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Orlov YL, Chen M, Kolchanov NA, Hofestädt R. BGRS: bioinformatics of genome regulation and data integration. J Integr Bioinform 2023; 20:jib-2023-0032. [PMID: 37972410 PMCID: PMC10757072 DOI: 10.1515/jib-2023-0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Affiliation(s)
- Yuriy L. Orlov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090Novosibirsk, Russia
- Life Sciences Department, Novosibirsk State University, 630090Novosibirsk, Russia
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119991Moscow, Russia
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia, 117198Moscow, Russia
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou310058, China
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090Novosibirsk, Russia
- Life Sciences Department, Novosibirsk State University, 630090Novosibirsk, Russia
| | - Ralf Hofestädt
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
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2
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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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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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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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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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Anashkina AA, Leberfarb EY, Orlov YL. Recent Trends in Cancer Genomics and Bioinformatics Tools Development. Int J Mol Sci 2021; 22:ijms222212146. [PMID: 34830028 PMCID: PMC8618360 DOI: 10.3390/ijms222212146] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 02/07/2023] Open
Affiliation(s)
- Anastasia A. Anashkina
- 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;
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elena Y. Leberfarb
- Department of Medicinal Chemistry, Novosibirsk State Medical University, 630091 Novosibirsk, Russia;
| | - 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), 119991 Moscow, Russia;
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Life Sciences Department, Novosibirsk State University, 630090 Novosibirsk, Russia
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia, 117198 Moscow, Russia
- Correspondence: or
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7
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Bioinformatics Applications to Reveal Molecular Mechanisms of Gene Expression Regulation in Model Organisms. Int J Mol Sci 2021; 22:ijms222111973. [PMID: 34769403 PMCID: PMC8584893 DOI: 10.3390/ijms222111973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 02/06/2023] Open
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Medical Genetics, Genomics and Bioinformatics Aid in Understanding Molecular Mechanisms of Human Diseases. Int J Mol Sci 2021; 22:ijms22189962. [PMID: 34576125 PMCID: PMC8467458 DOI: 10.3390/ijms22189962] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 12/14/2022] Open
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9
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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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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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