BGRS\SB-2014 Program
Bioinformatics of Genome Regulation and Structure\Systems Biology — BGRS\SB-2014 June 23 – 28, 2014 Novosibirsk, Akademgorodok
Chairmen: akad. Kolchanov N.A. (ICG SB RAS, Novosibirsk, Russia), Prof. Dr. Ralf Hofestaedt (Bielefeld University, Germany).
System Biology Symposium
Sections:
Genomics and epigenetics.Chairmen: Prof. K.G. Skryabin (Bioengineering Center, RAS, Moscow, Russia), Prof. Yijun Ruan (The Jackson Laboratory, USA).
Genomics and epigenetics.
Chairmen: Prof. K.G. Skryabin (Bioengineering Center, RAS, Moscow, Russia), Prof. Yijun Ruan (The Jackson Laboratory, USA).
The Human Genome Project had been completed more than a decade ago, however, challenge remains to study how genomic information guides the gene expression in cell space and time. “Structure determines function” is common approach to understand the nature laws. In biological systems, this approach if effective not only for organic molecules such as RNA and proteins, but applies also at macromolecules levels including chromosomes and whole genome. An emerging frontier of genomic researches is investigation of the three-dimensional (3D) of genome structure and understanding how gene transcription and other cell functions are regulated in 3D space of the cell nucleus. Recent studies have shown that many enhancers interact with their target genes through long distance and large numbers of genes topologically organize into multi-gene complexes, such as transcription factories, for coordinated transcription regulation. Further studies in 3D genomics require integrated systems approaches and represent many new interdisciplinary challenges including next generation sequencing, computational biology, single molecule imaging etc. The session will present some of the most recent advances and discuss new challenges in the forefronts of genomic researches.
Proteomics, metabolomics and computational pharmacology.Chairman: Prof. E.N. Nikolaev (Institute of Energy Problems of Chemical Physics RAS, Moscow, Russia), Chairlady: Prof. I.M. Larina (SSC RF Institute for Biomedical Problems, RAMS, Moscow, Russia), Chairlady: E. Schwartz (Ariadne Diagnostics LLC, USA)
Proteomics, metabolomics and computational pharmacology.
Chairman: Prof. E.N. Nikolaev (Institute of Energy Problems of Chemical Physics RAS, Moscow, Russia), Chairlady: Prof. I.M. Larina (SSC RF Institute for Biomedical Problems, RAMS, Moscow, Russia), Chairlady: E. Schwartz (Ariadne Diagnostics LLC, USA).
This session will be focused on biomarkers and specifically omics-based strategy to identify biomarkers and pharmacological targets in different diseases. The increasing amounts of data, generated by experimental methods, challenges researchers to extract biologically applicable information. New computational methods for data analysis improve the quality of prospective biomarkers, presenting approaches for more effective verification and validation of biomarkers. Systems biology and pathway analysis may be the key that researchers need to rapidly discover, qualify and select appropriate biomarkers before large investment spent for their development. In addition, the complex interactions of targeted biomarkers can be mapped across multiple cellular processes and diseases providing a window into potential risks and benefits, before and during clinical trials, allowing companies to maximize their resources towards the development of targeted and individualized therapies. Several software packages available now provide for researchers the flexibility to import their experimental profiling data, find key regulators that could also be biomarkers from this data, and store this information in searchable databases. This innovative technology is particularly appropriate for the identification of new biomarkers for different diseases in the field of personalized medicine. The technology works to select biological pathways that are closely related to a clinical outcome of interest, by using proteomics or other “omics” data; and leverages its comprehensive database of pathway-related information containing relationships between proteins, cell processes, small molecules, and more. Thus, computational approaches for precision medicine together with the emergence of new high-throughput technologies for biomarker discovery are enabling comprehensive profiling of new biological pathways and molecular targets that can be more specific indicators of many devastated diseases including cancer and neurodegenerative disease.
Section topics include, but are not limited to:
The role of proteomics in clinical pharmacology
Biomarkers: bioinformatics/mathematical point of view
Biomarkers in translational medicine
Cancer pharmacology
Proteomics in neuroscience
Computational approaches to developing surrogate biomarkers for clinical trials
Systems computational biology.Chairmen: Dr. A. Ratushny (Seattle BioMed and Institute for Systems Biology, Seattle, USA). Prof. V. P. Golubyatnikov (IM SB RAS, Novosibirsk, Russia), Prof. M.Dehmer (Institute for Bioinformatics and Translational Research, Austria).
