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1
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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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Zhang H, Yu F, Xie P, Sun S, Qiao X, Tang S, Chen C, Yang S, Mei C, Yang D, Wu Y, Xia R, Li X, Lu J, Liu Y, Xie X, Ma D, Xu X, Liang Z, Feng Z, Huang X, Yu H, Liu G, Wang Y, Li J, Zhang Q, Chen C, Ouyang Y, Xie Q. A Gγ protein regulates alkaline sensitivity in crops. Science 2023; 379:eade8416. [PMID: 36952416 DOI: 10.1126/science.ade8416] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The use of alkaline salt lands for crop production is hindered by a scarcity of knowledge and breeding efforts for plant alkaline tolerance. Through genome association analysis of sorghum, a naturally high-alkaline-tolerant crop, we detected a major locus, Alkaline Tolerance 1 (AT1), specifically related to alkaline-salinity sensitivity. An at1 allele with a carboxyl-terminal truncation increased sensitivity, whereas knockout of AT1 increased tolerance to alkalinity in sorghum, millet, rice, and maize. AT1 encodes an atypical G protein γ subunit that affects the phosphorylation of aquaporins to modulate the distribution of hydrogen peroxide (H2O2). These processes appear to protect plants against oxidative stress by alkali. Designing knockouts of AT1 homologs or selecting its natural nonfunctional alleles could improve crop productivity in sodic lands.
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Affiliation(s)
- Huili Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- Breeding Base of State Key Laboratory of Land Degradation and Ecological Restoration of North Western China, School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Feifei Yu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Grassland Science and Technology, China Agricultural University, Beijing 100083, China
| | - Peng Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengyuan Sun
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology and Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Xinhua Qiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sanyuan Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengxuan Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Sen Yang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cuo Mei
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dekai Yang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaorong Wu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Ran Xia
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xu Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jun Lu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuxi Liu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaowei Xie
- Breeding Base of State Key Laboratory of Land Degradation and Ecological Restoration of North Western China, School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Dongmei Ma
- Breeding Base of State Key Laboratory of Land Degradation and Ecological Restoration of North Western China, School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Xing Xu
- Breeding Base of State Key Laboratory of Land Degradation and Ecological Restoration of North Western China, School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Zhengwei Liang
- Northeast Institute of Geography and Agroecology, Daan National Station for Agro-ecosystem Observation and Research, Chinese Academy of Sciences, Changchun 130102, China
| | - Zhonghui Feng
- University of Chinese Academy of Sciences, Beijing 100049, China
- Northeast Institute of Geography and Agroecology, Daan National Station for Agro-ecosystem Observation and Research, Chinese Academy of Sciences, Changchun 130102, China
| | - Xiahe Huang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Hong Yu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Guifu Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingchun Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Chang Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Center of Technology Innovation for Maize, State Key Laboratory of Maize Germplasm Innovation and Molecular Breeding, Syngenta Group China, Beijing 102206, China
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3
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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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4
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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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5
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Orlov YL, Anashkina AA. Life: Computational Genomics Applications in Life Sciences. Life (Basel) 2021; 11:life11111211. [PMID: 34833087 PMCID: PMC8622464 DOI: 10.3390/life11111211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 01/19/2023] 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), 119991 Moscow, Russia;
- Life Sciences Department, Novosibirsk State University, 630090 Novosibirsk, Russia
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia, 117198 Moscow, Russia
- Correspondence:
| | - 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
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6
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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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7
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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: 17] [Impact Index Per Article: 5.7] [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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8
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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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9
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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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10
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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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11
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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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12
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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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13
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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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14
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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, 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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16
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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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17
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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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18
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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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19
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Baranova AV, Klimontov VV, Letyagin AY, Orlov YL. Medical genomics research at BGRS-2018. BMC Med Genomics 2019; 12:36. [PMID: 30871564 PMCID: PMC6416836 DOI: 10.1186/s12920-019-0480-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Ancha V Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, USA.,Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - Vadim V Klimontov
- Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia
| | - Andrey Y Letyagin
- Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia
| | - Yuriy L Orlov
- 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
- Novosibirsk State University, Novosibirsk, Russia. .,The A.O. Kovalevsky Institute of Marine Biological Research of RAS, Sevastopol, Russia.
