Deep learning for plant genomics and crop improvement

H Wang, E Cimen, N Singh, E Buckler - Current opinion in plant biology, 2020 - Elsevier
Our era has witnessed tremendous advances in plant genomics, characterized by an
explosion of high-throughput techniques to identify multi-dimensional genome-wide …

To bind or not to bind: how Auxin Response Factors select their target genes

J Rienstra, J Hernández-García… - Journal of Experimental …, 2023 - academic.oup.com
Most plant growth and development processes are regulated in one way or another by
auxin. The best-studied mechanism by which auxin exerts its regulatory effects is through …

Massively parallel assays and quantitative sequence–function relationships

JB Kinney, DM McCandlish - Annual review of genomics and …, 2019 - annualreviews.org
Over the last decade, a rich variety of massively parallel assays have revolutionized our
understanding of how biological sequences encode quantitative molecular phenotypes …

Deciphering transcriptional regulators of banana fruit ripening by regulatory network analysis

JF Kuang, CJ Wu, YF Guo, D Walther… - Plant biotechnology …, 2021 - Wiley Online Library
Fruit ripening is a critical phase in the production and marketing of fruits. Previous studies
have indicated that fruit ripening is a highly coordinated process, mainly regulated at the …

[HTML][HTML] Modern plant breeding techniques in crop improvement and genetic diversity: from molecular markers and gene editing to artificial intelligence—A critical …

L Sun, M Lai, F Ghouri, MA Nawaz, F Ali, FS Baloch… - Plants, 2024 - mdpi.com
With the development of new technologies in recent years, researchers have made
significant progress in crop breeding. Modern breeding differs from traditional breeding …

Transcriptional and post-transcriptional controls for tuning gene expression in plants

V Zhong, BN Archibald, JAN Brophy - Current Opinion in Plant Biology, 2023 - Elsevier
Plant biotechnologists seek to modify plants through genetic reprogramming, but our ability
to precisely control gene expression in plants is still limited. Here, we review transcription …

Deep learning-empowered crop breeding: intelligent, efficient and promising

X Wang, H Zeng, L Lin, Y Huang, H Lin… - Frontiers in Plant …, 2023 - frontiersin.org
Crop breeding is one of the main approaches to increase crop yield and improve crop
quality. However, the breeding process faces challenges such as complex data, difficulties …

Every cloud has a silver lining: how abiotic stresses affect gene expression in plant-pathogen interactions

M Zarattini, M Farjad, A Launay… - Journal of …, 2021 - academic.oup.com
Current environmental and climate changes are having a pronounced influence on the
outcome of plant–pathogen interactions, further highlighting the fact that abiotic stresses …

AUXIN RESPONSE FACTOR 18–HISTONE DEACETYLASE 6 module regulates floral organ identity in rose (Rosa hybrida)

J Chen, Y Li, Y Li, Y Li, Y Wang, C Jiang… - Plant …, 2021 - academic.oup.com
The phytohormone auxin plays a pivotal role in floral meristem initiation and gynoecium
development, but whether and how auxin controls floral organ identity remain largely …

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 …