 Functional Assessment of 2,177 U.S. and International Drugs Identifies the Quinoline Nitroxoline as a Potent Amoebicidal Agent against the Pathogen Balamuthia mandrillaris American Society for Microbiology, 2018
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 Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance Biology Open, 2018
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 Whole-Genome mRNA Gene Expression Differs Between Patients With and Without Delirium Sage Journals, 2018
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 Avian keratin disorder of Alaska black-capped chickadees is associated with Poecivirus infection Virology Journal, 2018
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 Low-Cost Touchscreen Driven Programmable Dual Syringe Pump for Life Science Applications Science Direct, 2018
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 Metagenomic next-generation sequencing reveals Miamiensis avidus (Ciliophora: Scuticociliatida) in the 2017 epizootic of leopard sharks (Triakis semifasciata) in San Francisco Bay, California BioRxiv, 2018
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 Chronic Meningitis Investigated via Metagenomic Next-Generation Sequencing JAMA Network, 2018
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 Depletion of Abundant Sequences by Hybridization (DASH): Using Cas9 to remove unwanted highabundance species in sequencing libraries and molecular counting applications
With widespread adoption of next-generation sequencing (NGS) technologies, the need has arisen for a broadly applicable method to remove unwanted high-abundance species prior to sequencing. We introduce DASH (Depletion of Abundant Sequences by Hybridization), a facile technique for targeted depletion of undesired sequences. Sequencing libraries are DASHed with recombinant Cas9 protein complexed with a library of single guide RNAs (sgRNAs) programmed to target unwanted species for cleavage, thus preventing them from consuming sequencing space. We demonstrate up to 99% reduction of mitochondrial ribosomal RNA (rRNA) in HeLa cells, and enrichment of pathogen sequences up to 4-fold in metagenomic samples from patients with infectious diseases. Similarly, we demonstrate the utility of DASH in the context of cancer diagnostics by significantly increasing the detectable fraction of KRAS mutant sequences over the predominant wild-type allele. This simple single-tube method is reprogrammable for virtually any sample type to increase sequencing yield without additional cost. Read full publication here |
 Balamuthia mandrillaris is a rare, but almost always fatal cause of meningoencephalitis. The DeRisi Lab seeks contributions to support research and small molecule screening to identify possible therapeutic compounds. See our recent publication, Diagnosing Balamuthia mandrillaris Encephalitis with Metagenomic Deep Sequencing for more information about Balamuthia.
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