In Silico Biology - Volume 11, issue 3-4

Authors: van den Ende, J.E.

Article Type: Other

DOI: 10.3233/ISB-2012-0450

Citation: In Silico Biology, vol. 11, no. 3-4, pp. 95-95, 2012

Authors: Vaskin, Y.Y. | Khomicheva, I.V. | Ignatieva, E.V. | Vityaev, E.E.

Article Type: Research Article

Abstract: The task of automatic extraction of the hierarchical structure of eukaryotic gene regulatory regions is in the junction of the fields of biology, mathematics and information technologies. A solution of the problem involves understanding of sophisticated mechanisms of eukaryotic gene regulation and applying advanced data mining technologies. In the paper the integrated system, implementing a powerful relation mining of biological data method, is discussed. The system allows taking into account prior information about the gene regulatory regions that is known by the biologist, performing the analysis on each hierarchical level, searching for a solution from a simple hypothesis to a …complex one. The integration of ExpertDiscovery system into UGENE toolkit provides a convenient environment for conducting complex research and automating the work of a biologist. For demonstration, the system has been applied for recognition of SF1, SREBP, HNF4 vertebrate binding sites and for the analysis the human gene regulatory regions that promote liver-specific transcription. Show more

Keywords: Complex signal, hierarchical analysis, recognition, gene regulatory regions, bioinformatics

DOI: 10.3233/ISB-2012-0448

Citation: In Silico Biology, vol. 11, no. 3-4, pp. 97-108, 2012

Authors: Gunbin, Konstantin V. | Suslov, Valentin V. | Genaev, Mikhail A. | Afonnikov, Dmitry A.

Article Type: Research Article

Abstract: SAMEM (System for Analysis of Molecular Evolution Modes), a web-based pipeline system for inferring modes of molecular evolution in genes and proteins (http://pixie.bionet.nsc.ru/samem/), is presented. Pipeline 1 performs analyses of protein-coding gene evolution; pipeline 2 performs analyses of protein evolution; pipeline 3 prepares datasets of genes and/or proteins, performs their primary analysis, and builds BLOSUM matrices; pipeline 4 checks if these genes really are protein-coding. Pipeline 1 has an all-new feature, which allows the user to obtain K R /K C estimates using several different methods. An important feature of pipeline 2 is an original method for analyzing the …rates of amino acid substitutions at the branches of a phylogenetic tree. The method is based on Markov modeling and a non-parametric permutation test, which compares expected and observed frequencies of amino acid substitutions, and infers the modes of molecular evolution at deep inner branches. Show more

Keywords: Molecular evolution, Markov modeling, permutation test, radical and conservative amino acid substitutions, web-based application

DOI: 10.3233/ISB-2012-0446

Citation: In Silico Biology, vol. 11, no. 3-4, pp. 109-123, 2012

Authors: Lashin, Sergey A. | Matushkin, Yury G.

Article Type: Research Article

Abstract: In this paper we consider the recent advances in methodology for modeling of prokaryotic communities evolution and new features of the software package “Haploid evolutionary constructor” (http://evol-constructor.bionet.nsc.ru). We show the principles of building complex computer models in our software tool. These models describe several levels of biological organization: genetic, metabolic, population, ecological. New features of the haploid evolutionary constructor include the modeling of gene networks and phage infections.

Keywords: Evolution modeling, simulation, prokaryotic community, gene network, phage

DOI: 10.3233/ISB-2012-0447

Citation: In Silico Biology, vol. 11, no. 3-4, pp. 125-135, 2012

Authors: Palyanov, Andrey | Khayrulin, Sergey | Larson, Stephen D. | Dibert, Alexander

Article Type: Research Article

Abstract: The nematode C. elegans is the only animal with a known neuronal wiring diagram, or “connectome”. During the last three decades, extensive studies of the C. elegans have provided wide-ranging data about it, but few systematic ways of integrating these data into a dynamic model have been put forward. Here we present a detailed demonstration of a virtual C. elegans aimed at integrating these data in the form of a 3D dynamic model operating in a simulated physical environment. Our current demonstration includes a realistic flexible worm body model, muscular system and a partially implemented ventral neural …cord. Our virtual C. elegans demonstrates successful forward and backward locomotion when sending sinusoidal patterns of neuronal activity to groups of motor neurons. To account for the relatively slow propagation velocity and the attenuation of neuronal signals, we introduced “pseudo neurons” into our model to simulate simplified neuronal dynamics. The pseudo neurons also provide a good way of visualizing the nervous system’s structure and activity dynamics. Show more

Keywords: Virtual organism, C. elegans, simulation, neuro-cybernetics, muscular system, ventral neural cord

DOI: 10.3233/ISB-2012-0445

Citation: In Silico Biology, vol. 11, no. 3-4, pp. 137-147, 2012

Authors: Demenkov, P.S. | Ivanisenko, T.V. | Kolchanov, N.A. | Ivanisenko, V.A.

Article Type: Research Article

Abstract: The ANDVisio tool is designed to reconstruct and analyze associative gene networks in the earlier developed Associative Network Discovery System (ANDSystem) software package. The ANDSystem incorporates utilities for automated extraction of knowledge from Pubmed published scientific texts, analysis of factographic databases, also the ANDCell database containing information on molecular-genetic events retrieved from texts and databases. ANDVisio is a new user’s interface to the ANDCell database stored in a remote server. ANDVisio provides graphic visualization, editing, search, also saving of associative gene networks in different formats resulting from user’s request. The associative gene networks describe semantic relationships between molecular-genetic objects (proteins, …genes, metabolites and others), biological processes, and diseases. ANDVisio is provided with various tools to support filtering by object types, relationships between objects and information sources; graph layout; search of the shortest pathway; cycles in graphs. Show more

Keywords: ANDVisio, ANDSystem, ANDCell, text-mining, associative gene networks, data integration

DOI: 10.3233/ISB-2012-0449

Citation: In Silico Biology, vol. 11, no. 3-4, pp. 149-161, 2012