Antonets Denis Viktorovich

Antonets Denis Viktorovich
Post
Head of Analytics Department
Academic degree
Candidate of Biological Sciences (Ph.D.)
in the Novel team
since 2010
Education
Department of Natural Sciences NSU (2003)
Projects
Protomenal and others
Interests
Bioinformatics, immunoinformatics, virology, metagenomics, NGS, statistics, machine learning, Data Science, Deep Learning

Links

LinkedIn
ResearchGate

List of publications

2024
Nearly complete genome sequences of the first two identified Colorado potato beetle viruses
Maria Antonets, Sergei Bodnev, Ulyana Rotskaya, Elena Kosman, Tatyana Tregubchak, Tatyana Bauer, Mamedyar Azaev, Vadim Kryukov & Denis Antonets
2023
The Metagenomic Analysis of Viral Diversity in Colorado Potato Beetle Public NGS Data
Maria Starchevskaya, Ekaterina Kamanova, Yuri Vyatkin, Tatyana Tregubchak, Tatyana Bauer, Sergei Bodnev, Ulyana Rotskaya, Olga Polenogova, Vadim Kryukov and Denis Antonets
RNAseq profiling of blood from patients with coronary artery disease: Signature of a T cell imbalance
Timothy A. McCaffrey, Ian Toma, Zhaoqing Yang, Richard Katz, Jonathan Reiner, Ramesh Mazhari, Palak Shah, Zachary Falk, Richard Wargowsky, Jennifer Goldman, Dan Jones, Dmitry Shtokalo, Denis Antonets, Tisha Jepson, Anastasia Fetisova, Kevin Jaatinen, Natalia Ree, Maxim Ri
2021
Very long intergenic non-coding (vlinc) RNAs directly regulate multiple genes in cis and trans
Cao H, Xu D, Cai Y, Han X, Tang L, Gao F, Qi Y, Cai D, Wang H, Ri M, Antonets D, Vyatkin Y, Chen Y, You X, Wang F, Nicolas E, Kapranov P.
BMC Biol. 2021 May 20;19(1):108. doi: 10.1186/s12915-021-01044-x. PMID: 34016118; PMCID: PMC8139166
RNAseq analysis of treatment-dependent signaling changes during inflammation in a mouse cutaneous wound healing model
St Laurent G 3rd, Toma I, Seilheimer B, Cesnulevicius K, Schultz M, Tackett M, Zhou J, Ri M, Shtokalo D, Antonets D, Jepson T, McCaffrey TA.
BMC Genomics. 2021 Nov 25;22(1):854. doi: 10.1186/s12864-021-08083-2.
RNA sequencing of blood in coronary artery disease: involvement of regulatory T cell imbalance
McCaffrey, T.A., Toma, I., Yang, Z., Katz, R., Reiner, J., Mazhari, R., Shah, P., Tackett, M., Jones, D., Jepson, T., Falk, Z., Wargodsky, R., Shtakalo, D., Antonets, D., Ertle, J., Kim, J., Lai, Y., Arslan, Z., Aledort, E., Alfaraidy M., St.Laurent III, G.
BMC Med Genomics 14, 216 (2021)
2020
Immunogenicity and Protective Efficacy of Influenza A DNA Vaccines Encoding Artificial Antigens Based on Conservative Hemagglutinin Stem Region and M2 Protein in Mice
Bazhan S, Antonets D, Starostina E, Ilyicheva T, Kaplina O, Marchenko V, Durymanov A, Oreshkova S, Karpenko L
Vaccines (Basel). 2020 Aug 9;8(3):448. doi: 10.3390/vaccines8030448. PMID: 32784907; PMCID: PMC7565880.
In silico design of influenza a virus artificial epitope-based T-cell antigens and the evaluation of their immunogenicity in mice
Bazhan SI, Antonets DV, Starostina EV, Ilyicheva TN, Kaplina ON, Marchenko VY, Volkova OY, Bakulina AY, Karpenko LI
