Tag: Computational Biology

Functional genomic studies across plants are incomplete without deciphering the putative gene functions in model as well as non-model plants. With an aim to facilitate gene function identification and cross-species expression analysis, Sreedasyam et al. describe the Joint Genome Institute (JGI) Plant…

It’s pretty obvious that plants are not simply balls of cells. Their shapes and patterns are determined in large part through processes that cause cells to grow and divide asymmetrically, through the establishment of cell polarity. When I set out to read this review I was a bit nervous, expecting to…

Life is spurred forward by the power of metabolic interactions. Within the plant microbiome, microbial communities use diverse mechanisms to thrive, survive, and multiply. In this review, Pacheco & Vorholt describe the interplay of metabolic interactions within plant microbiomes and review current…

Bending or folding in plants is influenced by different factors such as environmental conditions (nutrient, water, light, gravity), abiotic or biotic stress, cell wall properties, and cell differential growth. Jonsson et al. explain how bending is achieved by considering molecular mechanisms, mathematical…

Experimental or "wet lab" biologists look at data, develop a hypothesis to explain it, test the hypothesis, and repeat. Through these approaches, our understanding of life is continually being expanded and refined. A complementary approach involves developing mathematical models to explain observations,…

One of the well-known molecular pathways that regulate plant development is the one formed by the homeobox transcription factor WUSCHEL (WUS) and the secreted peptide CLAVATA 3 (CLV3). In the shoot apical meristem (SAM), WUS expression is constrained to the organizing center where it maintains the stem…

The AlphaFoldDB database recently made headlines by predicting the three-dimensional protein structure of millions of proteins based on their primary amino acid sequence. Most of these models remain to be tested, but it’s a place to start. Here, Dumortier et al. add an important complementary tool…

Knowing whether a given plant species forms a persistent soil seed bank is essential to understanding its ecological dynamics, yet soil seed bank studies are both labor-intensive and time-consuming. One could argue that models should help predict this. Still, seed persistence in the soil is shaped by…