메뉴 건너뛰기




Volumn 31, Issue 12, 2015, Pages i53-i61

Ig Repertoire Constructor: A novel algorithm for antibody repertoire construction and immunoproteogenomics analysis

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; IMMUNOGLOBULIN; PEPTIDE FRAGMENT; PROTEOME;

EID: 84931099165     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv238     Document Type: Conference Paper
Times cited : (37)

References (49)
  • 1
    • 79961160227 scopus 로고    scopus 로고
    • High-resolution description of antibody heavy-chain repertoires in humans
    • Arnaout R., et al. (2011). High-resolution description of antibody heavy-chain repertoires in humans. PloS One, 6, e22365
    • (2011) Plos One , vol.6 , pp. e22365
    • Arnaout, R.1
  • 2
    • 57449097186 scopus 로고    scopus 로고
    • Automated de novo protein sequencing of monoclonal antibodies
    • Bandeira N., et al. (2008). Automated de novo protein sequencing of monoclonal antibodies. Nat. Biotechnol., 26, 1336-1338
    • (2008) Nat. Biotechnol , vol.26 , pp. 1336-1338
    • Bandeira, N.1
  • 3
    • 84860771820 scopus 로고    scopus 로고
    • Spades: A new genome assembly algorithm and its applications to single-cell sequencing
    • Bankevich A., et al. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol., 19, 455-477
    • (2012) J. Comput. Biol , vol.19 , pp. 455-477
    • Bankevich, A.1
  • 4
    • 0032728081 scopus 로고    scopus 로고
    • Clustering gene expression patterns
    • Ben-Dor A., et al. (1999). Clustering gene expression patterns. J. Comp. Biol., 6, 281-297
    • (1999) J. Comp. Biol , vol.6 , pp. 281-297
    • Ben-Dor, A.1
  • 5
    • 84926350458 scopus 로고    scopus 로고
    • Immunoglobulin classification using the colored antibody graph
    • RECOMB 2015 Springer International Publishing
    • Bonissone S. and Pevzner P.A. (2015). Immunoglobulin Classification Using the Colored Antibody Graph. Lecture Notes in Computer Science, RECOMB 2015, Springer International Publishing, pp. 44-59
    • (2015) Lecture Notes in Computer Science , pp. 44-59
    • Bonissone, S.1    Pevzner, P.A.2
  • 6
    • 84901253129 scopus 로고    scopus 로고
    • Proteomic identification of monoclonal antibodies from serum
    • Boutz D.R., et al. (2014). Proteomic identification of monoclonal antibodies from serum. Anal. Chem., 86, 4758-4766
    • (2014) Anal. Chem , vol.86 , pp. 4758-4766
    • Boutz, D.R.1
  • 7
    • 48449094247 scopus 로고    scopus 로고
    • Imgt/v-quest: The highly customized and integrated system for ig and tr standardized vj and vdj sequence analysis
    • Brochet X., et al. (2008). IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized VJ and VDJ sequence analysis. Nucleic Acids Res., 36 (Suppl. 2) , W503-W508
    • (2008) Nucleic Acids Res , vol.36 , pp. W503-W508
    • Brochet, X.1
  • 8
    • 0017280292 scopus 로고
    • A modification of jerne's theory of antibody production using the concept of clonal selection
    • Burnet F.M. (1976). A modification of Jerne's theory of antibody production using the concept of clonal selection. CA Cancer J. Clin., 26, 119-121
    • (1976) CA Cancer J. Clin , vol.26 , pp. 119-121
    • Burnet, F.M.1
  • 9
    • 79251500018 scopus 로고    scopus 로고
    • Resurrection of a clinical antibody: Template proteogenomic de novo proteomic sequencing and reverse engineering of an anti-lymphotoxin-a antibody
    • Castellana N., et al. (2011). Resurrection of a clinical antibody: template proteogenomic de novo proteomic sequencing and reverse engineering of an anti-lymphotoxin-a antibody. Proteomics, 11, 395-405
    • (2011) Proteomics , vol.11 , pp. 395-405
    • Castellana, N.1
  • 10
    • 84860381828 scopus 로고    scopus 로고
    • A proteomics approach for the identification and cloning of monoclonal antibodies fromserum
    • Cheung W.C., et al. (2012). A proteomics approach for the identification and cloning of monoclonal antibodies fromserum. Nat. Biotechnol., 30, 447-452
    • (2012) Nat. Biotechnol , vol.30 , pp. 447-452
    • Cheung, W.C.1
  • 11
    • 70349318211 scopus 로고    scopus 로고
    • The impact of retrotransposons on human genome evolution
