{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,1,6]],"date-time":"2024-01-06T05:07:36Z","timestamp":1704517656915},"reference-count":45,"publisher":"Walter de Gruyter GmbH","issue":"3","license":[{"start":{"date-parts":[[2023,9,1]],"date-time":"2023-09-01T00:00:00Z","timestamp":1693526400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"RSF-NSFC joint project \"Smart Crop\" - Cognitive Platform for Reconstruction, Visualization and Analysis of Stress Response Networks based on ANDSystem and Multiomics in Rice and Wheat","award":["23-44-00030","32261133526"]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,1]]},"DOI":"10.1515\/jib-2023-0032","type":"journal-article","created":{"date-parts":[[2023,11,17]],"date-time":"2023-11-17T04:39:59Z","timestamp":1700195999000},"source":"Crossref","is-referenced-by-count":0,"title":["BGRS: bioinformatics of genome regulation and data integration"],"prefix":"10.1515","volume":"20","author":[{"ORCID":"http:\/\/orcid.org\/0000-0003-0587-1609","authenticated-orcid":false,"given":"Yuriy L.","family":"Orlov","sequence":"first","affiliation":[{"name":"Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences , 630090 Novosibirsk , Russia"},{"name":"Life Sciences Department , Novosibirsk State University , 630090 Novosibirsk , Russia"},{"name":"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"},{"name":"Agrarian and Technological Institute, Peoples\u2019 Friendship University of Russia , 117198 Moscow , Russia"}]},{"given":"Ming","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics , College of Life Sciences, Zhejiang University , Hangzhou 310058 , China"}]},{"given":"Nikolay A.","family":"Kolchanov","sequence":"additional","affiliation":[{"name":"Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences , 630090 Novosibirsk , Russia"},{"name":"Life Sciences Department , Novosibirsk State University , 630090 Novosibirsk , Russia"}]},{"given":"Ralf","family":"Hofest\u00e4dt","sequence":"additional","affiliation":[{"name":"Faculty of Technology, Bielefeld University , Bielefeld , Germany"}]}],"member":"374","published-online":{"date-parts":[[2023,11,16]]},"reference":[{"key":"2024010601120032168_j_jib-2023-0032_ref_001","doi-asserted-by":"crossref","unstructured":"Orlov, Y, Xu, H, Afonnikov, D, Lim, B, Heng, JC, Yuan, P, et al.. Computer and statistical analysis of transcription factor binding and chromatin modifications by ChIP-seq data in embryonic stem cell. J Integr Bioinform 2012;9:211. https:\/\/doi.org\/10.2390\/biecoll-jib-2012-211.","DOI":"10.1515\/jib-2012-211"},{"key":"2024010601120032168_j_jib-2023-0032_ref_002","doi-asserted-by":"crossref","unstructured":"Orlov, Y, Dobrovolskaya, O, Chen, M, Hofest\u00e4dt, R. Bioinformatics of genome regulation and structure \u2013 2020 papers collection. J Integr Bioinform 2020;17:20200038. https:\/\/doi.org\/10.1515\/jib-2020-0038.","DOI":"10.1515\/jib-2020-0038"},{"key":"2024010601120032168_j_jib-2023-0032_ref_003","doi-asserted-by":"crossref","unstructured":"Heinemeyer, T, Wingender, E, Reuter, I, Hermjakob, H, Kel, AE, Kel, OV, et al.. Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Res 1998;26:362\u20137. https:\/\/doi.org\/10.1093\/nar\/26.1.362.","DOI":"10.1093\/nar\/26.1.362"},{"key":"2024010601120032168_j_jib-2023-0032_ref_004","doi-asserted-by":"crossref","unstructured":"Chen, M, Harrison, A, Shanahan, H, Orlov, Y. Biological big bytes: integrative analysis of large biological datasets. J Integr Bioinform 2017;14:20170052. https:\/\/doi.org\/10.1515\/jib-2017-0052.","DOI":"10.1515\/jib-2017-0052"},{"key":"2024010601120032168_j_jib-2023-0032_ref_005","doi-asserted-by":"crossref","unstructured":"Dergilev, AI, Orlova, NG, Dobrovolskaya, OB, Orlov, YL. Statistical