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Items: 25


BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs.

Meleshko D, Mohimani H, Tracanna V, Hajirasouliha I, Medema MH, Korobeynikov A, Pevzner PA.

Genome Res. 2019 Aug;29(8):1352-1362. doi: 10.1101/gr.243477.118. Epub 2019 Jun 3.


Ketoreductase Domain Dysfunction Expands Chemodiversity: Malyngamide Biosynthesis in the Cyanobacterium Okeania hirsuta.

Moss NA, Leão T, Rankin MR, McCullough TM, Qu P, Korobeynikov A, Smith JL, Gerwick L, Gerwick WH.

ACS Chem Biol. 2018 Dec 21;13(12):3385-3395. doi: 10.1021/acschembio.8b00910. Epub 2018 Dec 3.


IonHammer: Homopolymer-Space Hamming Clustering for IonTorrent Read Error Correction.

Ershov V, Tarasov A, Lapidus A, Korobeynikov A.

J Comput Biol. 2019 Feb;26(2):124-127. doi: 10.1089/cmb.2018.0152. Epub 2018 Oct 16.


Dereplication of microbial metabolites through database search of mass spectra.

Mohimani H, Gurevich A, Shlemov A, Mikheenko A, Korobeynikov A, Cao L, Shcherbin E, Nothias LF, Dorrestein PC, Pevzner PA.

Nat Commun. 2018 Oct 2;9(1):4035. doi: 10.1038/s41467-018-06082-8.


Autoprobiotics as an Approach for Restoration of Personalised Microbiota.

Suvorov A, Karaseva A, Kotyleva M, Kondratenko Y, Lavrenova N, Korobeynikov A, Kozyrev P, Kramskaya T, Leontieva G, Kudryavtsev I, Guo D, Lapidus A, Ermolenko E.

Front Microbiol. 2018 Sep 12;9:1869. doi: 10.3389/fmicb.2018.01869. eCollection 2018.


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. doi: 10.1038/s41564-017-0094-2. Epub 2018 Jan 22.


Globular chitosan treatment of bovine jugular veins: evidence of anticalcification efficacy in the subcutaneous rat model.

Krasilnikova AA, Sergeevichev DS, Fomenko VV, Korobeynikov AA, Vasilyeva MB, Yunoshev AS, Karaskov AM, Pokushalov EA.

Cardiovasc Pathol. 2018 Jan - Feb;32:1-7. doi: 10.1016/j.carpath.2017.08.003. Epub 2017 Sep 14.


A Maldiisotopic Approach to Discover Natural Products: Cryptomaldamide, a Hybrid Tripeptide from the Marine Cyanobacterium Moorea producens.

Kinnel RB, Esquenazi E, Leao T, Moss N, Mevers E, Pereira AR, Monroe EA, Korobeynikov A, Murray TF, Sherman D, Gerwick L, Dorrestein PC, Gerwick WH.

J Nat Prod. 2017 May 26;80(5):1514-1521. doi: 10.1021/acs.jnatprod.7b00019. Epub 2017 Apr 27.


metaSPAdes: a new versatile metagenomic assembler.

Nurk S, Meleshko D, Korobeynikov A, Pevzner PA.

Genome Res. 2017 May;27(5):824-834. doi: 10.1101/gr.213959.116. Epub 2017 Mar 15.


Comparative genomics uncovers the prolific and distinctive metabolic potential of the cyanobacterial genus Moorea.

Leao T, Castelão G, Korobeynikov A, Monroe EA, Podell S, Glukhov E, Allen EE, Gerwick WH, Gerwick L.

Proc Natl Acad Sci U S A. 2017 Mar 21;114(12):3198-3203. doi: 10.1073/pnas.1618556114. Epub 2017 Mar 6.


Sequencing rare marine actinomycete genomes reveals high density of unique natural product biosynthetic gene clusters.

Schorn MA, Alanjary MM, Aguinaldo K, Korobeynikov A, Podell S, Patin N, Lincecum T, Jensen PR, Ziemert N, Moore BS.

Microbiology. 2016 Dec;162(12):2075-2086. doi: 10.1099/mic.0.000386. Epub 2016 Oct 27.


A novel uncultured heterotrophic bacterial associate of the cyanobacterium Moorea producens JHB.

Cummings SL, Barbé D, Leao TF, Korobeynikov A, Engene N, Glukhov E, Gerwick WH, Gerwick L.

BMC Microbiol. 2016 Aug 30;16(1):198. doi: 10.1186/s12866-016-0817-1.


The Phormidolide Biosynthetic Gene Cluster: A trans-AT PKS Pathway Encoding a Toxic Macrocyclic Polyketide.

Bertin MJ, Vulpanovici A, Monroe EA, Korobeynikov A, Sherman DH, Gerwick L, Gerwick WH.

