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 […]
The word2vec technique has become an essential part when building a text model and even adapted in other fields like building a recommendation system. In this blog, I will introduce the basic concepts and applications of word2vec. When building a machine learning model to understand text, the first challenge is to encode the text as […]
Metabolic Flux Analysis (MFA) is a technique used to quantify metabolic fluxes (the rate of turnover of molecules). MFA has at least two important applications: First, by studying metabolic flux, it is possible to adjust the amount of substrates/ingredients in the medium/protocol of cell culture [1] or mutate genes [2] to improve productivity. Second, by […]
Large-scale recombinant protein production is one of the most significant achievements of modern biotechnology. These proteins have wide applications in molecular biology, therapeutics, and industry. Efficient recombinant protein production using genetically manipulated organisms have saved several lives by providing the pure and accessible amount of therapeutic and prophylactic proteins. Today, more than 75 recombinant proteins […]
The threat of antibiotic resistance is well documented and frequently highlighted in the media, with constant mentions to “superbugs” and the potential end of effective antimicrobials. In the United States alone, over 2 million people become infected with antibiotic-resistant bacteria, and the death toll can reach 23,000 annually (1). In Europe, the estimations are that […]