 Community Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Disproportionately Affects the Latinx Population During Shelter-in-Place in San Francisco Infectious Disease Society of America, 2020
|
 IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring Oxford Academic, 2020
|
 Temporal airway microbiome changes related to ventilator associated pneumonia in children European Respiratory Journal, 2020
|
 ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens Cell Reports Medicine, 2020
|
 Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries PNAS, 2020
|
 Auto-antibodies against type I IFNs in patients with life-threatening COVID-19 Science, 2020
|
 High resolution epitope mapping of anti-Hu and anti-Yo autoimmunity by programmable phage display Oxford Academic, 2020
|
|  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 |
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 |
|