Author Archives: WeimerMicroLab

Tools for Hunting Antimicrobial Resistance (AMR) Genes

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Contributed by Cory Schlesener, B.S. Predicting bacterial isolate susceptibility for disease treatment and surveying resistance prevalence broadly is of great interest, especially as antibiotic resistance is increasing globally among clinical isolates. Screening sequence data for genes and alleles that confer antibiotic resistance has increased in availability but also in complexity over the past decade. There is now a myriad of bioinformatics tools […]

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Dr. Weimer & graduate student DJ Darwin Bandoy’s manuscript Analysis of SARS-CoV-2 genomic epidemiology reveals disease transmission coupled to variant emergence and allelic variation published in Nature

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This past week UC Davis did a press release for the new paper that Dr. Weimer and graduate student DJ Darwin Bandoy have being published in Nature. You can read the article Analysis of SARS-CoV-2 genomic epidemiology reveals disease transmission coupled to variant emergence and allelic variation, here.  You can also access the UC Davis […]

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Vaccines work!

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Contributed by Darwin Bandoy, PhD Candidate One year into the pandemic and I already managed to get my first dose of vaccine. The pandemic will end with the achievement of herd immunity and the best path towards herd immunity is via vaccination. Vaccines are generally safe. Several variants are causing trouble by reducing the efficacy […]

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Cell Line Makes the Phenotyp

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Contributed by Cory Schlesener, B.S. When conducting biological assays using mammalian cell tissue culture, the cell line used is crucial. It is a given to choose cells derived from the tissue of interest to study. However, as immortalized cell lines are not entirely normal, lines derived from the same tissue types can ultimately have differences in […]

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2021

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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

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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

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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

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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

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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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