Systems computational biology.
Chairmen: Dr. A. Ratushny (Institute for Systems Biology, Seattle, USA). Prof. V. P. Golubyatnikov (IM SB RAS, Novosibirsk, Russia), Prof. M.Dehmer (Institute for Bioinformatics and Translational Research, Austria).
The section is devoted to the problems and methods of mathematical analysis of complex biological networks (gene and metabolic networks, associative and semantic networks, protein-protein interactions).
Methods for describing and comparison of complex networks will be discussed, as well as methods for identifying and search for structural patterns, structural motifs and methods of model networks reconstruction. The session includes discussion of comparative analysis of biological networks and networks evolution patterns.
Multiscale modeling methods that combine large-scale globally predictive and small-scale detailed kinetic models represents an effective framework for exploring dynamical biomolecular systems. This combined approach allows the integration of the genome-scale ‘omics’ data, identification of key players in particular cellular functions and iterative investigation of underlying molecular mechanisms using the “experiment-model-hypothesis-experiment” systems biology cycle. While both large scale and detailed kinetic models are available and have shown success in predicting organism behavior, they have not yet been adequately integrated. We are developing computational approaches for multiscale modeling and systematic exploration of topological features and parametric space of dynamical biological systems. Using these approaches we have discovered and modeled novel biomolecular regulatory systems in various organisms including Saccharomyces cerevisiae and Halobacterium salinarum. These studies reveal evolutionary advantages of discovered regulatory systems, principles of operation, and mechanisms for control that are relevant for rational intervention and synthetic biology applications.
The section will include discussion on modeling methods in system computational biology.
Chairlady: Prof. E.A. Salina (ICG SB RAS, Novosibirsk, Russia).
Section is devoted to genomic and postgenomic approaches to analysis of structural and functional genome organization, integration of obtained knowledge into the system plant biology. Genetic models to solve the system biology problems will be discussed in the frames of this section. Particular emphasis will be placed on methods of bioinformatics analysis and de novo assembly of the sequenced plants’ genomes. The number of plants with available genome sequencing data has been significantly increased in recent years. The question is how successfully integrate these data into systems biology to understand the organization and functioning of plant genome, realized in development and environment interaction of the organism. The Application of systems biology techniques to address that question on plants, varying in genome size and ploidy will be considered at the section.
Evolutionary Biology.Chairman: Prof. David Liberles (University of Wyoming, USA). Invited speakers: Prof. Andy Clark (Cornell University, USA), Prof. David Penny (Massey University, New Zealand).
Evolutionary Biology.
Chairman: Prof. David Liberles (University of Wyoming, USA). Invited speakers: Prof. Andy Clark (Cornell University, USA), Prof. David Penny (Massey University, New Zealand).
Systems biology and bioinformatics are fields that are engaged in the ultimate question of how a genomic sequence and its encoded RNA and protein sequences lead to a cellular or organismal phenotype. Relatedly, in a comparative perspective, how do changes in these sequences lead to changes in cellular and organismal phenotypes? To mechanistically address this question, fundamental processes in population genetics, evolutionary biology, biochemistry, and physical chemistry must be integrated. The modern synthesis in evolutionary bioinformatics is aimed at this level of mechanistic understanding, integrating across multiple layers of biological organization. Statistical techniques that build upon these diverse processes are critical to inference in this field. The invited lecturers all draw upon these diverse fields to make inference on genome function and this will be the main emphasis for discussion.
Human genetics has become the focus of all achievements of genetics and other “omic” technologies. Actual trends in applied aspects are: translational medicine, personalized medicine, ethnogenomics.
Achievements in human genetics have become the basis for genomic medicine. Translational medicine, figuratively defined as “from base pairs to bedside”, just started its progress in relation to widespread multifactorial diseases, whereas most success has been achieved for Mendelian disorders, which, however, account for only 1% of all human diseases.
Main idea of personalized medicine is well known for two thousand years, and genomic technologies added only a little to its effectiveness. Still open is the question: in which cases medical care should be individualized, and in which cases it should be universal.
Ethnogenomics is one of the most advanced parts of human genetics in Russia, but inter-population analysis has been performed mostly for those genome regions which mark evolutionary and migration events. Little is known about population specific features of complex diseases susceptibility structure, and this knowledge is unconvincing.
In the last ten years, epigenetics becomes leading topic in human and medical genetics, so do the studies for genome structure variability in somatic cells, not only in carcinogenesis (traditionally) but also in other multifactorial diseases.
