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THE MAMMALIAN CIRCADIAN CLOCK: GENE REGULATORY NETWORK AND THEIR COMPUTER ANALYSIS

O. A. Podkolodnaya, N. N. Podkolodnaya, N. L. Podkolodnyy
2015 Vavilovskij Žurnal Genetiki i Selekcii  
This paper presents the results of the reconstruction and analysis of gene regulatory network of the circadian clock in mammals. Application of graph theory methods makes it possible to analyze the structure of the gene network and identify the central component of circadian clock regulation, which includes the basic regulatory circuits passing through the key element of the circadian clock, the Clock/Bmal1 protein. Cluster analysis has revealed subsystems with clear biological interpretation,
more » ... hich are involved in the functioning of the circadian clock by interacting with the central component. This structural model, which includes the central component and functional subsystems that interact with the central component, can provide grounds for the construction of a mathematical model of the dynamics of the gene network regulating the circadian rhythm.
doaj:b375865d1957442db6940b8f03381a35 fatcat:awddocquobgrbpwy6do33wjqzm

DISTRIBUTED RESTful WEB SERVICES FOR RECONSTRUCTION AND ANALYSIS OF GENE NETWORKS

N. L. Podkolodnyy, A. V. Semenychev, D. A. Rasskazov, V. G. Borowsky, E. A. Ananko, E. V. Ignatieva, N. N. Podkolodnaya, O. A. Podkolodnaya, N. A. Kolchanov
2014 Vavilovskij Žurnal Genetiki i Selekcii  
This paper describes a RESTful Web service-based distributed software system, which focuses on the reconstruction of gene networks by integrating data from heterogeneous data sources, including databases of molecular-genetic interactions, metabolic and signaling pathways, gene networks, etc.
doaj:86396da3431b49e19f2b44ee3c1180fc fatcat:azygodterfeg5bmntyhb4h5sya

Biomedical and candidate SN P markers of chronopathologies can significantly change affinity of ТАТА -binding protein for human gene promoters

D. A. Rasskazov, N. L. Podkolodnyy, O. A. Podkolodnaya, N. N. Podkolodnaya, V. V. Suslov, L. K. Savinkova, P. M. Ponomarenko, M. P. Ponomarenko
2016 Vavilov Journal of Genetics and Breeding  
.�� Podkolodnaya o .A.�� Podkolodnaya n.n .�� Suslov V.V.�� Savinkova l .K.�� Ponomarenko P.M.�� Ponoma-renko M.P.  ...  Podkolodnaya … l .K. Savinkova�� P.M. Ponomarenko�� M.P. Ponomarenko  ... 
doi:10.18699/vj15.083 fatcat:sbytvqqsdjhwlmdf3nb64jy6lm

Nucleosome formation potential of exons, introns, and Alu repeats

V. G. Levitsky, O. A. Podkolodnaya, N. A. Kolchanov, N. L. Podkolodny
2001 Bioinformatics  
A program for constructing nucleosome formation potential profile was applied for investigation of exons, introns, and repetitive sequences. The program is available at http: //wwwmgs.bionet.nsc.ru/mgs/programs/recon/. We have demonstrated that introns and repetitive sequences exhibit higher nucleosome formation potentials than exons. This fact may be explained by functional saturation of exons with genetic code, hindering the localization of efficient nucleosome positioning sites. Contact: levitsky@bionet.nsc.ru
doi:10.1093/bioinformatics/17.11.1062 pmid:11724736 fatcat:vwfddnhs2bedpe3xn3ghmpy2ym

Detection and analysis of dynamic patterns of diurnal expression of mammalian genes

O. V. Podkolodnaya, N. N. Tverdokhleb, N. L. Podkolodnyy
2019 Vavilovskij Žurnal Genetiki i Selekcii  
В нашем случае N = 24, k = 12, n j = 2. Пусть в результате получен уровень значимости α 0 .  ...  Для проверки нулевой гипотезы используется статистика: F = ∑ j n j (X . j -X .. ) 2 / (k -1) ∑ i ∑ j (X ij -X . j ) 2 / (N -k) , (1) которая имеет F распределение с степенями свободы k -1 и N -k.  ... 
doi:10.18699/vj18.450 fatcat:ijvveqtytnc5fjg2ew36wyjchy

Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis

V. G. Levitsky, O. A. Podkolodnaya, N. A. Kolchanov, N. L. Podkolodny
2001 Bioinformatics  
(1) n = f (1) i, p , n = 1, . . . , N , where N = 16 × P.  ...  f (1) n ) and the set of random sequences (vector f (2) n ) is found according to the following equation: R 2 = N k=1 N n=1 {[ f (2) n − f (1) n ] * S −1 n,k * [ f (2) k − f (1) k ]}, (1) where n = 1,  ... 
doi:10.1093/bioinformatics/17.11.998 pmid:11724728 fatcat:idofqh43bnez3bk3zatfk2w4xq

Analysis of the circadian rhythm of biological processes in mouse liver and kidney

I. N. Podkolodnyy, N. N. Tverdokhleb, O. A. Podkolodnaya
2017 Vavilovskij Žurnal Genetiki i Selekcii  
Podkolodnaya • 8  ... 
doi:10.18699/vj17.311 fatcat:wmmamt7zjrhq7f5fixirg5tr3y

The effects of SN Ps in the regions of positioning RNA polymerase II on the TBP/promoter affinity in the genes of human circadian clock

