G. Yaari

Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry

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.

A Novel Approach to T-Cell Receptor Beta Chain (TCRB) Repertoire Encoding Using Lossless String Compression

The paper introduces a lossless string compression method based on LZ-76 to encode T-cell receptor beta chain repertoires, enabling applications like diversity estimation and sequence generation.

IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data

The paper introduces a new V allele naming scheme and genotype inference method for adaptive immune receptor sequencing, validated with genomic long read data and implemented in an R package.

Altered somatic hypermutation patterns in COVID-19 patients classifies disease severity

This study uses machine learning to analyze B cell receptor sequencing data and identifies altered somatic hypermutation patterns in COVID-19 patients that correlate with disease severity.

FLAIRR-seq: A novel method for single molecule resolution of near full-length immunoglobulin heavy chain repertoires

FLAIRR-seq provides high-resolution, single-molecule characterization of immunoglobulin heavy chain repertoires, including constant region features, and identifies novel alleles.

A BALB/c IGHV Reference Set, defined by haplotype analysis of long-read VDJ-C sequences from F1 (BALB/c / C57BL/6) mice

The paper defines a BALB/c IGHV reference set by analyzing long-read VDJ-C sequences from F1 mice, identifying strain-specific variations and germline alleles not present in existing genome references.

Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma

The paper investigates OMAS in neuroblastoma, finding polyclonal B- and T-cell infiltration and TLS enrichment, linking them to autoimmune and anti-tumor responses.

T Cell Receptor Beta Germline Variability is Revealed by Inference From Repertoire Data

The paper identifies undocumented polymorphisms in T cell receptor Beta genes using AIRR-seq data and shows how a single SNP affects TCR repertoire composition.

Machine learning analysis of naïve B-cell receptor repertoires stratifies celiac disease patients and controls

The paper uses machine learning to analyze naive B-cell receptor repertoires to distinguish celiac disease patients from controls, achieving an F1 score of 85%.

Multi-Clonal Live SARS-CoV-2 In Vitro Neutralization by Antibodies Isolated from Severe COVID-19 Convalescent Donors

This study identifies multi-clonal neutralizing antibodies against SARS-CoV-2 in severe COVID-19 patients and shows their potential for combination therapy.

Polymorphisms in immunoglobulin heavy chain variable genes and their upstream regions

The paper identifies novel germline IGHV alleles and upstream sequence variability, challenging current immunoglobulin repertoire annotation methods.

Mice developing mammary tumors evolve T cell sequences shared with human breast cancer patients

The paper tracks TCR repertoire evolution in mice with mammary tumors and finds shared tumor-exclusive TCR sequences with human breast cancer patients.