Plant Gene Regulatory Networks

Characterization of gene regulatory networks in plants using new methods and data types.- Inducible, tissue-specific gene expression in Arabidopsis using GR-LhG4-mediated trans-activation.- Targeted activation of Arabidopsis genes by a potent CRISPR–Act3.0 system.- Single cell RNA-sequencing in Arabidopsis root tissues.- Analysis of Chromatin Accessibility, Histone Modifications, and Transcriptional States in Specific Cell Types Using Flow Cytometry.- Untargeted proteomics and metabolomics analysis of plant organ development.- DamID-seq: A DNA methylation method that captures both transient and stable TF-DNA interactions genome-wide in plant cells.- CUT&Tag for mapping in vivo protein-DNA interactions in plants.- Identification of plant transcription factor DNA-binding sites using seq-DAP-seq.- Estimating DNA-binding specificities of transcription factors using SELEX-seq.- Immunoprecipitation-mass spectrometry (IP-MS) of protein-protein interactions of nucleus-localized plant proteins.- Mapping active gene modules by ChIA-PET in rice.- Building high-confidence gene regulatory networks by integrating validated TF-target gene interactions using ConnecTF.- The ChIP-hub resource: towards plantEncode.- A practical guide to inferring multi-omics networks in plant systems.- Gene regulatory network modelling using single-cell multi-omics in plants.- Methodology for Constructing a Knowledgebase for Plant Gene Regulation Information.- Predicting gene regulatory interactions using natural genetic variation.- Prediction of transcription factor regulators and gene regulatory networks in tomato using binding site information.- AGENT for Exploring and Analyzing Gene Regulatory Networks from Arabidopsis.- A transferable machine learning framework for predicting transcriptional responses of gene across species.