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For: Cowell LG, Davila M, Kepler TB, Kelsoe G. Identification and utilization of arbitrary correlations in models of recombination signal sequences. Genome Biol 2002;3:RESEARCH0072. [PMID: 12537561 PMCID: PMC151174 DOI: 10.1186/gb-2002-3-12-research0072] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2002] [Revised: 09/04/2002] [Accepted: 10/10/2002] [Indexed: 01/26/2023]  Open
Number Cited by Other Article(s)
1
Jackson KJ. RAGging on recombination signal sequence strength for diffusion-mediated recombination. Immunol Cell Biol 2024. [PMID: 38973226 DOI: 10.1111/imcb.12803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
2
Zhang Y, Li X, Ba Z, Lou J, Gaertner KE, Zhu T, Lin X, Ye AY, Alt FW, Hu H. Molecular basis for differential Igk versus Igh V(D)J joining mechanisms. Nature 2024;630:189-197. [PMID: 38811728 PMCID: PMC11153149 DOI: 10.1038/s41586-024-07477-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/26/2024] [Indexed: 05/31/2024]
3
Früh SP, Früh MA, Kaufer BB, Göbel TW. Unraveling the chicken T cell repertoire with enhanced genome annotation. Front Immunol 2024;15:1359169. [PMID: 38550579 PMCID: PMC10972964 DOI: 10.3389/fimmu.2024.1359169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/23/2024] [Indexed: 04/02/2024]  Open
4
Hoolehan W, Harris JC, Byrum JN, Simpson DA, Rodgers K. An updated definition of V(D)J recombination signal sequences revealed by high-throughput recombination assays. Nucleic Acids Res 2022;50:11696-11711. [PMID: 36370096 PMCID: PMC9723617 DOI: 10.1093/nar/gkac1038] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/13/2022]  Open
5
Different classes of genomic inserts contribute to human antibody diversity. Proc Natl Acad Sci U S A 2022;119:e2205470119. [PMID: 36037353 PMCID: PMC9457163 DOI: 10.1073/pnas.2205470119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
6
Shinoda K, Maman Y, Canela A, Schatz DG, Livak F, Nussenzweig A. Intra-Vκ Cluster Recombination Shapes the Ig Kappa Locus Repertoire. Cell Rep 2020;29:4471-4481.e6. [PMID: 31875554 DOI: 10.1016/j.celrep.2019.11.088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/04/2019] [Accepted: 11/21/2019] [Indexed: 10/25/2022]  Open
7
Hirokawa S, Chure G, Belliveau NM, Lovely GA, Anaya M, Schatz DG, Baltimore D, Phillips R. Sequence-dependent dynamics of synthetic and endogenous RSSs in V(D)J recombination. Nucleic Acids Res 2020;48:6726-6739. [PMID: 32449932 PMCID: PMC7337519 DOI: 10.1093/nar/gkaa418] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/20/2020] [Accepted: 05/07/2020] [Indexed: 12/25/2022]  Open
8
Mika J, Kabacik S, Badie C, Polanska J, Candéias SM. Germline DNA Retention in Murine and Human Rearranged T Cell Receptor Gene Coding Joints: Alternative Recombination Signal Sequences and V(D)J Recombinase Errors. Front Immunol 2019;10:2637. [PMID: 31781122 PMCID: PMC6857471 DOI: 10.3389/fimmu.2019.02637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/24/2019] [Indexed: 12/02/2022]  Open
9
Patil P, Cieslak A, Bernhart SH, Toprak UH, Wagener R, López C, Wiehle L, Bens S, Altmüller J, Franitza M, Scholz I, Jayne S, Ahearne MJ, Scheffold A, Jebaraj BMC, Schneider C, Costa D, Braun T, Schrader A, Campo E, Dyer MJS, Nürnberg P, Dürig J, Johansson P, Böttcher S, Schlesner M, Herling M, Stilgenbauer S, Macintyre E, Siebert R. Reconstruction of rearranged T-cell receptor loci by whole genome and transcriptome sequencing gives insights into the initial steps of T-cell prolymphocytic leukemia. Genes Chromosomes Cancer 2019;59:261-267. [PMID: 31677197 DOI: 10.1002/gcc.22821] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 12/20/2022]  Open
