International Multiconference “Bioinformatics of Genome Regulation and Structure\Systems Biology”

Category

Systems computational biology: analysis, mathematical modeling and information technologies symposium

Showing: 1 - 10 of 21 RESULTS
Systems computational biology: analysis, mathematical modeling and information technologies symposiumA global human mitochondrial tree as a resource for population and evolutionary studies

A global human mitochondrial tree as a resource for population and evolutionary studies

No Comment on A global human mitochondrial tree as a resource for population and evolutionary studies

Kristina Ushakova1, Viktor Shamansky2, Alina A Mikhailova3, Alina G Mikhailova4, Evgeniy Tretiakov5, Ilia Mazunin6, Konstantin Popadin7, Konstantin Gunbin8
1ITMO University, IKBFU Center for Mitochondrial Functional Genomics, kristina.ushakova@outlook.com
2IKBFU Center for Mitochondrial Functional Genomics, v.a.shamanskiy@gmail.com
3IKBFU Center for Mitochondrial Functional Genomics, mihailovaalina777@yandex.ru
4IKBFU Center for Mitochondrial Functional Genomics, polarsong4@gmail.com
5Medizinische Universität Wien, Evgenii.O.Tretiakov@gmail.com
6Skoltech Center of Life Sciences, ilya.mazunin@yandex.ru
7Ecole polytechnique Federale de Lausanne, IKBFU Center for Mitochondrial Functional Genomics, konstantinpopadin@gmail.com
8Institute of Cytology and Genetics SB RAS, IKBFU Center for Mitochondrial Functional Genomics, genkvg@gmail.com

The mitochondrial DNA (mtDNA) is a highly streamlined genome with essential role for cellular metabolism. To create a resource for investigation of various aspects of human mtDNA evolution we reconstructed global human mtDNA tree using 40000 complete human mtDNAs. To make our reconstructions robust we used several alternative models of nucleotide substitutions (TN92, GTR); several alternative approaches to reconstruct ancestral states for each nucleotide in each node (parsimony, empirical Bayesian approach and ML marginal reconstruction) and tested statistical significance of each internal node (SH-like approximate likelihood ratio test, approximate Bayes test and ultrafast bootstrap approximation). As a result we obtained a detailed phylogenetic tree of human mitochondrial genomes with more than one million reconstructed single-nucleotide substitutions. We confirmed high quality of our reconstructions, demonstrating: (i) an absence of stop codons on internal nodes, (ii) strong expected excess of C>T and A>G transitions (heavy chain notation) among synonymous substitutions etc. As a first task demonstrating utility of our tree, we reconstructed detailed mtDNA germline mutational spectrum (global, gene-specific and with nucleotide context) based on a collection of more than 300’000 synonymous substitutions. Next we compared it with somatic mtDNA mutational spectrum, derived from cancer data. Globally, two mutational spectra were similar to each other, while local shifts in the frequency of several types of substitutions may be explained by different mutagenic environment between female gamete line and various somatic tissues. We hope that this resource will help to address numerous questions of human mtDNA evolution in the future. 

 

Systems computational biology: analysis, mathematical modeling and information technologies symposiumDevelopment and analysis of AIDS epidemic agent-based computer model applying an algorithm for explicit calculation of HIV replicability

Development and analysis of AIDS epidemic agent-based computer model applying an algorithm for explicit calculation of HIV replicability

No Comment on Development and analysis of AIDS epidemic agent-based computer model applying an algorithm for explicit calculation of HIV replicability

Anna Smirnova1, Mikhail Ponomarenko2, Sergey Lashin3
1ICG SB RAS, Novosibirsk, Russia NSU, Novosibirsk, Russia, asmirnova@bionet.nsc.ru
2ICG SB RAS, Novosibirsk, Russia, pon@bionet.nsc.ru
3ICG SB RAS, Novosibirsk, Russia NSU, Novosibirsk, Russia, lashin@bionet.nsc.ru

Different strains of HIV contribute differently to the course of the disease. For its evaluation, 1,336 HIV strains were analyzed. An agent model of the spread of HIV infection in the population has been developed. We analyzed 5 scenarios for the development of the HIV epidemic in Russia, depending on the initial data. Without additional measures, after 10 years, the percentage of HIV patients in Russia will increase from 1% to 2.45%. Comprehensive measures to increase the use of barrier contraception, reduce the number of joint injections among drug users and improve the situation with treatment coverage can reduce the percentage of patients from 1% to 0.3% and prevent the emergence of new patients.

Systems computational biology: analysis, mathematical modeling and information technologies symposiumThe Nosological Rate Of Incidents Congenital Anomalies In Neonatal Period In Novosibirsk

The Nosological Rate Of Incidents Congenital Anomalies In Neonatal Period In Novosibirsk

No Comment on The Nosological Rate Of Incidents Congenital Anomalies In Neonatal Period In Novosibirsk

MIKHAIL TRAVIN1
1Head of Laboratory of functional morphology of the lymphatic system Research Institute of Clinical and Experimental Lymрhology – Branch of the Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, mtravin@mail.ru

The results of the study demonstrate that the rate of congenital anomalies in the perinatal period was dominated by multiple anomalies among newborns and stillborn fetuses, mainly in premature infants. Among isolated anomalies, anomalies of cardiovascular system prevailed.

