Standard

Ig Repertoire Constructor : A novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. / Safonova, Yana; Bonissone, Stefano; Kurpilyansky, Eugene; Starostina, Ekaterina; Lapidus, Alla; Stinson, Jeremy; Depalatis, Laura; Sandoval, Wendy; Lill, Jennie; Pevzner, Pavel A.

In: Bioinformatics, Vol. 31, No. 12, 15.06.2015, p. i53-i61.

Research output: Contribution to journal › Article › peer-review

Harvard

Safonova, Y, Bonissone, S, Kurpilyansky, E, Starostina, E, Lapidus, A, Stinson, J, Depalatis, L, Sandoval, W, Lill, J & Pevzner, PA 2015, 'Ig Repertoire Constructor: A novel algorithm for antibody repertoire construction and immunoproteogenomics analysis', Bioinformatics, vol. 31, no. 12, pp. i53-i61. https://doi.org/10.1093/bioinformatics/btv238, https://doi.org/10.1093/bioinformatics/btv238

APA

Safonova, Y., Bonissone, S., Kurpilyansky, E., Starostina, E., Lapidus, A., Stinson, J., Depalatis, L., Sandoval, W., Lill, J., & Pevzner, P. A. (2015). Ig Repertoire Constructor: A novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. Bioinformatics, 31(12), i53-i61. https://doi.org/10.1093/bioinformatics/btv238, https://doi.org/10.1093/bioinformatics/btv238

Vancouver

Safonova Y, Bonissone S, Kurpilyansky E, Starostina E, Lapidus A, Stinson J et al. Ig Repertoire Constructor: A novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. Bioinformatics. 2015 Jun 15;31(12):i53-i61. https://doi.org/10.1093/bioinformatics/btv238, https://doi.org/10.1093/bioinformatics/btv238

Author

Safonova, Yana ; Bonissone, Stefano ; Kurpilyansky, Eugene ; Starostina, Ekaterina ; Lapidus, Alla ; Stinson, Jeremy ; Depalatis, Laura ; Sandoval, Wendy ; Lill, Jennie ; Pevzner, Pavel A. / Ig Repertoire Constructor : A novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. In: Bioinformatics. 2015 ; Vol. 31, No. 12. pp. i53-i61.

BibTeX

@article{37e2f0ad4d7847cb8741a06dade23903,
title = "Ig Repertoire Constructor: A novel algorithm for antibody repertoire construction and immunoproteogenomics analysis",
abstract = "The analysis of concentrations of circulating antibodies in serum (antibody repertoire) is a fundamental, yet poorly studied, problem in immunoinformatics. The two current approaches to the analysis of antibody repertoires [next generation sequencing (NGS) and mass spectrometry (MS)] present difficult computational challenges since antibodies are not directly encoded in the germline but are extensively diversified by somatic recombination and hypermutations. Therefore, the protein database required for the interpretation of spectra from circulating antibodies is custom for each individual. Although such a database can be constructed via NGS, the reads generated by NGS are error-prone and even a single nucleotide error precludes identification of a peptide by the standard proteomics tools. Here, we present the IgRepertoireConstructor algorithm that performs error-correction of immunosequencing reads and uses mass spectra to validate the constructed antibody repertoires.",
author = "Yana Safonova and Stefano Bonissone and Eugene Kurpilyansky and Ekaterina Starostina and Alla Lapidus and Jeremy Stinson and Laura Depalatis and Wendy Sandoval and Jennie Lill and Pevzner, {Pavel A.}",
note = "Publisher Copyright: {\textcopyright} The Author 2015. Published by Oxford University Press.",
year = "2015",
month = jun,
day = "15",
doi = "10.1093/bioinformatics/btv238",
language = "English",
volume = "31",
pages = "i53--i61",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "12",

}

RIS

TY - JOUR

T1 - Ig Repertoire Constructor

T2 - A novel algorithm for antibody repertoire construction and immunoproteogenomics analysis

AU - Safonova, Yana

AU - Bonissone, Stefano

AU - Kurpilyansky, Eugene

AU - Starostina, Ekaterina

AU - Lapidus, Alla

AU - Stinson, Jeremy

AU - Depalatis, Laura

AU - Sandoval, Wendy

AU - Lill, Jennie

AU - Pevzner, Pavel A.

N1 - Publisher Copyright: © The Author 2015. Published by Oxford University Press.

PY - 2015/6/15

Y1 - 2015/6/15

N2 - The analysis of concentrations of circulating antibodies in serum (antibody repertoire) is a fundamental, yet poorly studied, problem in immunoinformatics. The two current approaches to the analysis of antibody repertoires [next generation sequencing (NGS) and mass spectrometry (MS)] present difficult computational challenges since antibodies are not directly encoded in the germline but are extensively diversified by somatic recombination and hypermutations. Therefore, the protein database required for the interpretation of spectra from circulating antibodies is custom for each individual. Although such a database can be constructed via NGS, the reads generated by NGS are error-prone and even a single nucleotide error precludes identification of a peptide by the standard proteomics tools. Here, we present the IgRepertoireConstructor algorithm that performs error-correction of immunosequencing reads and uses mass spectra to validate the constructed antibody repertoires.

AB - The analysis of concentrations of circulating antibodies in serum (antibody repertoire) is a fundamental, yet poorly studied, problem in immunoinformatics. The two current approaches to the analysis of antibody repertoires [next generation sequencing (NGS) and mass spectrometry (MS)] present difficult computational challenges since antibodies are not directly encoded in the germline but are extensively diversified by somatic recombination and hypermutations. Therefore, the protein database required for the interpretation of spectra from circulating antibodies is custom for each individual. Although such a database can be constructed via NGS, the reads generated by NGS are error-prone and even a single nucleotide error precludes identification of a peptide by the standard proteomics tools. Here, we present the IgRepertoireConstructor algorithm that performs error-correction of immunosequencing reads and uses mass spectra to validate the constructed antibody repertoires.

UR - http://www.scopus.com/inward/record.url?scp=84931099165&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btv238

DO - 10.1093/bioinformatics/btv238

M3 - Article

C2 - 26072509

VL - 31

SP - i53-i61

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 12

ER -

ID: 5799294