Oscar L. Rodriguez

An integrated human immunoglobulin germline resource linking allele diversity to expressed repertoire structure

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 human IG heavy chain constant gene locus is enriched for large structural variants and coding polymorphisms that vary among human populations

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

Single dose alum adjuvanted RBD protein vaccine provides protection against homologous challenge with SARS-CoV-2 Washington strain and heterologous rechallenge with Delta and Omicron BA.5 variants in K18 hACE2 mouse model

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.

Identification of protective human monoclonal antibodies using a K18 hACE2 transgenic mouse SARS-CoV-2 challenge model

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.

Germline polymorphism in the immunoglobulin kappa and lambda loci explain variation in the expressed light chain antibody repertoire

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.

Human genetic variation shapes the antibody repertoire across B cell development

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.

Diverse priming outcomes under conditions of very rare precursor B cells

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.

A Broad Survey and Functional Analysis of Immunoglobulin Loci Variation in Rhesus Macaques

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

Addressing technical pitfalls in pursuit of molecular factors that mediate immunoglobulin gene regulation

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.

AIRR-C Human IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes

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

Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire

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

Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation

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

Targeted long-read sequencing facilitates phased diploid assembly and genotyping of the human T cell receptor alpha, delta and beta loci

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: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes using Short Read Data

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.

A phenome-wide association study identifies effects of copy number variation of VNTRs and multicopy genes on multiple human traits

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.

Limitations of lymphoblastoid cell lines for establishing genetic reference datasets in the immunoglobulin loci

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.

Pervasive cis effects of variation in copy number of large tandem repeats on local epigenetics and gene expression

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

A novel framework for characterizing genomic haplotype diversity in the human immunoglobulin heavy chain locus

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.

A survey of rare epigenetic variation in 23,116 human genomes identifies disease-relevant epivariations and novel CGG expansions

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.

A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types

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.

A robust benchmark for germline structural variant detection

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.

Multi-platform discovery of haplotype-resolved structural variation in human genomes

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.