Systems computational biology: analysis, mathematical modeling and information technologies symposiumRecognition of flavivirus species on the base of coding genome sequences

Recognition of flavivirus species on the base of coding genome sequences

No Comment on Recognition of flavivirus species on the base of coding genome sequences

Maria Chaley1, Vladimir Kutyrkin2
1Institute of Mathematical Problems of Biology RAS – Branch of KIAM RAS, maramaria@yandex.ru
2Department of Computational Mathematics and Mathematical Physics Moscow State Technical University n.a. N.E. Bauman, vkutyrkin@yandex.ru

Enter the abstract annotation ONLY here

Computational method for recognition the flavivirus species, including their subtypes, is proposed, that based on known sequence of viral genome. The method uses frequency characteristics of amino acid codons in the whole coding sequences of polyproteins. High reliability of this method is supported by correct recognizing of the 15 groups from different species and subtypes of flavivirus genomes.

Systems computational biology: analysis, mathematical modeling and information technologies symposiumTransfer of Genetic Algorithms to Directed Evolution of Macromolecules: Tests in Silico

Transfer of Genetic Algorithms to Directed Evolution of Macromolecules: Tests in Silico

No Comment on Transfer of Genetic Algorithms to Directed Evolution of Macromolecules: Tests in Silico

Ekaterina M. Myasnikova1
1Peter the Great St. Petersburg Polytechnical University, ekmyasnikova@yandex.ru

The ideas of evolutionary biology used to inspire computer scientists to develop a thriving nowadays field of genetic algorithms (GA). Nowadays, the directed evolution of biological macromolecules is reasonably interpreted as an implementation of GA in biochemical experiments. One of the theoretical foundations of GA, justifying the effectiveness of evolutionary search, is the concept of building blocks (BB). In GA, it is reasonable to match these BBs to domains / motifs of macromolecules in biology. Computer scientists have shown the importance of identifying and preserving already found BBs for the effectiveness of evolutionary search. For this purpose, dozens of procedures and algorithms have been developed. On the other hand, the experimental procedures finding and preserving domains (motifs) remain a poorly developed area in the techniques of evolution in vitro. In this report, we demonstrate how significantly some heuristic algorithms preserving the BBs can increase the efficiency of in vitro evolution in numerical experiments. As a benchmark test, we use such actual problem of synthetic biology as the evolutionary search for multi-domain RNA devices. The success of these primary tests with simple heuristic algorithms gives us every reason to expect that the implementation and application of more advanced and modern GA procedures will give an even greater increase in efficiency. In conclusion, we discuss the importance of such highly efficient heuristic algorithms for evolutionary and synthetic biology.

Systems computational biology: analysis, mathematical modeling and information technologies symposiumNamed entity recognition in medical texts in Russian using deep learning models

Named entity recognition in medical texts in Russian using deep learning models

No Comment on Named entity recognition in medical texts in Russian using deep learning models

Igor Viktorovich Moskalev1, Luybov\’ Anatol\’evna Khvorova2
1ASU, Barnaul, Russia, moskalev.igor.v@gmail.com
2ASU, Barnaul, Russia, khvorovala@gmail.com

The application of contextual and domain-specific pre-trained word embeddings for recognition of medical concepts in free-text clinical notes in Russian is considered. As it is known, a large amount of medical data is stored in electronic form, a significant part – in an unstructured form (medical history, extracts, description of the results of various tests). This data contains a large amount of useful information for the diagnosis of diseases. The results of the experiments showed the effectiveness of applying contextual language models which pre-trained on medical texts in the task biomedical named entity recognition.

Systems computational biology: analysis, mathematical modeling and information technologies symposiumErrors in miRNA Recognition

Errors in miRNA Recognition

No Comment on Errors in miRNA Recognition

Pavel Vorozheykin1, Igor Titov2
1NSU, pavel.vorozheykin@gmail.com
2ICG SB RAS, titov@bionet.nsc.ru

Selecting and using the key miRNA features are crucial for the identification of miRNA sequences. These criteria may help us to take out junk data from the miRNA databases and to improve the prediction of miRNA ends in order to obtain more accurate forecasting of the seed-related functions. We consider different processes of the miRNA identification to determine their role and influence on the prediction quality.

