Category Archives: uncategorized

2021

Contributed by Darwin Bandoy, PhD candidate It is the start of another year and we are still in the middle of the winter wave of COVID-19 with a record number of mortalities and new infections. What is different is the renewed interest in tracking mutational variants and emerging lineages, particularly B.1.1.7. While we expect new […]

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Parsing large data files to working chunks

Contributed by Cory Schlesener, B.S. When analyzing large data files in the realm of gigabytes, system memory and program/function set memory limits becomes an issue. Creating a smaller data set for analysis can bring the working data down to a manageable size. This downsizing would preferably be removing redundancy or features not relevant to analysis, […]

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AutoML, easier use of machine learning mode

Contributed by Cory Schlesener, B.S. Machine Learning (ML) enables powerful analysis of data to formulate models. These models can be utilized in applications or help dive into the data for insight on relationships between features.  There are many varieties of models and the algorithms that create them. Different varieties of core learning algorithms are better suited […]

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USDA Food Safety Fellow Day 1

Contributed by Darwin Bandoy, PhD Candidate We formally started the USDA Food Safety fellowship with a kick-off meeting. Our proposal is to utilize machine learning to parse the basis for virulence and antimicrobial resistance in Salmonella Dublin. This particular strain of Salmonella is notorious for causing systemic infections and uniquely adapted to cattle. The question […]

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Creating Prokaryotic Taxonomies with Whole Genomes

Contributed by Cory Schlesener, B.S. Historically it has been difficult to categorize prokaryotes into taxonomic units. Advances made have utilized DNA sequence identity to profile organisms at a higher resolution.  Older technologies based on genomic DNA hybridization, or sequence comparison of the 16s rDNA gene (PCR amplified), have greatly advanced our understanding of phylogeny, but […]

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Year Four

Contributed by DJ Darwin Bandoy, PhD Candidate I am now in my year four of my PhD studies in Integrative Pathobiology in UC Davis, still in the middle of the COVID-19 Pandemic. I presented in the lab meeting yesterday the theoretical framework of my epidemic modelling work from the UP Pandemic Response Team.  Understanding compartmental […]

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New Quality Control Program Optimized for Long Read Nucleotide Sequencing

Contributed by Cory Schlesener, B.S. DNA sequencing, in a high throughput process, generates errors in the reads, such as low confidence nucleotide based calling. Quality control is needed to evaluate the quality of the sequencing output and identify undesired features. The program FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc) has become one of the most popular tools for assessing quality […]

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Gut Microbiota and Unhealthy Aging

Contributed by Carol Huang, Sr. Research Specialist                      @BartWeimersLab The equilibrium of gut microbiota is fundamental to our health. The gut microbiota composition established at birth which changes with aging, diet, health condition and other factors.  As growing up the dynamic nature of gut microbiota getting […]

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Where is the metadata?

Contributed by DJ Darwin Bandoy, PhD Candidate One distinguishing feature of this pandemic is the rapid release of whole genome sequencing data. These sequences are usually uploaded in public databases with minimal accompanying metadata. While dates and geographic origin are useful for creation of phylogenetic analysis, further sophisticated analysis requires more metadata, particularly associated with […]

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Quantify Structural Similarity Comparisons of Genome Assemblies

Contributed by Cory Schlesener, B.S. One important component of a genome’s overall composition is the larger structure of how conserved blocks of genetic sequence are arranged. As segments of DNA recombine, sequences are introduced into new locations and/or orientations in a genome. However, this composition of large genetic blocks can artificially be rearranged in a constructed genome […]

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