10
Finney J, Yang G, Kuraoka M, Song S, Nojima T, Verkoczy L, Kitamura D, Haynes BF, Kelsoe G. Cross-Reactivity to Kynureninase Tolerizes B Cells That Express the HIV-1 Broadly Neutralizing Antibody 2F5. THE JOURNAL OF IMMUNOLOGY 2019;203:3268-3281. [PMID: 31732530 DOI: 10.4049/jimmunol.1900069] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 10/11/2019] [Indexed: 11/19/2022]
11
Zhang Y, Zhang X, Ba Z, Liang Z, Dring EW, Hu H, Lou J, Kyritsis N, Zurita J, Shamim MS, Presser Aiden A, Lieberman Aiden E, Alt FW. The fundamental role of chromatin loop extrusion in physiological V(D)J recombination. Nature 2019;573:600-604. [PMID: 31511698 PMCID: PMC6867615 DOI: 10.1038/s41586-019-1547-y] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/12/2019] [Indexed: 11/24/2022]
12
Matheson LS, Bolland DJ, Chovanec P, Krueger F, Andrews S, Koohy H, Corcoran AE. Local Chromatin Features Including PU.1 and IKAROS Binding and H3K4 Methylation Shape the Repertoire of Immunoglobulin Kappa Genes Chosen for V(D)J Recombination. Front Immunol 2017;8:1550. [PMID: 29204143 PMCID: PMC5698286 DOI: 10.3389/fimmu.2017.01550] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 10/31/2017] [Indexed: 11/25/2022]  Open
13
Dong Y, Wu C, Zhao X, Zhang P, Zhang H, Zheng M, Li S, Jiao J, Yu X, Lv Z, Ji Y. Epigenetic modifications of the VH region after DJH recombination in Pro-B cells. Immunology 2017;152:218-231. [PMID: 28502113 DOI: 10.1111/imm.12758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 04/27/2017] [Accepted: 05/08/2017] [Indexed: 12/19/2022]  Open
14
Rommel PC, Oliveira TY, Nussenzweig MC, Robbiani DF. RAG1/2 induces genomic insertions by mobilizing DNA into RAG1/2-independent breaks. J Exp Med 2017;214:815-831. [PMID: 28179379 PMCID: PMC5339680 DOI: 10.1084/jem.20161638] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/09/2016] [Accepted: 12/12/2016] [Indexed: 11/23/2022]  Open
15
Passagem-Santos D, Bonnet M, Sobral D, Trancoso I, Silva JG, Barreto VM, Athanasiadis A, Demengeot J, Pereira-Leal JB. RAG Recombinase as a Selective Pressure for Genome Evolution. Genome Biol Evol 2016;8:3364-3376. [PMID: 27979968 PMCID: PMC5203794 DOI: 10.1093/gbe/evw261] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
16
Regulated large-scale nucleosome density patterns and precise nucleosome positioning correlate with V(D)J recombination. Proc Natl Acad Sci U S A 2016;113:E6427-E6436. [PMID: 27698124 DOI: 10.1073/pnas.1605543113] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]  Open
17
Canela A, Sridharan S, Sciascia N, Tubbs A, Meltzer P, Sleckman BP, Nussenzweig A. DNA Breaks and End Resection Measured Genome-wide by End Sequencing. Mol Cell 2016;63:898-911. [PMID: 27477910 PMCID: PMC6299834 DOI: 10.1016/j.molcel.2016.06.034] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/14/2016] [Accepted: 06/21/2016] [Indexed: 12/18/2022]
18
Dong Y, Liu F, Wu C, Li S, Zhao X, Zhang P, Jiao J, Yu X, Ji Y, Zhang M. Illegitimate RAG-mediated recombination events are involved in IKZF1 Δ3-6 deletion in BCR-ABL1 lymphoblastic leukaemia. Clin Exp Immunol 2016;185:320-31. [PMID: 27198500 DOI: 10.1111/cei.12812] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/14/2016] [Accepted: 03/17/2016] [Indexed: 12/29/2022]  Open
19
Maman Y, Teng G, Seth R, Kleinstein SH, Schatz DG. RAG1 targeting in the genome is dominated by chromatin interactions mediated by the non-core regions of RAG1 and RAG2. Nucleic Acids Res 2016;44:9624-9637. [PMID: 27436288 PMCID: PMC5175335 DOI: 10.1093/nar/gkw633] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/16/2016] [Accepted: 07/02/2016] [Indexed: 02/01/2023]  Open
