Ayelet Peres
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View article: The current landscape of adaptive immune receptor genomic and repertoire data: OGRDB and VDJbase
The current landscape of adaptive immune receptor genomic and repertoire data: OGRDB and VDJbase Open
Accurate characterization of adaptive immune receptor repertoires through high-throughput sequencing is critical for understanding immune responses, disease biomarkers, vaccine design, and antibody engineering. However, progress depends on…
View article: The human IG heavy chain constant gene locus is enriched for large structural variants and coding polymorphisms that vary among human populations
The human IG heavy chain constant gene locus is enriched for large structural variants and coding polymorphisms that vary among human populations Open
The human immunoglobulin heavy chain constant (IGHC) domain of antibodies (Abs) is responsible for effector functions critical to immunity. This domain is encoded by genes in the IGHC locus, where descriptions of genomic diversity remain i…
View article: The gremlin in the works: why T cell receptor researchers need to pay more attention to germline reference sequences
The gremlin in the works: why T cell receptor researchers need to pay more attention to germline reference sequences Open
View article: Building immunoglobulin and T cell receptor gene databases for the future
Building immunoglobulin and T cell receptor gene databases for the future Open
View article: Germline polymorphisms in the immunoglobulin kappa and lambda loci explain variation in the expressed light chain antibody repertoire
Germline polymorphisms in the immunoglobulin kappa and lambda loci explain variation in the expressed light chain antibody repertoire Open
View article: Enhancing sequence alignment of adaptive immune receptors through multi-task deep learning
Enhancing sequence alignment of adaptive immune receptors through multi-task deep learning Open
Sequence alignment of immunoglobulin (Ig) sequences is central to the computational analysis of adaptive immune receptor repertoire sequencing (AIRR-seq) data, impacting adaptive immunity research and antibody engineering. Traditional Ig s…
View article: BLIMP1 controls GC B cell expansion and exit through regulating cell cycle progression and key transcription factors BCL6 and IRF4
BLIMP1 controls GC B cell expansion and exit through regulating cell cycle progression and key transcription factors BCL6 and IRF4 Open
In B cells, BLIMP1 is required for plasma cell differentiation. BLIMP1 is also expressed in some germinal center (GC) B cells (GCBC), yet the role of BLIMP1 in GCBC is not understood. Here we generated mixed bone marrow (BM) chimeric mice …
View article: Germline polymorphism in the immunoglobulin kappa and lambda loci explain variation in the expressed light chain antibody repertoire
Germline polymorphism in the immunoglobulin kappa and lambda loci explain variation in the expressed light chain antibody repertoire Open
Variation in antibody (Ab) responses contributes to variable disease outcomes and therapeutic responsiveness, the determinants of which are incompletely understood. This study demonstrates that polymorphisms in immunoglobulin (IG) light ch…
View article: The human IG heavy chain constant gene locus is enriched for large structural variants and coding polymorphisms that vary among human populations
The human IG heavy chain constant gene locus is enriched for large structural variants and coding polymorphisms that vary among human populations Open
The human immunoglobulin heavy chain constant (IGHC) domain of antibodies (Ab) is responsible for effector functions critical to immunity. This domain is encoded by genes in the IGHC locus, where descriptions of genomic diversity remain in…
View article: A Broad Survey and Functional Analysis of Immunoglobulin Loci Variation in Rhesus Macaques
A Broad Survey and Functional Analysis of Immunoglobulin Loci Variation in Rhesus Macaques Open
Rhesus macaques (RMs) are a vital model for studying human disease and invaluable to pre-clinical vaccine research, particularly for the study of broadly neutralizing antibody responses. Such studies require robust genetic resources for an…
View article: The Human Immunoglobulin Heavy Chain Constant Gene Locus is Enriched for Large Complex Structural Variants and Coding Polymorphisms that Vary in Frequency Among Human Populations
The Human Immunoglobulin Heavy Chain Constant Gene Locus is Enriched for Large Complex Structural Variants and Coding Polymorphisms that Vary in Frequency Among Human Populations Open
View article: An unbiased comparison of immunoglobulin sequence aligners
An unbiased comparison of immunoglobulin sequence aligners Open
Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is critical for our understanding of the adaptive immune system’s dynamics in health and disease. Reliable analysis of AIRR-seq data depends on accurate rearranged immunoglobulin (I…
View article: An unbiased comparison of immunoglobulin sequence aligners
An unbiased comparison of immunoglobulin sequence aligners Open
Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is critical for our under-standing of the adaptive immune system’s dynamics in health and disease. Reliable analysis of AIRR-seq data depends on accurate Immunoglobulin (Ig) sequenc…
View article: Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data
Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data Open
Enhancing the reproducibility and comprehension of adaptive immune receptor repertoire sequencing (AIRR-seq) data analysis is critical for scientific progress. This study presents guidelines for reproducible AIRR-seq data analysis, and a c…
View article: AIRR-C IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes
AIRR-C IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes Open
