Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data

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Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data is …
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scholarly articleQ13442814

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P356DOI10.3389/FIMMU.2013.00358
P932PMC publication ID3828525
P698PubMed publication ID24298272
P5875ResearchGate publication ID259115343

P50authorDavid A. HaflerQ25004567
Gur YaariQ41050662
P2093author name stringNamita Gupta
Francois Vigneault
Mohamed Uduman
Steven H Kleinstein
Kevin C O'Connor
Joel N H Stern
Uri Laserson
Daniel Gadala-Maria
Jason A Vander Heiden
P2860cites workEstimating Hypermutation Rates from Clonal Tree DataQ30882543
Cutting edge: DGYW/WRCH is a better predictor of mutability at G:C bases in Ig hypermutation than the widely accepted RGYW/WRCY motif and probably reflects a two-step activation-induced cytidine deaminase-triggered processQ33198930
Compartmentalized linkage of genes encoding interacting protein pairs.Q33832538
IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domainsQ34164031
Quantifying selection in high-throughput Immunoglobulin sequencing data setsQ34284964
Detecting selection in immunoglobulin sequencesQ35075665
Passenger transgenes reveal intrinsic specificity of the antibody hypermutation mechanism: clustering, polarity, and specific hot spotsQ36172034
AIDing antibody diversity by error-prone mismatch repairQ36173942
Generation of antibody diversity in the immune response of BALB/c mice to influenza virus hemagglutininQ36261566
The biochemistry of somatic hypermutationQ37096080
V-region mutation in vitro, in vivo, and in silico reveal the importance of the enzymatic properties of AID and the sequence environmentQ37193388
Biochemical analysis of hypermutational targeting by wild type and mutant activation-induced cytidine deaminaseQ40515192
Clone: a Monte-Carlo computer simulation of B cell clonal expansion, somatic mutation, and antigen-driven selectionQ41711157
Somatic hypermutation targeting is influenced by location within the immunoglobulin V regionQ42149724
Paratome: an online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structureQ42232982
Predicting regional mutability in antibody V genes based solely on di- and trinucleotide sequence compositionQ42604426
Di- and trinucleotide target preferences of somatic mutagenesis in normal and autoreactive B cellsQ42637489
The nucleotide-replacement spectrum under somatic hypermutation exhibits microsequence dependence that is strand-symmetric and distinct from that under germline mutationQ44872484
Hypermutation at A-T base pairs: the A nucleotide replacement spectrum is affected by adjacent nucleotides and there is no reverse complementarity of sequences flanking mutated A and T nucleotides.Q46740213
Sequence-specific targeting of two bases on both DNA strands by the somatic hypermutation mechanismQ47660823
The microenvironment of germ cell tumors harbors a prominent antigen-driven humoral responseQ48071040
Accurate estimation of substitution rates with neighbor-dependent models in a phylogenetic context.Q51423936
IgTree: creating Immunoglobulin variable region gene lineage trees.Q51871158
Problems in using statistical analysis of replacement and silent mutations in antibody genes for determining antigen-driven affinity selection.Q52992155
Somatic mutation hotspots correlate with DNA polymerase eta error spectrum.Q55034838
The Targeting of Somatic Hypermutation Closely Resembles That of Meiotic MutationQ57234192
Characteristics of sequences around individual nucleotide substitutions in IgVH genes suggest different GC and AT mutatorsQ77823529
P304page(s)358
P577publication date2013-11-15
P1433published inFrontiers in ImmunologyQ27723748
P1476titleModels of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data
P478volume4

