Year: 2019

  The term, FAIR, was officially coincided in 2016, which stands for findability, accessibility, interoperability, and reusability [1]. During my omics integration project, I realized the importance of practicing FAIR data management in scientific fields. In current days, not only the methods of storing data vary among different databases, but also the formats of datasets […]

A long time ago, I learned in school about the human digestive system. I learned how the food I ate, composed of proteins, carbohydrates, and fat, would be broken into less complex structures: amino acids, peptides, simple sugars, and fatty acids, by the enzymes present in my digestive tract. Those simpler structures would then be […]

Gut bacteria have co-evolved with animals for hundreds of thousands of years. There is, however, still potential for bacterial adaptation within each individual, according to recently published research (1). The researchers combined metagenomics with isolation, cultivation, and sequencing of  the bacterial content of 30 fecal samples to investigate how Bacteroides fragilis, a frequent commensal in […]

[latexpage] In this blog, we will walk through a probabilistic formulation of the well-known technique of principal component analysis (PCA). The probabilistic PCA (PPCA) was introduced by Bishop [1]. PPCA does not generate better results than PCA, but it permits a broad range of future extensions. Besides, PPCA falls in the category of Bayesian models, […]

Biofilms are the surface adhered aggregates of microorganisms embedded within a thick layer of exopolysaccharide (EPS) matrix. Bacteria in this polysaccharide matrix are well-organized structures that enable transport of nutrient and waste in-and-out of the biofilm. Most of the time biofilms are comprised of several bacterial species. Due to protective shielding by the polysaccharide matrix, […]

What is enzyme design? Enzyme catalysis is a key process in a wide range of industries from pharmaceutical to food sciences [1-6]. In evolutionary context, nature has optimized enzymes in living organisms to adapt to specific niches over millions, if not billions, of years. Despite the constant evolution, these enzymes might not meet our modern-day […]