Bioinformatics research at BGRS-2018

This thematic issue of BMC Bioinformatics continues the series of BioMed Central special post-conference journal issues presenting materials from the bioinformatics and systems biology summits BGRS\SB (Bioinformatics of Genome Regulation and Structure\Systems Biology). BGRS/SB conference is biannually conducted in Novosibirsk since 1998. In this issue we present five selected papers from the XI BGRS\SB-2018 multi-conference (http://conf.bionet.nsc.ru/bgrssb2018/en/). This Special Issue is accompanied by other BioMed Central Special Issues collecting presented works in the fields of genomics, evolutionary biology, plant biology, and genetics, published as BMC Genomics, BMC Evolutionary Biology, BMC Systems Biology and BMC Plant Biology supplements [1–4]. Recent works at Belyaev Conference-2017 (“Belyaev Readings-2017” http://conf.bionet.nsc.ru/ belyaev100/en) in Novosibirsk, Russia were presented at BioMed Central as well [5–7]. BGRS\SB-2018 included several symposia: “Cognitive Sciences, Genomics and Bioinformatics” (SCGB-2018), “Systems biology and biomedicine” (SbioMed-2018), “Biodiversity: genomics and evolution” (BioGenEvo-2018), “Mathematical modeling and high-performance computing in bioinformatics, biomedicine and biotechnology” (MM-HPC-BBB-2018), “Systems biology of DNA repair processes and programmed cell death” (SbPCD-2018). Each session had presentations of bioinformatics applications. Current special post-conference issue contains selected works on bioinformatics ranging from software for scientific literate mining to applications in plant biology. Below is a brief summary of the papers in this special issue. Ivanisenko et al. [8] presented a new version of the popular ANDSystem tool for automatic text mining of scientific publications, this time equipped with expanded functionality. Currently, there is a number of commercial automated services allowing users to reconstruct molecular-genetic networks using the data automatically extracted from the texts of scientific publications, for example: STRING (https://string-db.org), Pathway Commons (https://www.pathwaycommons.org/), MetaCore (https://portal.genego.com/), and Ingenuity (https://www.qiagenbioinformatics.com/). Presented tool ANDSystem reconstructs associative gene networks taking into account the tissue-specific gene expression. The system allows the reconstruction of combined gene networks, as well as performing the filtering of genes tissue-specific expression. As an example of the application of such filtering, gene network of the extrinsic apoptotic signaling pathway was analyzed. Note that previous publication of this tool was at BMC Systems Biology [9], and recent applications was published in BMC Medical Genomics by Saik et al. [10]. Ranajit Das and Priyanka Upadhyai [11] showed application of the Geographic Population Structure (GPS) and reAdmix algorithms [12, 13] to biogeographic analyses of captive gorillas. The Geographic Population Structure algorithm is an admixture based tool for inference of provenance and has been previously employed for the geo-localization of various human populations worldwide [14–17]. Given the strong correspondence between geography and genetics, a number of strategies have focused on the delineation of the precise geographic origin of human populations using high-resolution genetic data. Das and Upadhyai [11] applied the GPS tool for localization of the ancestral origins of wild and captive gorilla genomes, of unknown geographic source, available in the Great Ape Genome Project [18]. Determination of the source population of captive gorillas can provide valuable information to guide breeding programs and ensure their appropriate management at the population level. Finally, the authors’ findings shine light on the broader applicability of GPS for protecting the genetic integrity of endangered non-human species. Fedor Kazantsev and co-authors [19] presented an application in plant biology the database on Molecular * Correspondence: orlov@bionet.nsc.ru Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia Novosibirsk State University, 630090 Novosibirsk, Russia Full list of author information is available at the end of the article

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