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Page 1
SPAdes: a new genome assembly algorithm and its applications to single-cell 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. Bankevich A, et al. Among authors: nikolenko si. J Comput Biol. 2012 May;19(5):455-77. doi: 10.1089/cmb.2012.0021. Epub 2012 Apr 16. J Comput Biol. 2012. PMID: 22506599 Free PMC article.
BayesHammer: Bayesian clustering for error correction in single-cell sequencing.
Nikolenko SI, Korobeynikov AI, Alekseyev MA. Nikolenko SI, et al. BMC Genomics. 2013;14 Suppl 1(Suppl 1):S7. doi: 10.1186/1471-2164-14-S1-S7. Epub 2013 Jan 21. BMC Genomics. 2013. PMID: 23368723 Free PMC article.
Single cells within the Puerto Rico trench suggest hadal adaptation of microbial lineages.
León-Zayas R, Novotny M, Podell S, Shepard CM, Berkenpas E, Nikolenko S, Pevzner P, Lasken RS, Bartlett DH. León-Zayas R, et al. Appl Environ Microbiol. 2015 Dec;81(24):8265-76. doi: 10.1128/AEM.01659-15. Epub 2015 Sep 18. Appl Environ Microbiol. 2015. PMID: 26386059 Free PMC article.
Medical concept normalization in social media posts with recurrent neural networks.
Tutubalina E, Miftahutdinov Z, Nikolenko S, Malykh V. Tutubalina E, et al. J Biomed Inform. 2018 Aug;84:93-102. doi: 10.1016/j.jbi.2018.06.006. Epub 2018 Jun 12. J Biomed Inform. 2018. PMID: 29906585
druGAN: An Advanced Generative Adversarial Autoencoder Model for de Novo Generation of New Molecules with Desired Molecular Properties in Silico.
Kadurin A, Nikolenko S, Khrabrov K, Aliper A, Zhavoronkov A. Kadurin A, et al. Mol Pharm. 2017 Sep 5;14(9):3098-3104. doi: 10.1021/acs.molpharmaceut.7b00346. Epub 2017 Aug 4. Mol Pharm. 2017. PMID: 28703000
3D Molecular Representations Based on the Wave Transform for Convolutional Neural Networks.
Kuzminykh D, Polykovskiy D, Kadurin A, Zhebrak A, Baskov I, Nikolenko S, Shayakhmetov R, Zhavoronkov A. Kuzminykh D, et al. Mol Pharm. 2018 Oct 1;15(10):4378-4385. doi: 10.1021/acs.molpharmaceut.7b01134. Epub 2018 Mar 5. Mol Pharm. 2018. PMID: 29473756
Tooth detection and numbering in panoramic radiographs using convolutional neural networks.
Tuzoff DV, Tuzova LN, Bornstein MM, Krasnov AS, Kharchenko MA, Nikolenko SI, Sveshnikov MM, Bednenko GB. Tuzoff DV, et al. Among authors: nikolenko si. Dentomaxillofac Radiol. 2019 May;48(4):20180051. doi: 10.1259/dmfr.20180051. Epub 2019 Mar 5. Dentomaxillofac Radiol. 2019. PMID: 30835551 Free PMC article.
FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry.
Palmer A, Phapale P, Chernyavsky I, Lavigne R, Fay D, Tarasov A, Kovalev V, Fuchser J, Nikolenko S, Pineau C, Becker M, Alexandrov T. Palmer A, et al. Nat Methods. 2017 Jan;14(1):57-60. doi: 10.1038/nmeth.4072. Epub 2016 Nov 14. Nat Methods. 2017. PMID: 27842059
Analysis and interpretation of imaging mass spectrometry data by clustering mass-to-charge images according to their spatial similarity.
Alexandrov T, Chernyavsky I, Becker M, von Eggeling F, Nikolenko S. Alexandrov T, et al. Anal Chem. 2013 Dec 3;85(23):11189-95. doi: 10.1021/ac401420z. Epub 2013 Nov 15. Anal Chem. 2013. PMID: 24180335