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Gene Networks
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Untranslated Plant mRNAs
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TRRD: Database
Transcription Regulatory Regions DB


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Testimonial Laurent Favre, CEO


"We have been working with [ITC Software] for more than 2 years now. We started with contract basis work and finally came to ODC which is completely dedicated for our tasks. High team stability, good proficiency and efficient administration support are the factors which bring high value to our collaboration."  ..../more

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Climate Change >

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Publications

Publications

 

   UCI Benchmark Study


  About us >   Scientific Advisors  Publications  Meet the Team  Global Delivery

 

ITC Software and its partner's scientific staff are authors of many scientific publications that are published in leading worldwide journals and scientific conference proceedings. Below are selected scientific publications from members of our core team.

 

bullet Ecosystems Modeling
bullet Gene networks and signal trusduction pathways
bullet Sequence analysis
bullet Bioinformatics software development
bullet Biological database development
bullet Biomechanics

 


Ecosystems Modeling

 

Saveliev, Anatoly A; Romanov, Andrey V; Mukharamova, Svetlana S.

Automated Mapping using Multilevel B-Splines'

Applied GIS. 2005.; Monash University ePress: Victoria, Australia. http://www.epress.monash.edu.au/.: DOI:10.2104/ag050017

Abstract: This paper describes application of multilevel B-Splines approximation (MBA) algorithm to the SIC2004 exercise as a high performance automatic mapping means in emergency situations. MBA method was compared with kriging, and various flexible MBA method’s tuning “controls” were proposed and discussed. Outliers automatic detection and delineation techniques considered could be used to process outliers without the loss in performance. Prior data were used to adjust method parameters and discover the pattern of spatial correlation. The interpolation algorithm development did not assume any information about the phenomena in addition to values given.

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Anatoly A. Saveliev, Dmitry V. Dobrinin
The Application of Kohonen's Self-Organizing Maps and Markov Random Fields  for Thematic Interpretation of Nature Phenomena

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Rogova T., Saveliev A., Mukcharamova S.
Effect of Landscape fragmentation on Coniferous-Broadleaved Forests
Journal of Vegetation Science. Vol. Conference Proceedings 41 symposium IAVS, Sweden. 2000. P.174-177.

Anatoly A. Saveliev, Dmitry V. Dobrinin
Hierarchical Multispectral Image Classification Based on Self Organized Maps

IGARSS’99 IEEE 1999. International Geoscience and Remote Sensing Symposium, Hamburg, Germany, 1999, p.2510-2512.

Abstract: One of the problems in the thematic interpretation of the remote sensor (RS) data is the processing of the sets of multispectral, multydate images. The problem is that when we try to compare two and more RS image, we have to rectify their geometry and correct atmospheric effects. While the geometric correction could be done with any precision, the atmospheric correction for a set of images is a very complex task, and it could not be solved in a common case. We propose a new approach, based on the artificial neural networks, for a stable RS images classification and interpretation without the atmospheric correction. That approach, using the Kohonen’s Self Organized Maps (SOM) [1], has been realized as a part of the ScanEx image processing technology in a computer program NeRIS (Neural Raster Interpretation System). The Sammon’s mapping [2] of that SOM classification from the p dimensional input image space to the 2 dimensional points on a plane (whereby the distances between the mapped vectors tend to approximate to distances of the input vectors), was used for hierarchical classification and stable thematic interpretation of the RS images.
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Alain F. Zuur, Elena N. Ieno, Neil J. Walker, Anatoly A. Saveliev, Graham M. Smith

Mixed effects models and extensions in ecology with R

ISSN 1431-8776, ISBN 978-0-387-87457-9, Library of Congress No: 2008942429

Abstract: Building on the successful Analysing Ecological Data (2007) by Zuur, Ieno and Smith, the authors now provide an expanded introduction to using regression and its extensions in analysing ecological data. As with the earlier book, real data sets from postgraduate ecological studies or research projects are used throughout. The first part of the book is a largely non-mathematical introduction to linear mixed effects modelling, GLM and GAM, zero inflated models, GEE, GLMM and GAMM. The second part provides ten case studies that range from koalas to deep sea research. These chapters provide an invaluable insight into analysing complex ecological datasets, including comparisons of different approaches to the same problem. By matching ecological questions and data structure to a case study, these chapters provide an excellent starting point to analysing your own data. Data and R code from all chapters are available from www.highstat.com.

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Anatoly A. Saveliev, Svetlana S. Mucharamova, Gennady A. Piliugin
Modeling of the Daily Rainfall Values Using Surface Under Tension and Kriging
Journal of Geographic Information and Decision Analysis, Vol. 2., No. 2, pp. , 1998.

Category: Atmospheric physics and meteorology, Statistics and geostatistics
Abstract: Various estimation methods are discussed in respect of rainfall estimation. The potentialities of two methods were demonstrated by comparison of estimated daily rainfall values in unknown locations with the results of real observations in the same locations. The accuracy of prediction as well as applied properties of the estimations and methods used are discussed.

