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1
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Anashkina AA, Orlova NG, Ignatov AN, Chen M, Orlov YL. Editorial: Bioinformatics of genome regulation and systems biology, Volume III. Front Genet 2023; 14:1215987. [PMID: 37274783 PMCID: PMC10233740 DOI: 10.3389/fgene.2023.1215987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/10/2023] [Indexed: 06/07/2023] Open
Affiliation(s)
- Anastasia A. Anashkina
- The Digital Health Institute, I.M.Sechenov First Moscow State Medical University of the Russian Ministry of Health (Sechenov University), Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nina G. Orlova
- Department of Mathematics, Financial University Under the Government of the Russian Federation, Moscow, Russia
| | - Alexander N. Ignatov
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia (RUDN University), Moscow, Russia
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yuriy L. Orlov
- The Digital Health Institute, I.M.Sechenov First Moscow State Medical University of the Russian Ministry of Health (Sechenov University), Moscow, Russia
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia (RUDN University), Moscow, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Institute of Life Sciences and Biomedicine, Far East Federal University, Vladivostok, Russia
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2
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Orlov YL, Ivanisenko VA, Dobrovolskaya OB, Chen M. Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics. Int J Mol Sci 2022; 23:ijms23126759. [PMID: 35743200 PMCID: PMC9223720 DOI: 10.3390/ijms23126759] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 11/16/2022] Open
Abstract
The study of molecular mechanisms of plant stress response is important for agrobiotechnology applications as it was discussed at series of recent bioinformatics conferences [...].
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Affiliation(s)
- Yuriy L. Orlov
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia, 117198 Moscow, Russia;
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119991 Moscow, Russia
- Correspondence:
| | | | - Oxana B. Dobrovolskaya
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia, 117198 Moscow, Russia;
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China;
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3
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Das R, Tatarinova TV, Galieva ER, Orlov YL. Editorial: Association Between Individuals' Genomic Ancestry and Variation in Disease Susceptibility. Front Genet 2022; 13:831320. [PMID: 35186044 PMCID: PMC8847436 DOI: 10.3389/fgene.2022.831320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/14/2022] [Indexed: 12/18/2022] Open
Affiliation(s)
- Ranajit Das
- Yenepoya Research Centre, Yenepoya University, Mangalore, India
| | - Tatiana V Tatarinova
- Natural Science Division, La Verne University, La Verne, CA, United States.,Department of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Elvira R Galieva
- Life Sciences Department, Novosibirsk State University, Novosibirsk, Russia.,Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Yuriy L Orlov
- Life Sciences Department, Novosibirsk State University, Novosibirsk, Russia.,Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.,Agrarian and Technological Institute, Peoples' Friendship University of Russia (RUDN University), Moscow, Russia.,Institute of Digital Medicine, I.M.Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
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4
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Orlov YL, Tatarinova TV, Oparina NY, Galieva ER, Baranova AV. Editorial: Bioinformatics of Genome Regulation, Volume I. Front Genet 2021; 12:803273. [PMID: 34938326 PMCID: PMC8687738 DOI: 10.3389/fgene.2021.803273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/08/2021] [Indexed: 11/23/2022] Open
Affiliation(s)
- Yuriy L Orlov
- Institute of Digital Medicine, I.M.Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Agrarian and Technological Institute, Peoples' Friendship University of Russia (RUDN University), Moscow, Russia.,Life Sciences Department, Novosibirsk State University, Novosibirsk, Russia.,Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | | | - Nina Y Oparina
- Institute of Medicine, University of Gothenburg, Göteborg, Sweden
| | - Elvira R Galieva
- Life Sciences Department, Novosibirsk State University, Novosibirsk, Russia
| | - Ancha V Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, United States.,Research Centre for Medical Genetics, Moscow, Russia
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5
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Orlov YL, Anashkina AA, Tatarinova TV, Baranova AV. Editorial: Bioinformatics of Genome Regulation, Volume II. Front Genet 2021; 12:795257. [PMID: 34819949 PMCID: PMC8606529 DOI: 10.3389/fgene.2021.795257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 10/25/2021] [Indexed: 12/17/2022] Open
Affiliation(s)
- Yuriy L Orlov
- The Digital Health Institute, I.M.Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Agrobiotechnology Department, Agrarian and Technological Institute, Peoples' Friendship University of Russia (RUDN University), Moscow, Russia
| | - Anastasia A Anashkina
- The Digital Health Institute, I.M.Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Ancha V Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, United States.,Research Centre for Medical Genetics, Moscow, Russia
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6
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Orlov YL, Ignatov AN, Galieva ER, Dobrovolskaya OB. Microbiology research at the systems biology and bioinformatics - 2019 (SBB-2019) school. BMC Microbiol 2020; 20:348. [PMID: 33228539 PMCID: PMC7686665 DOI: 10.1186/s12866-020-02038-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yuriy L Orlov
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119146, Moscow, Russia. .,Novosibirsk State University, 630090, Novosibirsk, Russia. .,Agrarian and Technological Institute, Peoples' Friendship University of Russia (RUDN University), 117198, Moscow, Russia. .,Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia.
