Laboratory for Algorithmic Biology

Head: Pavel Pevzner

Визитная карточка коллектива (первый Российский бренд в биоинформатике):

SPADES

QUAST

Community feedback:

“SPAdes is a swiss-army knife of genome assembly tools”

 

10 Main  Biomedical  Projects:

 

1. Immunogenomics – tools for antibody repeater analysis

2. Transcriptome assembler

3. Genome assembly - Scaling SPAdes towards large genomes

4. Genome assembly evaluation  - Optimizing QUAST and evaluating genome assemblers.

5. Metagenomics - metaSPAdes genome assembler for metagenomic data 

6. SPArcle project Genome Comparison using de Bruijn graphs

7. Variation detection in human genome using Illumina TSLRs

8. Cancer Genomics  - Clinical data interpretation portal. Structural variants clinical reporting and NGS post-processing suite.

9. Peptidic Natural Products (PNPs)  discovery tools

10. Analysis of proteins from high-resolution tandem mass spectrometry data

 

Collaborators:

  • Prof.D. Chudakov at Institute of Bioorganic Chemistry, Moscow
  • Sonia Timberlake at AbVitro, Boston.
  • Terry Gaasterland, Rob Knight, Hosein Mohimani, Pieter Dorrestein  (UCSD)
  • JGI, JCVI, - USA
  • CAMI team (Bielefeld University, HZI Braunschweig, etc),
  • Dobzhansky center (St Petersburg).
  • Oleg Glotov, Andrey Glotov
  • Christopher Dupont (JCVI).
  • AstraZeneca Oncology.
  • Daniel Petras (TU Berlin)
  • Yury Tsybin (EPFL).
  • Theo Luider, Lennard Dekker , Martiijn VanDuijn (Eraumus MC)

 

Publications:

За первый год работы Центра алгоритмической биотехнологии в СПбГУ опубликовано и подготовлено к печати 25 публикаций:

- 9 опубликовано
- 3 приняты к публикации, одна из которых в журнале Nature Methods (impact factor 32.072).
- 6 направлено в печать
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