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 …
Microbiome multi-omics network analysis: statistical considerations, limitations, and opportunities
The advent of large-scale microbiome studies affords newfound analytical opportunities to
understand how these communities of microbes operate and relate to their environment …
understand how these communities of microbes operate and relate to their environment …
The single-cell eQTLGen consortium
In recent years, functional genomics approaches combining genetic information with bulk
RNA-sequencing data have identified the downstream expression effects of disease …
RNA-sequencing data have identified the downstream expression effects of disease …
Gene regulatory network inference using fused LASSO on multiple data sets
Devising computational methods to accurately reconstruct gene regulatory networks given
gene expression data is key to systems biology applications. Here we propose a method for …
gene expression data is key to systems biology applications. Here we propose a method for …
Inferring transcription factor regulatory networks from single-cell ATAC-seq data based on graph neural networks
H Li, Y Sun, H Hong, X Huang, H Tao… - Nature Machine …, 2022 - nature.com
Sequence-specific transcription factors (TFs) are the key effectors of eukaryotic gene control
and they regulate hundreds to thousands of downstream genes. Of particular interest are …
and they regulate hundreds to thousands of downstream genes. Of particular interest are …
Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells
Transcriptional regulatory networks (TRNs) provide insight into cellular behavior by
describing interactions between transcription factors (TFs) and their gene targets. The assay …
describing interactions between transcription factors (TFs) and their gene targets. The assay …
Group sparse optimization via lp, q regularization
In this paper, we investigate a group sparse optimization problem via lp, q regularization in
three aspects: theory, algorithm and application. In the theoretical aspect, by introducing a …
three aspects: theory, algorithm and application. In the theoretical aspect, by introducing a …
Multi-study inference of regulatory networks for more accurate models of gene regulation
Gene regulatory networks are composed of sub-networks that are often shared across
biological processes, cell-types, and organisms. Leveraging multiple sources of information …
biological processes, cell-types, and organisms. Leveraging multiple sources of information …
[HTML][HTML] Integration of single-cell multi-omics for gene regulatory network inference
The advancement of single-cell sequencing technology in recent years has provided an
opportunity to reconstruct gene regulatory networks (GRNs) with the data from thousands of …
opportunity to reconstruct gene regulatory networks (GRNs) with the data from thousands of …
scLink: inferring sparse gene co-expression networks from single-cell expression data
WV Li, Y Li - Genomics, Proteomics and Bioinformatics, 2021 - academic.oup.com
A system-level understanding of the regulation and coordination mechanisms of gene
expression is essential for studying the complexity of biological processes in health and …
expression is essential for studying the complexity of biological processes in health and …