Bioinformatics of Genome Regulation and Structure II

Part 1. Computational Structural, Functional and Evolutionary Genomics

1. Recognition of Coding Regions in Genome Alignment
T. V. Astakhova, S. V. Petrova, I. I. Tsitovich, M. A. Roytberg

2. Predicting sRNA Genes in the Genome of E. Coli by the Promoter-Search Algorithm PlatProm
A. S. Brok-Volchanski, I. S. Masulis, K. S. Shavkunov, V. I. Lukyanov, Yu. A. Purtov, E. G. Kostyanicina, A. A. Deev, O. N. Ozoline

3. Content Sensors Based on Codon Structure and DNA Methylation for Gene Finding in Vertebrate Genomes
X. Xia

4. The Sitega Tool for Recognition and Context Analysis of Transcription Factor Binding Sites: Significant Dinucleotide Features Besides the Canonical Consensus Exemplified By SF-1 Binding Site
V. Levitsky, E. Ignatieva, G. Vasiliev, N. Limova, T. Busygina, T. Merkulova, N. Kolchanov

5. Transcription Regulatory Regions Database (TRRD): A Source of Experimentally Confirmed Data on Transcription Regulatory Regions of Eukaryotic Genes
N. Kolchanov, E. Ignatieva, O. Podkolodnaya, E. Ananko, I. Stepanenko, T. Merkulova, T. Khlebodarova, V. Merkulov, N. Podkolodny, D. Grigorovich, A. Poplavsky, A. Romashchenko

6. Artsite Database: Comparison of In Vitro Selected and Natural Binding Sites of Eukaryotic Transcription Factors
T. Khlebodarova, O. Podkolodnaya, D. Oshchepkov, D. Miginsky, E. Ananko, E. Ignatieva

7. Comparative Analysis of Electrostatic Patterns for Promoter and Nonpromoter DNA in E. Coli Genome
S. G. Kamzolova, A. A. Sorokin, P. M. Beskaravainy, A. A. Osypov

8. Analysis of Nucleosome Formation Potential and Conformational Properties of Human J1-J2 and D2-D1 Type Alpha Satellite DNA
A. Katokhin, V. Levitsky, D. Oshchepkov, A. Poplavsky, V. Trifonov, D. Furman

9. VMM: A Variable Memory Markov Model Prediction of Nucleosome Formation Sites
Yu. L. Orlov, V. G. Levitsky, O. G. Smirnova, O. A. Podkolodnaya, T. M. Khlebodarova, N. A. Kolchanov

10. DNA Nucleosome Organization of the Promoter Gene Regions
V. G. Levitsky, A. G. Pichueva, A. V. Kochetov, L. Milanesi

11. A Toolbox for Analysis of RNA Secondary Structure Based on Genetic Algorithm
I. Titov, D. Vorobiev, A. Palyanov

12. Comparative Genomics and Evolution of Bacterial Regulatory Systems
M. S. Gelfand, A. V. Gerasimova, E. A. Kotelnikova, O. N. Laikova, V. Y. Makeev, A. A. Mironov, E. M. Panina, D. A. Ravcheev, D. A. Rodionov, A. G. Vitreschak

13. Comparative Whole Genome Sequence Analysis of Corynebacteria
Y. Nishio, Y. Usuda, T. Gojobori, K. Ikeo

14. New LTR Retrotransposable Elements from Eukaryotic Genomes
O. Novikova, M. Fursov, E. Beresikov, A. Blinov

15. A Genome-Wide Identification of Mitochondrial DNA Topoisomerase I in Arabidopsis
A. Katyshev, I.B. Rogozin, Yu. Konstantinov

16. Change in CpG Context is a Leading Cause of Correlation between the Rates of Non-Synonymous and Synonymous Substitutions in Rodents
G. Bazykin, A. Ogurtsov, A. Kondrashov

17. Universal Seven-Cluster Structure of Genome Fragment Distribution: Basic Symmetry in Triplet Frequencies
A. Gorban, A. Zinovyev, T. Popova

18. New Methods to Infer DNA Function from Sequence Information
I. Abnizova, R. Boekhorst, K. Walter, W. R. Gilks

19. Revelation and Classification of Dinucleotide Periodicity of Bacterial Genomes Using the Method of Information Decomposition
A. A. Shelenkov, M. B. Chaley, K. G. Skryabin, E. V. Korotkov

20. Algorithms to Reconstruct Evolutionary Events at Molecular Level and Infer Species Phylogeny
V. Lyubetsky, K. Gorbunov, L. Rusin, V. V’yugin

Part 2. Computational Structural and Functional Proteomics

21. Mining from Complete Proteomes to Identify Adhesins and Adhesin-Like Proteins: A Rapid Aid to Experimental Researchers
S. Ramachandran, P. Jain, K. Kumar, G. Sachdeva

