(Q31092433)

2 November 2017

repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data (English)

1 reference

2 November 2017

1 reference

Yuval Elhanati

1

1 reference

2 November 2017

Quentin Marcou

series ordinal

2

1 reference

2 November 2017

Thierry Mora

series ordinal

3

1 reference

2 November 2017

Aleksandra M Walczak

series ordinal

4

1 reference

2 November 2017

language of work or name

English

0 references

publication date

26 February 2016

1 reference

2 November 2017

9

1 reference

based on heuristic

inferred from page(s)

published in

Bioinformatics

1 reference

2 November 2017

32

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2 November 2017

13

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2 November 2017

1943-1951

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Creative Commons Attribution-NonCommercial 4.0 International

2 November 2017

start time

12 October 2016

1 reference

April 2023 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

Inferring processes underlying B-cell repertoire diversity

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

Assigning and visualizing germline genes in antibody repertoires

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

Distinctive properties of identical twins' TCR repertoires revealed by high-throughput sequencing.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

Huge Overlap of Individual TCR Beta Repertoires.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

Immunosequencing: applications of immune repertoire deep sequencing

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

IgBLAST: an immunoglobulin variable domain sequence analysis tool

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

Statistical inference of the generation probability of T-cell receptors from sequence repertoires

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

Next generation sequencing for TCR repertoire profiling: platform-specific features and correction algorithms.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

V(D)J recombination: mechanisms of initiation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

Recombination centres and the orchestration of V(D)J recombination

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

SoDA2: a Hidden Markov Model approach for identification of immunoglobulin rearrangements

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

Role for rearranged variable gene segments in directing secondary T cell receptor alpha recombination.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

Unraveling V(D)J recombination; insights into gene regulation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

Repertoires of antigen receptors in Tdt congenitally deficient mice

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4920122

MiXCR: software for comprehensive adaptive immunity profiling.

28 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW112

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/10.1093%2FBIOINFORMATICS%2FBTW112

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW112

NKT and MAIT invariant TCRα sequences can be produced efficiently by VJ gene recombination

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW112

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/10.1093%2FBIOINFORMATICS%2FBTW112

Predicting protein functions using incomplete hierarchical labels

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW112

Towards error-free profiling of immune repertoires.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW112

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW112

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.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW112

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW112

A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW112

The Targeting of Somatic Hypermutation Closely Resembles That of Meiotic Mutation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW112

Base-specific sequences that bias somatic hypermutation deduced by analysis of out-of-frame human IgVH 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=4920122

Ordered and coordinated rearrangement of the TCR alpha locus: role of secondary rearrangement in thymic selection

25 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27153709

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A model for TCR gene segment use

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27153709

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIOINFORMATICS/BTW112

1 reference

journals/bioinformatics/ElhanatiMMW16

2 November 2017

1 reference

1 reference

DBLP Dataset 2021-01-02

28 January 2021

0 references

1 reference

2 November 2017

PubMed publication ID

27153709

1 reference