estimates of multiple transcription factors binding in the model plant genomes based on ChIP-seq data. J Integr Bioinform 2022;19:20200036. https:\/\/doi.org\/10.1515\/jib-2020-0036.","DOI":"10.1515\/jib-2020-0036"},{"key":"2024010601120032168_j_jib-2023-0032_ref_006","doi-asserted-by":"crossref","unstructured":"Chao, H, Zhang, S, Hu, Y, Ni, Q, Xin, S, Zhao, L, et al.. Integrating omics databases for enhanced crop breeding. J Integr Bioinform 2023;20:20230012. https:\/\/doi.org\/10.1515\/jib-2023-0012.","DOI":"10.1515\/jib-2023-0012"},{"key":"2024010601120032168_j_jib-2023-0032_ref_007","doi-asserted-by":"crossref","unstructured":"Babenko, VN, Bragin, AO, Spitsina, AM, Chadaeva, IV, Galieva, ER, Orlova, GV, et al.. Analysis of differential gene expression by RNA-seq data in brain areas of laboratory animals. J Integr Bioinform 2016;13:292. https:\/\/doi.org\/10.2390\/biecoll-jib-2016-292.","DOI":"10.1515\/jib-2016-292"},{"key":"2024010601120032168_j_jib-2023-0032_ref_008","doi-asserted-by":"crossref","unstructured":"Babenko, VN, Gubanova, NV, Bragin, AO, Chadaeva, IV, Vasiliev, GV, Medvedeva, IV, et al.. Computer analysis of glioma transcriptome profiling: alternative splicing events. J Integr Bioinform 2017;14:20170022. https:\/\/doi.org\/10.1515\/jib-2017-0022.","DOI":"10.1515\/jib-2017-0022"},{"key":"2024010601120032168_j_jib-2023-0032_ref_009","doi-asserted-by":"crossref","unstructured":"Kratov, S, Zybarev, Y. To the question of the digital platform \u201cbioinformatics\u201d creating and its system-forming solutions. J Integr Bioinform 2020;17:20200029. https:\/\/doi.org\/10.1515\/jib-2020-0029.","DOI":"10.1515\/jib-2020-0029"},{"key":"2024010601120032168_j_jib-2023-0032_ref_010","doi-asserted-by":"crossref","unstructured":"K\u00f6nig, M, Gleeson, P, Golebiewski, M, Gorochowski, T, Hucka, M, Keating, SM, et al.. Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022. J Integr Bioinform 2023;20:20230004. https:\/\/doi.org\/10.1515\/jib-2023-0004.","DOI":"10.1515\/jib-2023-0004"},{"key":"2024010601120032168_j_jib-2023-0032_ref_011","doi-asserted-by":"crossref","unstructured":"Takan, S, Allmer, J. Community-wide collaboration is a must to reinstall trust in bioinformatics solutions and biomedical interpretation. J Integr Bioinform 2023;20:20220028. https:\/\/doi.org\/10.1515\/jib-2022-0028.","DOI":"10.1515\/jib-2022-0028"},{"key":"2024010601120032168_j_jib-2023-0032_ref_012","doi-asserted-by":"crossref","unstructured":"Casano, N, Santini, S, Vittorini, P, Sinatti, G, Carducci, P, Mastroianni, CM, et al.. Application of machine learning approach in emergency department to support clinical decision making for SARS-CoV-2 infected patients. J Integr Bioinform 2023;20:20220047. https:\/\/doi.org\/10.1515\/jib-2022-0047.","DOI":"10.1515\/jib-2022-0047"},{"key":"2024010601120032168_j_jib-2023-0032_ref_013","doi-asserted-by":"crossref","unstructured":"Orlov, YL, Baranova, AV, Hofestaedt, R, Kolchanov, A. Computational genomics at BGRS\\SB-2016: introductory note. BMC Genom 2016;17:996. https:\/\/doi.org\/10.1186\/s12864-016-3350-6.","DOI":"10.1186\/s12864-016-3350-6"},{"key":"2024010601120032168_j_jib-2023-0032_ref_014","doi-asserted-by":"crossref","unstructured":"Orlov, YL, Kolchanov, NA, Hofest\u00e4dt, R, Wong, L. Editorial \u2013 bioinformatics development at the BGRS\\SB conference series: 10th anniversary. J Bioinf Comput Biol 2017;15:1702001. https:\/\/doi.org\/10.1142\/S0219720017020012.","DOI":"10.1142\/S0219720017020012"},{"key":"2024010601120032168_j_jib-2023-0032_ref_015","doi-asserted-by":"crossref","unstructured":"Orlov, YL, Hofest\u00e4dt, R, Tatarinova, TV. Bioinformatics