22. Central Moments Based Statistical Analysis for the Determination of Functional Sites in Proteins with Thematics
L. F. Murga, J. Ko, Y. Wei, M. J. Ondrechen

23. Amino Acids Surface Patterns in Protein Domain Functionality Analysis
I. Merelli, L. Pattini, S. Cerutti, L. Milanesi

24. Computer Simulations of Anionic Unsaturated Lipid Bilayer—A Suitable Model to Study Membrane Interactions with A Cell-Penetrating Peptide
A. A. Polyansky, P. E. Volynsky, A. S. Arseniev, R. G. Efremov

25. The Role of Water in Homeodomain-DNA Interaction
A. Karyagina, A. Ershova, S. Spirin, A. Alexeevski

26. Molecular Modeling of Human MT1 and MT2 Melatonin Receptors
A. Chugunov, P. Chavatte, R. Efremov

27. Molecular Dynamics of Small Peptides Using Ergodic Trajectories
K. V. Shaitan, K. B. Tereshkina

28. A Periodical Nature of 94 Protein Families
V. P. Turutina, A. A. Laskin, N. A. Kudryashov, K. G. Skryabin, E. V. Korotkov

29. Prediction of Contact Numbers of Amino Acid Residues Using a Neural Network Model
D. A. Afonnikov

30. Fastprot: A Computational Workbench for Recognition of the Structural and Functional Determinants in Protein Tertiary Structures
V. A. Ivanisenko, S. S. Pintus, P. S. Demenkov, M. A. Krestyanova, E. K. Litvenko, D. A. Grigorovich, V. A. Debelov

31. A Markov Model for Protein Sequences
Y. Surya pavan, C. K. Mitra, S. M. Bendre

32. Proteome Complexity Measures Based on Counting of Domain-to-Protein Links for Replicative and Non-Replicative Domains
V. A. Kuznetsov, V. V. Pickalov, A. A. Kanapin

Part 3. Computational System Biology

33. A Software Architecture for Developmental Modeling in Plants: The Computable Plant Project
V. Gor, B. E. Shapiro, H. Jönsson, M. Heisler, G. V. Reddy, E. M. Meyerowitz, E. Mjolsness

34. Prediction and Alignment of Metabolic Pathways
M. Chen, R. Hofestaedt

35. General Principles of Organization and Laws of Functioning in Governing Gene Networks
R. N. Tchuraev

36. From Gradients to Stripes: A Logical Analysis of Drosophila Segmentation Genetic Network
D. Thieffry, C. Chaouiya, L. Sánchez

37. Self-Oscillations in Hypothetical Gene Networks
V. A. Likhoshvai, V. V. Kogai, S. I. Fadeev

38. Periodic Trajectories and Andronov-Hopf Bifurcations in Models of Gene Networks
V. P. Golubyatnikov, V. A. Likhoshvai, E. P. Volokitin, Yu. A. Gaidov, A. F. Osipov

39. On the Problem of Search for Stationary Points in Regulatory Circuits of Gene Networks
V. A. Likhoshvai

40. Modeling of Gene Expression by the Delay Equation
V. A. Likhoshvai, G. V. Demidenko, S. I. Fadeev

41. AGNS—A Database on Expression of Arabidopsis Genes
N. Omelyanchuk, V. Mironova, A. Poplavsky, N. Podkoldny, N. Kolchanov, E. Mjolsness, E. Meyerowitz

42. Study of the Interactions between Viral and Human Genomes During Transformation of B Cells with Epstein-Barr Virus
E. Ananko, D. Oshchepkov, E. Nedosekina, V. Levitsky, I. Lokhova, O. Smirnova, V. Likhoshvai, N. Kolchanov

43. Probing Gene Expression: Sequence-Specific Hybridization on Microarrays
H. Binder

44. Determination of the Developmental Age of a Drosophila Embryo from Confocal Images of its Segmentation Gene Expression Patterns
E. Myasnikova, A. Samsonova, S. Surkova, M. Samsonova, J. Reinitz

Part 4. Biomolecular Data and Processes Analysis

45. Topical Clustering of Biomedical Abstracts by Self-Organizing Maps
M. Fattore, P. Arrigo

46. Software for Analysis of Gene Regulatory Sequences by Knowledge Discovery Methods
E. E. Vityaev, T. I. Shipilov, M. A. Pozdnyakov, O. V. Vishnevsky, A. L. Proscura, Yu. L. Orlov, P. Arrigo

47. A Mathematical Model of the Discontinuous Genetic Structures Fixation Process
E. Ya. Frisman, O. L. Zhdanova

Keywords: Life Sciences, Bioinformatics, Mathematical Biology in General, Computer Appl. in Life Sciences, Proteomics, Cell Biology, Evolutionary Biology