Pavel Pevzner

from Wikipedia, the free encyclopedia
Pavel Pevzner

Pavel Pevzner , Russian Павел Аркадьевич Певзнер , transcription Pawel Arkadjewitsch Pewsner, (* in Kursk ) is a Russian-American bioinformatician.

Life

Pevszner studied mathematics and physics at the Moscow Institute of Physics and Technology, where he received his PhD while working at the Russian Research Institute of Genetics (NII Genetics). In 1990 he went to the University of Southern California in the laboratory of Michael Waterman . In 1992 he became associate professor at Pennsylvania State University and in 1995 professor of mathematics, computer science and molecular biology at the University of Southern California. In 2000 he became Professor of Computer Science at the University of California, San Diego . There he is the Ronald R. Taylor Professor and Director of the NIH Center for Computational Mass Spectrometry.

plant

Pevzner specializes in genome sequencing, immunoproteogenomics , antibiotic sequencing and comparative genomics.

In 1989 he published an algorithm for the analysis of DNA arrays based on De Bruijn graphs in genome sequencing . In 2004 he introduced their generalization A-Bruijn graphs. Pevzner was involved in various genome sequencing projects (mouse, rat, chicken). He also applied the results of genome sequencing to the study of the evolution of living things, for example in the reconstruction of the genome architecture of extinct mammals. In 2003 he and G. Tesler proposed an alternative to the old Random Breakage Model (RBM) of genome rearrangements and chromosome evolution ( Susumu Ohno 1971), the Fragile Breakage Model (FBM). It is based on the concept of the breakpoint graph and an accumulation of genome breaks at weak points and not breaks at randomly chosen places. Polynomial algorithms for genome arrangements and associated databases are based on this.

From 1999 he contributed to the development of de novo peptide sequencing for the identification of proteins. Pevszner invented a method of evaluating mass spectrometer data with spectral networks (molecular networks) and applied this in 2008 to the development of the first antibody sequencing method. He applied that in his company Digital Proteomics. With his laboratory he is taking steps in the direction of personalized immunogenomics, that is, the investigation of the antibody spectrum of individual individuals for diagnosis and therapy.

Using spectral networks, he developed a method of antibiotic sequencing, which he uses to search for new antibiotics. He was one of the founders of the spectral network Global Natural Product Social (GNPS), to which thousands of laboratories are affiliated.

Honors and memberships

Pevzner received a Presidential Young Investigator Award from the NSF. In 2010 he became a Fellow of the Association for Computing Machinery . In 2011 he received an honorary doctorate from Simon Fraser University , he received a professorship from the Howard Hughes Medical Institute and in 2018 he received the Paris Kanellakis Prize .

Pevszner is one of the most highly cited scientists. He is on the editorial board of PLoS Computational Biology.

Fonts (selection)

So far not listed in the footnotes.

  • Computational Molecular Biology, MIT Press, 2000
  • with Neil Jones: An Introduction to Bioinformatics Algorithms, MIT Press, 2004
  • with Ron Shamir (Ed.): Bioinformatics for Biologists, Cambridge University Press, 2011
  • with Phillip Compeau: Bioinformatics Algorithms: An Active Learning Approach, Active Learning Publishers, 2014

Some essays:

