(Q36370482)

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Prospective estimation of recombination signal efficiency and identification of functional cryptic signals in the genome by statistical modeling

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scholarly article

1 reference

Europe PubMed Central

13 August 2017

Prospective estimation of recombination signal efficiency and identification of functional cryptic signals in the genome by statistical modeling (English)

1 reference

Europe PubMed Central

13 August 2017

0 references

Thomas B. Kepler

object named as

Thomas B Kepler

4

0 references

5

object named as

Garnett Kelsoe

1 reference

Europe PubMed Central

13 August 2017

author name string

Lindsay G Cowell

1

1 reference

Europe PubMed Central

13 August 2017

Marco Davila

2

1 reference

Europe PubMed Central

13 August 2017

Kaiyong Yang

3

1 reference

Europe PubMed Central

13 August 2017

language of work or name

0 references

publication date

1 January 2003

1 reference

Europe PubMed Central

13 August 2017

Journal of Experimental Medicine

1 reference

Europe PubMed Central

13 August 2017

197

1 reference

Europe PubMed Central

13 August 2017

207-220

1 reference

Europe PubMed Central

13 August 2017

2

1 reference

Europe PubMed Central

13 August 2017

From IMGT-ONTOLOGY CLASSIFICATION Axiom to IMGT standardized gene and allele nomenclature: for immunoglobulins (IG) and T cell receptors (TR).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Identification and utilization of arbitrary correlations in models of recombination signal sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

The "dispensable" portion of RAG2 is necessary for efficient V-to-DJ rearrangement during B and T cell development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Regulation of V(D)J recombination: a dominant role for promoter positioning in gene segment accessibility

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Targeted transposition by the V(D)J recombinase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

V(D)J-mediated translocations in lymphoid neoplasms: a functional assessment of genomic instability by cryptic sites.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Comparative genomics of the human and mouse T cell receptor loci

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

A role for secondary V(D)J recombination in oncogenic chromosomal translocations?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Transcription factor NF-kappa B regulates Ig lambda light chain gene rearrangement

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

The RAG proteins in V(D)J recombination: more than just a nuclease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Genetic modulation of T cell receptor gene segment usage during somatic recombination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

B-cell repertoire formation: role of the recombination signal sequence in non-random V segment utilization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Mechanisms that direct ordered assembly of T cell receptor beta locus V, D, and J gene segments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Recombination signal sequences restrict chromosomal V(D)J recombination beyond the 12/23 rule.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

The RAG proteins and V(D)J recombination: complexes, ends, and transposition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Rearrangement of immunoglobulin genes in shark germ cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

A highly ordered structure in V(D)J recombination cleavage complexes is facilitated by HMG1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Mechanistic basis for coding end sequence effects in the initiation of V(D)J recombination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

The RAG1 homeodomain recruits HMG1 and HMG2 to facilitate recombination signal sequence binding and to enhance the intrinsic DNA-bending activity of RAG1-RAG2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Analysis of mice with single and multiple copies of transgenes reveals a novel arrangement for the lambda5-VpreB1 locus control region

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

RAG reexpression and DNA recombination at T cell receptor loci in peripheral CD4+ T cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

V(D)J recombination signal recognition: distinct, overlapping DNA-protein contacts in complexes containing RAG1 with and without RAG2.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Sequence of the spacer in the recombination signal sequence affects V(D)J rearrangement frequency and correlates with nonrandom Vkappa usage in vivo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Cryptic signals and the fidelity of V(D)J joining

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Construction of a representative cDNA library from prostatic intraepithelial neoplasia

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

RAG1 mediates signal sequence recognition and recruitment of RAG2 in V(D)J recombination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Conservation of sequence in recombination signal sequence spacers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Tandemly repeated transgenes of the human minisatellite MS32 (D1S8), with novel mouse gamma satellite integration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

An active v-abl protein tyrosine kinase blocks immunoglobulin light-chain gene rearrangement

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Transcripts from opposite strands of gamma satellite DNA are differentially expressed during mouse development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

A modified tetracycline-regulated system provides autoregulatory, inducible gene expression in cultured cells and transgenic mice

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Use of the ‘Perceptron’ algorithm to distinguish translational initiation sites inE. coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Somatic generation of antibody diversity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Information content of binding sites on nucleotide sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

