Joseph L. DeRisi

Genome-wide within-host evolution during prolonged SARS-CoV-2 infection in a person with advanced HIV infection

The paper tracks SARS-CoV-2 mutations over 90 days in an HIV-positive individual and tests their functional impact on viral entry and replication.

Longitudinal linear-epitope profiling of SLE identifies novel antigens associated with disease and disease activity

This study identifies novel SLE autoantigens and links EBV-driven immunity to autoimmunity through longitudinal PhIP-seq and machine learning analysis.

Humoral Immune Dysregulation Defines High-Risk Cirrhotic Ascites

The paper analyzes human ascites fluid to identify immune dysregulation features associated with poor outcomes in cirrhosis, finding that B cell dysfunction, not microbial translocation, defines high-risk cases.

AEGIS reveals epitope- and clone-resolved convergence of CNS B and T cell autoreactivity in ROHHAD

AEGIS identifies epitope- and clone-specific autoimmunity in ROHHAD by linking immune repertoires to self-epitopes, revealing convergence on ZSCAN1 epitopes in the CNS.

ORION: An agentic reasoning construct for the analysis of complex human immune profiling

ORION uses AI to analyze immune profiling data, reducing analysis time from months to hours and generating testable hypotheses.

IL-6 underlies microenvironment immunosuppression and resistance to therapy in glioblastoma

This study identifies IL-6 as a driver of immunosuppression in glioblastoma, showing that its inhibition enhances response to immune checkpoint therapy and radiotherapy in preclinical models.

Autoreactomes in Healthy Individuals Vary According to HLA Class II Genotype

This study identifies distinct autoreactomes in healthy individuals based on HLA-DRB1 genotype using PhIP-Seq, showing genotype-specific autoantibody profiles and potential pathogenic autoantibodies before disease onset.

Structure-guided design of a targeted autoantibody degrader for neurologic disease

This paper designs a targeted autoantibody degrader to treat neurologic diseases by specifically clearing pathogenic autoantibodies while preserving the immune system.

Defining the host dependencies and the transcriptional landscape of RSV infection and bystander activation

This study uses CRISPR screening and single-cell RNA sequencing to analyze host factors and transcriptional changes in RSV-infected and bystander cells, revealing distinct gene expression patterns and host dependencies.

Nitroxoline treatment of Balamuthia mandrillaris triggers genomic crisis, transcriptional collapse, and incomplete encystment via copper and iron chelation

This paper investigates how nitroxoline induces genomic instability, transcriptional collapse, and incomplete encystment in Balamuthia mandrillaris by chelating copper and iron.

Proteomic profiling of the local and systemic immune response to pediatric respiratory viral infections

This study uses proteomics to analyze immune responses in tracheal aspirate and plasma from critically ill children with viral lower respiratory tract infections, identifying diagnostic biomarkers and correlations with viral load and coinfections.

Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq

This study uses Perturb-seq to functionally interrogate SARS-CoV-2 host factors in human lung epithelial cells, identifying key factors that influence infection and host response.

Rubella virus tropism and single cell responses in human primary tissue and microglia-containing organoids

This study investigates rubella virus tropism in human brain slices and organoids, showing microglia as the primary target and revealing an interferon response in non-microglial cells.

PhIP-Seq uncovers novel autoantibodies and unique endotypes in interstitial lung disease

This study uses PhIP-Seq to identify novel autoantibodies in ILD patients, revealing a new molecular endotype associated with inflammation and fibrosis.

Functional characterization of 5' UTR cis-acting sequence elements that modulate translational efficiency in P. falciparum and humans

The paper compares cis-acting sequence elements affecting translational efficiency in Plasmodium falciparum and humans using in vitro translation assays.

IDseq - An Open Source Cloud-based Pipeline and Analysis Service for Metagenomic Pathogen Detection and Monitoring

IDseq provides a cloud-based metagenomics pipeline for pathogen detection, enabling analysis of mNGS data with tools for taxonomic assignment and novel pathogen identification.

Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by a widely-used RT-PCR assay

The paper identifies a SARS-CoV-2 N gene polymorphism that reduces RT-PCR assay sensitivity and emphasizes the need for multi-target testing.

Unbiased metagenomic sequencing for pediatric meningitis in Bangladesh reveals neuroinvasive Chikungunya virus outbreak and other unrealized pathogens

This study uses metagenomic sequencing to identify pathogens in pediatric meningitis cases in Bangladesh, revealing a Chikungunya virus outbreak and other previously undetected causes.

An exploration of ambigrammatic sequences in narnaviruses

The paper explores the ambigrammatic sequences in narnaviruses, showing that codon alignment allows for stop codon elimination in the reverse strand through synonymous substitutions, suggesting a mechanism for de novo gene creation.

Miniaturization and optimization of 384-well compatible metagenomic sequencing library preparation

This paper describes a miniaturized and automated method for metagenomic sequencing library preparation that reduces costs and time while maintaining quality.

The Plasmodium falciparum cytoplasmic translation apparatus: a promising therapeutic target not yet exploited by clinically approved antimalarials.

The paper develops and validates a direct assay to measure Plasmodium falciparum translation, showing no clinically approved antimalarials inhibit it.

Integrating Host Response and Unbiased Microbe Detection for Lower Respiratory Tract Infection Diagnosis in Critically Ill Adults

This paper develops a metagenomic sequencing approach to diagnose lower respiratory tract infections by integrating pathogen detection, microbiome analysis, and host transcriptome data.

Pediatric Brainstem Encephalitis Outbreak Investigation with Metagenomic Next-Generation Sequencing

The paper investigates a pediatric brainstem encephalitis outbreak using metagenomic next-generation sequencing, finding that mNGS significantly improves EV-A71 detection in CSF and confirms the outbreak strain's relation to a neuroinvasive isolate.

Etiology of fever in Ugandan children: identification of microbial pathogens using metagenomic next-generation sequencing and IDseq, a platform for unbiased metagenomic analysis

This study uses metagenomic sequencing and the IDseq platform to identify microbial pathogens in Ugandan children with fever, revealing common pathogens and novel viruses.

Extending Chemical Perturbations Of The Ubiquitin Fitness Landscape In A Classroom Setting

The paper uses deep mutational scanning to explore how chemical perturbations affect ubiquitin's mutational tolerance, revealing sensitization of most positions except two.

Genomic characterization of serial-passaged Ebola virus in a boa constrictor cell line

This study shows Ebola virus can infect boa constrictor cells without causing cytopathic effect or requiring genomic adaptation, while Marburg virus cannot.

Repurposing the quinoline antibiotic nitroxoline to treat infections caused by the brain-eating amoeba Balamuthia mandrillaris

This paper identifies nitroxoline as a potent inhibitor of Balamuthia mandrillaris, showing greater efficacy than current treatments for granulomatous amoebic encephalitis.

Evidence for Alternative Complement Cascade Activation in Primary CNS Vasculitis

The paper analyzes cerebrospinal fluid proteomes to identify complement pathway activation in PACNS, suggesting C5 inhibitors as potential therapies.

Single-cell transcriptomic characterization of 20 organs and tissues from individual mice creates a Tabula Muris

The paper creates a single-cell transcriptomic atlas of 20 mouse organs and tissues, providing a resource for studying gene expression across cell types.

Silver microwires from treating tooth decay with silver diamine fluoride

This paper investigates the structural changes in tooth decay treated with silver diamine fluoride, identifying silver microwires formed in situ and confirming their chemical composition.