Systems computational biology: analysis, mathematical modeling and information technologies symposiumCandidate SNP markers of rheumatoid arthritis changing the affinity of TATA-binding protein for the human gene promoters expo disruptive selection of immunoactivative and immunosuppressive genenets that provoke and prevent this disorder, respectively, as if it could be a self-domestication syndrome

Candidate SNP markers of rheumatoid arthritis changing the affinity of TATA-binding protein for the human gene promoters expo disruptive selection of immunoactivative and immunosuppressive genenets that provoke and prevent this disorder, respectively, as if it could be a self-domestication syndrome

No Comment on Candidate SNP markers of rheumatoid arthritis changing the affinity of TATA-binding protein for the human gene promoters expo disruptive selection of immunoactivative and immunosuppressive genenets that provoke and prevent this disorder, respectively, as if it could be a self-domestication syndrome

Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/435.pdf”]
Natalya Klimova1, Dmitry Oshchepkov2, Irina Chadaeva3, Mikhail Ponomarenko4, Evgeniya Oshchepkova5, academician Vladimir Kozlov6
1Molecular Genetics Department, Institute of Cytology and Genetics, ICG SB RAS, Novosibirsk, Russia, klimova@bionet.nsc.ru
2Systems Biology Department, Institute of Cytology and Genetics, ICG SB RAS, Novosibirsk, Russia, diman@bionet.nsc.ru
3Systems Biology Department, Institute of Cytology and Genetics, ICG SB RAS, Novosibirsk, Russia, ichadaeva@bionet.nsc.ru
4Systems Biology Department, Institute of Cytology and Genetics, ICG SB RAS, Novosibirsk, Russia, pon@bionen.nsc.ru
5Systems Biology Department, Institute of Cytology and Genetics, ICG SB RAS, Novosibirsk, Russia, nzhenia@bionet.nsc.ru
6Research Institute of Fundamental and Clinical Immunology, RIFCI SB RAS, Novosibirsk, Russia, niiki01@online.nsk.su

Here we conducted a computational genome-wide study of the all known single-nucleotide polymorphism (SNP) of 70 bp proximal promoters of 67 human rheumatoid arthritis (RA)-related genes that displayed disruptive natural selections of immunoactivative or immunosuppressive genes raising or reducing risks of RA, respectively, as if it maybe a domestication syndrome. That is why, we confirmed it in vivo using the genome-wide transcriptome profiling (RNA-seq assay) of the differentially expressed genes (DEGs) within hypothalamus of adult male rats (Rattus norvegicus) of two unique outbred lines bred in aggressiveness and tameness as an animal model of human diseases (statistical significance padj < 0.025 at Pearson\’s П‡2 criterion with Bonferroni\’s correction).

Systems computational biology: analysis, mathematical modeling and information technologies symposiumThe algorithm for finding potentially oscillating behavior in enzymatic systems

The algorithm for finding potentially oscillating behavior in enzymatic systems

No Comment on The algorithm for finding potentially oscillating behavior in enzymatic systems

Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/425.pdf”]
Tatiana N. Lakhova1, Fedor V. Kazantsev2, Yuriy G. Matushkin3, Sergey A. Lashin4
1Bioinformatics and Information Technologies in Genetics, Kurchatov genome center ICG SB RAS, tlakhova@bionet.nsc.ru
2Sector for computer analysis and simulations of biological systems, Kurchatov genomics center ICG SB RAS, kazfdr@bionet.nsc.ru
3Laboratory of molecular genetic systems ICG SB RAS, mat@bionet.nsc.ru
4Sector of Bioinformatics and Information Technologies in Genetics, Kurchatov genomics center ICG SB RAS, Novosibirsk State University, lashin@bionet.nsc.ru

Enzymatic reactions regulate Р° lot of processes in a cell. Chemical compounds such as various inhibitors, activators, cofactors, allosteric regulators, etc. may influence reaction rate. We are interested in the oscillatory processes that play role in the functioning of biological systems. It is known that oscillatory behavior frequently emerges via influence of the positive and/or negative feedback loops. Development and analysis of mathematical and computer models may be the tools to explore such behavior. Therefore, the aim of our research is to develop the technology that can help find potentially oscillating microbial enzymatic subsystems and to explore their behavior.

Systems computational biology: analysis, mathematical modeling and information technologies symposiumComputer reconstruction of the ecological structure of intestinal microbiota communities based on high-throughput sequencing data

Computer reconstruction of the ecological structure of intestinal microbiota communities based on high-throughput sequencing data

No Comment on Computer reconstruction of the ecological structure of intestinal microbiota communities based on high-throughput sequencing data

Andrew Kopochev1, Alexandra Klimenko2, S.A. Lashin3
1Kurchatov Genomics Center, Institute of Cytology and Genetics, andrew.kropochev@gmail.com
2Kurchatov Genomics Center, Institute of Cytology and Genetics, klimenko@bionet.nsc.ru
3Kurchatov Genomics Center, Institute of Cytology and Genetics, lashin@bionet.nsc.ru

Human gut microbiota is essential for human health. Under the recent avalanche of metagenomic high-throughput sequencing data methods for its bioinformatic analysis and ecological reconstruction gain particular relevance. In this study, we employ the trait-based ecology approach to create a method of computer reconstruction of the ecological structure of intestinal microbiota communities based on high-throughput sequencing data and apply it to the synthetic community comprised of the key representatives of the human gut microbiota. Using this structure allowed us to evaluate the abundance of respective functional groups and infer a knowledge about the processes associated with them. The developed method can be applied to analyze intestinal microbial communities of other related species.