20
Bolland DJ, Koohy H, Wood AL, Matheson LS, Krueger F, Stubbington MJT, Baizan-Edge A, Chovanec P, Stubbs BA, Tabbada K, Andrews SR, Spivakov M, Corcoran AE. Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination. Cell Rep 2016;15:2475-87. [PMID: 27264181 PMCID: PMC4914699 DOI: 10.1016/j.celrep.2016.05.020] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/01/2016] [Accepted: 05/02/2016] [Indexed: 12/02/2022]  Open
21
Mijušković M, Chou YF, Gigi V, Lindsay CR, Shestova O, Lewis SM, Roth DB. Off-Target V(D)J Recombination Drives Lymphomagenesis and Is Escalated by Loss of the Rag2 C Terminus. Cell Rep 2015;12:1842-52. [PMID: 26365182 DOI: 10.1016/j.celrep.2015.08.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/07/2015] [Accepted: 08/08/2015] [Indexed: 11/29/2022]  Open
22
Chen C, Bartenhagen C, Gombert M, Okpanyi V, Binder V, Röttgers S, Bradtke J, Teigler-Schlegel A, Harbott J, Ginzel S, Thiele R, Husemann P, Krell PF, Borkhardt A, Dugas M, Hu J, Fischer U. Next-generation-sequencing of recurrent childhood high hyperdiploid acute lymphoblastic leukemia reveals mutations typically associated with high risk patients. Leuk Res 2015;39:990-1001. [DOI: 10.1016/j.leukres.2015.06.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 06/08/2015] [Accepted: 06/10/2015] [Indexed: 01/07/2023]
23
Recruitment of RAG1 and RAG2 to Chromatinized DNA during V(D)J Recombination. Mol Cell Biol 2015;35:3701-13. [PMID: 26303526 DOI: 10.1128/mcb.00219-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 06/09/2015] [Indexed: 11/20/2022]  Open
24
Teng G, Maman Y, Resch W, Kim M, Yamane A, Qian J, Kieffer-Kwon KR, Mandal M, Ji Y, Meffre E, Clark MR, Cowell LG, Casellas R, Schatz DG. RAG Represents a Widespread Threat to the Lymphocyte Genome. Cell 2015;162:751-65. [PMID: 26234156 PMCID: PMC4537821 DOI: 10.1016/j.cell.2015.07.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 04/14/2015] [Accepted: 06/02/2015] [Indexed: 11/26/2022]
25
Regulation and Evolution of the RAG Recombinase. Adv Immunol 2015;128:1-39. [PMID: 26477364 DOI: 10.1016/bs.ai.2015.07.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
26
The proximal J kappa germline-transcript promoter facilitates receptor editing through control of ordered recombination. PLoS One 2015;10:e0113824. [PMID: 25559567 PMCID: PMC4283955 DOI: 10.1371/journal.pone.0113824] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 10/31/2014] [Indexed: 12/31/2022]  Open
27
Parkinson NJ, Roddis M, Ferneyhough B, Zhang G, Marsden AJ, Maslau S, Sanchez-Pearson Y, Barthlott T, Humphreys IR, Ladell K, Price DA, Ponting CP, Hollander G, Fischer MD. Violation of the 12/23 rule of genomic V(D)J recombination is common in lymphocytes. Genome Res 2014;25:226-34. [PMID: 25367293 PMCID: PMC4315296 DOI: 10.1101/gr.179770.114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
28
PTEN microdeletions in T-cell acute lymphoblastic leukemia are caused by illegitimate RAG-mediated recombination events. Blood 2014;124:567-78. [PMID: 24904117 DOI: 10.1182/blood-2014-03-562751] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
29
Illegitimate V(D)J recombination-mediated deletions in Notch1 and Bcl11b are not sufficient for extensive clonal expansion and show minimal age or sex bias in frequency or junctional processing. Mutat Res 2014;761:34-48. [PMID: 24530429 DOI: 10.1016/j.mrfmmm.2014.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 12/23/2013] [Accepted: 01/28/2014] [Indexed: 01/22/2023]