J Biomol Struct Dyn. 2022 Apr;40(7):3196-3212. doi: 10.1080/07391102.2020.1845978. Epub 2020 Nov 23. PMID: 33222632.
Cationic Polymers for the Delivery of the Ebola DNA Vaccine Encoding Artificial T-Cell Immunogen
Karpenko LI, Apartsin EK, Dudko SG, Starostina EV, Kaplina ON, Antonets DV, Volosnikova EA, Zaitsev BN, Bakulina AY, Venyaminova AG, Ilyichev AA, Bazhan SI.
Vaccines (Basel). 2020 Dec 1;8(4):718. doi: 10.3390/vaccines8040718. PMID: 33271964; PMCID: PMC7760684.
Biomarker discovery in attention deficit hyperactivity disorder: RNA sequencing of whole blood in discordant twin and case-controlled cohorts
McCaffrey TA, St Laurent G 3rd, Shtokalo D, Antonets D, Vyatkin Y, Jones D, Battison E, Nigg JT.
BMC Med Genomics. 2020 Oct 28;13(1):160. doi: 10.1186/s12920-020-00808-8. PMID: 33115496; PMCID: PMC7594430.
CellCountCV-A Web-Application for Accurate Cell Counting and Automated Batch Processing of Microscopic Images Using Fully Convolutional Neural Networks
Denis Antonets, Nikolai Russkikh, Antoine Sanchez, Victoria Kovalenko, Elvira Bairamova, Dmitry Shtokalo, Sergey Medvedev, Suren Zakian
Sensors (Basel). 2020 Jun 29;20(13):3653. doi: 10.3390/s20133653.
Style transfer with variational autoencoders is a promising approach to RNA-Seq data harmonization and analysis
Nikolai Russkikh, Denis Antonets, Dmitry Shtokalo, Alexander Makarov, Yuri Vyatkin, Alexey Zakharov, Evgeny Terentyev
Bioinformatics, Volume 36, Issue 20, 15 October 2020
2019
Artificial Anti-HIV-1 Immunogen Comprising Epitopes of Broadly Neutralizing Antibodies 2F5, 10E8, and a Peptide Mimic of VRC01 Discontinuous Epitope
Rudometov AP, Chikaev AN, Rudometova NB, Antonets DV, Lomzov AA, Kaplina ON, Ilyichev AA, Karpenko LI
Vaccines (Basel). 2019 Aug 6;7(3):83. doi: 10.3390/vaccines7030083. PMID: 31390770; PMCID: PMC6789618.
2018
The search of CAR, AhR, ESRs binding sites in promoters of intronic and intergenic microRNAs
Ovchinnikov VY, Antonets DV, Gulyaeva LF
J Bioinform Comput Biol. 2018 Feb;16(1):1750029. doi: 10.1142/S0219720017500299. Epub 2017 Dec 10. PMID: 29301444.
Design of Artificial Immunogens Containing Melanoma-associated T-cell Epitopes
Borobova EA, Antonets DV, Starostina EV, Karpenko LI, Ilyichev AA, Bazhan SI.
Curr Gene Ther. 2018;18(6):375-385. doi: 10.2174/1566523218666181113112829. PMID: 30421674.
2016
Functional annotation of the vlinc class of non-coding RNAs using systems biology approach
G. St. Laurent, Y. Vyatkin, D. Antonets, M. Ri, Y. Qi, O. Saik, D. Shtokalo, M. J.L. de Hoon, H. Kawaji, M. Itoh, T. Lassmann, E. Arner, A.R.R. Forrest, The FANTOM consortium, E. Nicolas, T.A. McCaffrey, P. Carninci, Y. Hayashizaki, C. Wahlestedt, and P. Kapranov.
Nucl. Acids Res. (2016) doi: 10.1093/nar/gkw162
2013
Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila
St Laurent G, Tackett MR, Nechkin S, Shtokalo D, Antonets D, Savva YA, Maloney R, Kapranov P, Lawrence CE, Reenan RA
Nature Structural and Molecular Biology. 2013 Sep 29. doi: 10.1038/nsmb.2675

