 Kelch-like Protein 11 Seminoma-associated Paraneoplastic Encephalitis NEJM 2019
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 Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children Oxford Academic, 2019
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 Towards precision quantification of contamination in metagenomic sequencing experiments Microbiome, 2019
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 Metagenomic comparison of tracheal aspirate and mini-bronchial alveolar lavage for assessment of respiratory microbiota American Journal of Physiology, 2019
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 Miniaturization and optimization of 384-well compatible RNA sequencing library preparation PLOS One, 2019
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 Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults PNAS, 2018
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 Clinicopathology conference: 41‐year‐old woman with chronic relapsing meningitis Annuls of Neurology, 2018
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|  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 |
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