Computational principles and challenges in single-cell data integration
The development of single-cell multimodal assays provides a powerful tool for investigating
multiple dimensions of cellular heterogeneity, enabling new insights into development …
multiple dimensions of cellular heterogeneity, enabling new insights into development …
Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics
AS Nam, R Chaligne, DA Landau - Nature Reviews Genetics, 2021 - nature.com
Cancer represents an evolutionary process through which growing malignant populations
genetically diversify, leading to tumour progression, relapse and resistance to therapy. In …
genetically diversify, leading to tumour progression, relapse and resistance to therapy. In …
Genome-wide enhancer maps link risk variants to disease genes
Genome-wide association studies (GWAS) have identified thousands of noncoding loci that
are associated with human diseases and complex traits, each of which could reveal insights …
are associated with human diseases and complex traits, each of which could reveal insights …
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 …
scATAC-seq (single-cell assay for transposase accessible chromatin by sequencing). Here …
Joint probabilistic modeling of single-cell multi-omic data with totalVI
The paired measurement of RNA and surface proteins in single cells with cellular indexing
of transcriptomes and epitopes by sequencing (CITE-seq) is a promising approach to …
of transcriptomes and epitopes by sequencing (CITE-seq) is a promising approach to …
[HTML][HTML] ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis
The advent of single-cell chromatin accessibility profiling has accelerated the ability to map
gene regulatory landscapes but has outpaced the development of scalable software to …
gene regulatory landscapes but has outpaced the development of scalable software to …
[HTML][HTML] Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution
Genetic perturbations of cortical development can lead to neurodevelopmental disease,
including autism spectrum disorder (ASD). To identify genomic regions crucial to …
including autism spectrum disorder (ASD). To identify genomic regions crucial to …
Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19
Our understanding of protective versus pathological immune responses to SARS-CoV-2, the
virus that causes coronavirus disease 2019 (COVID-19), is limited by inadequate profiling of …
virus that causes coronavirus disease 2019 (COVID-19), is limited by inadequate profiling of …
Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling
Natural mitochondrial DNA (mtDNA) mutations enable the inference of clonal relationships
among cells. mtDNA can be profiled along with measures of cell state, but has not yet been …
among cells. mtDNA can be profiled along with measures of cell state, but has not yet been …
[HTML][HTML] Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney
The integration of single cell transcriptome and chromatin accessibility datasets enables a
deeper understanding of cell heterogeneity. We performed single nucleus ATAC (snATAC …
deeper understanding of cell heterogeneity. We performed single nucleus ATAC (snATAC …