Evidence map›Paper›PMID 26072509›Full record

ArticleBioinformatics (Oxford, England)2015

IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis.

Yana Safonova, Stefano Bonissone, Eugene Kurpilyansky, Ekaterina Starostina, Alla Lapidus, Jeremy Stinson, Laura DePalatis, Wendy Sandoval, Jennie Lill, Pavel A Pevzner

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.

0numbers the graph read from it
0cells of the map it votes in
22citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

22 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Antibody repertoire sequencing analysis.Acta biochimica et biophysica Sinica · 2022
    Review
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Review
  12. Article
  13. Analyzing Immunoglobulin Repertoires.Frontiers in immunology · 2018
    Review
  14. The Antibody Repertoire of Colorectal Cancer.Molecular & cellular proteomics : MCP · 2017
    Article
  15. Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads.Journal of immunology (Baltimore, Md. : 1950) · 2017
    Article
  16. Article
  17. De Novo MS/MS Sequencing of Native Human Antibodies.Journal of proteome research · 2017
    Article
  18. Article
  19. Article
  20. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Yana SafonovaCenter for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA.
Stefano BonissoneCenter for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA.
Eugene KurpilyanskyCenter for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA.
Ekaterina StarostinaCenter for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA.
Alla LapidusCenter for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA.
Jeremy StinsonCenter for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA.
Laura DePalatisCenter for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA.
Wendy SandovalCenter for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA.
Jennie LillCenter for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA.
Pavel A PevznerCenter for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA.

Funding

TrainingP41GM103484 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PEVZNER, PAVEL A · 2012 to 2018
$8.7M
NIGMS NIH HHS 5P41GM103484NIGMS NIH HHS P41 GM103484
6 · The paper itself

Abstract

unlabelledThe 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. AVAILABILITY AND IMPLEMENTATION: IgRepertoireConstructor is open source and freely available as a C++ and Python program running on all Unix-compatible platforms. The source code is available from http://bioinf.spbau.ru/igtools. CONTACT: ppevzner@ucsd.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Indexed as

AlgorithmsGenome, HumanSoftwareAntibodiesDatabases, FactualHigh-Throughput Nucleotide SequencingHumansImmunoglobulinsMass SpectrometryPeptide FragmentsProteomeSequence Analysis, DNAAntibodiesImmunoglobulinsPeptide FragmentsProteome

Identifiers

PMID26072509
PMCPMC4542777

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.