| | | | - Ancha V Baranova
- Research Centre of Medical Genetics, Moscow, Russia.,Moscow Institute of Physics and Technology (State University), Dolgoprudnyi, Russia
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Orlov YL, Tatarinova TV, Zakhartsev MV, Kolchanov NA. Introduction to the 9th Young Scientists School on Systems Biology and Bioinformatics (SBB'2017). J Bioinform Comput Biol 2018; 16:1802001. [PMID: 29439645 DOI: 10.1142/s0219720018020018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Yuriy L Orlov
- 1 Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.,2 Novosibirsk State University, Novosibirsk, Russia.,3 Institute of Marine Biology Researches of the RAS, Sevastopol, Russia
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Affiliation(s)
- Yuriy L Orlov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
| | | | - Ming Chen
- Zhejiang University, Hangzhou, China
| | - Ancha V Baranova
- Research Centre of Medical Genetics, Moscow, Russia
- George Mason University, Fairfax, VA, USA
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Affiliation(s)
- Yuriy L Orlov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
| | - Ancha V Baranova
- Research Centre of Medical Genetics, Moscow, Russia
- George Mason University, Fairfax, VA, USA
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Orlov YL, Baranova AV, Chen M, Salina EA. Plant Biology at Belyaev Conference - 2017. BMC PLANT BIOLOGY 2017; 17:257. [PMID: 29297331 PMCID: PMC5751566 DOI: 10.1186/s12870-017-1189-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Yuriy L Orlov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
| | - Ancha V Baranova
- Research Centre of Medical Genetics, Moscow, Russia
- George Mason University, Fairfax, VA, USA
| | - Ming Chen
- Zhejiang University, Hangzhou, China
| | - Elena A Salina
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
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Orlov YL, Baranova AV, Tatarinova TV, Kolchanov NA. Genetics at Belyaev Conference - 2017: introductory note. BMC Genet 2017; 18:116. [PMID: 29297300 PMCID: PMC5751695 DOI: 10.1186/s12863-017-0577-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Yuriy L Orlov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia. .,Novosibirsk State University, Novosibirsk, Russia.
| | - Ancha V Baranova
- Research Centre of Medical Genetics, Moscow, Russia.,George Mason University, Fairfax, VA, USA
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Affiliation(s)
- Ancha V Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, 22030, USA.
- Research Centre for Medical Genetics, Moskvorechie, 1, Moscow, Russia.
| | - Yuriy L Orlov
- Institute of Cytology and Genetics SB RAS, Lavrentyeva, 10, 630090, Novosibirsk, Russia
- Novosibirsk State University, Pirogova, 2, 630090, Novosibirsk, Russia
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Orlov YL, Baranova AV, Hofestädt R, Kolchanov NA. Computational genomics at BGRS\SB-2016: introductory note. BMC Genomics 2016; 17:996. [PMID: 28105925 PMCID: PMC5249040 DOI: 10.1186/s12864-016-3350-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Yuriy L Orlov
- Institute of Cytology and Genetics SB RAS, Lavrentyeva, 10, 630090, Novosibirsk, Russia. .,Novosibirsk State University, Pirogova, 2, 630090, Novosibirsk, Russia.
| | - Ancha V Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, 22030, USA.,Research Centre for Medical Genetics, Moskvorechie, 1, Moscow, Russia
| | | | - Nikolay A Kolchanov
- Institute of Cytology and Genetics SB RAS, Lavrentyeva, 10, 630090, Novosibirsk, Russia
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Orlov YL, Baranova AV, Markel AL. Computational models in genetics at BGRS\SB-2016: introductory note. BMC Genet 2016; 17:155. [PMID: 28105935 PMCID: PMC5249000 DOI: 10.1186/s12863-016-0465-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Affiliation(s)
- Yuriy L Orlov
- Institute of Cytology and Genetics SB RAS, Lavrentyeva, 10, 630090, Novosibirsk, Russia. .,Novosibirsk State University, Pirogova, 2, 630090, Novosibirsk, Russia.
| | - Ancha V Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, 22030, USA.,Research Centre for Medical Genetics, Moskvorechie 1, Moscow, Russia
| | - Arcady L Markel
- Institute of Cytology and Genetics SB RAS, Lavrentyeva, 10, 630090, Novosibirsk, Russia.,Novosibirsk State University, Pirogova, 2, 630090, Novosibirsk, Russia
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Orlov YL, Baranova AV, Salina EA. Computational plant bioscience at BGRS\SB-2016: introductory note. BMC PLANT BIOLOGY 2016; 16:243. [PMID: 28105950 PMCID: PMC5123298 DOI: 10.1186/s12870-016-0923-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Yuriy L Orlov
- Institute of Cytology and Genetics SB RAS, Lavrentyeva, 10, 630090, Novosibirsk, Russia.
- Novosibirsk State University, 630090, Novosibirsk, Russia.
| | - Ancha V Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, 22030, USA
| | - Elena A Salina
- Institute of Cytology and Genetics SB RAS, Lavrentyeva, 10, 630090, Novosibirsk, Russia
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