Claire Bertelli, Keith E Tilley, Fiona S L Brinkman
Briefings in Bioinformatics (September 2019)
Contributed by Ashleigh Flores
Contributed by DJ Bandoy, DVM
Covid-19 is the name given by the World Health Organization to the severe respiratory disease due to 2019-nCOV. What is astonishing is the speed of release of preprints in Biorkiv of several studies from phylogenetics to virus pseudotyping. While public health concern triumphs over the need for peer review, uncurated papers lead to wild conspiracy theories. This is where social media scientists play a role, hence the heavily criticized paper linking coronavirus with HIV virus is retracted. All of my papers so far are biorkived because coming from a Third World country, my inability to access journal articles hindered my research before coming to UC Davis.
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 large scale sequencing data, you need to tame the metadata. This requires at the minimum scripting techniques in Excel, which is practically a form of coding. But transposition of multimillion rows and columns is limited in Excel, hence the need for more robust tools like OpenRefine and eventually command-line tools. So yes, a biologist should and must code.
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 harmonization of standards make it difficult to compare the AMR profile across different countries. Whole-genome sequencing has recently been used to profile antimicrobial resistance and is shown to be robust in detecting the antibiotic resistance genes for the most commonly used antibiotics. One of my favorite tools is Abricate by Torsten Seeman (who also developed the hugely popular Prokka tool). This tool allows me to perform in silico AMR profiling of whole genomes of pathogenic organisms.
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 trajectory. One form of innovation is applying a technique from another field.
This is where Twitter is useful. I view Twitter as a source of curated scientific material for discovery from peripheral fields. It allows me to sample the minds of the brightest people, and see the hottest publications. I have encountered a lot of bioinformatic tools by eavesdropping on the tweets of the leading bioinformaticians.