    • Cordaux R. and Batzer M.A. (2009). The impact of retrotransposons on human genome evolution. Nat. Rev. Genet., 10, 691-703
    • (2009) Nat. Rev. Genet , vol.10 , pp. 691-703
    • Cordaux, R.1    Batzer, M.A.2
  • 12
    • 70349648171 scopus 로고    scopus 로고
    • Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing
    • Freeman J., et al. (2009). Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res., 19, 1817-1824
    • (2009) Genome Res , vol.19 , pp. 1817-1824
    • Freeman, J.1
  • 13
    • 34547840205 scopus 로고    scopus 로고
    • Ihmmune-align: Hidden markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences
    • Gaëta B.A., et al. (2007). iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences. Bioinformatics, 23, 1580-1587
    • (2007) Bioinformatics , vol.23 , pp. 1580-1587
    • Gaëta, B.A.1
  • 16
    • 84893831480 scopus 로고    scopus 로고
    • The promise and challenge of high-throughput sequencing of the antibody repertoire
    • Georgiou G., et al. (2014). The promise and challenge of high-throughput sequencing of the antibody repertoire. Nat. Biotechnol., 32, 158-168
    • (2014) Nat. Biotechnol , vol.32 , pp. 158-168
    • Georgiou, G.1
  • 17
    • 84923870910 scopus 로고    scopus 로고
    • Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice
    • Greiff V., et al. (2014). Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice. BMC Immunol., 15, 40
    • (2014) BMC Immunol , vol.15 , pp. 40
    • Greiff, V.1
  • 18
    • 79959960525 scopus 로고    scopus 로고
    • Target-decoy approach and false discovery rate: When things may go wrong
    • Gupta N., et al. (2011). Target-decoy approach and false discovery rate: when things may go wrong. J. Am. Soc. Mass. Spectr., 22, 1111-1120
    • (2011) J. Am. Soc. Mass. Spectr , vol.22 , pp. 1111-1120
    • Gupta, N.1
  • 19
    • 79955109675 scopus 로고    scopus 로고
    • Determinism and stochasticity during maturation of the zebra fish antibody repertoire
    • Jiang N., et al. (2011). Determinism and stochasticity during maturation of the zebra fish antibody repertoire. Proc.Natl. Acad. Sci.USA, 108, 5348-5353
    • (2011) Proc.Natl. Acad. Sci.USA , vol.108 , pp. 5348-5353
    • Jiang, N.1
  • 20
    • 84874092680 scopus 로고    scopus 로고
    • Lineage structure of the human antibody repertoire in response to influenza vaccination
    • 171ra19
    • Jiang N., et al. (2013). Lineage structure of the human antibody repertoire in response to influenza vaccination. Sci. Transl. Med., 5, 171ra19
    • (2013) Sci. Transl. Med , vol.5
    • Jiang, N.1
  • 21
    • 0032131147 scopus 로고    scopus 로고
    • A fast and high quality multilevel scheme for partitioning irregular graphs
    • Karypis G. and Kumar V. (1999). A fast and high quality multilevel scheme for partitioning irregular graphs. SIAM J. Sci. Comput., 20, 35992
    • (1999) SIAM J. Sci. Comput , vol.20 , pp. 35992
    • Karypis, G.1    Kumar, V.2
  • 22
    • 78649358717 scopus 로고    scopus 로고
    • Quake: Quality-aware detection and correction of sequencing errors
    • Kelley D., et al. (2010). Quake: quality-aware detection and correction of sequencing errors. Genome Biol., 11, R116
    • (2010) Genome Biol , vol.11 , pp. R116
    • Kelley, D.1
  • 23
    • 84923247212 scopus 로고    scopus 로고
    • MS-GF+ makes progress towards a universal database search tool for proteomics
    • Kim S. and Pevzner P.A. (2014). MS-GF+ makes progress towards a universal database search tool for proteomics. Nat. Commun., 5, 5277
    • (2014) Nat. Commun , vol.5 , pp. 5277
    • Kim, S.1    Pevzner, P.A.2
  • 24
    • 50149117169 scopus 로고    scopus 로고
    • Spectral probabilities and generating functions of tandem mass spectra: A strike against decoy databases
    • Kim S., et al. (2008). Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J. Proteome Res., 7, 3354-3363
    • (2008) J. Proteome Res , vol.7 , pp. 3354-3363
    • Kim, S.1
  • 25
    • 84897549848 scopus 로고    scopus 로고
    • High-resolution antibody dynamics of vaccineinduced immune responses
