Identification of Plasmodium falciparum specific translation inhibitors from the MMV Malaria Box using a high throughput in vitro translation screenMalaria Journal, 2016
Depletion of Abundant Sequences by Hybridization (DASH): Using Cas9 to remove unwanted highabundance species in sequencing libraries and molecular counting applicationsBioRxiv, 2015 and Genome Biology, 2016
Diagnosing Balamuthia mandrillaris Encephalitis With Metagenomic Deep SequencingAnnals of Neurology, 2015
Genome Announcements Collection 2: Tombunodavirus UC1; Picalivirus D; Laverivirus UC1Genome Announcements, 2015
Genome Announcements Collection 1: Ciliovirus, Brinovirus; Marine RNA Viruses SF-1, SF-2, SF-3; Leviviridae RNA Phages EC and MBGenome Announcements, 2015
Widespread Recombination, Reassortment, and Transmission of Unbalanced Compound Viral Genotypes in Natural Arenavirus InfectionsPLoS, 2015
Destructin-1 is a Collagen-Degrading Endopeptidase Secreted by P. destructans, the Causative Agent of White-Nose SyndromePNAS, 2015
We are currently accepting applications for summer research positions in the DeRisi Lab for 2016. To begin the application process with Joe DeRisi as a mentor, please send your cover letter, CV/resume, and list of references to our Lab Manager, Jennifer Mann, at email@example.com.
[ UCSF SRTP ]
Application deadline: February 1, 2016
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
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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