SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell Transcripts (Q37271866)

19 August 2017

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

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19 August 2017

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4

John R Mascola

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19 August 2017

5

Peter D Kwong

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19 August 2017

1

Chaim A Schramm

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19 August 2017

2

Zizhang Sheng

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19 August 2017

Zhenhai Zhang

3

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19 August 2017

Lawrence Shapiro

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6

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19 August 2017

21 September 2016

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19 August 2017

Frontiers in Immunology

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19 August 2017

7

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19 August 2017

372

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describes a project that uses

19 August 2017

ggplot2

object named as

ggplot2

2 references

10 June 2022

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=5030719

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

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

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Clonify: unseeded antibody lineage assignment from next-generation sequencing data

6 September 2017

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Optimization of the Solubility of HIV-1-Neutralizing Antibody 10E8 through Somatic Variation and Structure-Based Design

6 September 2017

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HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen

6 September 2017

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

6 September 2017

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Breakthrough therapies in B-cell non-Hodgkin lymphoma.

6 September 2017

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

6 September 2017

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Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design

6 September 2017

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Practical guidelines for B-cell receptor repertoire sequencing analysis

6 September 2017

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Utilities for High-Throughput Analysis of B-Cell Clonal Lineages.

6 September 2017

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New Member of the V1V2-Directed CAP256-VRC26 Lineage That Shows Increased Breadth and Exceptional Potency

6 September 2017

1 reference

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

6 September 2017

1 reference

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IMonitor: A Robust Pipeline for TCR and BCR Repertoire Analysis

6 September 2017

1 reference

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The analysis of clonal expansions in normal and autoimmune B cell repertoires

6 September 2017

1 reference

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HTJoinSolver: Human immunoglobulin VDJ partitioning using approximate dynamic programming constrained by conserved motifs

6 September 2017

1 reference

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

6 September 2017

1 reference

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Ability to develop broadly neutralizing HIV-1 antibodies is not restricted by the germline Ig gene repertoire

6 September 2017

1 reference

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B-cell receptor signaling in diffuse large B-cell lymphoma

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

VDJSeq-Solver: in silico V(D)J recombination detection tool

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

IMGT®, the international ImMunoGeneTics information system® 25 years on.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

Enhanced potency of a broadly neutralizing HIV-1 antibody in vitro improves protection against lentiviral infection in vivo

6 September 2017

1 reference

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Human responses to influenza vaccination show seroconversion signatures and convergent antibody rearrangements

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

Reconstructing a B-Cell Clonal Lineage. II. Mutation, Selection, and Affinity Maturation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

BEAST 2: a software platform for Bayesian evolutionary analysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

High-resolution antibody dynamics of vaccine-induced immune responses

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

The promise and challenge of high-throughput sequencing of the antibody repertoire.

6 September 2017

1 reference

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The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis

6 September 2017

1 reference

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De novo identification of VRC01 class HIV-1-neutralizing antibodies by next-generation sequencing of B-cell transcripts

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

Genetic measurement of memory B-cell recall using antibody repertoire sequencing

6 September 2017

1 reference

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IgBLAST: an immunoglobulin variable domain sequence analysis tool

6 September 2017

1 reference

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Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus

6 September 2017

1 reference

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Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

Lineage structure of the human antibody repertoire in response to influenza vaccination

6 September 2017

1 reference

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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

6 September 2017

1 reference

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Somatic Populations of PGT135-137 HIV-1-Neutralizing Antibodies Identified by 454 Pyrosequencing and Bioinformatics

6 September 2017

1 reference

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Monoclonal antibody therapeutics: history and future

6 September 2017

1 reference

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Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

Search and clustering orders of magnitude faster than BLAST

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

Correlates of protection induced by vaccination

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

ETE: a python Environment for Tree Exploration

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

BLAST : architecture and applications

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

Sequencing technologies - the next generation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

Biopython: freely available Python tools for computational molecular biology and bioinformatics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

Next-generation DNA sequencing

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

MUSCLE: multiple sequence alignment with high accuracy and high throughput

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

The Bioperl toolkit: Perl modules for the life sciences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

From T to B and back again: positive feedback in systemic autoimmune disease

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

A Hidden Markov Model approach to variation among sites in rate of evolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

Safety, pharmacokinetics and neutralization of the broadly neutralizing HIV-1 human monoclonal antibody VRC01 in healthy adults

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

Reconstructing and mining the B cell repertoire with ImmunediveRsity

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestors

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

IgTree: creating Immunoglobulin variable region gene lineage trees

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

Characterization of the human Ig heavy chain antigen binding complementarity determining region 3 using a newly developed software algorithm, JOINSOLVER.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030719

3 September 2018

Identifiers

DOI

10.3389/FIMMU.2016.00372

0 references

1 reference

19 August 2017

PubMed publication ID

27708645

1 reference