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A.A.Saveliev, G.A.Evtugyn, D.A.Semanov
Pollution assessment of industrial waste waters based on artificial neural nets approach

Environmental Radioecology and Appl. Ecology.- 2001.- V.7.-No. 2- P.47-54.

Abstract: A novel approach to the general estimation of waste waters pollution based on general biochemical, toxicological and hydrochemical parameters and artificial neural nets has been proposed. As shown expert system proposed makes it possible, at best, to predict the pollution class for more than 80% of the samples of industrial waste waters examined. Bibliography 9 references. Download: ....

Saveliev A.A., Dobrinin D.V.
The use of Kohonen's neural nets for the detection of land-cover transitions
Proceedings of the First International Workshop on the Analysis of Multitemporal Remote Sensing Images. Proceedings of Multytemp 2001. Series in Remote Sensing, World Scientific, Singapore, 2002, V.2, P.148-155.

Yermolaev O., Saveliev A.
Usage of artificial neural networks for regioning (classification) conditions and factors of erosion.
2nd Internat. Symposium on Gully Erosion under Global Change. GEGC – II (22-25.05.2002), Chengdy, 2002. 1 p.
 

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Gene networks and signal trusduction pathways


Kolpakov F.A., Ananko E.A., Kolesov G.B. and Kolchanov N.A.
GeneNet: a database for gene networks and its automated visualization.
Bioinformatics. 1998;14(6):529-537.

Abstract: MOTIVATION: Gene networks that provide the regulation of physiological processes are the basic feature of organisms. Information regarding the regulation of gene expression and signal transduction pathways is increasing rapidly. However, the information is hard to formalize and systematize. Ways and means for automated visualization of the gene networks based on their formalized description are needed.
RESULTS: The object-oriented database GeneNet and the software for its automated visualization have been developed. The main principles of a formalized description of the gene network have been worked out. Antiviral response and erythropoiesis are provided as examples to show how this is achieved. The GeneNet graphical user interface written in Java provides automated generation of the gene network diagrams and allows visualization and exploration of the GeneNet database through the Internet. A system of filters allows the selection of particular components of the network for visualization.
AVAILABILITY: For the GeneNet database and its graphical user interface please contact info(at)itcsoftware.com.  [PMID: 9694992]

Kolpakov F.A., Ananko E.A.
Interactive data input into the GeneNet database.
Bioinformatics. 1999;15(7-8):713-714.

Abstract: SUMMARY: The GeneNet database has been developed for a formalized hierarchical description of the gene networks. To provide rapid data accumulation in the database, the Java graphical interface for data input through the Internet by independent experts equipped with convenient visual tools is developed. AVAILABILITY: please contact info (at) itcsoftware.com
Full article  [PMID: 10487877]

Kolchanov N.A., Anan'ko E.A., Kolpakov F.A., Podkolodnaia O.A., Ignat'eva E.V., Goriachkovskaia T.N., Stepanenko E.L.
Gene networks.
Mol. Biol. (Mosk.). 2000;34(4):533-544. Russian.
[PMID: 11042846]

Ananko E.A., Kolpakov F.A., Kolesov G.B., Kolchanov N.A.
Gene Networks: a database and its automated visualization through the internet in the genenet computing system.
Proc. Int. Conf. Bioinf. of Genome Regulation and Structure (BGRS'98). 1998;1:82-85.

Abstract: Gene networks provide the regulation of physiological processes in eukaryotic organisms. Ways and means for automated visualization of the gene networks based on their formalized description are needed. Rapidly increasing information regarding the regulation of gene expression and signal transduction pathways is hard to formalize and systematize. The main principles of a formalized description of various regulatory processes have been worked out for the GeneNet computer system designed for accumulation of the data on gene networks and their visualization through the Internet. The GeneNet system is bipartite and includes: (1) a database containing information on gene networks and (2) a Java program for automated construction of the gene network diagrams based on their formalized description in the database. The GeneNet graphical user interface allows visualization and exploration of the GeneNet database through the Internet.
The GeneNet is a part of GeneExpress - a system for analysis of genomic regulatory sequences (http://wwwmgs.bionet.nsc.ru/systems/GeneExpress/ >>) , developed in the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences. GeneNet is available at http://wwwmgs.bionet.nsc.ru/systems/MGL/GeneNet/ >>

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Sequence analysis


Kolpakov F.A., Kel' A.E., Ponomarenko M.P., Kolchanov N.A.
High heterogeneity of higher eukaryotic gene promoters, transcribed by RNA polymerase II.
Dokl Akad Nauk. 1997;375(5):693-995. Russian.

