J. L. DeRisi

Validation of a murine proteome-wide phage display library for the identification of autoantibody specificities

This paper validates a murine proteome-wide PhIP-seq library to identify autoantibody specificities in autoimmune disease models.

Broad sensitivity of Candida auris strains to quinolones and mechanisms of resistance

This paper identifies dihalogenated hydroxyquinolines as effective inhibitors of Candida auris with limited resistance development and characterizes the resistance mechanisms.

Proteome-wide antigenic profiling in Ugandan cohorts identifies associations between age, exposure intensity, and responses to repeat-containing antigens in Plasmodium falciparum

The paper profiles antibody responses to Plasmodium falciparum antigens in Ugandan cohorts, finding that repeat-containing antigens show stronger exposure-dependent responses and shared cross-reactive motifs.

Discovery and Genomic Characterization of a Novel Henipavirus, Angavokely virus, from fruit bats in Madagascar

This paper discovers and characterizes Angavokely virus, a novel henipavirus from Madagascar fruit bats, revealing genomic features and potential pathogenicity.

Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-Seq

This paper scales PhIP-Seq for autoantibody discovery across multiple autoimmune diseases and COVID19, enabling machine learning predictions and identification of disease-specific autoantigens.

Full genome Nobecovirus sequences from Malagasy fruit bats define a unique evolutionary history for this coronavirus clade

The paper reports full genome sequences of Nobecoviruses from Malagasy fruit bats, revealing distinct phylogenetic clades and recombination events.

Elevated N-glycosylation of immunoglobulin G variable regions in myasthenia gravis highlights a commonality across autoantibody-associated diseases

This study identifies elevated N-glycosylation in IgG variable regions in myasthenia gravis patients and shows it is not required for autoantigen binding.

Persistence of ambigrammatic narnaviruses requires translation of the reverse open reading frame

This paper shows that ambigrammatic narnaviruses require translation of a reverse open reading frame for persistence, suggesting a novel viral strategy involving ribosome-mediated protection of viral RNA.

Exploratory neuroimmune profiling identifies CNS-specific alterations in COVID-19 patients with neurological involvement

The paper identifies CNS-specific immune alterations in COVID-19 patients with neurological symptoms, suggesting neuroinvasion and anti-neural autoimmunity as potential causes.

Identification of novel, clinically correlated autoantigens in the monogenic autoimmune syndrome APS1 by PhIP-Seq

This study uses PhIP-Seq to identify novel autoantigens in APS1, linking specific autoantibodies to clinical phenotypes like ovarian insufficiency and intestinal dysfunction.

FLASH: A next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences

FLASH is a CRISPR-based diagnostic method that enhances detection of low-abundance antimicrobial resistance sequences in metagenomic data.

Exploration of Anti-Yo and Anti-Hu paraneoplastic neurological disorders by PhIP-Seq reveals a highly restricted pattern of antibody epitopes

This study uses PhIP-Seq to identify epitopes of anti-Yo and anti-Hu autoantibodies in PND patients, revealing restricted antigenic patterns and potential biomarkers.

A Metagenomic Comparison of Tracheal Aspirate and Mini-Bronchial Alveolar Lavage for Assessment of Respiratory Microbiota

This paper compares metagenomic sequencing of tracheal aspirates and mini-bronchial alveolar lavage to assess respiratory microbiota and develop diagnostic models for lower respiratory tract infections.

Metagenomic next-generation sequencing reveals Miamiensis avidus (Ciliophora: Scuticociliatida) in the 2017 epizootic of leopard sharks (Triakis semifasciata) in San Francisco Bay, California

The paper uses metagenomic sequencing to identify Miamiensis avidus in leopard sharks during a 2017 epizootic, linking it to meningoencephalitis and highlighting its presence in wild elasmobranchs for the first time.

Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children

This study develops a metagenomic sequencing assay to detect missed pathogens in immunocompromised children, finding increased sensitivity for identifying potential pathogens in lung samples.

Metagenomics for chronic meningitis: clarifying interpretation and diagnosis

This study uses metagenomic next-generation sequencing of cerebrospinal fluid to identify pathogens in patients with subacute or chronic meningitis, using a z-score based scoring algorithm to distinguish true pathogens from environmental contaminants.