  • with V. Bafna: Genome rearrangements and sorting by reversals, SIAM Journal on Computing, Volume 25, 1996, pp. 272-289
  • with S. Hannenhalli: Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals, Journal of the ACM (JACM), Volume 46, 1999, pp. 1-27
  • with SH Sze: Combinatorial approaches to finding subtle signals in DNA sequences, ISMB, Volume 8, 2000, pp. 269-278.
  • with H. Tang, MS Waterman: An Eulerian path approach to DNA fragment assembly, Proc. Nat. Acad. USA, Vol. 98, 2001, pp. 9748-9753
  • with S. Tanner u. a .: InsPecT: Identification of post-translationally modified peptides from tandem mass spectra, Analytical Chemistry, Volume 77, 2005, pp. 4626-4639
  • with G. Tesler: Genome rearrangements in mammalian evolution: lessons from human and mouse genomes, Genome Res., Volume 13, 2003, pp. 37-45, PMID 12529304 .
  • with WJ Murphy: Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps, Science, Volume 309, 2005, pp. 613-617
  • with AL Price, NC Jones: De novo identification of repeat families in large genomes, Bioinformatics, Volume 21, Suppl. 1, 2005, i351-i358
  • with A. Frank: PepNovo: De novo peptide sequencing via probabilistic network modeling, Analytical Chemistry, Volume 77, 2005, pp. 964-973
  • with Mark Chaisson: Short Read Fragment Assembly of Bacterial Genomes, Genome Res., Volume 18, 2008, pp. 324-330
  • with MA Alekseyev: Breakpoint graphs and ancestral genome reconstructions, Genome Res., Volume 19, 2009, pp. 943-957, PMID 19218533
  • with PEC Compeau, G. Tesler: How to apply de Bruijn graphs to genome assembly, Nature Biotechnology, Volume 29, 2011, pp. 987-991, PMID 22068540
  • with S. Nurk u. a .: Assembling single-cell genomes and mini-metagenomes from chimeric MDA products, Journal of Computational Biology, Volume 20, 2013, pp. 714-737
  • with A. Bankevich u. a .: SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, Journal of Computational Biology, Volume 19, 2012, pp. 455-477
  • with S. Kim: MS-GF + makes progress towards a universal database search tool for proteomics, Nature Communications, Volume 5, 2014, p. 5277
  • with S. Nurk, D. Meleshko, A. Korobeynikov: metaSPAdes: a new versatile metagenomic assembler, Genome Research, Volume 27, 2017, pp. 824-834
  • with M.Kolmogorov u. a .: Assembly of long, error-prone reads using repeat graphs, Nature Biotechnology, Volume 37, 2019, pp. 540-546, PMID 30936562 .
  • with D. Antipov a. a .: metaviralSPAdes: Assembly of Viruses From Metagenomic Data, Bioinformatics, May 15, 2020, PMID 32413137

Web links

Commons : Pavel A. Pevzner  - collection of pictures, videos and audio files

Individual evidence

  1. ↑ Pevzner, one-tuple DNA Sequencing: Computer Analysis, J. Biomol. Struct. Dyn., Vol. 7, 1989, pp. 63-73
  2. ↑ RH Waterston, Pevzner u. a .: Initial sequencing and comparative analysis of the mouse genome, Nature, Volume 420, 2002, pp. 520-562
  3. ↑ RA Gibbs, Pevzner u. a .: Genome sequence of the Brown Norway rat yields insights into mammalian evolution, Nature, Volume 428, 2004, pp. 493-520
  4. ↑ LDW Hillier, Pevzner et al. a .: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution, Nature, Volume 423, 2014, pp. 695-777
  5. ↑ G. Bourque, Pevzner, G. Tesler: Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes, Genome Res, vol 14, 2004, pp 507-516. PMID 15059991
  6. ↑ Pevzner, Tesler, Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution, Proc. Nat. Acad. USA, Vol. 100, 2003, pp. 7672-7677
  7. ↑ V. Dancik, TA Addona, KR Clauser, JE Vath, PA Pevzner: De Novo Peptide Sequencing via Tandem Mass Spectrometry, Journal of Computational Biology, Volume 6, 1999, pp 327-341
  8. ↑ Bandeira et al. a., Automated de novo protein sequencing of monoclonal antibodies, Nature-Biotechnology, Volume 26, 2008, pp. 1336-1338
  9. ↑ Ng u. a., Dereplication and de novo sequencing of nonribosomal peptides, Nature Methods, Volume 6, 2009, pp. 596-599
  10. ↑ M. Wang, Pevzner et al. a .: Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking, Nature Biotechnology, Volume 34, 2016, pp. 828-837
personal data
SURNAME Pevzner, Pavel
ALTERNATIVE NAMES Pewsner, Pavel Arkadyevich
BRIEF DESCRIPTION Russian-American bioinformatician
DATE OF BIRTH 20th century
PLACE OF BIRTH Kursk