Nature – Pathogens
- Faster detection of asymptomatic COVID-19 cases among care home staff in England through the combination of SARS-CoV-2 testing technologies March 29, 2024
- Diving into the proteomic atlas of SARS-CoV-2 infected cells March 28, 2024
- Transmission dynamics of Zika virus with multiple infection routes and a case study in Brazil March 28, 2024
- Genomic insights into anthropozoonotic tuberculosis in captive sun bears (Helarctos malayanus) and an Asiatic black bear (Ursus thibetanus) in Cambodia March 28, 2024
- Period of hospitalization and mortality in transferred versus non-transferred COVID-19 patients: results from Germany March 28, 2024
Nature – AMR
- Going to extremes: progress in exploring new environments for novel antibiotics March 25, 2024
- Mutations in the efflux pump regulator MexZ shift tissue colonization by Pseudomonas aeruginosa to a state of antibiotic tolerance March 22, 2024
- Drug-resistant tuberculosis: a persistent global health concern March 22, 2024
- Emergence and clonal expansion of a qacA-harbouring sequence type 45 lineage of methicillin-resistant Staphylococcus aureus March 21, 2024
- Evaluation of synergistic/antagonistic antibacterial activities of fatty oils from apricot, date, grape, and black seeds March 19, 2024
Outbreaks
CDC
Food Safety News
- Two states consider allowing sales of unpasteurized, raw milk March 29, 2024
- Farm Aid adds its voice to food and farm policy March 29, 2024
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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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