Oscar L. Rodriguez

This paper constructs HUSA, a comprehensive germline resource linking allele diversity to expressed antibody repertoires by integrating long-read sequencing and AIRR-seq data.

The paper identifies structural variants and coding polymorphisms in the human IGHC locus, revealing population-specific diversity and potential functional impacts.

A single dose of alum-adjuvanted RBD protein vaccine from the Wuhan strain protects against homologous SARS-CoV-2 WA strain challenge but not heterologous Delta and Omicron BA.5 rechallenge, unless mice survive the initial WA challenge.

This study identifies protective human monoclonal antibodies against SARS-CoV-2 using a K18 hACE2 transgenic mouse model, showing that in vivo testing improves accuracy over in vitro assays.

This study shows that genetic variations in immunoglobulin light chain loci influence the diversity of expressed light chain antibodies, affecting amino acid sequences and gene usage.

The paper investigates how genetic variation and selection shape antibody repertoires across B cell development stages, finding distinct roles for genetics and selection in heavy and light chain repertoires.

The paper investigates how vaccine antigen delivery and adjuvant selection affect the priming of rare HIV broadly neutralizing antibody-precursor B cells in non-human primates, finding that specific dosing and adjuvant combinations enhance their detection in germinal centers.

The paper develops methodologies to generate and analyze immunoglobulin loci variation in rhesus macaques, revealing extensive diversity and expanding existing allele sets by 60%.

The paper identifies limitations of short-read sequencing in analyzing IGH regulatory regions and advocates for long-read tools to better understand germline variation's impact on antibody repertoires.

The paper uses long-read sequencing to resolve haplotype variation and genetic architecture in the human IGK locus across diverse ancestries, identifying novel variants and population-specific allele frequencies.

The paper curates high-quality human immunoglobulin germline gene reference sets to improve AIRR-seq analysis accuracy and facilitate immunoglobulin gene studies.

The paper shows that genetic variation in the immunoglobulin heavy chain locus influences the diversity and characteristics of the human antibody repertoire.

The paper characterizes the immunoglobulin lambda chain locus in diverse populations, identifying novel alleles and highlighting limitations of short-read sequencing.

This paper uses targeted long-read sequencing to accurately assemble and genotype TCR loci, discovering new alleles and improving variant detection compared to short-read methods.

ImmunoTyper-SR genotypes IGHV alleles from short read data and identifies associations between IGHV alleles and anti-type I IFN autoantibodies in COVID-19 patients.

This study identifies 32 traits associated with copy number variation of 38 VNTRs and multicopy genes in a large cohort, suggesting structural variants contribute to missing heritability.

This study identifies how V(D)J recombination in lymphoblastoid cell lines affects genetic data quality in immunoglobulin loci, impacting allele frequency and linkage disequilibrium estimates.

The paper identifies VNTRs associated with gene expression and DNA methylation, validates their associations, and links them to human phenotypes through GWAS.

The paper introduces a framework combining long-read sequencing and a new tool to fully characterize haplotype diversity in the human immunoglobulin heavy chain locus, demonstrating high accuracy and scalability.

The paper surveys rare epigenetic variation in 23,116 human genomes, identifies disease-relevant epivariations, and discovers novel CGG expansions linked to folate-sensitive fragile sites.

The paper develops a fully automated method to annotate 164 human cell types using 1,615 genomics datasets, creating a unified encyclopedia of functional DNA elements with a new importance measure.

Genome in a Bottle benchmark of 12745 sequence-resolved insertions and deletions of 50 bp or more, integrating 19 calling methods, scores false negatives and false positives alike.

This study identifies a large number of structural variants in human genomes using multiple sequencing technologies and presents them as a gold standard for future studies.