The V(D)J recombination activating gene, RAG-1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Mouse kappa light-chain recombination signal sequences mediate recombination more frequently than do those of lambda light chain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Sequences at the somatic recombination sites of immunoglobulin light-chain genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Essential residues in V(D)J recombination signals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

Mouse VH7183 recombination signal sequences mediate recombination more frequently than those of VHJ558.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

30 September 2017

IMGT, the international ImMunoGeneTics database: a high-quality information system for comparative immunogenetics and immunology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

28 June 2018

Individual V(H) promoters vary in strength, but the frequency of rearrangement of those V(H) genes does not correlate with promoter strength nor enhancer-independence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

28 June 2018

V(H) gene replacement occurs in the spleen and bone marrow of non-autoimmune quasi-monoclonal mice

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

28 June 2018

DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

28 June 2018

Molecular mechanisms involved in receptor editing at the Ig heavy chain locus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

28 June 2018

A statistical model for locating regulatory regions in genomic DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

28 June 2018

Coding end sequence can markedly affect the initiation of V(D)J recombination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

28 June 2018

Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

28 June 2018

Extrachromosomal DNA substrates in pre-B cells undergo inversion or deletion at immunoglobulin V-(D)-J joining signals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

28 June 2018

Two pairs of recombination signals are sufficient to cause immunoglobulin V-(D)-J joining

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

28 June 2018

Structure of the T15 VH gene subfamily: identification of immunoglobulin gene promotor homologies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

28 June 2018

Recombination between an expressed immunoglobulin heavy-chain gene and a germline variable gene segment in a Ly 1+ B-cell lymphoma

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

28 June 2018

Consensus patterns in DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

28 June 2018

Evolution and distribution of (GT)n repetitive sequences in mammalian genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

28 June 2018

Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

28 June 2018

The cleavage efficiency of the human immunoglobulin heavy chain VH elements by the RAG complex: implications for the immune repertoire

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

21 September 2018

Promoter sequences and algorithmical methods for identifying them.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

21 September 2018

Phase Variation: Evolution of a Controlling Element

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

21 September 2018

T cell receptor DJ but not VDJ rearrangement within a recombination substrate introduced into a pre-B cell line.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

21 September 2018

The homeodomain region of Rag-1 reveals the parallel mechanisms of bacterial and V(D)J recombination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2193808

21 October 2018

Rearrangement of upstream DH and VH genes to a rearranged immunoglobulin variable region gene inserted into the DQ52-JH region of the immunoglobulin heavy chain locus

1 reference

https://api.crossref.org/works/10.1084%2FJEM.20020250

21 January 2018

V(H) replacement is unlikely to contribute significantly to receptor editing due to an ineffectual embedded recombination signal sequence

1 reference

https://pubmed.ncbi.nlm.nih.gov/12538660

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

V(D)J recombinase activity in a subset of germinal center B lymphocytes

1 reference

https://pubmed.ncbi.nlm.nih.gov/12538660

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Deletion and editing of B cells that express antibodies to DNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/12538660

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Activation of immunoglobulin kappa gene rearrangement correlates with induction of germline kappa gene transcription

1 reference

https://pubmed.ncbi.nlm.nih.gov/12538660

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Immunoglobulin heavy chain gene replacement: a mechanism of receptor editing

1 reference

https://pubmed.ncbi.nlm.nih.gov/12538660

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mouse major (gamma) satellite DNA is highly conserved and organized into extremely long tandem arrays: implications for recombination between nonhomologous chromosomes

1 reference

https://pubmed.ncbi.nlm.nih.gov/12538660

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

V(D)J recombination: a functional definition of the joining signals

1 reference

https://pubmed.ncbi.nlm.nih.gov/12538660

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Double-strand signal sequence breaks in V(D)J recombination are blunt, 5'-phosphorylated, RAG-dependent, and cell cycle regulated

1 reference

https://pubmed.ncbi.nlm.nih.gov/12538660

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1084/JEM.20020250

1 reference

Europe PubMed Central

13 August 2017

1 reference

Europe PubMed Central

13 August 2017

1 reference

Europe PubMed Central

13 August 2017

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