    • Laserson U., et al. (2014). High-resolution antibody dynamics of vaccineinduced immune responses. Proc. Natl. Acad. Sci. U.S.A, 111, 492833
    • (2014) Proc. Natl. Acad. Sci. U.S.A , vol.111 , pp. 492833
    • Laserson, U.1
  • 26
    • 84893840611 scopus 로고    scopus 로고
    • Identification and characterization of the constituent human serum antibodies elicited by vaccination
    • Lavinder J.J., et al. (2014). Identification and characterization of the constituent human serum antibodies elicited by vaccination. Proc. Natl. Acad. Sci. U.S.A, 111, 2259-2264
    • (2014) Proc. Natl. Acad. Sci. U.S.A , vol.111 , pp. 2259-2264
    • Lavinder, J.J.1
  • 27
    • 58149316094 scopus 로고    scopus 로고
    • Imgtvr, the international immunogenetics information systemvr
    • Lefranc M.-P., et al. (2009). IMGTVR , the international ImMunoGeneTics information systemVR . Nucleic Acids Res., 37 (Suppl. 1) , D1006-D1012
    • (2009) Nucleic Acids Res , vol.37 , pp. D1006-D1012
    • Lefranc, M.-P.1
  • 28
    • 69949152299 scopus 로고    scopus 로고
    • Automated protein (re) sequencing with MS/MS and a homologous database yields almost full coverage and accuracy
    • Liu X., et al. (2009). Automated protein (re) sequencing with MS/MS and a homologous database yields almost full coverage and accuracy. Bioinformatics, 25, 2174-2180
    • (2009) Bioinformatics , vol.25 , pp. 2174-2180
    • Liu, X.1
  • 29
    • 79959485321 scopus 로고    scopus 로고
    • Error correction of high-throughput sequencing datasets with non-uniform coverage
    • Medvedev P., et al. (2011). Error correction of high-throughput sequencing datasets with non-uniform coverage. Bioinformatics, 27, i137-i141
    • (2011) Bioinformatics , vol.27 , pp. i137-i141
    • Medvedev, P.1
  • 30
    • 84859877187 scopus 로고    scopus 로고
    • Fast multi-blind modification search through tandem mass spectrometry
    • Na S., et al. (2012). Fast multi-blind modification search through tandem mass spectrometry. Mol. Cell. Proteomics, 11, M111.010199
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. M111010199
    • Na, S.1
  • 31
    • 84908540871 scopus 로고    scopus 로고
    • Proteogenomics: Concepts, applications and computational strategies
    • Nesvizhskii A.I. (2014). Proteogenomics: concepts, applications and computational strategies. Nat. Methods., 11, 1114-1125
    • (2014) Nat. Methods , vol.11 , pp. 1114-1125
    • Nesvizhskii, A.I.1
  • 32
    • 84881309354 scopus 로고    scopus 로고
    • BayesHammer: Bayesian clustering for error correction in single-cell sequencing
    • Nikolenko S., et al. (2013). BayesHammer: bayesian clustering for error correction in single-cell sequencing. BMC Genomics, 14, S7
    • (2013) BMC Genomics , vol.14 , pp. S7
    • Nikolenko, S.1
  • 33
    • 0035859921 scopus 로고    scopus 로고
    • An Eulerian path approach to DNA fragment assembly
    • Pevzner P., et al. (2001). An Eulerian path approach to DNA fragment assembly. Proc. Natl. Acad. Sci. U.S.A, 98, 9748-9753
    • (2001) Proc. Natl. Acad. Sci. U.S.A , vol.98 , pp. 9748-9753
    • Pevzner, P.1
  • 34
    • 8744242187 scopus 로고    scopus 로고
    • Whole-genome analysis of Alu repeat elements reveals complex evolutionary history
    • Price A.L., et al. (2004). Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. Genome Res., 14, 2245-2252
    • (2004) Genome Res , vol.14 , pp. 2245-2252
    • Price, A.L.1
  • 35
    • 77956688921 scopus 로고    scopus 로고
    • Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells
    • Reddy S., et al. (2010). Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells. Nat. Biotechnol., 28, 965-969
    • (2010) Nat. Biotechnol , vol.28 , pp. 965-969
    • Reddy, S.1
  • 36
    • 77950541195 scopus 로고    scopus 로고
    • Comprehensive assessment of T-cell receptor betachain diversity in alphabeta T cells
    • Robins H., et al. (2009). Comprehensive assessment of T-cell receptor betachain diversity in alphabeta T cells. Blood, 114, 4099-4107
    • (2009) Blood , vol.114 , pp. 4099-4107
    • Robins, H.1
  • 37
    • 77956460339 scopus 로고    scopus 로고
    • Overlap and effective size of the human CD8+ T cell receptor repertoire