Abstract: The degree of similarity between higher eukarotic promoter sequences transcribed by RNA-polymerase II was to be estimated depending on the species or tissue-specific expression of the corresponding genes. Samples of promoter fragments ([-190; +20] region relative to the transcription start was divided into 7 fragments of 30 bp in length each) have been analyzed for homo sapiens, bos taurus, mus musculus, rat norvegicus, gallus gallus, xenopus laevis and drosophila melanogaster. The sequences were extracted from the EMBL data library, tissue specificity data from the EPD. The similarity between the sequences of the i-th fragments of two promoters (i=1,..7) was assumed non-random if a higher alignment score was obtained for them using the program FASTA than for random sequences with the same oligonucleotide content in 95% of cases. The measure of similarity for the group as a whole was the ratio of the number of non-randomly similar pairs of sequences to the total number of all possible pairs in the group. As turned out, the degree of similarity for the promoters of a species just insignificantly exceeded the random threshold, the highest similarity being observed in the TATA-box and its vicinity. As to the tissue-specific promoters, it was typical of them to have on the whole higher degrees of similarity within a species. That the promoters of non-homologous genes contain non-randomly similar fragments uncovers an important role of convergence in the evolution of promoters. [PMID: 9493004]

Kel A.E., Kondrakhin Yu.V., Kolpakov F.A., Ponomarenko M.P., Wingender E., Kolchanov N.A.
Computer analyses of the structure of transcription factor binding sites.
SAMS. 1995;18-19:819-822. Overseas Publishers Association, Amsterdam.

Abstract: A method for revealing of correlated nucleotide positions in CRE based on entropy coefficient is described. Runs of related positions are found. Connection of the correlations with DNA helical structure and possible application for recognition is discussed.
Full article

Kondrakhin Yu.V., Kolpakov F.A., Kel A.E., Milanesi L., Kolchanov N.A.
Computer analysis and recognition of the transcription regulatory elements in eukaryotic genomes.
Proc. German Conf. on Bioinformatics (GSB'96). 1996; p..

Abstract: A feature of transcription regulatory regions of eukaryotic genes is a clear-cut hierarchy and modular structure (Kel, at al., 1995a). Binding sites for individual transcription factors are at the bottom. Composite elements are at the intermediate level; these are composed of closely located (adjacent or even overlapping) transcription factor binding sites that function as one by virtue of intensive protein-protein interaction between the transcription factors. At the highest level are promoters and enhancers. On the background of the projects for total sequence of the human, mouse, Drosophila and other eukaryotic genome, computer analysis and identification of transcription regulatory units is an extremely important problem. We report results of computer analysis and identification of transcription factor binding sites, composite elements, promoters.
Full article

Seledtsov I.A., Kolpakov F.A.
Rapid estimates of statistical significance of the pairwise nucleotide sequence alignment.
Proc. Int. Conf. Bioinf. of Genome Regulation and Structure (BGRS'98). 1998;2:301-304.

Abstract: Statistical significance of the similarity observed is the main question while comparing sequences. This problem has not yet been solved mathematically for optimal aligning of the sequences containing insertions and deletions. We have carried out the regression analysis of the observed similarity of random sequences depending on their length and nucleotide composition and are proposing a practical method to estimate the probability of the similarity observed to be statistically significant. The regression parameters being determined for a given alignment scheme (similarity matrix and penalties for deletions) for a pair of nucleotide sequences, the statistical significance of the similarity observed can be precisely estimated basing on only their lengths and nucleotide composition.
Full article

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Kolesov G.B., Kolpakov F.A., Kolchanov N.A.
New method for the study of the modular structure of transcription regulatory regions.
Proc. Int. Conf. Bioinf. of Genome Regulation and Structure (BGRS'98). 1998;2:430-433.

Abstract:  It is known that transcription regulatory regions have a modular structure and contain transcription factor binding sites, composite elements, enhancers, silencers, and other functional modules. The situation when the same functional module is located in different positions relative to the transcription start. We propose to solve this problem by combining the methods of pairwise and multiple alignment with analysis of the similarity profiles of the sequences. The promoters of interferon-induced and erythroid-specific genes were investigated. Analysis of similarity profiles for this group promoters reveals that their have large number of similar motifs. The motifs revealed on promoters of interferon-induced genes were subjected to multiple alignment using Gibbs algorithm and was shown their correspondence to binding sites of transcription factor regulating antiviral response.
Full article

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Kochetov A.V., Pilugin M.V., Kolpakov F.A., Babenko V.N., Kvashnina E.V., Shumny V.K.
Structural and compositional features of 5' untranslated regions of higher plant mRNAs.
Proc. Int. Conf. Bioinf. of Genome Regulation and Structure (BGRS'98). 1998;1:210-213.

Abstract: Computer analysis of the 5'untranslated regions (5'UTRs) of plant mRNA sequences is reported. In comparison with 3'UTRs, the nucleotide composition of 5'UTRs is characterized by a considerable asymmetry in the content of the complementary nucleotides (G/C and A/U) and a strong decrease in the frequency of AUG triplet. It has been also shown that mRNA 5'UTRs of dicot and monocot genes differ in a number of characteristics (length, nucleotide content, and context of translational start codon). Statistically, leaders of dicot mRNAs are A+U-rich sequences, and most of them (77%) vary in length between 11 and 120 nt; whereas 5'UTRs of monocot mRNAs are C-rich, and their lengths are mainly distributed between 40 and 120 nt (68% in analyzed sample). Consensus sequences of translational start contexts are aaaaaaaaaAaaAUGGCu for the dicot and ggggcggccA/GCcAUGGCG for the monocot mRNAs. AUG codon contexts in monocot mRNAs appeared to be considerably different from those in dicots by the occurrence of certain combinations of nucleotides in -3 and +4 positions around AUG. The doublet G-3/G+4 was found to be the most frequent combination in monocot mRNAs (35.3%), whereas the doublet A-3/G+4 was the most frequent in dicot mRNAs (35.9%). 

