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 …

Navigating the pitfalls of applying machine learning in genomics

S Whalen, J Schreiber, WS Noble… - Nature Reviews Genetics, 2022 - nature.com
The scale of genetic, epigenomic, transcriptomic, cheminformatic and proteomic data
available today, coupled with easy-to-use machine learning (ML) toolkits, has propelled the …

Eleven grand challenges in single-cell data science

D Lähnemann, J Köster, E Szczurek, DJ McCarthy… - Genome biology, 2020 - Springer
The recent boom in microfluidics and combinatorial indexing strategies, combined with low
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …

Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data

TS Andrews, VY Kiselev, D McCarthy, M Hemberg - Nature protocols, 2021 - nature.com
Single-cell RNA sequencing (scRNA-seq) is a popular and powerful technology that allows
you to profile the whole transcriptome of a large number of individual cells. However, the …

Confronting false discoveries in single-cell differential expression

JW Squair, M Gautier, C Kathe, MA Anderson… - Nature …, 2021 - nature.com
Differential expression analysis in single-cell transcriptomics enables the dissection of cell-
type-specific responses to perturbations such as disease, trauma, or experimental …

Epigenetic age prediction

DJ Simpson, T Chandra - Aging cell, 2021 - Wiley Online Library
Advanced age is the main common risk factor for cancer, cardiovascular disease and
neurodegeneration. Yet, more is known about the molecular basis of any of these groups of …

Significance analysis for clustering with single-cell RNA-sequencing data

IN Grabski, K Street, RA Irizarry - Nature Methods, 2023 - nature.com
Unsupervised clustering of single-cell RNA-sequencing data enables the identification of
distinct cell populations. However, the most widely used clustering algorithms are heuristic …

Multifunctional barcoding with ClonMapper enables high-resolution study of clonal dynamics during tumor evolution and treatment

C Gutierrez, AM Al'Khafaji, E Brenner, KE Johnson… - Nature Cancer, 2021 - nature.com
Lineage-tracing methods have enabled characterization of clonal dynamics in complex
populations, but generally lack the ability to integrate genomic, epigenomic and …

Molecular design of hypothalamus development

RA Romanov, EO Tretiakov, ME Kastriti, M Zupancic… - Nature, 2020 - nature.com
A wealth of specialized neuroendocrine command systems intercalated within the
hypothalamus control the most fundamental physiological needs in vertebrates …

Selective inference for hierarchical clustering

LL Gao, J Bien, D Witten - Journal of the American Statistical …, 2024 - Taylor & Francis
Classical tests for a difference in means control the Type I error rate when the groups are
defined a priori. However, when the groups are instead defined via clustering, then applying …