Gene regulatory network inference in the era of single-cell multi-omics

P Badia-i-Mompel, L Wessels, S Müller-Dott… - Nature Reviews …, 2023 - nature.com
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …

Mapping gene regulatory networks from single-cell omics data

MWEJ Fiers, L Minnoye, S Aibar… - Briefings in …, 2018 - academic.oup.com
Single-cell techniques are advancing rapidly and are yielding unprecedented insight into
cellular heterogeneity. Mapping the gene regulatory networks (GRNs) underlying cell states …

Gene regulatory network inference resources: A practical overview

D Mercatelli, L Scalambra, L Triboli, F Ray… - Biochimica et Biophysica …, 2020 - Elsevier
Transcriptional regulation is a fundamental molecular mechanism involved in almost every
aspect of life, from homeostasis to development, from metabolism to behavior, from reaction …

Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics

L Wang, N Trasanidis, T Wu, G Dong, M Hu… - Nature …, 2023 - nature.com
Gene regulatory networks (GRNs) are key determinants of cell function and identity and are
dynamically rewired during development and disease. Despite decades of advancement …

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

C Bravo González-Blas, S De Winter, G Hulselmans… - Nature …, 2023 - nature.com
Joint profiling of chromatin accessibility and gene expression in individual cells provides an
opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present …

Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets

S Zhang, S Pyne, S Pietrzak, S Halberg… - Nature …, 2023 - nature.com
Cell type-specific gene expression patterns are outputs of transcriptional gene regulatory
networks (GRNs) that connect transcription factors and signaling proteins to target genes …

A hybrid deep learning framework for gene regulatory network inference from single-cell transcriptomic data

M Zhao, W He, J Tang, Q Zou… - Briefings in bioinformatics, 2022 - academic.oup.com
Inferring gene regulatory networks (GRNs) based on gene expression profiles is able to
provide an insight into a number of cellular phenotypes from the genomic level and reveal …

Leveraging models of cell regulation and GWAS data in integrative network-based association studies

A Califano, AJ Butte, S Friend, T Ideker, E Schadt - Nature genetics, 2012 - nature.com
PERSPECTIVE interplay of signal transduction, transcriptional, post-transcriptional,
metabolic and other regulatory events that determine cell behavior. Even today, entirely new …

[PDF][PDF] Functional inference of gene regulation using single-cell multi-omics

VK Kartha, FM Duarte, Y Hu, S Ma, JG Chew… - Cell genomics, 2022 - cell.com
Cells require coordinated control over gene expression when responding to environmental
stimuli. Here we apply scATAC-seq and single-cell RNA sequencing (scRNA-seq) in resting …

Inference of gene regulatory network from single-cell transcriptomic data using pySCENIC

N Kumar, B Mishra, M Athar, S Mukhtar - … Regulation: Methods and …, 2021 - Springer
With the advent of recent next-generation sequencing (NGS) technologies in genomics,
transcriptomics, and epigenomics, profiling single-cell sequencing became possible. The …