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Evolutionary biology at BGRS\SB-2016
BMC Evolutionary Biology volume 17, Article number: 21 (2017)
This special BMC Evolutionary Biology BGRS\SB-2016 issue is an integral part of the collection of manuscripts presented at “Bioinformatics of Genome Regulation and Structure\Systems Biology” (BGRS\SB-2016) conference which took place at August 29 - September 2, 2016 in Novosibirsk, Russia. Other issues in this collection include BMC Genetics , BMC Plant Biology , BMC Genomics , BMC Bioinformatics and BMC Systems Biology releases.
International Conference BGRS\SB-2016 (http://conf.bionet.nsc.ru/bgrssb2016/) is 10th installment of the biannual BGRS event which has a long history starting from 1998 in Novosibirsk. The conference organized by Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences (ICG SB RAS) has focuses on evolutionary biology, systems biology and bioinformatics, gene network analysis, post-genomics and sequencing technologies. Since 1998, BGRS series has grown to large international multi-conference forum where medical doctors, mathematicians, biologists could share their recent theoretical and experimental insights.
In 2016, the BGRS included several parallel events and symposia: the international Symposium “Systems Biology and Biomedicine” (SBioMed-2016) (http://conf.bionet.nsc.ru/ishg2016/en/), Symposium “Cognitive Sciences, Genomics and Bioinformatics” (CSGB-2016) (http://physiol.ru/csgb2016/), and the Second International Conference on the Mathematical Modeling and High-Performance Computing in Bioinformatics, Biomedicine and Biotechnology (MM-HPC-BBB-2016) (http://conf.bionet.nsc.ru/mm-hpc-bbb-2016/en/).
Since 2014, The BGRS Program Committee collaborates with BioMed Central on full-text thematic issues of relevant BMC journals. In recent years, BioMed Central had published several special issues based on best materials presented at the conference, including ones in BMC Genomics (http://www.biomedcentral.com/bmcgenomics/supplements/15/S12), BMC Genetics , BMC Evolutionary Biology (http://www.biomedcentral.com/bmcevolbiol/supplements/15/S1), and BMC Systems Biology (http://www.biomedcentral.com/bmcsystbiol/supplements/9/S2).
Additionally, special issues on bioinformatics were published at the “Journal of Bioinformatics and Computational Biology”  and “Vavilov Journal of Selection and Breeding” (http://vavilov.elpub.ru/jour/) (in Russian). This year, a special issue in “Molecular Biology” (Springer) was added to the list (http://www.springer.com/life+sciences/journal/11008).
Current issue of BMC Genomics presents reports on genome-wide studies in computational biology discussed at the BGRS\SB-2016 conference.
The paper by Oleg Balanovsky et al.  opens this special issue by presenting the results of combined efforts of population geneticists and genetic genealogists in reconstructing phylogeography of human haplogroup Q3. In addition to important conclusions about history of human migrations, this study provides positive example of collaboration between academic and citizen science and demonstrates possibility of well-balanced and careful interpretation of the paternal-side history of human populations.
The work of Vladimir Babenko and colleagues  utilizes high resolution map of human genome for genome-wide study of CpG islands and Alu-repeats. Authors demonstrated that the landscapes of these elements are related to chromatin accessibility. As particular example, authors analyzed CpG-rich genome of dog and unearthed its unique features.
Jelena Guzina and Marko Djordjevic  explored the evolution of σ70 family of the factors by quantitative investigation of mix-and-matching in two canonical ECFfamily members (σE and σW) and proposed an evolutionary anchored simple model which relates the size of σfactor regulon with the extent of mix-and-matching.
Aleksandra Chertkova and colleagues  employed in silico evolution of Drosophila gap gene regulatory sequence to demonstrate that elevated mutational pressure leads to produce regulatory sequence organizations with fewer, albeit on average stronger, functional transcription factor binding sites that support preservation of adjacent regulatory sequences.
The paper by Evgenii Konorov et al.  presents their insights into the genomics of urban populations of ants. Authors showed that the success of Lasius niger in urbanized areas may result from the expansion of the CYP9 cytochrome family, the diversification of DNA repair systems, and reduced odorant communication.
Finally, Ilyas Jetybaev et al.  studied short horned grasshoppers of the family Pamphagidae in the Anatolian region, and found two neo-XY sex chromosome systems, belonging to two different evolutionary lineages. They point at high density of species carrying neo-XY systems, and the different evolutionary stage for the two lineages found, one being older than the other.
The works presented above employ a variety of evolutionary analysis techniques, from karyotyping to genome sequencing and then to in silico evolution and to building kinetic models.
Returning back to the tenth anniversary BGRS\SB event, note that 2016’ thematic collection of the manuscripts is augmented by Special Issues covering various Satellite events, including already traditional Young Scientists School “Systems Biology and Bioinformatics” (SBB-2016) (http://conf.bionet.nsc.ru/sbb2016/en/). The CSGB-2016 Symposium on cognitive sciences has presented special issue at IEEE Xplore Digital Library (http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=7587661). “Journal of Bioinformatics and Computational Biology” (http://www.worldscientific.com/worldscinet/jbcb) continues traditional special issues after BGRS\SB on mathematical problems of bioinformatics and biomedicine as well as “Journal of Integrative Bioinformatics” (http://journal.imbio.de/). Experimental research manuscripts fallen into the scope of BGRS\SB2016 have been collated in Special Issue of “Molecular Biology” (Springer) (http://www.springer.com/life+sciences/journal/11008) that will be published in 2017. In addition, special issue on bioinformatics and evolutionary biology is published at the “Vavilov Journal of Selection and Breeding” (http://www.bionet.nsc.ru/vogis).