    • Robins H., et al. (2010). Overlap and effective size of the human CD8+ T cell receptor repertoire. Sci. Transl. Med., 2, 47-64
    • (2010) Sci. Transl. Med , vol.2 , pp. 47-64
    • Robins, H.1
  • 38
    • 0026443954 scopus 로고
    • Somatic hypermutagenesis in immunoglobulin genes ii influence of neighbouring base sequences on mutagenesis
    • Rogozin I. and Kolchanov N. (1992). Somatic hypermutagenesis in immunoglobulin genes. ii. influence of neighbouring base sequences on mutagenesis. Biochim. Biophys. Acta., 1171, 11-18
    • (1992) Biochim. Biophys. Acta , vol.1171 , pp. 11-18
    • Rogozin, I.1    Kolchanov, N.2
  • 39
    • 0001580189 scopus 로고
    • Algorithmic aspects of vertex elimination on graphs
    • Rose D.J., et al. (1976). Algorithmic aspects of vertex elimination on graphs. SIAM J. Comput., 2, 26683
    • (1976) SIAM J. Comput , vol.2 , pp. 26683
    • Rose, D.J.1
  • 40
    • 84869438827 scopus 로고    scopus 로고
    • Proteomics-directed cloning of circulating antiviral human monoclonal antibodies
    • Sato S., et al. (2012). Proteomics-directed cloning of circulating antiviral human monoclonal antibodies. Nat. Biotechnol., 30, 1039-1043
    • (2012) Nat. Biotechnol , vol.30 , pp. 1039-1043
    • Sato, S.1
  • 41
    • 84901857468 scopus 로고    scopus 로고
    • Towards error-free profiling of immune repertoires
    • Shugay M., et al. (2014). Towards error-free profiling of immune repertoires. Nat. Methods, 11, 653-655
    • (2014) Nat. Methods , vol.11 , pp. 653-655
    • Shugay, M.1
  • 42
    • 84882432416 scopus 로고    scopus 로고
    • Genetic measurement of memory B-cell recall using antibody repertoire sequencing
    • Vollmers C., et al. (2013). Genetic measurement of memory B-cell recall using antibody repertoire sequencing. Proc. Natl. Acad. Sci. U.S.A, 110, 13463-13468
    • (2013) Proc. Natl. Acad. Sci. U.S.A , vol.110 , pp. 13463-13468
    • Vollmers, C.1
  • 43
    • 32544437698 scopus 로고    scopus 로고
    • Soda: Implementation of a 3d alignment algorithm for inference of antigen receptor recombinations
    • Volpe J.M., et al. (2006). SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations. Bioinformatics, 22, 438-444
    • (2006) Bioinformatics , vol.22 , pp. 438-444
    • Volpe, J.M.1
  • 44
    • 79955554975 scopus 로고    scopus 로고
    • Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes
    • Warren R., et al. (2011). Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes. Genome Res., 21, 790-797
    • (2011) Genome Res , vol.21 , pp. 790-797
    • Warren, R.1
  • 45
    • 65649122270 scopus 로고    scopus 로고
    • High-throughput sequencing of the zebrafish antibody repertoire
    • Weinstein J., et al. (2009). High-throughput sequencing of the zebrafish antibody repertoire. Science, 324, 807-810
    • (2009) Science , vol.324 , pp. 807-810
    • Weinstein, J.1
  • 46
    • 84874223925 scopus 로고    scopus 로고
    • Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response
    • Wine Y., et al. (2013). Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response. Proc. Natl. Acad. Sci. U.S.A, 110, 2993-2998
    • (2013) Proc. Natl. Acad. Sci. U.S.A , vol.110 , pp. 2993-2998
    • Wine, Y.1
  • 47
    • 84920956731 scopus 로고    scopus 로고
    • Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing
    • Yadav M., et al. (2014). Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing. Nature, 515, 572-576
    • (2014) Nature , vol.515 , pp. 572-576
    • Yadav, M.1
  • 48
    • 0002463920 scopus 로고
    • Computing the minimum fill-in is NP-complete
    • Yannakakis M. (1981). Computing the minimum fill-in is NP-complete. SIAM J. Alg. Disc. Meth., 2, 77-79
    • (1981) SIAM J. Alg. Disc. Meth , vol.2 , pp. 77-79
    • Yannakakis, M.1
  • 49
    • 84883563447 scopus 로고    scopus 로고
    • IgBlast: An immunoglobulin variable domain sequence analysis tool
    • Ye J., et al. (2013). IgBlast: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res., 41, W34-W40
    • (2013) Nucleic Acids Res , vol.41 , pp. W34-W40
    • Ye, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.