Category Archives: uncategorized

Biological machine learning combined with bacterial population genomics reveals common and rare allelic variants of genes to cause disease

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.”  

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Machine Learning How to Culture UnCulturables?

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, … Continue reading

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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 … Continue reading

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Qualifying Exam Preparation for PhD students in Life Sciences and Biotechnology

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, … Continue reading

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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, … Continue reading

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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 … Continue reading

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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 … Continue reading

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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 … Continue reading

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Pangenome guided pharmacophore modelling of enterohemorrhagic Escherichia coli sdiA

Contributed by Darwin Bandoy, DVM I am proud to present my published work in the F1000Research journal. This journal is unique due to the open peer review platform. Open peer review publishes the article first after a basic editorial screening … Continue reading

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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 … Continue reading

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