[HTML][HTML] Building transcription factor binding site models to understand gene regulation in plants
Transcription factors (TFs) are key cellular components that control gene expression. They
recognize specific DNA sequences, the TF binding sites (TFBSs), and thus are targeted to …
recognize specific DNA sequences, the TF binding sites (TFBSs), and thus are targeted to …
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 …
Elucidating the biology of transcription factor–DNA interaction for accurate identification of cis-regulatory elements
M Hajheidari, SC Huang - Current opinion in plant biology, 2022 - Elsevier
Transcription factors (TFs) play a critical role in determining cell fate decisions by integrating
developmental and environmental signals through binding to specific cis-regulatory …
developmental and environmental signals through binding to specific cis-regulatory …
JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles
I Rauluseviciute, R Riudavets-Puig… - Nucleic Acids …, 2024 - academic.oup.com
Abstract JASPAR (https://jaspar. elixir. no/) is a widely-used open-access database
presenting manually curated high-quality and non-redundant DNA-binding profiles for …
presenting manually curated high-quality and non-redundant DNA-binding profiles for …
Exploiting genomic features to improve the prediction of transcription factor-binding sites in plants
The identification of transcription factor (TF) target genes is central in biology. A popular
approach is based on the location by pattern matching of potential cis-regulatory elements …
approach is based on the location by pattern matching of potential cis-regulatory elements …
Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors
Maize is a major crop and a model plant for studying C4 photosynthesis and leaf
development. However, a genomewide regulatory network of leaf development is not yet …
development. However, a genomewide regulatory network of leaf development is not yet …
PlantRegMap: charting functional regulatory maps in plants
With the goal of charting plant transcriptional regulatory maps (ie transcription factors (TFs),
cis-elements and interactions between them), we have upgraded the TF-centred database …
cis-elements and interactions between them), we have upgraded the TF-centred database …
[HTML][HTML] Base-resolution prediction of transcription factor binding signals by a deep learning framework
Transcription factors (TFs) play an important role in regulating gene expression, thus the
identification of the sites bound by them has become a fundamental step for molecular and …
identification of the sites bound by them has become a fundamental step for molecular and …
DeepSTF: predicting transcription factor binding sites by interpretable deep neural networks combining sequence and shape
P Ding, Y Wang, X Zhang, X Gao, G Liu… - Briefings in …, 2023 - academic.oup.com
Precise targeting of transcription factor binding sites (TFBSs) is essential to comprehending
transcriptional regulatory processes and investigating cellular function. Although several …
transcriptional regulatory processes and investigating cellular function. Although several …
[HTML][HTML] Positional distribution of transcription factor binding sites in Arabidopsis thaliana
Binding of a transcription factor (TF) to its DNA binding sites (TFBSs) is a critical step to
initiate the transcription of its target genes. It is therefore interesting to know where the …
initiate the transcription of its target genes. It is therefore interesting to know where the …
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