Introduction Analysis of an individual’s immunoglobulin (IG) gene repertoire requires the use of high-quality germline gene reference sets. When sets only contain alleles supported by strong evidence, AIRR sequencing (AIRR-seq) data analys…
View article: AIRR-C Human IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes
AIRR-C Human IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes Open
Analysis of an individual’s immunoglobulin (IG) gene repertoire requires the use of high-quality germline gene Reference Sets. The Adaptive Immune Receptor Repertoire-Community (AIRR-C) Reference Sets have been developed to include only hu…
View article: IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data
IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data Open
In adaptive immune receptor repertoire analysis, determining the germline variable (V) allele associated with each T- and B-cell receptor sequence is a crucial step. This process is highly impacted by allele annotations. Aligning sequences…
View article: Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma
Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma Open
View article: piglet: Program for Inferring Immunoglobulin Allele Similarity Clusters and Genotypes
piglet: Program for Inferring Immunoglobulin Allele Similarity Clusters and Genotypes Open
View article: FLAIRR-Seq: A Method for Single-Molecule Resolution of Near Full-Length Antibody H Chain Repertoires
FLAIRR-Seq: A Method for Single-Molecule Resolution of Near Full-Length Antibody H Chain Repertoires Open
Current Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) using short-read sequencing strategies resolve expressed Ab transcripts with limited resolution of the C region. In this article, we present the near-full-length AIRR-seq (F…
View article: B cell class switch recombination is regulated by DYRK1A through MSH6 phosphorylation
B cell class switch recombination is regulated by DYRK1A through MSH6 phosphorylation Open
Protection from viral infections depends on immunoglobulin isotype switching, which endows antibodies with effector functions. Here, we find that the protein kinase DYRK1A is essential for B cell-mediated protection from viral infection an…
View article: AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets
AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets Open
Analysis of an individual's immunoglobulin or T cell receptor gene repertoire can provide important insights into immune function. High-quality analysis of adaptive immune receptor repertoire sequencing data depends upon accurate and relat…
View article: IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data
IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data Open
In adaptive immune receptor repertoire analysis, determining the germline variable (V) allele associated with each T- and B-cell receptor sequence is a crucial step. This process is highly impacted by allele annotations. Aligning sequences…
View article: A somatic hypermutation–based machine learning model stratifies individuals with Crohn's disease and controls
A somatic hypermutation–based machine learning model stratifies individuals with Crohn's disease and controls Open
Crohn's disease (CD) is a chronic relapsing–remitting inflammatory disorder of the gastrointestinal tract that is characterized by altered innate and adaptive immune function. Although massively parallel sequencing studies of the T cell re…
View article: FLAIRR-seq: A novel method for single molecule resolution of near full-length immunoglobulin heavy chain repertoires
FLAIRR-seq: A novel method for single molecule resolution of near full-length immunoglobulin heavy chain repertoires Open
Current Adaptive Immune Receptor Repertoire Sequencing (AIRR-seq) strategies resolve expressed antibody (Ab) transcripts with limited resolution of the constant region. Here we present a novel near full-length AIRR-seq (FLAIRR-Seq) method …
View article: B cell class switch recombination is regulated by DYRK1A through MSH6 phosphorylation
B cell class switch recombination is regulated by DYRK1A through MSH6 phosphorylation Open
Protection from viral infections depends on immunoglobulin isotype switching, which endows antibodies with effector functions. Here, we found that the protein kinase DYRK1A is essential for B cell-mediated protection from viral infection a…
View article: A BALB/c IGHV Reference Set, Defined by Haplotype Analysis of Long-Read VDJ-C Sequences From F1 (BALB/c x C57BL/6) Mice
A BALB/c IGHV Reference Set, Defined by Haplotype Analysis of Long-Read VDJ-C Sequences From F1 (BALB/c x C57BL/6) Mice Open
The immunoglobulin genes of inbred mouse strains that are commonly used in models of antibody-mediated human diseases are poorly characterized. This compromises data analysis. To infer the immunoglobulin genes of BALB/c mice, we used long-…
View article: A BALB/c IGHV Reference Set, defined by haplotype analysis of long-read VDJ-C sequences from F1 (BALB/c / C57BL/6) mice
A BALB/c IGHV Reference Set, defined by haplotype analysis of long-read VDJ-C sequences from F1 (BALB/c / C57BL/6) mice Open
The immunoglobulin genes of inbred mouse strains that are commonly used in models of antibody-mediated human diseases are poorly characterized. This compromises data analysis. To infer the immunoglobulin genes of BALB/c mice, we used long-…
View article: T cell receptor beta germline variability is revealed by inference from repertoire data
T cell receptor beta germline variability is revealed by inference from repertoire data Open
View article: Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma
Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma Open
Summary Neuroblastoma is a lethal childhood solid tumor of developing peripheral nerves. Two percent of children with neuroblastoma develop Opsoclonus Myoclonus Ataxia Syndrome (OMAS), a paraneoplastic disease characterized by cerebellar a…