Concepts and new developments in droplet-based single cell multi-omics
Single cell sequencing technologies have become a fixture in the molecular profiling of cells
due to their ease, flexibility, and commercial availability. In particular, partitioning individual …
due to their ease, flexibility, and commercial availability. In particular, partitioning individual …
Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome and epigenome
E Metzner, KM Southard, TM Norman - Cell systems, 2025 - cell.com
Single-cell CRISPR screens link genetic perturbations to transcriptional states, but high-
throughput methods connecting these induced changes to their regulatory foundations are …
throughput methods connecting these induced changes to their regulatory foundations are …
Perspective on recent developments and challenges in regulatory and systems genomics
Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular,
and molecular levels requires deciphering the cis-regulatory code, the sequence rules by …
and molecular levels requires deciphering the cis-regulatory code, the sequence rules by …
Controlled noise: evidence of epigenetic regulation of single-cell expression variability
Motivation Understanding single-cell expression variability (scEV) or gene expression noise
among cells of the same type and state is crucial for delineating population-level cellular …
among cells of the same type and state is crucial for delineating population-level cellular …
ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning
W Saelens, O Pushkarev, B Deplancke - Nature Communications, 2025 - nature.com
Gene regulation is inherently multiscale, but scale-adaptive machine learning methods that
fully exploit this property in single-nucleus accessibility data are still lacking. Here, we …
fully exploit this property in single-nucleus accessibility data are still lacking. Here, we …
GEEES: inferring cell-specific gene–enhancer interactions from multi-modal single-cell data
S Chen, S Keleş - Bioinformatics, 2024 - academic.oup.com
Motivation Gene–enhancer interactions are central to transcriptional regulation. Current
multi-modal single-cell datasets that profile transcriptome and chromatin accessibility …
multi-modal single-cell datasets that profile transcriptome and chromatin accessibility …
Mapping enhancer-gene regulatory interactions from single-cell data
Mapping enhancers and their target genes in specific cell types is crucial for understanding
gene regulation and human disease genetics. However, accurately predicting enhancer …
gene regulation and human disease genetics. However, accurately predicting enhancer …
Super-enhancers: drivers of cells' identities and cells' debacles
M Lavaud, R Tesfaye, L Lassous, B Brounais… - …, 2024 - Taylor & Francis
Precise spatiotemporal regulations of gene expression are essential for determining cells'
fates and functions. Enhancers are cis-acting DNA elements that act as periodic …
fates and functions. Enhancers are cis-acting DNA elements that act as periodic …
Single-cell multiomics: a new frontier in drug research and development
J Ma, C Dong, A He, H Xiong - Frontiers in Drug Discovery, 2024 - frontiersin.org
Single-cell multiomics (sc-multiomics) is a burgeoning field that simultaneously integrates
multiple layers of molecular information, enabling the characterization of dynamic cell states …
multiple layers of molecular information, enabling the characterization of dynamic cell states …
Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance
ER Dorans, K Jagadeesh, K Dey, AL Price - medRxiv, 2024 - medrxiv.org
Methods that analyze single-cell paired RNA-seq and ATAC-seq multiome data have shown
great promise in linking regulatory elements to genes. However, existing methods differ in …
great promise in linking regulatory elements to genes. However, existing methods differ in …