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Bioinformatics software development


Kolpakov F.A., Babenko V.N.
The MGL computer system--an instrument for generating, graphically representing, and analyzing regulatory genomic sequences.
Mol Biol (Mosk). 1997;4(31):647-655. Russian.

Abstract: A computer system MGL (Molecular Genetic Language) was designed for search, extraction from databases, sample generation, visualization, and analysis of regulatory genomic sequences (RGS): regions of DNA/RNA sequences involved in regulation of various molecular genetic processes: replication, transcription, splicing, translation, etc. The MGL system offers a wide range of possibilities for searching and extracting the information on RGS from the EMBL, TRANSFAC, TRRD, Compel, EPD, and Nucleo databases. MGL generates samples of promoters, transcription factor binding sites, and nucleosome positioning sites in an automatic mode using the EMBL database as a source of nucleotide sequences, while the data on RGS location in the sequences are extracted from the EPD, TRRD, and Nucleo databases, respectively. The MGL system also generates automatically nucleotide sequence samples of various RGS (promoters, splicing sites, mRNA, CDS, 5'- and 3'-untranslated regions, polyadenylation sites) basing on semantic analysis of the EMBL FEATURE TABLE information. The MGL system provides visualization of data on the RGS location in nucleotide sequences from TRRD and EMBL databases as well as from results of transcription factor binding sites search in a map form. The MGL system is provided with specialized script language allowing a user to carry out sample generation and analysis of RGS in automatic mode. The MGL system has a user friendly interface designed for Windows3.x and Windows 95. [PMID: 9340492]

Kel A.E., Kondrakhin Y.V., Kolpakov F.A., Kel O.V., Romashenko A.G.,Wingender E., Milanesi L., Kolchanov N.A.
Computer tool FUNSITE for analysis of eukaryotic regulatory genomic sequences.
Proc. Int. Conf. Intell. Syst. Mol. Biol. (ISMB). 1995; p.197-205.

Abstract: We present the computer tool FUNSITE for description and analysis of regulatory sequences of eukaryotic genomes. The tool consists of the following main parts: 1) An integrated database for genomic regulatory sequences. The integrated database was designed on the basis of the databases TRANSFAC (Wingender 1994) and TRRD (Kel et al. 1995) that are currently under development. The following functions are performed: i) linkage to the EMBL database; ii) preparing samples of definite types of functional sites with their flanking sequences; iii) preparing samples of promoter sequences; iv) preparing samples of transcription factors classified with regard to structural and functional features of DNA binding and activating domains, functional families of the factors, their tissue specificity and other functional features; v) access to data on mutual disposition of cis-elements within the regulatory regions. 2) The second component of FUNSITE tool is the set of programs for analysis of the structural organization of regulatory sequences: i) Program for revealing of potential transcription factors binding sites based on their consensi; ii) program for revealing of the potential binding sites using homology search with nucleotide sequences of real binding sites; iii) program for analysis of oligonucleotide context features which are characteristic of flank sequences of the binding sites; iv) program for design of recognition method for the functional sites based on generalized weight matrix; v) program for revealing potential composite elements. The results of analysis of the promoter sequences of eukaryotic genes with the FUNSITE are presented, too. [PMID: 7584437]
Full article

Kolchanov N.A., Ponomarenko M.P., Frolov A.S., Ananko E.A., Kolpakov F.A., Ignatieva E.V., Podkolodnaya O.A., Goryachkovskaya T.N., Stepanenko I.L., Merkulova T.I., Babenko V.N., Ponomarenko J.V., Kochetov A.V., Podkolodny N.L., Vorobyev D.G., Lavrushev S.V., Grigorovich D.A., Kondrakhin Yu.V., Milanesi L., Wingender E., Solovyev V.V., and Overton G.C.
Integrated databases and computer systems for studying eukaryotic gene expression.
Bioinformatics. 1999;15(7-8):669-686.

Abstract: MOTIVATION: The goal of the work was to develop a WWW-oriented computer system providing a maximal integration of informational and software resources on the regulation of gene expression and navigation through them. Rapid growth of the variety and volume of information accumulated in the databases on regulation of gene expression necessarily requires the development of computer systems for automated discovery of the knowledge that can be further used for analysis of regulatory genomic sequences. RESULTS: The GeneExpress system developed includes the following major informational and software modules: (1) Transcription Regulation (TRRD) module, which contains the databases on transcription regulatory regions of eukaryotic genes and TRRD Viewer for data visualization; (2) Site Activity Prediction (ACTIVITY), the module for analysis of functional site activity and its prediction; (3) Site Recognition module, which comprises (a) B-DNA-VIDEO system for detecting the conformational and physicochemical properties of DNA sites significant for their recognition, (b) Consensus and Weight Matrices (ConsFrec) and (c) Transcription Factor Binding Sites Recognition (TFBSR) systems for detecting conservative contextual regions of functional sites and their recognition; (4) Gene Networks (GeneNet), which contains an object-oriented database accumulating the data on gene networks and signal transduction pathways, and the Java-based Viewer for exploration and visualization of the GeneNet information; (5) mRNA Translation (Leader mRNA), designed to analyze structural and contextual properties of mRNA 5'-untranslated regions (5'-UTRs) and predict their translation efficiency; (6) other program modules designed to study the structure-function organization of regulatory genomic sequences and regulatory proteins. [PMID: 99419257]