research at BGRS\\SB-2018. J Bioinf Comput Biol 2019;17:1902001. https:\/\/doi.org\/10.1142\/S0219720019020013.","DOI":"10.1142\/S0219720019020013"},{"key":"2024010601120032168_j_jib-2023-0032_ref_016","doi-asserted-by":"crossref","unstructured":"Ahsan, M, Liu, Y, Feng, C, Hofest\u00e4dt, R, Chen, M. OverCOVID: an integrative web portal for SARS-CoV-2 bioinformatics resources. J Integr Bioinform 2021;18:9\u201317. https:\/\/doi.org\/10.1515\/jib-2020-0046.","DOI":"10.1515\/jib-2020-0046"},{"key":"2024010601120032168_j_jib-2023-0032_ref_017","unstructured":"Orlov, Y, Xu, H, Afonnikov, D, Lim, B, Heng, J-C, Yuan, P, et al.. Computer and statistical analysis of transcription factor binding and chromatin modifications by ChIP-seq data in embryonic stem cell. In: Proceedings IB 2012 (international symposium on integrative bioinformatics. The 8th annual meeting). Hangzhou, China: Zhejiang University Press; 2012:80\u201392 pp."},{"key":"2024010601120032168_j_jib-2023-0032_ref_018","doi-asserted-by":"crossref","unstructured":"Orlov, YL, Baranova, AV, Hofest\u00e4dt, R, Kolchanov, NA. Genomics at Belyaev conference \u2013 2017. BMC Genom 2018;19:79. https:\/\/doi.org\/10.1186\/s12864-018-4476-5.","DOI":"10.1186\/s12864-018-4476-5"},{"key":"2024010601120032168_j_jib-2023-0032_ref_019","doi-asserted-by":"crossref","unstructured":"Shumny, VK. To the centenary of the birth of outstanding evolutionist Dmitri Konstantinovich Belyaev. Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov. J Genet Breed 2017;21:387\u201391. https:\/\/doi.org\/10.18699\/VJ17.256.","DOI":"10.18699\/VJ17.256"},{"key":"2024010601120032168_j_jib-2023-0032_ref_020","doi-asserted-by":"crossref","unstructured":"Shumny, VK. Development of genetic research in the USSR. Genome 1989;31:900\u20134. https:\/\/doi.org\/10.1139\/g89-160. 2698850.","DOI":"10.1139\/g89-160"},{"key":"2024010601120032168_j_jib-2023-0032_ref_021","unstructured":"Ratner, VA. PRINTSIP SVIAZNOSTI SERI\u2019I I OPREDELENIE PORIADKA OSNOVANI I V KODONAKH [Principles of series coherence and the determination of the basic order of codones]. Biofizika 1964;9:621\u20135."},{"key":"2024010601120032168_j_jib-2023-0032_ref_022","unstructured":"Churaev, RN, Ratner, VA. The modelling of operon systems in the language of the theory of automata. Sov Genet 1974;9:267\u20138."},{"key":"2024010601120032168_j_jib-2023-0032_ref_023","unstructured":"Ratner, VA. Geneticheski\u012d iazyk: grammatika, semantika, \u00e9voliutsiia [The genetic language: grammar, semantics, evolution]. Genetika 1993;29:709\u201319."},{"key":"2024010601120032168_j_jib-2023-0032_ref_024","unstructured":"Likhoshva\u012d, VA, IuG, M, Ratushny\u012d, AV, Anan\u2019ko, EA, Ignat\u2019eva, EV, Podkolodnaia, OA. Obobshchenny\u012d khimiko-kineticheski\u012d metod modelirovaniia gennykh sete\u012d [A generalized chemical-kinetic method for modeling gene networks]. Mol Biol 2001;35:1072\u20139."},{"key":"2024010601120032168_j_jib-2023-0032_ref_025","doi-asserted-by":"crossref","unstructured":"Likhoshvai, VA, Fadeev, SI, Kogai, VV, Khlebodarova, TM. On the chaos in gene networks. J Bioinf Comput Biol 2013;11:1340009. https:\/\/doi.org\/10.1142\/S021972001340009X.","DOI":"10.1142\/S021972001340009X"},{"key":"2024010601120032168_j_jib-2023-0032_ref_026","doi-asserted-by":"crossref","unstructured":"Baranova, AV, Orlov, YL. The papers presented at 7th young scientists school \u201csystems biology and bioinformatics\u201d (SBB\u201915): introductory note. BMC Genet 