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Items: 1 to 20 of 89

1.

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

Volpe JM, Cowell LG, Kepler TB.

Bioinformatics. 2006 Feb 15;22(4):438-44. Epub 2005 Dec 15.

2.

GARD: a genetic algorithm for recombination detection.

Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD.

Bioinformatics. 2006 Dec 15;22(24):3096-8. Epub 2006 Nov 16.

3.

Haplotypes histories as pathways of recombinations.

El-Mabrouk N, Labuda D.

Bioinformatics. 2004 Aug 12;20(12):1836-41. Epub 2004 Feb 26.

4.

Detecting recombination with MCMC.

Husmeier D, McGuire G.

Bioinformatics. 2002;18 Suppl 1:S345-53.

5.

A new antigen receptor gene family that undergoes rearrangement and extensive somatic diversification in sharks.

Greenberg AS, Avila D, Hughes M, Hughes A, McKinney EC, Flajnik MF.

Nature. 1995 Mar 9;374(6518):168-73.

PMID:
7877689
6.

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

Gaëta BA, Malming HR, Jackson KJ, Bain ME, Wilson P, Collins AM.

Bioinformatics. 2007 Jul 1;23(13):1580-7. Epub 2007 Apr 26.

7.

Antigen-receptor genes of the agnathan lamprey are assembled by a process involving copy choice.

Nagawa F, Kishishita N, Shimizu K, Hirose S, Miyoshi M, Nezu J, Nishimura T, Nishizumi H, Takahashi Y, Hashimoto S, Takeuchi M, Miyajima A, Takemori T, Otsuka AJ, Sakano H.

Nat Immunol. 2007 Feb;8(2):206-13. Epub 2006 Dec 24.

PMID:
17187071
8.

Mechanisms of antigen receptor evolution.

Eason DD, Cannon JP, Haire RN, Rast JP, Ostrov DA, Litman GW.

Semin Immunol. 2004 Aug;16(4):215-26. Review.

PMID:
15522620
9.
11.

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

Munshaw S, Kepler TB.

Bioinformatics. 2010 Apr 1;26(7):867-72. doi: 10.1093/bioinformatics/btq056. Epub 2010 Feb 9.

12.

Efficient filtering methods for clustering cDNAs with spliced sequence alignment.

Shibuya T, Kashima H, Konagaya A.

Bioinformatics. 2004 Jan 1;20(1):29-39.

13.

IMGT/PhyloGene: an on-line tool for comparative analysis of immunoglobulin and T cell receptor genes.

Elemento O, Lefranc MP.

Dev Comp Immunol. 2003 Oct;27(9):763-79.

PMID:
12818634
14.

IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs.

Yousfi Monod M, Giudicelli V, Chaume D, Lefranc MP.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i379-85.

15.

Homology search for genes.

Cui X, Vinar T, Brejová B, Shasha D, Li M.

Bioinformatics. 2007 Jul 1;23(13):i97-103.

16.

Efficient multiple genome alignment.

Höhl M, Kurtz S, Ohlebusch E.

Bioinformatics. 2002;18 Suppl 1:S312-20.

17.

Using bioinformatics tools for the sequence analysis of immunoglobulins and T cell receptors.

Lefranc MP.

Curr Protoc Immunol. 2006 Mar;Appendix 1:Appendix 1W. doi: 10.1002/0471142735.ima01ws71.

PMID:
18432961
18.

A probabilistic measure for alignment-free sequence comparison.

Pham TD, Zuegg J.

Bioinformatics. 2004 Dec 12;20(18):3455-61. Epub 2004 Jul 22.

19.

Pattern locator: a new tool for finding local sequence patterns in genomic DNA sequences.

Mrázek J, Xie S.

Bioinformatics. 2006 Dec 15;22(24):3099-100. Epub 2006 Nov 8.

20.

Optimal, efficient reconstruction of phylogenetic networks with constrained recombination.

Gusfield D, Eddhu S, Langley C.

J Bioinform Comput Biol. 2004 Mar;2(1):173-213.

PMID:
15272438
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