Kolchanov N.A., Ponomarenko M.P., Kel A.E., Kondrakhin Yu.V., Frolov A.S., Kolpakov F.A., Goriachkovsky T.N., Kel-Margulis O.V., Ananko E.A., Ignatieva E.V., et al.
GeneExpress: an integrator for databases and computer systems accessible by the Internet and intended for studying eukaryotic gene expression.
Biofizika. 1999;44(5):837-841. Russian.

Abstract: We have developed GeneExpress that is the WWW-oriented integrator for the databases and systems supporting the investigation of gene expression. The total number of the Web-based resources integrated is 30. The database GeneNet on molecular events forming gene networks was assigned its integrative core. [PMID: 10624523]

Kolchanov N.A., Ponomarenko M.P., Kel A.E., Kondrakhin Yu.V., Frolov A.S., Kolpakov F.A., Goryachkovsky T.N., Kel O.V., Ananko E.A., Ignatieva E.V., Podkolodnaya O.A., Babenko V.N., Stepanenko I.L., Romashchenko A.G., Merkulova T.I, Vorobiev D.G., Lavryushev S.V., Ponomarenko Yu.V., Kochetov A.V., Kolesov G.B., Solovyev V.V., Milanesi L., Podkolodny N.L., Wingender E., Heinemeyer T.
GeneExpress: a computer system for description, analysis, and recognition of regulatory sequences in eukaryotic genome.
Proc. Int. Conf. Intell. Syst. Mol. Biol. (ISMB). 1998;6:95-104.

Abstract: GeneExpress system has been designed to integrate description, analysis, and recognition of eukaryotic regulatory sequences. The system includes 5 basic units: (1) GeneNet contains an object-oriented database for accumulation of data on gene networks and signal transduction pathways and a Java-based viewer that allows an exploration and visualization of the GeneNet information; (2) Transcription Regulation combines the database on transcription regulatory regions of eukaryotic genes (TRRD) and TRRD Viewer; (3) Transcription Factor Binding Site Recognition contains a compilation of transcription factor binding sites (TFBSC) and programs for their analysis and recognition; (4) mRNA Translation is designed for analysis of structural and contextual features of mRNA 5'UTRs and prediction of their translation efficiency; and (5) ACTIVITY is the module for analysis and site activity prediction of a given nucleotide sequence. Integration of the databases in the GeneExpress is based on the Sequence Retrieval System (SRS) created in the European Bioinformatics Institute.[PMID: 9783214]
Full article

Kolpakov F.A., Babenko V.N.
MGL: an object-oriented computer system for molecular genetic data management, analysis, and visualization.
Proc. Int. Conf. Bioinf. of Genome Regulation and Structure (BGRS'98). 1998;2:434-437.

Abstract: The object-oriented computer system MGL is designed for (1) searching for and extracting the information from molecular genetics databases; (2) automated generation of nucleotide sequence samples of various gene components basing on semantic analysis of the EMBL FEATURE TABLE information and samples of promoters and transcription factor binding sites basing on the information from the EPD and TRRD databases, respectively; (3) nucleotide sequences analysis; and (4) visualization of the database-contained information and the results of analyses performed. The core of the MGL is the class library based on the idea that the set of classes corresponds directly to the main concepts of molecular genetic data. A specialized high-level object-oriented language allows a user to generate samples and analyze nucleotide sequences in an automatic mode. The MGL system has a friendly user interface designed for Windows.
Full article  

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Biological database development


Kolchanov N.A., Podkolodnaya O.A., Ananko E.A., Ignatieva E.V., Stepanenko I.L., Kel-Margoulis O.V., Kel A.E., Merkulova T.I., Goryachkovskaya T.N., Busygina T.V., Kolpakov F.A., Podkolodny N.L., Naumochkin A.N., Korostishevskaya I.M., Romashchenko A.G., Overton G.C.
Transcription regulatory regions database (TRRD): its status in 2000.
Nucleic Acids Res.. 2000;28(1):298-301.