Teaching

2021–2022
NSU

Special course on the analysis of metagenomic data

NSU

Special course: introduction to data analysis and machine learning

2020–2021
NSU

Special course on the analysis of metagenomic data

NSU

Special course: introduction to data analysis and machine learning

2019–2020
NSU

Special course on the analysis of metagenomic data

NSU

Special course: introduction to data analysis and machine learning

Antonets Denis Viktorovich

Links

LinkedIn
ResearchGate

Antonets Denis Viktorovich

Post
Head of Analytics Department
Academic degree
Candidate of Biological Sciences (Ph.D.)
in the Novel team
since 2010
Education
Department of Natural Sciences NSU (2003)
Projects
Protomenal and others
Interests
Bioinformatics, immunoinformatics, virology, metagenomics, NGS, statistics, machine learning, Data Science, Deep Learning

List of publications

2024
Nearly complete genome sequences of the first two identified Colorado potato beetle viruses
Maria Antonets, Sergei Bodnev, Ulyana Rotskaya, Elena Kosman, Tatyana Tregubchak, Tatyana Bauer, Mamedyar Azaev, Vadim Kryukov & Denis Antonets
2023
The Metagenomic Analysis of Viral Diversity in Colorado Potato Beetle Public NGS Data
Maria Starchevskaya, Ekaterina Kamanova, Yuri Vyatkin, Tatyana Tregubchak, Tatyana Bauer, Sergei Bodnev, Ulyana Rotskaya, Olga Polenogova, Vadim Kryukov and Denis Antonets
RNAseq profiling of blood from patients with coronary artery disease: Signature of a T cell imbalance
Timothy A. McCaffrey, Ian Toma, Zhaoqing Yang, Richard Katz, Jonathan Reiner, Ramesh Mazhari, Palak Shah, Zachary Falk, Richard Wargowsky, Jennifer Goldman, Dan Jones, Dmitry Shtokalo, Denis Antonets, Tisha Jepson, Anastasia Fetisova, Kevin Jaatinen, Natalia Ree, Maxim Ri
2021
Very long intergenic non-coding (vlinc) RNAs directly regulate multiple genes in cis and trans
Cao H, Xu D, Cai Y, Han X, Tang L, Gao F, Qi Y, Cai D, Wang H, Ri M, Antonets D, Vyatkin Y, Chen Y, You X, Wang F, Nicolas E, Kapranov P.
BMC Biol. 2021 May 20;19(1):108. doi: 10.1186/s12915-021-01044-x. PMID: 34016118; PMCID: PMC8139166
RNAseq analysis of treatment-dependent signaling changes during inflammation in a mouse cutaneous wound healing model
St Laurent G 3rd, Toma I, Seilheimer B, Cesnulevicius K, Schultz M, Tackett M, Zhou J, Ri M, Shtokalo D, Antonets D, Jepson T, McCaffrey TA.
BMC Genomics. 2021 Nov 25;22(1):854. doi: 10.1186/s12864-021-08083-2.
RNA sequencing of blood in coronary artery disease: involvement of regulatory T cell imbalance
McCaffrey, T.A., Toma, I., Yang, Z., Katz, R., Reiner, J., Mazhari, R., Shah, P., Tackett, M., Jones, D., Jepson, T., Falk, Z., Wargodsky, R., Shtakalo, D., Antonets, D., Ertle, J., Kim, J., Lai, Y., Arslan, Z., Aledort, E., Alfaraidy M., St.Laurent III, G.
BMC Med Genomics 14, 216 (2021)
2020
Immunogenicity and Protective Efficacy of Influenza A DNA Vaccines Encoding Artificial Antigens Based on Conservative Hemagglutinin Stem Region and M2 Protein in Mice
Bazhan S, Antonets D, Starostina E, Ilyicheva T, Kaplina O, Marchenko V, Durymanov A, Oreshkova S, Karpenko L
Vaccines (Basel). 2020 Aug 9;8(3):448. doi: 10.3390/vaccines8030448. PMID: 32784907; PMCID: PMC7565880.
In silico design of influenza a virus artificial epitope-based T-cell antigens and the evaluation of their immunogenicity in mice
Bazhan SI, Antonets DV, Starostina EV, Ilyicheva TN, Kaplina ON, Marchenko VY, Volkova OY, Bakulina AY, Karpenko LI