It is supposed that these and other related topics will be discussed in the section reports. Section:
Translational Medicine. Chairman: Prof. M.P. Moshkin (ICG SB RAS)
Translational medicine deals with a number of problems regarding an implementation of data obtained in an experiment in clinical practice: research informatization, approaching of experimental research to real clinical problems, development of the infrastructure for research, biobanks and Phase I of clinical trials.
Medical genetics.Chairmen: Chairmen: Prof. V.P. Puzyrev (IMG SB RAS, Tomsk, Russia), M.I. Voevoda (IIM, SB RAS, Novosibirsk, Russia).
Medical genetics. Chairmen: Chairmen: Prof. V.P. Puzyrev (IMG SB RAS, Tomsk, Russia), M.I. Voevoda (IIM, SB RAS, Novosibirsk, Russia).
Discoveries in the basic sciences with evidence are the source of advances in modern medicine. Personalized medicine is based on the data of molecular diagnostics, genetics and pharmacogenomics. The session will address the challenges of medical genetics and personalized medicine - when health care should be individualized, and when universal.
Interantional Conference
Mathematical Modeling and High Performance Computing in Bioinformatics, Biomedicine and Biotechnology (MM-HPC-BBB-2014)
Chairman of international program committee: RAS corresponding member Prof. S.I. Kabanikhin, Institute of Computational Mathematics and Mathematical Geophysics SB RAS, Novosibirsk, Russia
Innovate computer technology development gives opportunity to solve problems of modeling in life sciences, biology and biomedicine at a totally new level. Rise of new parallel computation systems architecture requires new algorithm design for solving problems of modeling cell molecular processes, for prediction and analysis of 3D protein structure, analysis of chromosomal structures and genomic information.
Development of high-performance computing, cloud computing and services of data storage for Life Sciences are of special interest.
The results of recent researches in the following fields will be discussed:
High-performance and distributed computing in system biology and biomedicine.
Data mining methods in natural sciences.
Problems of mathematical modeling in life sciences: direct and inverse problems.
Mathematical modeling of gene and metabolic networks.
Mathematical modeling in biomedicine.
Mathematical modeling of biopolymers structure and dynamics.
Modeling of DNA-protein and protein-protein interactions.
Use of application program packs for solving problems of bioinformatics and biomedicine.
Modeling of pharmacokinetic processes in the body. Numerical methods of solving direct and inverse problems.
Mathematical models of immune processes. Direct and inverse problems in immunology.
Researching and classification of phase portraits of nonlinear dynamic systems.
Mathematical modeling in biomedicine and High performance computing and software tools for bioinformatics and biomedicine. Chairman: Corresponding Member of Russian Academy of Sciences, Dr. Sc., Professor S. I Kabanikhin, Sobolev Institute of Mathematics SB RAS, Y.L. Orlov, ICG SB RAS, Novosibirsk, Prof. S.K. Golushko, ICT SB RAS.
The questions of mathematical modeling in biomedicine, direct and inverse problems of determining the parameters of biophysical processes with the help of computer simulations will be discussed as part of this section.
The section topics include methods of high performance computing and data analysis in system biology, problems of algorithms parallelization. The following problems will be discussed: optimization computer genomics algorithms, high-throughput sequencing data analysis, mapping and short sequence assembly algorithms.
Text-mining and intelligent analysis of knowledge in databases. Chairmen: Prof. Andrey Rzhetsky (The University of Chicago, USA), Prof. Goncharov S.S., Zagoruiko N.G. (IM SB RAS, Novosibirsk, Russia).
Scientists today cannot hope to manually track all of the published science papers relevant to their work. A cancer biologist, for instance, can find more than 2 million relevant papers in the PubMed archive, more than 200 million Web pages by a Google search, and databases holding experimental results contain millions of gigabytes of data. This explosion of knowledge is changing the landscape of science. Computers already play an important role in helping scientists to store, manipulate, and analyze data. New capabilities, however, are extending the reach of computers from analysis to hypothesis. Drawing on approaches from artificial intelligence, computer programs increasingly are able to integrate published knowledge with experimental data, search for patterns and logical relations, and enable new hypotheses to emerge with little human intervention. Scientists have used such computational approaches to repurpose drugs, functionally characterize genes, identify elements of cellular biochemical pathways, and highlight essential breaches of logic and inconsistency in scientific understanding. We predict that within a decade, even more powerful tools will enable automated, high-volume hypothesis generation to guide high-throughput experiments in biomedicine, chemistry, physics, and even the social sciences.