30
Choi NM, Loguercio S, Verma-Gaur J, Degner SC, Torkamani A, Su AI, Oltz EM, Artyomov M, Feeney AJ. Deep sequencing of the murine IgH repertoire reveals complex regulation of nonrandom V gene rearrangement frequencies. THE JOURNAL OF IMMUNOLOGY 2013;191:2393-402. [PMID: 23898036 DOI: 10.4049/jimmunol.1301279] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
31
Trancoso I, Bonnet M, Gardner R, Carneiro J, Barreto VM, Demengeot J, Sarmento LM. A Novel Quantitative Fluorescent Reporter Assay for RAG Targets and RAG Activity. Front Immunol 2013;4:110. [PMID: 23720659 PMCID: PMC3655321 DOI: 10.3389/fimmu.2013.00110] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 04/27/2013] [Indexed: 12/11/2022]  Open
32
Chen C, Bartenhagen C, Gombert M, Okpanyi V, Binder V, Röttgers S, Bradtke J, Teigler-Schlegel A, Harbott J, Ginzel S, Thiele R, Fischer U, Dugas M, Hu J, Borkhardt A. Next-generation-sequencing-based risk stratification and identification of new genes involved in structural and sequence variations in near haploid lymphoblastic leukemia. Genes Chromosomes Cancer 2013;52:564-79. [DOI: 10.1002/gcc.22054] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/29/2013] [Indexed: 01/10/2023]  Open
33
Merelli I, Guffanti A, Fabbri M, Cocito A, Furia L, Grazini U, Bonnal RJ, Milanesi L, McBlane F. RSSsite: a reference database and prediction tool for the identification of cryptic Recombination Signal Sequences in human and murine genomes. Nucleic Acids Res 2010;38:W262-7. [PMID: 20478831 PMCID: PMC2896083 DOI: 10.1093/nar/gkq391] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
34
Aberrantly resolved RAG-mediated DNA breaks in Atm-deficient lymphocytes target chromosomal breakpoints in cis. Proc Natl Acad Sci U S A 2009;106:18339-44. [PMID: 19820166 DOI: 10.1073/pnas.0902545106] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]  Open
35
Lieberman AE, Kuraoka M, Davila M, Kelsoe G, Cowell LG. Conserved cryptic recombination signals in Vkappa gene segments are cleaved in small pre-B cells. BMC Immunol 2009;10:37. [PMID: 19555491 PMCID: PMC2711918 DOI: 10.1186/1471-2172-10-37] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Accepted: 06/25/2009] [Indexed: 12/01/2022]  Open
36
Lange MD, Waldbieser GC, Lobb CJ. Patterns of receptor revision in the immunoglobulin heavy chains of a teleost fish. THE JOURNAL OF IMMUNOLOGY 2009;182:5605-22. [PMID: 19380808 DOI: 10.4049/jimmunol.0801013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
37
Characterization of arrangement and expression of the T cell receptor gamma locus in the sandbar shark. Proc Natl Acad Sci U S A 2009;106:8591-6. [PMID: 19439654 DOI: 10.1073/pnas.0811283106] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
38
Leaky severe combined immunodeficiency and aberrant DNA rearrangements due to a hypomorphic RAG1 mutation. Blood 2009;113:2965-75. [PMID: 19126872 DOI: 10.1182/blood-2008-07-165167] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
39
Levitsky VG, Ignatieva EV, Ananko EA, Turnaev II, Merkulova TI, Kolchanov NA, Hodgman TC. Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions. BMC Bioinformatics 2007;8:481. [PMID: 18093302 PMCID: PMC2265442 DOI: 10.1186/1471-2105-8-481] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2007] [Accepted: 12/19/2007] [Indexed: 12/22/2022]  Open
40
Davila M, Liu F, Cowell LG, Lieberman AE, Heikamp E, Patel A, Kelsoe G. Multiple, conserved cryptic recombination signals in VH gene segments: detection of cleavage products only in pro B cells. ACTA ACUST UNITED AC 2007;204:3195-208. [PMID: 18056287 PMCID: PMC2150985 DOI: 10.1084/jem.20071224] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