J Biomol Struct Dyn. 2022 Apr;40(7):3196-3212. doi: 10.1080/07391102.2020.1845978. Epub 2020 Nov 23. PMID: 33222632.
Cationic Polymers for the Delivery of the Ebola DNA Vaccine Encoding Artificial T-Cell Immunogen
Karpenko LI, Apartsin EK, Dudko SG, Starostina EV, Kaplina ON, Antonets DV, Volosnikova EA, Zaitsev BN, Bakulina AY, Venyaminova AG, Ilyichev AA, Bazhan SI.
Vaccines (Basel). 2020 Dec 1;8(4):718. doi: 10.3390/vaccines8040718. PMID: 33271964; PMCID: PMC7760684.
Biomarker discovery in attention deficit hyperactivity disorder: RNA sequencing of whole blood in discordant twin and case-controlled cohorts
McCaffrey TA, St Laurent G 3rd, Shtokalo D, Antonets D, Vyatkin Y, Jones D, Battison E, Nigg JT.
BMC Med Genomics. 2020 Oct 28;13(1):160. doi: 10.1186/s12920-020-00808-8. PMID: 33115496; PMCID: PMC7594430.
CellCountCV-A Web-Application for Accurate Cell Counting and Automated Batch Processing of Microscopic Images Using Fully Convolutional Neural Networks
Denis Antonets, Nikolai Russkikh, Antoine Sanchez, Victoria Kovalenko, Elvira Bairamova, Dmitry Shtokalo, Sergey Medvedev, Suren Zakian
Sensors (Basel). 2020 Jun 29;20(13):3653. doi: 10.3390/s20133653.
Style transfer with variational autoencoders is a promising approach to RNA-Seq data harmonization and analysis
Nikolai Russkikh, Denis Antonets, Dmitry Shtokalo, Alexander Makarov, Yuri Vyatkin, Alexey Zakharov, Evgeny Terentyev
Bioinformatics, Volume 36, Issue 20, 15 October 2020
2019
Artificial Anti-HIV-1 Immunogen Comprising Epitopes of Broadly Neutralizing Antibodies 2F5, 10E8, and a Peptide Mimic of VRC01 Discontinuous Epitope
Rudometov AP, Chikaev AN, Rudometova NB, Antonets DV, Lomzov AA, Kaplina ON, Ilyichev AA, Karpenko LI
Vaccines (Basel). 2019 Aug 6;7(3):83. doi: 10.3390/vaccines7030083. PMID: 31390770; PMCID: PMC6789618.
2018
The search of CAR, AhR, ESRs binding sites in promoters of intronic and intergenic microRNAs
Ovchinnikov VY, Antonets DV, Gulyaeva LF
J Bioinform Comput Biol. 2018 Feb;16(1):1750029. doi: 10.1142/S0219720017500299. Epub 2017 Dec 10. PMID: 29301444.
Design of Artificial Immunogens Containing Melanoma-associated T-cell Epitopes
Borobova EA, Antonets DV, Starostina EV, Karpenko LI, Ilyichev AA, Bazhan SI.
Curr Gene Ther. 2018;18(6):375-385. doi: 10.2174/1566523218666181113112829. PMID: 30421674.
2016
Functional annotation of the vlinc class of non-coding RNAs using systems biology approach
G. St. Laurent, Y. Vyatkin, D. Antonets, M. Ri, Y. Qi, O. Saik, D. Shtokalo, M. J.L. de Hoon, H. Kawaji, M. Itoh, T. Lassmann, E. Arner, A.R.R. Forrest, The FANTOM consortium, E. Nicolas, T.A. McCaffrey, P. Carninci, Y. Hayashizaki, C. Wahlestedt, and P. Kapranov.
Nucl. Acids Res. (2016) doi: 10.1093/nar/gkw162
2013
Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila
St Laurent G, Tackett MR, Nechkin S, Shtokalo D, Antonets D, Savva YA, Maloney R, Kapranov P, Lawrence CE, Reenan RA
Nature Structural and Molecular Biology. 2013 Sep 29. doi: 10.1038/nsmb.2675

Teaching

2021–2022
NSU

Special course on the analysis of metagenomic data

NSU

Special course: introduction to data analysis and machine learning

2020–2021
NSU

Special course on the analysis of metagenomic data

NSU

Special course: introduction to data analysis and machine learning

2019–2020
NSU

Special course on the analysis of metagenomic data

NSU

Special course: introduction to data analysis and machine learning