SPbU Center for Algorithmic Biotechnology
Development of software products for data analysis in the fields of genomics, transcriptomics, proteomics, immunoinformatics, and the search for new antibiotics.
Organization type: Laboratory
Field of science: Computer and information sciences
Goals and Objectives
Project Goal:Creation of new algorithms and software for genomics and proteomics — extremely relevant areas of modern biology studying the structures and functions of genomes and proteins
Other results
- The SPAdes software product, created at the CAB, is one of the most popular programs for bacterial genome assembly in the world, despite high competition, including from research teams at the Massachusetts Institute of Technology and Harvard University. The scientific publication in the Journal of Computational Biology describing SPAdes has been cited nearly 2,000 times in the 5 years since its publication.
- A comparative analysis of leading metagenomic DNA assemblers conducted by German scientists showed that metaSPAdes, created by the CAB, 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).
Scientific Results
- The SPAdes software product was created, recognized as the world's best in the field of genome assembly from short fragments produced by modern sequencing technologies.
- A new universal de novo metagenomic assembler, metaSPAdes, has been created.
- The QUAST software product was created to assess the quality of assemblies produced in the laboratory.
- Notable results have been achieved in the fields of transcriptomics and proteomics.
Implementation of research results:
The Center for Algorithmic Biotechnology provides bioinformatics support for the largest current human microbiome research project, dedicated to analyzing the microbiome of Larry Smarr, who has become a "living laboratory" over the last 12 years due to his Crohn's disease. CAB researchers Dmitry Meleshko and Sergey Nurk were allocated one million hours on a supercomputer in San Diego to analyze this microbiome, while Alla Mikheenko and Alexey Gurevich are analyzing its metabolome.
Education and personnel retraining
- Saint Petersburg State University's educational activities have been modernized through the creation and implementation of online courses, disciplines, and a core educational program in Bioinformatics into the curricula.
- The "Introduction to Bioinformatics" online course was created and launched in 2014, becoming the first Russian-language bioinformatics course on the Coursera platform. Since its launch, the course has been taken by more than 25,000 people from Russia, Belarus, Kazakhstan, the USA, Germany, Israel, and other countries.
- The second online course "Introduction to Bioinformatics: Metagenomics" was created and launched in 2016 on the Coursera, Stepik, and Open Education platforms. The course won an award at the EdCrunch Award OOC 2018 international open online course competition.
- A Master's degree program in "Bioinformatics" was developed at Saint Petersburg State University (headed by A. L. Lapidus). The first successful intake for the "Bioinformatics" Master's program took place in 2018.
Cooperation
Joint Genome Institute (USA), University of California San Diego (USA), Scripps Research (USA), J. Craig Venter Institute (USA), AstraZeneca (USA), Roche International Group of Companies, EMC (Russia), Illumina (USA, UK), Juno Therapeutics (USA), Genentech (USA), Nabsys (USA), EMBL-EBI (UK), Institute for Agricultural and Forest Systems in the Mediterranean (Italy): joint scientific research.Website: http://cab.spbu.ru/
Contact person: Pavel Arkadyevich Pevzner
Address: 21 Bolshoy Prospekt, Vasilyevsky Island
Phone: +7 (812) 363-60-42
Contact person: Pavel Arkadyevich Pevzner
Address: 21 Bolshoy Prospekt, Vasilyevsky Island
Phone: +7 (812) 363-60-42
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