O. A. Podkolodnaya, D. A. Rasskazov, N. L. Podkolodnyy, N. N. Podkolodnaya, V. V. Suslov, L. K. Savinkova, P. M. Ponomarenko, M. P. Ponomarenko
2016 Vavilov Journal of Genetics and Breeding  
Podkolodnaya o .A.�� r asskazov D.A.�� Podkolodnyy n.l .�� Podkolodnaya n.n .�� Suslov V.V.�� Savinkova l .K.�� Ponomarenko P.M.�� Ponoma-renko M.P.  ...  Podkolodnaya�� D.A. Rasskazov�� N.l . Podkolodnyy … l.K. Savinkova�� P.P. Ponomarenko�� M.P. Ponomarenko O .A. Podkolodnaya�� D.A. Rasskazov�� N.l . Podkolodnyy … l .K. Savinkova�� P.P.  ... 
doi:10.18699/vj15.089 fatcat:ejr3476cybff7owuvyyifxiacu

Ontologies in bioinformatics and systems biology

N. L. Podkolodnyy, O. A. Podkolodnaya
2016 Vavilov Journal of Genetics and Breeding  
Podkolodnyy n .l .�� Podkolodnaya o .A. o ntologies in bioinformatics and systems biology.  ...  Podkolodnaya 2015 19 • 6 ontologies 655  ... 
doi:10.18699/vj15.090 fatcat:2wuouiukdnemhejxl356v7zkqi

INFORMATION SUPPORT OF RESEARCH ON TRANSCRIPTIONAL REGULATORY MECHANISMS: AN ONTOLOGICAL APPROACH

N. L. Podkolodnyy, E. V. Ignatieva, O. A. Podkolodnaya, N. A. Kolchanov
2014 Vavilovskij Žurnal Genetiki i Selekcii  
Совы (http://www.jfsowa.com/ontology/) и работа N. Baumgartner с соавт. (2006) . В описание понятия «процесс» входят следующие компоненты. − Контекст.  ... 
doaj:689e125c3db144f79ae73a69d77e7f03 fatcat:cbho2sunivhplcrsesdu55vcwi

Computational model for mammalian circadian oscillator: interacting with NAD+/SIRT1 pathway and age-related changes in gene expression of circadian oscillator

N. L. Podkolodnyy, N. N. Tverdokhleb, O. A. Podkolodnaya
2016 Vavilovskij Žurnal Genetiki i Selekcii  
Podkolodnaya • 6  ...  селекции • 20 • 6 • 2016 Математическая модель циркадного осциллятора: взаимодействие с системой NAD+/SIRT1 CLOCK PER2 Degradation a SIRT1 NAD+ BMAL1 PER2 CRY a E-Box CLOCK N  ... 
doi:10.18699/vj16.201 fatcat:x2lwco246rgf3eorgecnghtmni

Ontologies in bioinformatics and systems biology

N. L. Podkolodnyy, O. A. Podkolodnaya
2016 Russian Journal of Genetics Applied Research  
Podkolodnyy n .l .�� Podkolodnaya o .A. o ntologies in bioinformatics and systems biology.  ...  Podkolodnaya 2015 19 • 6 ontologies 655  ... 
doi:10.1134/s2079059716070091 fatcat:bwcpufmgynbqlpwiqlhrxb52x4

Transcription Regulatory Regions Database (TRRD): its status in 1999

N. A. Kolchanov, E. A. Ananko, O. A. Podkolodnaya, E. V. Ignatieva, I. L. Stepanenko, O. V. Kel-Margoulis, A. E. Kel, T. I. Merkulova, T. N. Goryachkovskaya, T. V. Busygina, F. A. Kolpakov, N. L. Podkolodny (+2 others)
1999 Nucleic Acids Research  
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
more » ... 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. TRRD 4.1 is installed under SRS and is available through the WWW at http://www.bionet.nsc.ru/trrd/
doi:10.1093/nar/27.1.303 pmid:9847210 pmcid:PMC148165 fatcat:u2pzqpx375eqfmko5qvsh4b4qu

Computational modeling of the cell-autonomous mammalian circadian oscillator

Olga A. Podkolodnaya, Natalya N. Tverdokhleb, Nikolay L. Podkolodnyy
2017 BMC Systems Biology  
This review summarizes various mathematical models of cell-autonomous mammalian circadian clock. We present the basics necessary for understanding of the cell-autonomous mammalian circadian oscillator, modern experimental data essential for its reconstruction and some special problems related to the validation of mathematical circadian oscillator models. This work compares existing mathematical models of circadian oscillator and the results of the computational studies of the oscillating
more » ... . Finally, we discuss applications of the mathematical models of mammalian circadian oscillator for solving specific problems in circadian rhythm biology.
doi:10.1186/s12918-016-0379-8 pmid:28466791 fatcat:gfjmzpsnnfeghhxzkpfcmwrklm

Oligonucleotide frequency matrices addressed to recognizing functional DNA sites

M. P. Ponomarenko, J. V. Ponomarenko, A. S. Frolov, O. A. Podkolodnaya, D. G. Vorobyev, N. A. Kolchanov, G. C. Overton
1999 Bioinformatics  
N > 65 and, finally, to alphabet #5 when N > 200.  ...  In these definitions, the oligonucleotide frequency matrix F L -m + 1,k = {f ij } is calculated as follows: f ij + 1 ) ȍ N n+1 Ȋ m z+1 d(s i)z-1,n Ů e zj ) N ) k (1) where δ(true) = 1, δ(false) = 0.  ... 
doi:10.1093/bioinformatics/15.7.631 pmid:10487871 fatcat:pzmq5ewb2vhd5cg5y552fzaiue
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