Automatic construction of Petri net models for computational simulations of molecular interaction network.

Petri nets are commonly applied in modeling biological systems. However, construction of a Petri net model for complex biological systems is often time consuming, and requires expertise in the research area, limiting their application. To address this challenge, we developed GINtoSPN, an R package that automates the conversion of multi-omics molecular interaction network extracted from the Global Integrative Network (GIN) into Petri nets in GraphML format.

Silica-Polymer Heterogeneous Hybrid Integrated Mach-Zehnder Interferometer Optical Waveguide Temperature Sensor.

In this paper, a temperature sensor based on a polymer-silica heterogeneous integrated Mach-Zehnder interferometer (MZI) structure is proposed. The MZI structure consists of a polymer waveguide arm and a doped silica waveguide arm. Due to the opposite thermal optical coefficients of polymers and silica, the hybrid integrated MZI structure enhances the temperature sensing characteristics.

GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases.

Knowledge bases have been instrumental in advancing biological research, facilitating pathway analysis and data visualization, which are now widely employed in the scientific community. Despite the establishment of several prominent knowledge bases focusing on signaling, metabolic networks, or both, integrating these networks into a unified topological network has proven to be challenging. The intricacy of molecular interactions and the diverse formats employed to store and display them contribute to the complexity of this task.

Design, synthesis and biological evaluations of diverse Michael acceptor-based phenazine hybrid molecules as TrxR1 inhibitors.

A series of novel phenazine derivatives (1~27) containing the Michael acceptor scaffolds were designed and synthesized in this study. Some compounds exhibited selective cytotoxicity against Bel-7402 cancer cell line in vitro, in which compound 26 were found to have the best antiproliferative activity. Meanwhile, compound 26 showed no obvious cell toxicity against human normal liver epithelial L02 cells, which means this compound possessed a better safety potential.