Welcome to the DeRisi Lab

Time 2021-01-04 15:05:48

Web Name: Welcome to the DeRisi Lab

WebSite: http://derisilab.ucsf.edu

ID:156424

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Community Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Disproportionately Affects the Latinx Population During Shelter-in-Place in San FranciscoInfectious Disease Society of America, 2020 IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoringOxford Academic, 2020 Temporal airway microbiome changes related to ventilator associated pneumonia in childrenEuropean Respiratory Journal, 2020 ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 AntigensCell Reports Medicine, 2020 Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage librariesPNAS, 2020 Auto-antibodies against type I IFNs in patients with life-threatening COVID-19Science, 2020 High resolution epitope mapping of anti-Hu and anti-Yo autoimmunity by programmable phage displayOxford Academic, 2020 2019-07-04 :: New Autoimmune Disease Discovered! More... Scientists at Chan Zuckerberg (CZ) Biohub, Mayo Clinic and University of California, San Francisco (UCSF), have discovered an autoimmune disease that appears to affect men with testicular cancer. A postdoctoral fellow in the DeRisi lab, Caleigh Mandel-Brehm, led the study together with a clinical fellow at the Mayo Clinic, Divyanshu Dubey. Using a combination of customized programmable phage display, immunohistochemical staining, and other techniques, antibodies to the protein Kelch-like Protein 11 (KLHL11) was identified as a highly specific marker of a new paraneoplastic autoimmune syndrome associated with seminoma in men. Click Here for the Full Press Release 2016-07-06 :: The UCSF Center for Next-Gen Precision Diagnostics More... Now open for patients and providers! 2015-12-07 :: DASH More... Depletion of Abundant Sequences by Hybridization (DASH): Using Cas9 to remove unwanted highabundance species in sequencing libraries and molecular counting applicationsWith 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

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