Blog

Preprint is Out!

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 […]

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Comprehensive Carbohydrate Active Enzyme Analysis with meta-dbCAN

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 […]

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Post Conference Reflections: Bay Area Microbial Pathogenesis Symposium

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 […]

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Analyzing RNAseq Data with DESeq2

Contributed by Shawn Higdon RNA sequencing experiments are extremely powerful in terms of the amount of information that is capable of being revealed for a given experimental system. While performing these experiments demands passing through several hurdles in the lab that require a high degree of technical skill, careful planning, and seemingly flawless execution, analyzing […]

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Metagenome wide association studies: data mining the microbiome

Contributed by Darwin Bandoy, DVM Increased sequencing capability offers an unprecedented look into the microbiome and the association with complex diseases. Associations are mined to determine the changes occurring with microbiome and metabolic conditions like diabetes and obesity, as well as chronic diseases such as colorectal cancer and rheumatoid arthritis. While initially microbial community membership […]

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Fast Transcript Quantification with Salmon

Contributed by Shawn Higdon Interpretation of Sequencing data from experiments targeting gene expression in any biological system requires a series of computational and analytical steps. After going through the motions of pre-processing sequencing reads into a state of high quality (trimming low-quality base calls and removing adapter sequences that slip through the cracks), the next […]

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Post ASM Conference reflections

Contributed by Darwin Bandoy, DVM I participated in the 2018 ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines, September 23–26, 2018, in Tysons, Virginia and presented my work in the lab using next-generation sequencing of Campylobacter hyointestinalis. The most interesting talk for me, surprisingly, is the use of data analytics by the […]

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