Frontiers and techniques in plant gene regulation

T Jores, M Hamm, JT Cuperus, C Queitsch - Current Opinion in Plant …, 2023 - Elsevier
Understanding plant gene regulation has been a priority for generations of plant scientists.
However, due to its complex nature, the regulatory code governing plant gene expression …

Enhancers in Plant Development, Adaptation, and Evolution

BM Beernink, JP Vogel, L Lei - Plant and Cell Physiology, 2024 - academic.oup.com
Understanding plant responses to developmental and environmental cues is crucial for
studying morphological divergence and local adaptation. Gene expression changes …

Deep learning‐enabled discovery and characterization of HKT genes in Spartina alterniflora

M Yang, S Chen, Z Huang, S Gao, T Yu, T Du… - The Plant …, 2023 - Wiley Online Library
Spartina alterniflora is a halophyte that can survive in high‐salinity environments, and it is
phylogenetically close to important cereal crops, such as maize and rice. It is of scientific …

PTFSpot: deep co-learning on transcription factors and their binding regions attains impeccable universality in plants

S Gupta, V Kesarwani, U Bhati, Jyoti… - Briefings in …, 2024 - academic.oup.com
Unlike animals, variability in transcription factors (TFs) and their binding regions (TFBRs)
across the plants species is a major problem that most of the existing TFBR finding software …

TSPTFBS 2.0: trans-species prediction of transcription factor binding sites and identification of their core motifs in plants

H Cheng, L Liu, Y Zhou, K Deng, Y Ge… - Frontiers in Plant …, 2023 - frontiersin.org
Introduction An emerging approach using promoter tiling deletion via genome editing is
beginning to become popular in plants. Identifying the precise positions of core motifs within …

The bHLH transcription factor OsPRI1 activates the Setaria viridis PEPC1 promoter in rice

P Carvalho, C Gomes, I Gonçalves… - New …, 2024 - Wiley Online Library
Photosynthetic efficiency is reduced by the dual role of Rubisco, which acts either as a
carboxylase or as an oxygenase, the latter leading to photorespiration. C4 photosynthesis …

[HTML][HTML] Comprehensive analysis of computational approaches in plant transcription factors binding regions discovery

S Gupta, R Shankar - Heliyon, 2024 - cell.com
Transcription factors (TFs) are regulatory proteins which bind to a specific DNA region
known as the transcription factor binding regions (TFBRs) to regulate the rate of transcription …

Comprehensive evaluation of plant transcription factors binding sites discovery tools

Jyoti, Ritu, S Gupta, R Shankar - bioRxiv, 2023 - biorxiv.org
Transcription factors (TFs) are regulatory proteins that bind to a specific DNA sequence,
known as the transcription factor binding site (TFBS), to regulate the rate of transcription …

Deep co-learning on transcription factors and their binding regions attains impeccable universality in plants

S Gupta, V Kesarwani, U Bhati, Jyoti, R Shankar - bioRxiv, 2023 - biorxiv.org
Unlike animals, variability in transcription factors (TF) and their binding sites (TFBS) across
the plants species is a major problem which most of the existing TFBS finding software fail to …