41
Haynes MR, Wu GE. Gene discovery at the human T-cell receptor alpha/delta locus. Immunogenetics 2006;59:109-21. [PMID: 17165047 DOI: 10.1007/s00251-006-0165-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Accepted: 10/03/2006] [Indexed: 10/23/2022]
42
Almeida JS, Vinga S. Computing distribution of scale independent motifs in biological sequences. Algorithms Mol Biol 2006;1:18. [PMID: 17049089 PMCID: PMC1630425 DOI: 10.1186/1748-7188-1-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Accepted: 10/18/2006] [Indexed: 11/10/2022]  Open
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Murray JM, O’Neill JP, Messier T, Rivers J, Walker VE, McGonagle B, Trombley L, Cowell LG, Kelsoe G, McBlane F, Finette BA. V(D)J recombinase-mediated processing of coding junctions at cryptic recombination signal sequences in peripheral T cells during human development. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2006;177:5393-404. [PMID: 17015725 PMCID: PMC1937029 DOI: 10.4049/jimmunol.177.8.5393] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Touvrey C, Cowell LG, Lieberman AE, Marche PN, Jouvin-Marche E, Candéias SM. Reassignment of the murine 3'TRDD1 recombination signal sequence. Immunogenetics 2006;58:895-903. [PMID: 17021860 PMCID: PMC1876511 DOI: 10.1007/s00251-006-0150-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2006] [Accepted: 08/03/2006] [Indexed: 11/30/2022]
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Marculescu R, Vanura K, Montpellier B, Roulland S, Le T, Navarro JM, Jäger U, McBlane F, Nadel B. Recombinase, chromosomal translocations and lymphoid neoplasia: targeting mistakes and repair failures. DNA Repair (Amst) 2006;5:1246-58. [PMID: 16798110 DOI: 10.1016/j.dnarep.2006.05.015] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Larijani M, Chen S, Cunningham LA, Volpe JM, Cowell LG, Lewis SM, Wu GE. The recombination difference between mouse kappa and lambda segments is mediated by a pair-wise regulation mechanism. Mol Immunol 2005;43:870-81. [PMID: 16054218 DOI: 10.1016/j.molimm.2005.06.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Indexed: 10/25/2022]
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Danilova N. Analysis of recombination signal sequences in zebrafish. Mol Immunol 2005;42:1243-9. [PMID: 15829313 DOI: 10.1016/j.molimm.2004.11.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2004] [Indexed: 11/28/2022]
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Cowell LG, Davila M, Ramsden D, Kelsoe G. Computational tools for understanding sequence variability in recombination signals. Immunol Rev 2004;200:57-69. [PMID: 15242396 DOI: 10.1111/j.0105-2896.2004.00171.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Lee AI, Fugmann SD, Cowell LG, Ptaszek LM, Kelsoe G, Schatz DG. A functional analysis of the spacer of V(D)J recombination signal sequences. PLoS Biol 2003;1:E1. [PMID: 14551903 PMCID: PMC212687 DOI: 10.1371/journal.pbio.0000001] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2003] [Accepted: 07/10/2003] [Indexed: 11/18/2022]  Open
50
Cowell LG, Davila M, Yang K, Kepler TB, Kelsoe G. Prospective estimation of recombination signal efficiency and identification of functional cryptic signals in the genome by statistical modeling. J Exp Med 2003;197:207-20. [PMID: 12538660 PMCID: PMC2193808 DOI: 10.1084/jem.20020250] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2002] [Accepted: 12/05/2002] [Indexed: 12/03/2022]  Open
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