The BGRS\SB-2016 Proceedings including “Evolutionary bioinformatics” section are available at the multi-conference web-site: http://www.bionet.nsc.ru/files/2016/conference/BGRS2016.pdf.
Next BGRS conference will take place in 2018. Welcome to Novosibirsk!
Orlov YL, Baranova AV, Markel AL. Computational models in genetics at BGRS\SB-2016: Introductory note. BMC Genet. 2016.
Orlov YL, Baranova AV, Salina EA. Computational plant bioscience at BGRS\SB-2016: Introductory note. BMC Plant Biol. 2016.
Orlov YL, Baranova AV, Hofestadt R, Kolchanov N. Computational genomics at BGRS\SB-2016: Introductory note. BMC Genomics. 2016.
Baranova AV, Orlov YL. The papers presented at 7th Young Scientists School “Systems Biology and Bioinformatics” (SBB’15): Introductory Note. BMC Genet. 2016;17(S1).
Orlov YL, Hofestädt RM, Kolchanov NA. Introductory note for BGRS\SB-2014 special issue. J Bioinform Comput Biol. 2015;13:1502001. http://dx.doi.org/10.1142/S0219720015020011.
Balanovsky O, Gurianov V, Zaporozhchenko V, Balaganskaya O, Urasin V, Zhabagin M, Grugni V, Canada R,Al-Zahery N, Raveane A, Shao-Qing W, Yan S, Wang X, Zalloua P, Marafi A, Koshel A, Semino O, Tyler-Smith C, Balanovska E. Phylogeography of human Y-chromosome haplogroup Q3-L275 from an academic/citizen science collaboration. BMC Genomics. 2016: S:2. (this issue).
Babenko VN, Chadaeva IV, Orlov YL. Genomic landscape of CpG rich elements in human. BMC Evol Biol. 2016: S:3. (this issue).
Guzina J, Djordjevic M. Mix-and-matching as a promoter recognition mechanism by ECF σ factors. BMC Evolutionary Biology. 2016: S:4. (this issue).
Chertkova AA, Schiman JS, Nuzhdin SV, Kozlov KN, Samsonova MG, Gursky VV. In silico evolution of the Drosophila gap gene regulatory sequence under elevated mutational pressure. BMC Evol Biol. 2016: S:5. (this issue)
Konorov EA, Nikitin MA, Mikhailov KV, Lysenkov SN, Belenky M, Chang PL, Nuzhdin SV, Scobeyeva VA. Genomic exaptation enables Lasius niger adaptation to urban environments. BMC Evol Biol. 2016: S:6. (this issue)
Jetybayev IE, Bugrov AG, Unal M, Buleu OG Rubtsov NB. Molecular cytogenetic analysis reveals the existence of two independent neo-XY sex chromosome systems in Anatolian Pamphagidae grasshoppers. BMC Evol Biol. 2016: S:7. (this issue)
The authors are grateful to the BGRS Program Committee, Prof. N.A. Kolchanov and Dr. F. Kondrashov, the Chairman of Evolutionary Bioinformatics section. The authors acknowledge the organizations and societies for general support of the BGRS\SB-2016 conference: the Institute of Cytology and Genetics SB RAS (www.bionet.nsc.ru) (budget project 0324-2015-0003), the Novosibirsk State University (www.nsu.ru), the Russian Foundation for Basic Research (www.rfbr.ru/rffi/) and the Vavilov Society of Geneticists and Breeders (http://www.bionet.nsc.ru/vogis/).
About this supplement
This article has been published as part of BMC Evolutionary Biology Vol 17 Suppl 1, 2017: Selected articles from BGRS\SB-2016: evolutionary biology. The full contents of the supplement are available online at https://bmcevolbiol.biomedcentral.com/articles/supplements/volume-17-supplement-1.
AB acknowledges the support from the Ministry of Science and Education, Russia (Project no. RFMEFI60714X0098). YLO acknowledges ICG SB RAS budget project 0324-2015-0003.
Publication of this article has been funded by the authors.
AB and YLO wrote the article. YLO and AB are guest editors at BioMed Central for several thematic post-conference issues. Both authors read and approved the final manuscript.
AB is Member of BGRS\SB-2016 Program Committee, Guest Editor at BioMed Central, Associate Professor, School of Systems Biology, George Mason University, Fairfax, Virginia, USA.
YO is Professor of the Russian Academy of Sciences, Member of BGRS\SB Program Committee, Guest editor at BioMed Central, “Journal of Bioinformatics and Computational Biology” and “Journal of Integrative Bioinformatics”, Head of the Lab at Novosibirsk State University and the Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
The authors declare that they have no competing interests.
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Baranova, A.V., Orlov, Y.L. Evolutionary biology at BGRS\SB-2016. BMC Evol Biol 17, 21 (2017). https://doi.org/10.1186/s12862-016-0869-8
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