Software
Genome sequencing
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. J Comput Biol. 2012 May;19(5):455-77.
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. Genome Res. 2017 May;27(5):824-834.
Antipov D, Hartwick N, Shen M, Raiko M, Lapidus A, Pevzner PA. Bioinformatics. 2016 Nov 15;32(22):3380-3387.
Antipov D, Korobeynikov A, McLean JS, Pevzner PA.
Bioinformatics. 2016 Apr 1;32(7):1009-15.
Lin Y, Yuan J, Kolmogorov M, Shen MW, Chaisson M, Pevzner PA. Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):E8396-E8405.
Kolmogorov M, Yuan J, Lin Y, Pevzner PA. (2019) Nature Biotechnology
Proteomics / Immunoproteogenomics
Shlemov A, Bankevich S, Bzikadze A, Turchaninova MA, Safonova Y, Pevzner PA.
J Immunol. 2017 Nov 1;199(9):3369-3380.
Kim S, Pevzner PA. Nat Commun. 2014 Oct 31;5:5277
Jeong K, Kim S, Pevzner PA. Bioinformatics. 2013 Aug 15;29(16):1953-62.
Liu X, Sirotkin Y, Shen Y, Anderson G, Tsai YS, Ting YS, Goodlett DR, Smith RD, Bafna V, Pevzner PA. Mol Cell Proteomics. 2012 Jun;11(6):M111.008524.
MS-Cluster
Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra.
Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra.
Frank AM, Monroe ME, Shah AR, Carver JJ, Bandeira N, Moore RJ, Anderson GA, Smith RD, Pevzner PA. Nat Methods. 2011 May 15;8(7):587-91.
Frank A, Pevzner P. Anal Chem. 2005 Feb 15;77(4):964-73.
IgScout
De novo Inference of Diversity Genes and Analysis of Non-canonical V(DD)J Recombination in Immunoglobulins
De novo Inference of Diversity Genes and Analysis of Non-canonical V(DD)J Recombination in Immunoglobulins
Safonova, Y., Pevzner, P.A. De novo inference of diversity genes and analysis of non-canonical V(DD)J recombination in immunoglobulins. Frontiers in Immunology. 2019, 10, 987
MINING-D
Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species
Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species
Bhardwaj, V, Franceschetti, M, Rao, R., Pevzner, P.A., Safonova, Y. Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species. PLOS Computational Biology 2020, 16, e1007837
Antibiotics Discovery
VarQuest
Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra.
Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra.
Gurevich A, Mikheenko A, Shlemov A, Korobeynikov A, Mohimani H, Pevzner PA. Nat Microbiol. 2018 Mar;3(3):319-327.
Mohimani H, Gurevich A, Mikheenko A, Garg N, Nothias LF, Ninomiya A, Takada K, Dorrestein PC, Pevzner PA. Nat Chem Biol. 2017 Jan;13(1):30-37.
CycloNovo
De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments.
De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments.
De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments. B. Behsaz, H. Mohimani, A. Gurevich, A. Prjibelski, M. F. Fisher, L. Smarr, P. C. Dorrestein, J. S. Mylne, and P. A. Pevzner. Cell Systems, 2020, 10, 99-108
Comparative genomics
Pu L, Lin Y, Pevzner PA. Genome Res. 2018 Jun;28(6):901-909.
Alekseyev MA, Pevzner PA. Genome Res. 2009 May;19(5):943-57.
Price AL, Jones NC, Pevzner PA. Bioinformatics. 2005 Jun;21 Suppl 1:i351-8.