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cites work (P2860)
Q525976305' Rapid Amplification of cDNA Ends and Illumina MiSeq Reveals B Cell Receptor Features in Healthy Adults, Adults With Chronic HIV-1 Infection, Cord Blood, and Humanized Mice.
Q31135078A Model of Somatic Hypermutation Targeting in Mice Based on High-Throughput Ig Sequencing Data
Q41996650A Phylogenetic Codon Substitution Model for Antibody Lineages
Q92454312A review of canine B cell clonality assays and primer set optimization using large-scale repertoire data
Q36349113Antigen Receptor Galaxy: A User-Friendly, Web-Based Tool for Analysis and Visualization of T and B Cell Receptor Repertoire Data
Q56376231Antihomotypic affinity maturation improves human B cell responses against a repetitive epitope
Q28640605Assigning and visualizing germline genes in antibody repertoires
Q30891515Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles
Q35155724B cell variable genes have evolved their codon usage to focus the targeted patterns of somatic mutation on the complementarity determining regions
Q59133570Benchmarking Tree and Ancestral Sequence Inference for B Cell Receptor Sequences
Q58781552Beyond Hot Spots: Biases in Antibody Somatic Hypermutation and Implications for Vaccine Design
Q30970597Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data
Q50420437Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires
Q64091957DSab-origin: a novel IGHD sensitive VDJ mapping method and its application on antibody response after influenza vaccination
Q47754080Dynamics of the human antibody repertoire after B cell depletion in systemic sclerosis.
Q48352173Dysregulation of B Cell Repertoire Formation in Myasthenia Gravis Patients Revealed through Deep Sequencing.
Q36020766Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection
Q37342726Evaluation of the Antigen-Experienced B-Cell Receptor Repertoire in Healthy Children and Adults
Q49860297Evidence for Alternate Modes of B cell Activation Involving Fab Acquired-N-Glycosylations in Antibody Secreting Cells Infiltrating the Labial Salivary Glands of Sjögren's Syndrome Patients
Q92446647Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies
Q92827369Fierce Selection and Interference in B-Cell Repertoire Response to Chronic HIV-1
Q58610902Filtering Next-Generation Sequencing of the Ig Gene Repertoire Data Using Antibody Structural Information
Q55356257Functional Relevance of Improbable Antibody Mutations for HIV Broadly Neutralizing Antibody Development.
Q33654599Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation
Q52352265HIV envelope V3 region mimic embodies key features of a broadly neutralizing antibody lineage epitope.
Q36274750Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data.
Q48297980High-Throughput Single-Cell Analysis of B Cell Receptor Usage among Autoantigen-Specific Plasma Cells in Celiac Disease.
Q49187352High-throughput immune repertoire analysis with IGoR.
Q42261577Human IgG2- and IgG4-expressing memory B cells display enhanced molecular and phenotypic signs of maturity and accumulate with age.
Q59812460Identification of CVID Patients With Defects in Immune Repertoire Formation or Specification
Q90239275Immune Profiling of Human Gut-Associated Lymphoid Tissue Identifies a Role for Isolated Lymphoid Follicles in Priming of Region-Specific Immunity
Q41963347Immune system modeling and analysis.
Q28640380Inferring processes underlying B-cell repertoire diversity
Q31107783Integrating multiple immunogenetic data sources for feature extraction and mining somatic hypermutation patterns: the case of "towards analysis" in chronic lymphocytic leukaemia
Q64066934Large-scale network analysis reveals the sequence space architecture of antibody repertoires
Q57159578Local Clonal Diversification and Dissemination of B Lymphocytes in the Human Bronchial Mucosa
Q36985671Long-lived antigen-induced IgM plasma cells demonstrate somatic mutations and contribute to long-term protection.
Q36584038Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing.
Q38811964Oncogenic events rather than antigen selection pressure may be the main driving forces for relapse in diffuse large B-cell lymphomas
Q40368519Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging
Q28607156Practical guidelines for B-cell receptor repertoire sequencing analysis
Q28640162Quantifying evolutionary constraints on B-cell affinity maturation
Q46209629Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads
Q35685749Responsive population dynamics and wide seeding into the duodenal lamina propria of transglutaminase-2-specific plasma cells in celiac disease
Q55003119Selection and Neutral Mutations Drive Pervasive Mutability Losses in Long-Lived Anti-HIV B-Cell Lineages.
Q42667029Shared VH1-46 gene usage by pemphigus vulgaris autoantibodies indicates common humoral immune responses among patients.
Q90335423Somatic hypermutation to counter a globally rare viral immunotype drove off-track antibodies in the CAP256-VRC26 HIV-1 V2-directed bNAb lineage
Q58705788Spatiotemporal segregation of human marginal zone and memory B cell populations in lymphoid tissue
Q40290521Staged induction of HIV-1 glycan-dependent broadly neutralizing antibodies.
Q41926663Stereotyped antibody responses target posttranslationally modified gluten in celiac disease
Q57093739Structural Insights from HIV-Antibody Coevolution and Related Immunization Studies
Q89759205Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice
Q38592595T-cell receptor profiling in cancer
Q57178227The Bayesian optimist's guide to adaptive immune receptor repertoire analysis
Q38708644The Diversity and Molecular Evolution of B-Cell Receptors during Infection
Q36261329The Number of Overlapping AID Hotspots in Germline IGHV Genes Is Inversely Correlated with Mutation Frequency in Chronic Lymphocytic Leukemia
Q64078703The Pipeline Repertoire for Ig-Seq Analysis
Q42015134The mutation patterns in B-cell immunoglobulin receptors reflect the influence of selection acting at multiple time-scales
Q36330081The preferred nucleotide contexts of the AID/APOBEC cytidine deaminases have differential effects when mutating retrotransposon and virus sequences compared to host genes
Q58586481Tracing Antibody Repertoire Evolution by Systems Phylogeny
Q96816315Ultrasensitive amplicon barcoding for next-generation sequencing facilitating sequence error and amplification-bias correction
Q52688244Using Genotype Abundance to Improve Phylogenetic Inference.
Q90644755VDJbase: an adaptive immune receptor genotype and haplotype database
Q33807674pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires