(Q33654599)

28 July 2017

title

Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation (English)

1 reference

28 July 2017

6

John R Mascola

1 reference

NISC Comparative Sequencing Program

28 July 2017

series ordinal

4

object named as

NISC Comparative Sequencing Program

1 reference

28 July 2017

5

James C Mullikin

1 reference

28 July 2017

7

Peter D Kwong

1 reference

28 July 2017

2

Chaim A Schramm

1 reference

28 July 2017

1

Zizhang Sheng

1 reference

28 July 2017

Rui Kong

3

1 reference

28 July 2017

Lawrence Shapiro

series ordinal

8

1 reference

28 July 2017

publication date

10 May 2017

1 reference

28 July 2017

published in

Frontiers in Immunology

1 reference

28 July 2017

volume

8

1 reference

28 July 2017

page(s)

537

1 reference

Mutational landscape of antibody variable domains reveals a switch modulating the interdomain conformational dynamics and antigen binding

28 July 2017

cites work

1 reference

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SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell Transcripts

21 June 2018

1 reference

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A Model of Somatic Hypermutation Targeting in Mice Based on High-Throughput Ig Sequencing Data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Induction of HIV Neutralizing Antibody Lineages in Mice with Diverse Precursor Repertoires

21 June 2018

1 reference

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Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Maturation Pathway from Germline to Broad HIV-1 Neutralizer of a CD4-Mimic Antibody

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Optimizing antibody expression by using the naturally occurring framework diversity in a live bacterial antibody display system

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Sequence-Intrinsic Mechanisms that Target AID Mutational Outcomes on Antibody Genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Viral variants that initiate and drive maturation of V1V2-directed HIV-1 broadly neutralizing antibodies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

AID targeting: old mysteries and new challenges

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Quantifying evolutionary constraints on B-cell affinity maturation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Inferring processes underlying B-cell repertoire diversity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Restricted, canonical, stereotyped and convergent immunoglobulin responses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Antibody-specific model of amino acid substitution for immunological inferences from alignments of antibody sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Integrating B cell lineage information into statistical tests for detecting selection in Ig sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Somatic Mutations of the Immunoglobulin Framework Are Generally Required for Broad and Potent HIV-1 Neutralization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Human peripheral blood antibodies with long HCDR3s are established primarily at original recombination using a limited subset of germline genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Somatic hypermutation targeting is influenced by location within the immunoglobulin V region

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Search and clustering orders of magnitude faster than BLAST

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Structural Basis for Broad and Potent Neutralization of HIV-1 by Antibody VRC01

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Molecular mechanisms of antibody somatic hypermutation.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Targeting of somatic hypermutation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

MSH2-MSH6 stimulates DNA polymerase eta, suggesting a role for A:T mutations in antibody genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

WebLogo: A Sequence Logo Generator

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Pairwise sequence alignment below the twilight zone

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Modifying the sequence of an immunoglobulin V-gene alters the resulting pattern of hypermutation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Passenger transgenes reveal intrinsic specificity of the antibody hypermutation mechanism: clustering, polarity, and specific hot spots

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

The immunohistology of lymph nodes in HIV infection: a review.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Somatic hypermutagenesis in immunoglobulin genes. II. Influence of neighbouring base sequences on mutagenesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Two levels of protection for the B cell genome during somatic hypermutation.

21 June 2018

1 reference

https://api.crossref.org/works/10.3389%2FFIMMU.2017.00537

The nucleotide-replacement spectrum under somatic hypermutation exhibits microsequence dependence that is strand-symmetric and distinct from that under germline mutation

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFIMMU.2017.00537

Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFIMMU.2017.00537

Sequence-specific targeting of two bases on both DNA strands by the somatic hypermutation mechanism

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFIMMU.2017.00537

No evidence for the use of DIR, D-D fusions, chromosome 15 open reading frames or VH replacement in the peripheral repertoire was found on application of an improved algorithm, JointML, to 6329 human immunoglobulin H rearrangements.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFIMMU.2017.00537

High-throughput antibody sequencing reveals genetic evidence of global regulation of the naïve and memory repertoires that extends across individuals.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFIMMU.2017.00537

A mechanism for TCR sharing between T cell subsets and individuals revealed by pyrosequencing.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFIMMU.2017.00537

Analysis of the frequency and pattern of somatic mutations within nonproductively rearranged human variable heavy chain genes.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Di- and trinucleotide target preferences of somatic mutagenesis in normal and autoreactive B cells

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5424261

Codon bias targets mutation.

30 October 2018

1 reference

https://api.crossref.org/works/10.3389%2FFIMMU.2017.00537

Evolution of Ig DNA sequence to target specific base positions within codons for somatic hypermutation

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28539926

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.3389/FIMMU.2017.00537

1 reference

28 July 2017

1 reference

28 July 2017

1 reference