-
1
-
-
79961160227
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
|