Gene regulatory network inference in the era of single-cell multi-omics
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 …
Discerning molecular interactions: a comprehensive review on biomolecular interaction databases and network analysis tools
Computational analysis of biomolecular interaction networks is now gaining a lot of
importance to understand the functions of novel genes/proteins. Gene interaction (GI) …
importance to understand the functions of novel genes/proteins. Gene interaction (GI) …
Spatially organized multicellular immune hubs in human colorectal cancer
Immune responses to cancer are highly variable, with mismatch repair-deficient (MMRd)
tumors exhibiting more anti-tumor immunity than mismatch repair-proficient (MMRp) tumors …
tumors exhibiting more anti-tumor immunity than mismatch repair-proficient (MMRp) tumors …
NicheNet: modeling intercellular communication by linking ligands to target genes
Computational methods that model how gene expression of a cell is influenced by
interacting cells are lacking. We present NicheNet (https://github. com/saeyslab/nichenetr), a …
interacting cells are lacking. We present NicheNet (https://github. com/saeyslab/nichenetr), a …
Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics
Abstract Knowledge of therapeutic targets and early drug candidates is useful for improved
drug discovery. In particular, information about target regulators and the patented …
drug discovery. In particular, information about target regulators and the patented …
NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis
The growing application of gene expression profiling demands powerful yet user-friendly
bioinformatics tools to support systems-level data understanding. NetworkAnalyst was first …
bioinformatics tools to support systems-level data understanding. NetworkAnalyst was first …
Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data
We present a systematic evaluation of state-of-the-art algorithms for inferring gene
regulatory networks from single-cell transcriptional data. As the ground truth for assessing …
regulatory networks from single-cell transcriptional data. As the ground truth for assessing …
Benchmark and integration of resources for the estimation of human transcription factor activities
The prediction of transcription factor (TF) activities from the gene expression of their targets
(ie, TF regulon) is becoming a widely used approach to characterize the functional status of …
(ie, TF regulon) is becoming a widely used approach to characterize the functional status of …
CellCall: integrating paired ligand–receptor and transcription factor activities for cell–cell communication
With the dramatic development of single-cell RNA sequencing (scRNA-seq) technologies,
the systematic decoding of cell-cell communication has received great research interest. To …
the systematic decoding of cell-cell communication has received great research interest. To …
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
Background RNA-seq is widely used for transcriptomic profiling, but the bioinformatics
analysis of resultant data can be time-consuming and challenging, especially for biologists …
analysis of resultant data can be time-consuming and challenging, especially for biologists …