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As of 30.01.2020

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scientific publications
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General information

Name of the project:  Computational biology

Strategy for Scientific and Technological Development Priority Level:  в

Goals and objectives

Research directions: Developing software for data analysis in genomics, transcriptomics, protenics, immunoinformatics and search for new antibiotics

Project objective: Creating new algorithms and software for genomics and proteomics – incredibly relevant areas of modern biology studying structures and functions of genomes and proteins

The practical value of the study

  • We have created the SPAdes software complex that has been named the best in the world in the field of genome assembly from short fragments produced by modern sequencing technologies.
  • The new universal de novo metagenome assembler metaSPAdes has been developed.
  • The QUAST software has been created for assessing quality of assemblies produced at the Laboratory.
  • We have produced notable results in transcriptomics and proteomics.

Implemented results of research:

The Center for Algorithmic Biotechnology provides bioinformatics support to the largest project in research of human microbiome   devoted to analysis of microbiome of Larry Smarr who has become a «living laboratory» due to Crohn's disease that has developed in his organism. The Center's employees Dmitriy Meleshko and Sergey Nurku have received opportunity to use a supercomputer in San Diego to analyze this microbiomme while Alla Mikheenko and Alexey Gureev analyze his metabolome.

Education and career development:

  • We have modernized educational activities of the Saint Petersburg State University as a result of creation and implementation of online courses into education programs in Bioinformatics.
  • In 2014 we created and launched the «Introduction to bioinformatics» online course that is the first course in bioinformatics on the Coursera platform. Since its launch the course has been completed by over 25 000 people from, Russia, Belarus, Kazakhstan, the United States, Germany, Israel and other countries.
  • In 2016 we created and launched the second online course «Introduction to bioinformatics: metgenomics» at Coursera, Stepik, and Open Education platforms. The course received a prize at the EdCrunch Award OOC 2018 competition of online courses. 
  • We have developed the «Bioinformatics» masters program for the Saint Petersburg State University (lead by A. L. Lapidus). Admission to the «Bioinformatics» masters program has been successfully completed for the first time in 2018.

Other results:

  • The SPAdes software package created by the Center is one of the most popular programs for assembling bacterial genomes in the world despite tight competition with such institutions as the Massachusetts Institute of Technology and the Harvard University. The publication describing SPAdes at the «Journal of Computational Biology» has been cited more than 2000 times over the 5 years since publications.
  • Comparative analysis of leading metagenome DNA assemblers conducted by German researchers has shown that metaSPAdes is number 1: «metaSPAdes showed the overall best assembly size statistics while also capturing a relatively large fraction of the expected diversity» (Vollmers et al., PlOS One, 2017).

Collaborations: Joint Genome Institute (USA), University of San Diego (USA), Scripps Institute (USA), J. Craig Venter Institute (USA), AstraZeneca (USA), EMC International Group (Russia), Illumina (USA, United Kingdom), Juno Therapeutics (USA), Genentech (USA), Nabsys (USA), EMBL-EBI (United Kingdom), Institute for Agricultural and Forest Systems in the Mediterranean (Italy): joint scientific research

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Bankevich A.L., Nurk S., Antipov D., Gurevich A.A., Dvorkin M., Kulikov A.S., Lesin V.M., Nikolenko S.I., … Pevzner P.A.
SPAdes: a New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of computational biology 19(5): 455–477 (2012).
Bankevich A., Pevzner P.A.
TruSPAdes: Barcode Assembly of TruSeq Synthetic Long Reads. Nature Methods 13(3): 248–250 (2016).
Mohimani H., Gurevich A., Shlemov A., Mikheenko A., Korobeynikov A., Cao L., Shcherbin E., Nothias L.F., Dorrestein P.C., Pevzner P.A.
Dereplication of microbial metabolites through database search of mass spectra. Nature Communications 9(1): 4035 (2018).
Antipov D., Hartwick N., Shen M., Raiko M., Lapidus A., Pevzner P.A.
plasmidSPAdes: assembling plasmids from whole genome sequencing data. Bioinformatics 32(22): 3380-3387 (2016).
Bushmanova E., Antipov D., Lapidus A., Suvorov V., Prjibelski A.D.
rnaQUAST: a quality assessment tool for de novo transcriptome assemblies. Bioinformatics 32(14): 2210-2 (2016).
Safonova Y., Lapidus A., Lill J.
IgSimulator: a versatile immunosequencing simulator. Bioinformatics 31(19):3213-5 (2015).
Prjibelski A.D., Vasilinetc I., Bankevich A., Gurevich A., Krivosheeva T., Nurk S., Pham S., Korobeynikov A., Lapidus A., Pevzner P.A.
ExSPAnder: a universal repeat resolver for DNA fragment assembly. Bioinformatics 30(12): 293-301 (2014).
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