TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information
SR Kulkarni, D Vaneechoutte… - Nucleic acids …, 2018 - academic.oup.com
A gene regulatory network (GRN) is a collection of regulatory interactions between
transcription factors (TFs) and their target genes. GRNs control different biological processes …
transcription factors (TFs) and their target genes. GRNs control different biological processes …
Inference of plant gene regulatory networks using data-driven methods: A practical overview
SR Kulkarni, K Vandepoele - Biochimica et Biophysica Acta (BBA)-Gene …, 2020 - Elsevier
Transcriptional regulation is a complex and dynamic process that plays a vital role in plant
growth and development. A key component in the regulation of genes is transcription factors …
growth and development. A key component in the regulation of genes is transcription factors …
Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators
Gene regulation is a dynamic process in which transcription factors (TFs) play an important
role in controlling spatiotemporal gene expression. To enhance our global understanding of …
role in controlling spatiotemporal gene expression. To enhance our global understanding of …
ConnecTF: A platform to integrate transcription factor–gene interactions and validate regulatory networks
Deciphering gene regulatory networks (GRNs) is both a promise and challenge of systems
biology. The promise lies in identifying key transcription factors (TFs) that enable an …
biology. The promise lies in identifying key transcription factors (TFs) that enable an …
[HTML][HTML] A machine learning approach to predict gene regulatory networks in seed development in Arabidopsis
Y Ni, D Aghamirzaie, H Elmarakeby… - Frontiers in plant …, 2016 - frontiersin.org
Gene regulatory networks (GRNs) provide a representation of relationships between
regulators and their target genes. Several methods for GRN inference, both unsupervised …
regulators and their target genes. Several methods for GRN inference, both unsupervised …
[HTML][HTML] Gene regulatory network inference: connecting plant biology and mathematical modeling
Plant responses to environmental and intrinsic signals are tightly controlled by multiple
transcription factors (TFs). These TFs and their regulatory connections form gene regulatory …
transcription factors (TFs). These TFs and their regulatory connections form gene regulatory …
Computational prediction of gene regulatory networks in plant growth and development
Highlights•GRNs represent causal relationships among regulators and their downstream
genes.•Biological hypothesis drives data collection and the subsequent inferred …
genes.•Biological hypothesis drives data collection and the subsequent inferred …
[HTML][HTML] LegumeGRN: a gene regulatory network prediction server for functional and comparative studies
Building accurate gene regulatory networks (GRNs) from high-throughput gene expression
data is a long-standing challenge. However, with the emergence of new algorithms …
data is a long-standing challenge. However, with the emergence of new algorithms …
PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants
With the goal of providing a comprehensive, high-quality resource for both plant transcription
factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF …
factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF …
[HTML][HTML] Statistical and machine learning approaches to predict gene regulatory networks from transcriptome datasets
K Mochida, S Koda, K Inoue, R Nishii - Frontiers in Plant Science, 2018 - frontiersin.org
Statistical and machine learning (ML)-based methods have recently advanced in
construction of gene regulatory network (GRNs) based on high-throughput biological …
construction of gene regulatory network (GRNs) based on high-throughput biological …