2016;17:S20. https:\/\/doi.org\/10.1186\/s12863-015-0326-5.","DOI":"10.1186\/s12863-015-0326-5"},{"key":"2024010601120032168_j_jib-2023-0032_ref_027","doi-asserted-by":"crossref","unstructured":"Orlov, YL, Voropaeva, EN, Chen, M, Baranova, AV. Medical genomics at the systems biology and bioinformatics (SBB-2019) school. BMC Med Genom 2020;13:127. https:\/\/doi.org\/10.1186\/s12920-020-00786-x.13.","DOI":"10.1186\/s12920-020-00786-x"},{"key":"2024010601120032168_j_jib-2023-0032_ref_028","doi-asserted-by":"crossref","unstructured":"Orlov, YL, Ignatov, AN, Galieva, ER, Dobrovolskaya, OB. Microbiology research at the systems biology and bioinformatics \u2013 2019 (SBB-2019) school. BMC Microbiol 2020;20:348. https:\/\/doi.org\/10.1186\/s12866-020-02038-5.","DOI":"10.1186\/s12866-020-02038-5"},{"key":"2024010601120032168_j_jib-2023-0032_ref_029","doi-asserted-by":"crossref","unstructured":"Orlov, YL, Chen, WL, Sekacheva, MI, Cai, G, Li, H. Editorial: high-throughput sequencing-based investigation of chronic disease Markers and mechanisms. Front Genet 2022;13:922206. https:\/\/doi.org\/10.3389\/fgene.2022.922206.","DOI":"10.3389\/fgene.2022.922206"},{"key":"2024010601120032168_j_jib-2023-0032_ref_030","doi-asserted-by":"crossref","unstructured":"Anashkina, AA, Leberfarb, EY, Orlov, YL. Recent trends in cancer genomics and bioinformatics tools development. Int J Mol Sci 2021;22:12146. https:\/\/doi.org\/10.3390\/ijms222212146.","DOI":"10.3390\/ijms222212146"},{"key":"2024010601120032168_j_jib-2023-0032_ref_031","doi-asserted-by":"crossref","unstructured":"Klimontov, VV, Koshechkin, KA, Orlova, NG, Sekacheva, MI, Orlov, YL. Medical genetics, genomics and bioinformatics\u20142022. Int J Mol Sci 2023;24:8968. https:\/\/doi.org\/10.3390\/ijms24108968.","DOI":"10.3390\/ijms24108968"},{"key":"2024010601120032168_j_jib-2023-0032_ref_032","doi-asserted-by":"crossref","unstructured":"Orlov, YL, Ivanisenko, VA, Dobrovolskaya, OB, Chen, M. Plant biology and Biotechnology: focus on genomics and bioinformatics. Int J Mol Sci 2022;23:6759. https:\/\/doi.org\/10.3390\/ijms23126759.","DOI":"10.3390\/ijms23126759"},{"key":"2024010601120032168_j_jib-2023-0032_ref_033","doi-asserted-by":"crossref","unstructured":"Orlov, YL, Anashkina, AA, Kumeiko, VV, Chen, M, Kolchanov, NA. Research topics of the bioinformatics of gene regulation. Int J Mol Sci 2023;24:8774. https:\/\/doi.org\/10.3390\/ijms24108774.","DOI":"10.3390\/ijms24108774"},{"key":"2024010601120032168_j_jib-2023-0032_ref_034","doi-asserted-by":"crossref","unstructured":"Orlov, YL, Baranova, AV. Editorial: bioinformatics of genome regulation and systems biology. Front Genet 2020;11:625. https:\/\/doi.org\/10.3389\/fgene.2020.00625.","DOI":"10.3389\/fgene.2020.00625"},{"key":"2024010601120032168_j_jib-2023-0032_ref_035","doi-asserted-by":"crossref","unstructured":"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. https:\/\/doi.org\/10.3389\/fgene.2023.1215987.","DOI":"10.3389\/fgene.2023.1215987"},{"key":"2024010601120032168_j_jib-2023-0032_ref_036","doi-asserted-by":"crossref","unstructured":"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 Genom 2019;20:322. https:\/\/doi.org\/10.1186\/s12864-019-5534-3.","DOI":"10.1186\/s12864-019-5707-0"},{"key":"2024010601120032168_j_jib-2023-0032_ref_037","doi-asserted-by":"crossref","unstructured":"Voropaeva, EN, Pospelova, TI, Voevoda, MI, Maksimov, VN, Orlov, YL, Seregina, OB. Clinical aspects of TP53 gene inactivation in diffuse large B-cell lymphoma. BMC Med Genom 2019;12:35. https:\/\/doi.org\/10.1186\/s12920-019-0484-9.","DOI":"10.1186\/s12920-019-0484-9"},{"key":"2024010601120032168_j_jib-2023-0032_ref_038","doi-asserted-by":"crossref","unstructured":"Orlov, YL, Hofestaedt, RM, Kolchanov, NA. Introductory