Abstract: Transcription Regulatory Regions Database (TRRD) has been developed for accumulation of experimental information on the structure-function features of regulatory regions of eukaryotic genes. Each entry in TRRD corresponds to a particular gene and contains a description of structure-function features of its regulatory regions (transcription factor binding sites, promoters, enhancers, silencers, etc.) and gene expression regulation patterns. The current release, TRRD 4.2.5, comprises the description of 760 genes, 3403 expression patterns, and >4600 regulatory elements including 3604 transcription factor binding sites, 600 promoters and 152 enhancers. This information was obtained through annotation of 2537 scientific publications. [PMID: 20063287]
Full article

Kolchanov N.A., Ananko E.A., Podkolodnaya O.A., Ignatieva E.V., Stepanenko I.L., Kel-Margoulis O.V., Kel A.E., Merkulova T.I., Goryachkovskaya T.N., Busygina T.V., Kolpakov F.A., Podkolodny N.L., Naumochkin A.N., Romashchenko A.G.
Transcription Regulatory Regions Database (TRRD):its status in 1999.
Nucleic Acids Res.. 1999;27(1):303-306.

Abstract: The Transcription Regulatory Regions Database (TRRD) is a curated database designed for accumulation of experimental data on extended regulatory regions of eukaryotic genes, the regulatory elements they contain, i.e., transcription factor binding sites, promoters, enhancers, silencers, etc., and expression patterns of the genes. Release 4.1 of TRRD offers a number of significant improvements, in particular, a more detailed description of transcription factor binding sites, transcription factors per se, and gene expression patterns in a computer-readable format. In addition, the new TRRD release provides considerably more references to other molecular biological databases. [PMID: 99063721]
Full article

Heinmeyer T., Wingender E., Reuter I., Hermjakob H., Kel A.E., Kel O.V., Ignatieva E.V., Ananko E.A., Podkolodnaya O.A., Kolpakov F.A., Podkolodny N.L., and Kolchanov N.A.
Databases on transcription regulation: TRANSFAC, TRRD and COMPEL.
Nucleic Acids Res.. 1998;26(1):362-367.  Gesellschaft fur Biotechnologische Forschung mbH, Mascheroder Weg 1, D-38124 Braunschweig, Germany.

Abstract: TRANSFAC, TRRD (Transcription Regulatory Region Database) and COMPEL are databases which store information about transcriptional regulation in eukaryotic cells. The three databases provide distinct views on the components involved in transcription: transcription factors and their binding sites and binding profiles (TRANSFAC), the regulatory hierarchy of whole genes (TRRD), and the structural and functional properties of composite elements (COMPEL). The quantitative and qualitative changes of all three databases and connected programs are described. [PMID: 98062468]
Full article

Kel A.E., Kolchanov N.A., Kel O.V., Romaschenko A.G., Ananko E.A., Ignatieva E.V., Merkulova T.I., Podkolodnaya O.A., Stepanenko I.L., Kochetov A.V., Kolpakov F.A., Podkolodnyi N.L., Naumochkin A.N.
TRRD: a database of transcription regulatory regions in eukaryotic genes.
Mol. Biol. (Mosk.). 1997;31(4):626-636.
[PMID: 9340490 ]

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Kolchanov N.A., Ignatieva E.V., Kel-Margoulis O.V., Kel A.E., Ananko E.A., Podkolodnaya O.A., Stepanenko I.L., Merkulova T.I., Goryachkovsky T.N., Kolpakov F.A., Podkolodny N.L., Lavryushev S.V., Grigorovich D.A., Frolov A.S., Romashchenko A.G.
Transcription Regulatory Regions Database (TRRD): new possibilities provided by release 4.0.
Proc. Int. Conf. Bioinf. of Genome Regulation and Structure (BGRS'98). 1998;1:25-28.

Abstract: Current state of the TRRD database is described including the new possibilities of experimental data formalized representation connected with TRRD format modification. Structure of the database and the means for its integration with other databases are detailed. Contents of the TRRD, Release 4.0, are briefly analyzed.

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Biomechanics


PUBLICATIONS IN COMPUTER MODELING IN BIOENGINEERING

M. Kojic, S. Mijailovic, N. Zdravkovic,
A numerical algorithm for stress integration of a fiber-fiber kinetics model with Coulomb friction for connective tissue,  Computational Mechanics, Vol. 21, No. 2, pp. 189-198, 1998.

M. Kojic, S. Mijailovic, N. Zdravkovic,
Modelling of muscle behavior by the finite element method using Hill's three-element model,  Int. J. Num. Meth. Engng., Vol. 43, pp. 941-953, 1998.

M. Kojic, N. Filipovic, S. Vulovic, S. Mijailovic,
A finite element solution procedure for porous medium with fluid flow and electromechanical coupling, Comm. Num. Meth. Engng, Vol. 14, pp. 381-392, 1998.

S. Radlović, M. Kojić, Z. Petrović, I. Vlastelica, B. Stojanović,
Finite element method application in implantology, Stom. Glasnik (Serbian), Vol. 45, 137-140, 1998.

M. Kojic, N. Filipovic, S. Mijailovic,
A large strain finite element analysis of cartilage deformation with electrokinetic coupling, Comp. Meth. Appl. Mech. Engng., Vol. 190, pp.  2447-2464,  2001.

S. Mijailovich, M. Kojic, M. Zivkovic, B. Fabry, J. Fredberg,
A finite el
еment model of cell deformation during magnetic bead twisting, J. Appl. Physiol., Vol. 93, pp. 1429-1436, 2002.

