Positive-unlabeled learning in bioinformatics and computational biology: a brief review.

Conventional supervised binary classification algorithms have been widely applied to address significant research questions using biological and biomedical data. This classification scheme requires two fully labeled classes of data (e.g.

The pattern of DNA methylation alteration, and its association with the changes of gene expression and alternative splicing during phosphate starvation in tomato.

DNA methylation is changed and associates with gene expression alterations in plant response to phosphate starvation (Pi-), a common stress that impacts plant growth and productivity. However, in the horticultural model species Solanum lycopersicum (tomato), the dynamics of DNA methylation and its relationship with changes in gene transcription and alternative splicing (AS) under Pi- are unknown. Here, we performed integrative methylome and transcriptome analyses of tomato seedlings under Pi-deficient and -sufficient conditions.

The Class III peroxidase gene OsPrx30, transcriptionally modulated by the AT-hook protein OsATH1, mediates rice bacterial blight-induced ROS accumulation.

Class III peroxidases (CIII Prxs) play critical roles in plant immunity by scavenging reactive oxygen species (ROS). However, the functions of CIII Prxs in rice (Oryza sativa L.) immunity are largely unexplored.

NBS-LRR Protein Pik-H4 Interacts with OsBIHD1 to Balance Rice Blast Resistance and Growth by Coordinating Ethylene-Brassinosteroid Pathway.

The regulation of innate immunity and plant growth, along with the trade-off between them, affects the defense and recovery mechanisms of the plant after it is attacked by pathogens. Although it is known that hormonal crosstalk plays a major role in regulating interaction of plant growth and PAMP-triggered immunity, the relationship between plant growth and effector-triggered immunity (ETI) remains unclear. In a large-scale yeast two-hybrid screening for Pik-H4-interacting proteins, a homeodomain transcription factor OsBIHD1 was identified, which is previously known to function in biotic and abiotic stress responses.

4-Coumarate-CoA Ligase-Like Gene Negatively Mediates the Rice Blast Resistance, Floret Development and Lignin Biosynthesis.

Although adenosine monophosphate (AMP) binding domain is widely distributed in multiple plant species, detailed molecular functions of AMP binding proteins (AMPBPs) in plant development and plant-pathogen interaction remain unclear. In the present study, we identified an AMPBP from a previous analysis of early responsive genes in rice during infection. is a homolog of Arabidopsis in rice, which encodes a 4-coumarate-Co-A ligase (4CL) like protein.

CONSTANS-Like 9 (OsCOL9) Interacts with Receptor for Activated C-Kinase 1(OsRACK1) to Regulate Blast Resistance through Salicylic Acid and Ethylene Signaling Pathways.

In a previous transcriptome analysis of early response genes in rice during Magnaporthe oryzae infection, we identified a CONSTANS-like (COL) gene OsCOL9. In the present study, we investigated the functional roles of OsCOL9 in blast resistance. OsCOL9 belonged to group II of the COL protein family, and it contained a BB-box and a C-terminal CCT (CONSTANS, COL and TOC1) domain.

CONSTANS-like 9 (COL9) delays the flowering time in Oryza sativa by repressing the Ehd1 pathway.

Flowering or heading is one of most important agronomic traits in rice. It has been characterized that CONSTANS (CO) and CONSTANS-like (COL) proteins are critical flowering regulators in response to photoperiodic stress in plants. We have previously identified that the COL family member OsCOL9 can positively enhance the rice blast resistance.