note for BGRS\\SB-2014 special issue. J Bioinf Comput Biol 2015;13:1502001. https:\/\/doi.org\/10.1142\/S0219720015020011.","DOI":"10.1142\/S0219720015020011"},{"key":"2024010601120032168_j_jib-2023-0032_ref_039","doi-asserted-by":"crossref","unstructured":"Antropova, EA, Khlebodarova, TM, Demenkov, PS, Volianskaia, AR, Venzel, AS, Ivanisenko, NV, et al.. Reconstruction of the regulatory hypermethylation network controlling hepatocellular carcinoma development during hepatitis C viral infection. J Integr Bioinform 2023;20:20230013. https:\/\/doi.org\/10.1515\/jib-2023-0013.","DOI":"10.1515\/jib-2023-0013"},{"key":"2024010601120032168_j_jib-2023-0032_ref_040","doi-asserted-by":"crossref","unstructured":"Ivanisenko, TV, Demenkov, PS, Kolchanov, NA, Ivanisenko, VA. The new version of the ANDDigest tool with improved AI-based short names recognition. Int J Mol Sci 2023;23:14934. https:\/\/doi.org\/10.3390\/ijms232314934.","DOI":"10.3390\/ijms232314934"},{"key":"2024010601120032168_j_jib-2023-0032_ref_041","doi-asserted-by":"crossref","unstructured":"Veljkovic, AN, Orlov, YL, Mitic, NS. BioGraph: data model for linking and querying diverse biological metadata. Int J Mol Sci 2023;24:6954. https:\/\/doi.org\/10.3390\/ijms24086954.","DOI":"10.3390\/ijms24086954"},{"key":"2024010601120032168_j_jib-2023-0032_ref_042","doi-asserted-by":"crossref","unstructured":"Akbari Rokn Abadi, S, Mohammadi, A, Koohi, S. A new profiling approach for DNA sequences based on the nucleotides\u2019 physicochemical features for accurate analysis of SARS-CoV-2 genomes. BMC Genom 2023;24:266. https:\/\/doi.org\/10.1186\/s12864-023-09373-7.","DOI":"10.1186\/s12864-023-09373-7"},{"key":"2024010601120032168_j_jib-2023-0032_ref_043","doi-asserted-by":"crossref","unstructured":"Pablo, R, Roberto, D, Victor, S, Isabel, G, Paul, C, Elizabeth, O. Big data in the healthcare system: a synergy with artificial intelligence and blockchain technology. J Integr Bioinform 2022;19:20200035. https:\/\/doi.org\/10.1515\/jib-2020-0035.","DOI":"10.1515\/jib-2020-0035"},{"key":"2024010601120032168_j_jib-2023-0032_ref_044","doi-asserted-by":"crossref","unstructured":"Anashkina, AA, Rubin, AB, Gudimchuk, NB, Vanin, AF, Tsygankov, AA, Orlov, YL. An open call for contributions to a special issue of Biophysical Reviews highlighting the research themes of VII Congress of Russian Biophysicists 2023. Biophys Rev 2022;14:1081\u20132. https:\/\/doi.org\/10.1007\/s12551-022-00998-8.","DOI":"10.1007\/s12551-022-00998-8"},{"key":"2024010601120032168_j_jib-2023-0032_ref_045","doi-asserted-by":"crossref","unstructured":"Anashkina, AA, Rubin, AB, Gudimchuk, NB, Vanin, AF, Tsygankov, AA, Orlov, YL. VII Congress of Russian Biophysicists\u20142023, Krasnodar, Russia. Biophys Rev 2023;15. https:\/\/doi.org\/10.1007\/s12551-023-01164-4.","DOI":"10.1007\/s12551-023-01164-4"}],"container-title":["Journal of Integrative Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2023-0032\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2023-0032\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,6]],"date-time":"2024-01-06T01:35:51Z","timestamp":1704504951000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2023-0032\/html"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,9,1]]},"references-count":45,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2023,11,16]]},"published-print":{"date-parts":[[2024,12,1]]}},"alternative-id":["10.1515\/jib-2023-0032"],"URL":"https:\/\/doi.org\/10.1515\/jib-2023-0032","relation":{},"ISSN":["1613-4516"],"issn-type":[{"value":"1613-4516","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,9,1]]}}}