M. Kojic, N. Zdravkovic, S. Mijailovic,
A numerical stress calculation procedure for a fiber-fiber kinetics model with Coulomb and viscous friction of connective tissue, Computational Mechanics, Vol. 30, pp. 185-195, 2003.

 N. Filipović, M. Kojić,  
Computer simulations of blood flow with mass transport through the carotid artery bifurcation, Theoret. Appl. Mech. (Serbian), Vol. 31, No. 1, pp. 1-33, 2004.

M. Kojic, A. Tsuda,
Gravitational deposition of aerosols from oscillatory laminar pipe flows, J. Aerosol Science, Vol. 35, pp. 245-261, 2004.

N. Kojic, M. Kojic, S. Gudlavalleti, G. McKinley,

Solvent removal during synthetic and Nephila fiber spinning, Biomacromolecules, Vol. 5, No. 5, 1698-1707, 2004.

 

C. Y. Tang, B. Stojanovic, C. P. Tsui, M. Kojic,

Modeling of muscle fatigue using Hill's model, Bio-Medical Materials and Engng., Vol. 15, No. 5, 2005.

Milos Kojic and K. J. Bathe,
Inelastic Analysis of Solids and Structures
, Springer Verlag, 2005. 

N. Filipovic, S. Mijailovic, A. Tsuda, M. Kojic,
An implicit algorithm within the arbitrary Lagrangian-Eurlerian formulation for solving incompressible fluid flow with large boundary motions, Comp. Meth. Appl. Mech. Eng., 95, 6347-6361, 2006.

N. Kojic, M. Kojic, D. Tschumperlin,
Computational modeling of extracellular mechanotransduction, Biophysical Journal, Vol 90, 4, Issue 11, 4261-4270, 2006.

N. Kojic, A. Kojic, M. Kojic,
Numerical determination of the solvent diffusion coefficient in a concentrated polymer solution, Comm. Num. Meth. Eng., Vol. 22, 1003-1013, 2006.

S. Haber, N. Filipovic, M. Kojic, A. Tsuda,
Dissipative particle dynamics simulation of flow generated by two rotating concentric cylinders. Part I: Boundary conditions, Physical Review E, Vol. 74, 1-8, 2006.

M. Kojic, I. Vlastelica, B. Stojanovic, V. Rankovic, A. Tsuda, 

Stress integration procedures for a biaxial isotropic material model of biological membranes and for hysteretic models of muscle fibers and surfactant, Int. J. Num. Meth. Engng., Vol 68, 893-909, 2006.

B. Stojanovic, M. Kojic, M. Rosic, C.P. Tsui, C.Y. Tang,   
An extension of Hill’s three-component model to include different fiber types in finite element modelling of muscle, Int. J. Num. Meth. Eng., 71, 801-817, 2007.

M. Kojic, N. Filipovic, A. Tsuda, 
A mesoscopic bridging scale method for fluids and coupling dissipative particle dynamics with continuum finite element method, Comp. Meth. Appl. Mech. Eng., 197, 821-833, 2008

Filipovic N, Haber S, Kojic M. and Tsuda A.,
Dissipative Particle Dynamics Simulation of Flow Generated by Two Rotating Concentric Cylinders. Part II: Lateral Dissipative and Random Forces, Phys. Rev. E.
, in review.

CY Tang, CP Tsui, B Stojanovic, M Kojic.

Finite element modelling of skeletal muscles coupled with fatigue, Int. J. Mech. Sciences, 49,  1179-1191, 2007.

N. Filipovic, D. Ravnic, M. Kojic, S.J. Mentzer, S. Haber, A. Tsuda,
Interactions of blood cell constituents: Experimental investigation and computatonal modeling by
discrete particle dynamics algorithm,  Microvascular Research, 75, 279-284, 2008.

M. Rosic, S. Pantovic, V. Rankovic, Z. Obradovic, N. Filipovic, M. Kojic, 

Evaluatiopn of dynamic response and biomechanical properties of isolated blood vessels, J. Biochem. Biophys. Methods, in press.

M. Kojić, N. Filipović, B. Stojanović, N. Kojic,
Computer Modeling in Bioengineering – Theoretical Background, Examples and Software
, J. Wiley and Sons, in press.

______

Kojic M. Filipovic N. Mijailovic S.,
A large strain finite element analysis of cartilage deformation with electrokinetic coupling. Computer Methods in Applied Mechanics & Engineering.
190(18-19):2447-2464, 2001.

Mijailovich, S.M. , Butler J.P. , and Fredberg, J.J..
Perturbed Equilibria of Myosin Binding Airway Smooth Muscle: Bond-Length Distributions, Mechanics and ATP Metabolism,
Biophys. J. 79, 2667-2681, 2000.

Kojic M. Mijailovic S. Zdravkovic N.,
Modelling of muscle behaviour by the finite element method using Hill’s three-element model. International Journal for Numerical Methods in Engineering.
43(5):941-953, 1998.

