Contributed by DJ Darwin Bandoy, DVM I personally believe that biology is a big data puzzle. That is also the main reason why I took my PhD in the Weimer lab with the 100K Pathogen Genome Project. But when I started in the lab, I also realized that before you can do any biology with […]
Click on the link to read the latest manuscript that Dr. Weimer was involved with which has been published in Nature. Food authentication from shotgun sequencing reads with an application on high protein powders.
Contributed by Darwin Bandoy, DVM Antimicrobial resistance is a key issue as pathogens develop resistance due to the misuse of antimicrobials in food animals. While some countries have already banned the use of antibiotics as growth promotants, emerging economies find it difficult to implement due to numerous factors. From a monitoring point of view, large […]
Contributed by DJ Darwin Bandoy, DVM Catching up with scientific literature is definitely a big challenge. While Google makes it easy to find materials you are searching for, it is not easy for articles that are tangential to your interest. These are the type of readings outside your field of interest but can complement your […]
WeimerMicroLab’s latest manuscript by DJ Darwin R. Bandoy & Bart C. Weimer is out! Click here to read “Biological machine learning combined with bacterial population genomics reveals common and rare allelic variants of genes to cause disease.”
Contributed by Shawn Higdon How much of the microbial biodiversity on planet Earth has mankind managed to grow in the laboratory? I think the number thrown around as a rough approximation in early biology classes is 5 percent. Five percent, right? Or is it one percent? One percent sounds more realistic…or is it one tenth […]
Contributed by Darwin Bandoy, DVM We are proud to announce the preprint publication of our paper wherein we identified a misclassified species of Hungatella from the Human Microbiome Project. This project demonstrates the power of pangenome analysis to resolve species identity by clustering. The impact of the misclassification is amplified because of numerous microbiome papers using […]
Contributed by Darwin Bandoy, DVM I am still over the clouds for passing my qualifying exam. And I am pretty sure most PhD students are curious how I made my preparations. So, I will be describing what I did. Read, read, read.I read all available materials for my topic (genomics of Campylobacter). This means getting […]
Contributed by Shawn Higdon The focus of my graduate research involves the investigation of nitrogen-fixing bacteria inhabiting a terrestrial environment that is rich in complex carbohydrate – the aerial root exudate (mucilage) of an isolated maize landrace. Within this arc, I have embarked on a quest to characterize the genomes of cultured bacteria derived from […]
Contributed by Darwin Bandoy DVM I presented a poster at BAMPS (Bay Area Microbial Pathogenesis Symposium) with my work on using machine learning bacterial genome-wide association study. First of all, it was radically different as most posters focus on defining a mechanism for a single gene, while my work is about extracting insights from population-scale […]