. A commonly used multiplexing technique involves …

A village in a dish model system for population-scale hiPSC studies

DR Neavin, AM Steinmann, N Farbehi, HS Chiu… - Nature …, 2023 - nature.com
The mechanisms by which DNA alleles contribute to disease risk, drug response, and other
human phenotypes are highly context-specific, varying across cell types and different …

A risk-reward examination of sample multiplexing reagents for single cell RNA-Seq

DV Brown, CJA Anttila, L Ling, P Grave, TM Baldwin… - Genomics, 2024 - Elsevier
Single-cell RNA sequencing (scRNA-Seq) has emerged as a powerful tool for
understanding cellular heterogeneity and function. However the choice of sample …

[HTML][HTML] Novel human pluripotent stem cell-derived hypothalamus organoids demonstrate cellular diversity

L Sarrafha, DR Neavin, GM Parfitt, IA Kruglikov… - iScience, 2023 - cell.com
The hypothalamus is a region of the brain that plays an important role in regulating body
functions and behaviors. There is a growing interest in human pluripotent stem cells …

Evaluation of genetic demultiplexing of single-cell sequencing data from model species

JF Cardiello, AJ Araus, S Giatrellis… - Life Science …, 2023 - life-science-alliance.org
Single-cell sequencing (sc-seq) provides a species agnostic tool to study cellular processes.
However, these technologies are expensive and require sufficient cell quantities and …