Kojic M. Filipovic N. Vulovic S. Mijailovic S.
A finite element solution procedure for porous medium with fluid flow and electromechanical coupling. Communications in Numerical Methods in Engineering.
14(4):381-392, 1998.

Kojic M. Mijailovic S. Zdravkovic N.
A numerical algorithm for stress integration of a fiber-fiber kinetics model with Coulomb friction for connective tissue.
Computational Mechanics. 21(2):189-198, 1998 .

 

Rosic M. A., Andjelkovic I., Mojovic M., Mitrovic D. and Maskic J.
Characterization of 3H-Histamine transport at the Sarcolemal Membrane of the Isolated Guinea-pig Heart in the Presence of Glucagon and H1 and H2 Receptors Antagonist.
Biomed Biochim Acta, 46 (10): 736-740, 1987

Kojic, M. and Bathe K. J.,
The "Effective Stress-Function" Algorithm for Thermo-Elasto-Plasticity and Creep,

Int. J. Num. Meth., Engng., pp. 1509-1532, 1987

Mitrovic D., Rosic M. A., Mojovic M. and Kostic M.,
Characteristics of Thiamin Transport in the Isolated Guinea-Pig Heart
,
Arch Int Physiol Biophys, 101: 325, 1993

Rosic M. A., Kostic M., Segal M., Williams S. and Preston H., L-Arginine
Transport in the Isolated Guinea-Pig Heart,
J physiol, 467: 154P, 1993

Rosic M. A., Segal M., Collis C. and Andjelkovic I.,
The Interaction if Digoxine and Cimetidine in the Isolated Guinea-Pig Heart
,
J Physiol, 449;221P, 1993

Rosic M. A., Segal M., Collis C., Egleton R. and Andjelkovic I.,
Propranolol Inhibits Cimetidine Potentation of Digoxine Effects in the Langedorff Perfused Guinea-Pig Heart
,
J Physiol, 467: 58P, 1993

Kojic, M., Grujovic, N., Slavkovic, R. and Zivkovic, M.,
A General Orthotropic von Mises Plasticity Material Model with Mixed Hardening Model Definition and Implicit Stress Integration Procedure
,
Transactions of ASME J. Applied Mechanics, Vol. 63, pp. 376-382, 1996

Rosic M., Pantovic S., Trtic T., Ribarac-Stepic N., Andjelkovic I., Lucic A., Mitrovic D.,
Thyroxine Uptake by the Isolated Rat Heart
,
Farmacia & Therapia, 13 (4): 100-104, 1996

Cvetkovic N., Necic M., Moracic V. and Rosic M. A.,
Design of Method for in Vitro Studies of Plimer Adhesion
,
Die Pharmazie, 52, 7, 536-639, 1997

Kojic, M., Filipovic, N., Vulovic, S., and Mijailovic, S.,
A Finite Element Solution Procedure for Porous Medium with Fluid Flow and Electromechanical Coupling
,
Comm. Num. Meth. Engng, Vol. 14, pp. 381-392,1998

Kojic, M., Mijailovic, S., Zdravkovic, N.,
A Numerical Algorithm for Stress Integration of a Fiber-Fiber Kinetics Model with Coulomb Friction for Connective Tissue
,
Computational Mechanics, 21(2):189-198, 1998

Kojic, M., Mijailovic, S., Zdravkovic, N.,
Modeling of Muscle Behavior by the Finite Element Method Using Hill's Three-Element Model
,
Int. J. Num. Meth. Engng., 43:941-953, 1998

Rosic M. A., Pantovic S. B., Lucic A. P., Ribarac-Stepic N., Trtic T., Andjelkovic I., Segal M. B., Triodothyronine Uptake by the Isolated Rat Heart, Die Pharmazie, 53, 350-352, 1998

Kojic, M. Filipovic, N, Mijailovic, N.,
A Large Strain Finite Element Analysis of Cartilage Deformation with Electrokinetic Coupling
,
Comput. Methods Appl. Mech. Engrg., Vol 190, pp. 2447-2464, 2001
Srboljub pp. 2447-2464
Bibliographic Page and Abstract | Article Full Text PDF (1.29 MB)

Rosic, M.A., Pantovic S.B., Lucic A. P., Ribarac-Stepic N., Andelkovic I.,
Kinetics of Thyroxine (T-4) and Triiodothyronine (T-3) Transport in the Isolated Rat Heart
,
Exp Physiol 2001, 86 (1), 13-18, 2001

Kojic, M. and Bathe, K. J., Inelastic Analysis of Solids and Structures, Springer-Verlag, Goettingen, New York, in press.

Kojic, M., Zdravkovic, N., Mijailovic, S.,
A Numerical Stress Calculation Procedure for a Fiber-Fiber Kinetics Model with Coulomb and Viscous Friction of Connective Tissue
,
Computational Mechanics, in press.

Kojic, M., Zdravkovic, N., Rosic, M., and Mijailovic, S.,
A Material Model for Passive Response of Urinary Bladder
, submitted

Filipovic, N. and Kojic, M.,
Computer Simulation of Blood Flow with Mass Transport Through the Carotid Artery Bifurcation
, submitted

 

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