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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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Pan-Genome Analysis with Roary

Contributed by Shawn Higdon Microbial Genomics involves the isolation of microbes from environmental samples, often times with the intent of generating a pure culture comprised by an organism of a single type of strain. While many isolation events lead to the generation of such cultures, large-scale isolation endeavors often lead to collections of banked isolates […]

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Diabetes and Gut Microbiome Study

Contributed by Carol Huang Metabolic disease diabetes and obesity have impacted quite some percentage of the population, over 600 million people in the world are obese, and over 400 million have diabetes. Type I diabetes often involves the loss of beta islet cells which produce insulin; Type II diabetes is a disorder of elevated blood […]

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Non-mammals and mammal gut defense

Contributed by Nguyet Kong Chitin is a fibrous substance containing polysaccharides and form the exoskeleton of arthropods such as insects and crustaceans and are commonly found on the cell walls of fungi. Non- mammals protect their gut walls with a layer of chitin and that layer will prevent bacterial infections. Whereas a mammal’s gut is […]

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