Chembiochem. 2016 Jan;17(2):164-73. doi: 10.1002/cbic.201500467. Epub 2015 Dec 23.


hybridSPAdes: an algorithm for hybrid assembly of short and long reads.

Antipov D, Korobeynikov A, McLean JS, Pevzner PA.

Bioinformatics. 2016 Apr 1;32(7):1009-15. doi: 10.1093/bioinformatics/btv688. Epub 2015 Nov 20.


Expanding the Described Metabolome of the Marine Cyanobacterium Moorea producens JHB through Orthogonal Natural Products Workflows.

Boudreau PD, Monroe EA, Mehrotra S, Desfor S, Korobeynikov A, Sherman DH, Murray TF, Gerwick L, Dorrestein PC, Gerwick WH.

PLoS One. 2015 Jul 29;10(7):e0133297. doi: 10.1371/journal.pone.0133297. eCollection 2015.


Combining Mass Spectrometric Metabolic Profiling with Genomic Analysis: A Powerful Approach for Discovering Natural Products from Cyanobacteria.

Kleigrewe K, Almaliti J, Tian IY, Kinnel RB, Korobeynikov A, Monroe EA, Duggan BM, Di Marzo V, Sherman DH, Dorrestein PC, Gerwick L, Gerwick WH.

J Nat Prod. 2015 Jul 24;78(7):1671-82. doi: 10.1021/acs.jnatprod.5b00301. Epub 2015 Jul 7.


Assembling short reads from jumping libraries with large insert sizes.

Vasilinetc I, Prjibelski AD, Gurevich A, Korobeynikov A, Pevzner PA.

Bioinformatics. 2015 Oct 15;31(20):3262-8. doi: 10.1093/bioinformatics/btv337. Epub 2015 Jun 3.


Spongosine production by a Vibrio harveyi strain associated with the sponge Tectitethya crypta.

Bertin MJ, Schwartz SL, Lee J, Korobeynikov A, Dorrestein PC, Gerwick L, Gerwick WH.

J Nat Prod. 2015 Mar 27;78(3):493-9. doi: 10.1021/np5009762. Epub 2015 Feb 10.


ExSPAnder: a universal repeat resolver for DNA fragment assembly.

Prjibelski AD, Vasilinetc I, Bankevich A, Gurevich A, Krivosheeva T, Nurk S, Pham S, Korobeynikov A, Lapidus A, Pevzner PA.

Bioinformatics. 2014 Jun 15;30(12):i293-301. doi: 10.1093/bioinformatics/btu266.


Single cell genome analysis of an uncultured heterotrophic stramenopile.

Roy RS, Price DC, Schliep A, Cai G, Korobeynikov A, Yoon HS, Yang EC, Bhattacharya D.

Sci Rep. 2014 Apr 24;4:4780. doi: 10.1038/srep04780.


Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways.

Coates RC, Podell S, Korobeynikov A, Lapidus A, Pevzner P, Sherman DH, Allen EE, Gerwick L, Gerwick WH.

PLoS One. 2014 Jan 27;9(1):e85140. doi: 10.1371/journal.pone.0085140. eCollection 2014.


Assembling single-cell genomes and mini-metagenomes from chimeric MDA products.

Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clingenpeel SR, Woyke T, McLean JS, Lasken R, Tesler G, Alekseyev MA, Pevzner PA.

J Comput Biol. 2013 Oct;20(10):714-37. doi: 10.1089/cmb.2013.0084.


BayesHammer: Bayesian clustering for error correction in single-cell sequencing.

Nikolenko SI, Korobeynikov AI, Alekseyev MA.

BMC Genomics. 2013;14 Suppl 1:S7. doi: 10.1186/1471-2164-14-S1-S7. Epub 2013 Jan 21.


Synthesis and evaluation of a glibenclamide glucose-conjugate: a potential new lead compound for substituted glibenclamide derivatives as islet imaging agents.

Schneider S, Ueberberg S, Korobeynikov A, Schechinger W, Schwanstecher C, Schwanstecher M, Klein HH, Schirrmacher E.

Regul Pept. 2007 Mar 1;139(1-3):122-7. Epub 2007 Jan 10.


In vitro and in vivo evaluation of novel glibenclamide derivatives as imaging agents for the non-invasive assessment of the pancreatic islet cell mass in animals and humans.

Schneider S, Feilen PJ, Schreckenberger M, Schwanstecher M, Schwanstecher C, Buchholz HG, Thews O, Oberholzer K, Korobeynikov A, Bauman A, Comagic S, Piel M, Schirrmacher E, Shiue CY, Alavi AA, Bartenstein P, Rösch F, Weber MM, Klein HH, Schirrmacher R.

Exp Clin Endocrinol Diabetes. 2005 Jul;113(7):388-95.


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