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 …
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …
The diversification of methods for studying cell–cell interactions and communication
No cell lives in a vacuum, and the molecular interactions between cells define most
phenotypes. Transcriptomics provides rich information to infer cell–cell interactions and …
phenotypes. Transcriptomics provides rich information to infer cell–cell interactions and …
A new gene set identifies senescent cells and predicts senescence-associated pathways across tissues
Although cellular senescence drives multiple age-related co-morbidities through the
senescence-associated secretory phenotype, in vivo senescent cell identification remains …
senescence-associated secretory phenotype, in vivo senescent cell identification remains …
Cell–cell communication inference and analysis in the tumour microenvironments from single-cell transcriptomics: data resources and computational strategies
Carcinomas are complex ecosystems composed of cancer, stromal and immune cells.
Communication between these cells and their microenvironments induces cancer …
Communication between these cells and their microenvironments induces cancer …
Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application
Alzheimer's disease (AD) is the most common form of dementia, characterized by
progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic …
progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic …
Single-cell network biology for resolving cellular heterogeneity in human diseases
Understanding cellular heterogeneity is the holy grail of biology and medicine. Cells
harboring identical genomes show a wide variety of behaviors in multicellular organisms …
harboring identical genomes show a wide variety of behaviors in multicellular organisms …
Understanding cell‐cell communication and signaling in the colorectal cancer microenvironment
Carcinomas are complex heterocellular systems containing epithelial cancer cells, stromal
fibroblasts, and multiple immune cell‐types. Cell‐cell communication between these tumor …
fibroblasts, and multiple immune cell‐types. Cell‐cell communication between these tumor …
Omics in systems biology: current progress and future outlook
TD Veenstra - Proteomics, 2021 - Wiley Online Library
Biological research has undergone tremendous changes over the past three decades.
Research used to almost exclusively focus on a single aspect of a single molecule per …
Research used to almost exclusively focus on a single aspect of a single molecule per …
Computational methods for single-cell RNA sequencing
Single-cell RNA sequencing (scRNA-seq) has provided a high-dimensional catalog of
millions of cells across species and diseases. These data have spurred the development of …
millions of cells across species and diseases. These data have spurred the development of …
[HTML][HTML] Network-based approaches for modeling disease regulation and progression
Molecular interaction networks lay the foundation for studying how biological functions are
controlled by the complex interplay of genes and proteins. Investigating perturbed processes …
controlled by the complex interplay of genes and proteins. Investigating perturbed processes …