Tag: Computational Biology

Genetic and molecular studies have revealed a complex exchange of signals and metabolites accompanying the development and process of symbiotic nitrogen fixation. Clearly, the photosynthesis-capable plant provides fixed carbon to the bacterial symbiont, which uses some of this energy for its core metabolism…

In Star Wars Episode 2, Obi Wan identifies the location of a missing planet by walking through a 3D projection of the galaxy. I’ve always hoped that if we obtain enough data and figure out how to display it properly, we’ll “see” what parts are out of place or missing. But getting from simple…

Growth is driven by cell expansion, which is driven by both synthesis of metabolites and osmotically-driven expansion. This latter contribution is typically overlooked in metabolic flux analysis. To remedy this, Shameer et al. have developed a model, GrOE-FBA (Growth by Osmotic Expansion- Flux Balance…

In recent years, a number of tools have been developed to describe and model plant morphogenesis, and these approaches have greatly informed our understanding of the molecular processes that underpin the control of growth. This excellent review by Pałubicki et al. is “an attempt to bring together…

Machine learning is a booming research field, also in Plant Science. Here, Wu et al. use chromatin modifications and transcription factors to predict transcription levels in Arabidopsis and rice. This is not only important for prediction but also to understand the mechanisms underlying epigenetic regulation.…

With the need to feed the growing population and the threat of global climate change, there is an imminent need to increase crop yields. One commonly accepted method of accomplishing this is by enhancing the photosynthetic capability of major crop plants, which may result in an increased yield. A recent…

I really enjoyed this review article, which very successfully introduces the reader to the why and how of how to apply network science to plant science. Bassel never veers off into abstraction or “math-speak”, but instead roots his explanations in familiar biological or ordinary terms. As an example,…

Cyber-agriculture is a computer-controlled plant growing environment which regulates climatic conditions through machine learning, finding optimized variables (“recipes”) to maximize a specific plant trait. Here, Johnson et al. applied cyber-agriculture to chemotype optimization for flavor in basil…