A Database for Small Molecules with Functional Implications in Plants
We developed SMART v1.0 (http://smart.omicstudio.cloud), the first database for small molecules with functional implications in plants. The SMART database is devoted to providing and managing small molecules and their associated structural data, …
Epigenetic modifications play important roles in genome evolution and innovation. However, most analyses have focused on the evolutionary role of DNA modifications, and little is understood about the influence of post-transcriptional RNA …
microRNAs (miRNAs) are short, noncoding regulatory RNAs derived from hairpin precursors (pre-miRNAs). In synergy with experimental approaches, computational approaches have become an invaluable tool for identifying miRNAs at the genome scale. We have …
Development of the cereal endosperm involves cell differentiation processes that enable nutrient uptake from the maternal plant, accumulation of storage products, and their utilization during germination. However, little is known about the regulatory …
Wheat (Triticum aestivum), one of the world's most important crops, is facing unprecedented challenges due to global warming. To evaluate the gene resources for heat adaptation in hexaploid wheat, small heat shock proteins (sHSPs), the key plant heat …
The endosperm is a major organ of the seed that plays vital roles in determining seed weight and quality. However, genome-wide transcriptome patterns throughout maize endosperm development have not been comprehensively investigated to date. …
Endosperm is an absorptive structure that supports embryo development or seedling germination in angiosperms. The endosperm of cereals is a main source of food, feed, and industrial raw materials worldwide. However, the genetic networks that regulate …
Machine learning (ML) is an intelligent data mining technique that builds a prediction model based on the learning of prior knowledge to recognize patterns in large-scale data sets. We present an ML-based methodology for transcriptome analysis via …
Machine learning-based differential network analysis
One of the computational challenges in plant systems biology is to accurately infer transcriptional regulation relationships based on correlation analyses of gene expression patterns. Despite several correlation methods that are applied in biology to …
Gini-based transcriptiome analysis
Karyotype-based genome assembly for Brassicaceae species
**MOTIVATION**:
The Brassicaceae family includes the most important plant model Arabidopsis thaliana and many cruciferous vegetable crops. A number of close relatives of Arabidopsis and economically important Brassica species are being sequenced with …