| | - Alexander N Ignatov
- Agrarian and Technological Institute, Peoples' Friendship University of Russia (RUDN University), 117198, Moscow, Russia.,PhytoEngineering R&D Centre, 141880, Moscow Region, Moscow, Russia
| | | | - Oxana B Dobrovolskaya
- Agrarian and Technological Institute, Peoples' Friendship University of Russia (RUDN University), 117198, Moscow, Russia.,Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia
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7
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Tatarinova TV, Tabikhanova LE, Eslami G, Bai H, Orlov YL. Genetics research at the "Centenary of human population genetics" conference and SBB-2019. BMC Genet 2020; 21:109. [PMID: 33092531 PMCID: PMC7580810 DOI: 10.1186/s12863-020-00906-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Tatiana V Tatarinova
- Department of Biology, University of La Verne, La Verne, CA, 91750, USA
- Department of Fundamental Biology and Biotechnology, Siberian Federal University, 660074, Krasnoyarsk, Russia
- N.I.Vavilov Institute of General Genetics RAS, 119991, Moscow, Russia
| | - Ludmila E Tabikhanova
- Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia
- Novosibirsk State University, 630090, Novosibirsk, Russia
| | - Gilda Eslami
- Research Center for Food Hygiene and Safety, School of Public Health, Shahid Sadoughi University of Medical Sciences, Yazd, 8916188638, Iran
- Department of Parasitology and Mycology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, 8916188638, Iran
| | - Haihua Bai
- Inner Mongolia University for the Nationalities, 028000, Tongliao, China
| | - Yuriy L Orlov
- Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia.
- Novosibirsk State University, 630090, Novosibirsk, Russia.
- The Digital Health Institute, I.M.Sechenov First Moscow State Medical University (Sechenov University), 119991, Moscow, Russia.
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8
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Baranova AV, Leberfarb EY, Lebedev GS, Orlov YL. Medical genetics studies at the SBB-2019 and MGNGS-2019 conferences. BMC MEDICAL GENETICS 2020; 21:186. [PMID: 33092553 PMCID: PMC7579857 DOI: 10.1186/s12881-020-01109-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Ancha V. Baranova
- George Mason University, Fairfax, VA 22030 USA
- Research Centre for Medical Genetics, 115522 Moscow, Russia
| | | | - Georgy S. Lebedev
- The Digital Health Institute, I.M.Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Yuriy L. Orlov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- The Digital Health Institute, I.M.Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
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9
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Orlov YL, Voropaeva EN, Chen M, Baranova AV. Medical genomics at the Systems Biology and Bioinformatics (SBB-2019) school. BMC Med Genomics 2020; 13:127. [PMID: 32948185 PMCID: PMC7500028 DOI: 10.1186/s12920-020-00786-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Yuriy L. Orlov
- The Digital Health Institute, I.M.Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Research Institute of Internal and Preventive Medicine - Branch of the Institute of Cytology and Genetics SB RAS, 630089 Novosibirsk, Russia
| | - Elena N. Voropaeva
- Research Institute of Internal and Preventive Medicine - Branch of the Institute of Cytology and Genetics SB RAS, 630089 Novosibirsk, Russia
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, First Affiliated Hospital of Medical School, Zhejiang University, Hangzhou, 310058 China
| | - Ancha V. Baranova
- George Mason University, Fairfax, VA 22030 USA
- Research Centre for Medical Genetics, 115522 Moscow, Russia
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10
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Affiliation(s)
- Yuriy L. Orlov
- The Digital Health Institute, I.M.Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia (RUDN), 117198 Moscow, Russia
| | - Elvira R. Galieva
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia (RUDN), 117198 Moscow, Russia
| | - Tatiana V. Tatarinova
- La Verne University, La Verne, CA 91750 USA
- Department of Fundamental Biology and Biotechnology, Siberian Federal University, 660074 Krasnoyarsk, Russia
- Vavilov Instutute of General Genetics RAS, 119991 Moscow, Russia
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11
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Tatarinova TV, Baranova AV, Anashkina AA, Orlov YL. Genomics and Systems Biology at the "Century of Human Population Genetics" conference. BMC Genomics 2020; 21:592. [PMID: 32912158 PMCID: PMC7487983 DOI: 10.1186/s12864-020-06993-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Tatiana V Tatarinova
- La Verne University, La Verne, CA, 91750, USA
- Department of Fundamental Biology and Biotechnology, Siberian Federal University, 660074, Krasnoyarsk, Russia
- George Mason University, Fairfax, VA, 22030, USA
| | - Ancha V Baranova
- George Mason University, Fairfax, VA, 22030, USA
- Research Centre for Medical Genetics, 115522, Moscow, Russia
| | | | - Yuriy L Orlov
- The Digital Health Institute, I.M.Sechenov First Moscow State Medical University (Sechenov University), 119991, Moscow, Russia.
- Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia.
- Novosibirsk State University, 630090, Novosibirsk, Russia.
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12
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Bioinformatics Methods in Medical Genetics and Genomics. Int J Mol Sci 2020; 21:ijms21176224. [PMID: 32872128 PMCID: PMC7504073 DOI: 10.3390/ijms21176224] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
Medical genomics relies on next-gen sequencing methods to decipher underlying molecular mechanisms of gene expression. This special issue collects materials originally presented at the “Centenary of Human Population Genetics” Conference-2019, in Moscow. Here we present some recent developments in computational methods tested on actual medical genetics problems dissected through genomics, transcriptomics and proteomics data analysis, gene networks, protein–protein interactions and biomedical literature mining. We have selected materials based on systems biology approaches, database mining. These methods and algorithms were discussed at the Digital Medical Forum-2019, organized by I.M. Sechenov First Moscow State Medical University presenting bioinformatics approaches for the drug targets discovery in cancer, its computational support, and digitalization of medical research, as well as at “Systems Biology and Bioinformatics”-2019 (SBB-2019) Young Scientists School in Novosibirsk, Russia. Selected recent advancements discussed at these events in the medical genomics and genetics areas are based on novel bioinformatics tools.
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Orlov YL, Baranova AV. Editorial: Bioinformatics of Genome Regulation and Systems Biology. Front Genet 2020; 11:625. [PMID: 32849761 PMCID: PMC7399369 DOI: 10.3389/fgene.2020.00625] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 05/26/2020] [Indexed: 12/31/2022] Open
Affiliation(s)
- Yuriy L Orlov
- Institute of Digital Medicine, I.M.Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Life Sciences Department, Novosibirsk State University, Novosibirsk, Russia.,Agrobiotechnology Department, Agrarian and Technological Institute, Peoples' Friendship University of Russia, Moscow, Russia
| | - Ancha V Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, United States
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14
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Orlov YL, Galieva ER, Melerzanov AV. Computer genomics research at the bioinformatics conference series in Novosibirsk. BMC Genomics 2019; 20:537. [PMID: 31291908 PMCID: PMC6620193 DOI: 10.1186/s12864-019-5846-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Yuriy L. Orlov
- Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119991 Moscow, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | | | - Alexander V. Melerzanov
- Moscow Institute of Physics and Technology (MIPT), 141700, Dolgoprudny, Moscow Region, Russia
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Orlov YL, Kochetov AV, Li G, Kolchanov NA. Genomics research at Bioinformatics of Genome Regulation and Structure\ Systems Biology (BGRS\SB) conferences in Novosibirsk. BMC Genomics 2019; 20:322. [PMID: 32039700 PMCID: PMC7227187 DOI: 10.1186/s12864-019-5707-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Yuriy L Orlov
- Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia. .,Novosibirsk State University, 630090, Novosibirsk, Russia. .,A.O.Kovalevsky Institute of Marine Biological Research of RAS, 119334, Moscow, Russia.
| | - Alex V Kochetov
- Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia
| | - Guoliang Li
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nikolay A Kolchanov
- Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia.,Novosibirsk State University, 630090, Novosibirsk, Russia
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Baranova AV, Skoblov MY, Voropaeva EN, Shanmughavel P, Orlov YL. Medical genetics studies at BGRS conference series. BMC MEDICAL GENETICS 2019; 20:50. [PMID: 30967129 PMCID: PMC6454589 DOI: 10.1186/s12881-019-0769-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Ancha V. Baranova
- School of Systems Biology, George Mason University, Fairfax, VA USA
- Research Centre for Medical Genetics, 115478 Moscow, Russia
| | | | - Elena N. Voropaeva
- Research Institute of Internal and Preventive Medicine - Branch of the Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | | | - Yuriy L. Orlov
- Research Institute of Internal and Preventive Medicine - Branch of the Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
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Affiliation(s)
- Yuriy L. Orlov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Tatiana V. Tatarinova
- Department of Biology, University of La Verne, La Verne, CA USA
- Vavilov Institute for General Genetics, Moscow, Russia
- Siberian Federal University, Krasnoyarsk, Russia
| | - Alex V. Kochetov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
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