S2SNET: A tool for transforming characters and numeric sequences into star network topological indices in chemoinformatics, bioinformatics, biomedical, and social-legal sciences

Current Bioinformatics

Volumn 8, Issue 4, 2013, Pages 429-437

  Munteanu, Cristian R ^a   Magalhães, Alexandre L ^b   Duardo Sánchez, Aliuska ^a,c   Pazos, Alejandro ^a   González Díaz, Humberto ^d,e  

^a UNIVERSITY OF A CORUÑA   (Spain)

^b UNIVERSITY OF PORTO   (Portugal)

^c UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

^d UNIVERSITY OF THE BASQUE COUNTRY UPV EHU   (Spain)

^e BASQUE FOUNDATION FOR SCIENCE   (Spain)

Author keywords

Complex network; Financial law network; Graph indices; Interaction; Network; Protein; Python application; Social network

Indexed keywords

BIOINFORMATICS; BLOOD; COMPLEX NETWORKS; COMPUTER SOFTWARE REUSABILITY; DNA SEQUENCES; GENES; GRAPHICAL USER INTERFACES; LEARNING SYSTEMS; MASS SPECTROMETERS; MASS SPECTROMETRY; METADATA; MOLECULAR BIOLOGY; PROTEINS; STARS; TOPOLOGY;

CLASSIFICATION MODELS; FINANCIAL LAW NETWORK; GRAPH INDEX; INTERACTION; NETWORK; PYTHON APPLICATION; SOCIAL NETWORK; STAR NETWORK; TAX LAWS; TOPOLOGICAL INDEX;

PYTHON;

ARTICLE; ARTIFICIAL NEURAL NETWORK; BIOINFORMATICS; BIOMEDICINE; CHEMOINFORMATICS; COMPUTER PROGRAM; DNA SEQUENCE; MACHINE LEARNING; PRIORITY JOURNAL; S2SNET TOOL; SCIENCE; SOCIAL LEGAL SCIENCE;

EID: 84882804172     PISSN: 15748936     EISSN: None     Source Type: Journal    
DOI: 10.2174/1574893611308040005     Document Type: Article

References (45)

1. Barabasi AL. Sociology. Network theory--the emergence of the creative enterprise. Science 2005; 308(5722): 639-41.
2. Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004; 5(2): 101-13.
3. Bornholdt S, Schuster HG. Handbook of Graphs and Complex Networks: From the Genome to the Internet. WILEY-VCH GmbH & CO. KGa: Wheinheim 2003.
4. González-Díaz H, Vilar S, Santana L, Uriarte E. Medicinal chemistry and bioinformatics - current trends in drugs discovery with networks topological indices. Curr Top Med Chem 2007; 7(10): 1025-39.
5. Mason O, Verwoerd M. Graph theory and networks in Biology. IET Syst Biol 2007; 1(2): 89-119.
6. Yook SH, Jeong H, Barabasi AL. Modeling the Internet's largescale topology. Proc Natl Acad Sci USA 2002; 99(21): 13382-6.
7. García-Domenech R, Gálvez J, Julián-Ortiz JV, Pogliani L. Some new trends in chemical graph theory. Chem Rev 2008; 108(3): 1127-69.
8. Gonzalez-Diaz H, Gonzalez-Diaz Y, Santana L, Ubeira FM, Uriarte E. Proteomics, networks and connectivity indices. Proteomics 2008; 8(4): 750-78.
9. Concu R, Podda G, Uriarte E, González-Díaz H. A new computational chemistry & complex networks approach to structure - function and similarity relationships in protein enzymes. In: Handbook of Computational Chemistry Research; Collett CTaR, CD., ed., Nova Science Publishers 2009.
10. Dall'asta L, Alvarez-Hamelin I, Barrat A, Vazquez A, Vespignani A. Statistical theory of Internet exploration. Phys Rev E Stat Nonlin Soft Matter Phys 2005; 71(3 Pt 2A): 036135.
11. Estrada E, Uriarte E. Recent advances on the role of topological indices in drug discovery research. Curr Med Chem 2001; 8: 1573-88.
12. Gonzalez-Diaz H, Prado-Prado F, Ubeira FM. Predicting antimicrobial drugs and targets with the MARCH-INSIDE approach. Curr Top Med Chem 2008; 8(18): 1676-90.
13. Todeschini R, Consonni V. Handbook of Molecular Descriptors. Wiley-VCH 2002.
14. Munteanu CR, Gonzáles-Diáz H. S2SNet - Sequence to Star Network, Reg. No. 03/2008/1338, Santiago de Compostela, Spain. Santiago de Compostela, Spain 2008.
15. Rappin N, Dunn R. wxPython in Action. Manning Publications Co.: Greenwich, CT 2006.
16. Ferino G, Delogu G, Podda G, Uriarte E, González-Díaz H. Quantitative Proteome-Disease Relationships (QPDRs) in Clinical Chemistry: Prediction of Prostate Cancer with Spectral Moments of PSA/MS Star Networks. In: Clinical Chemistry Research; Mitchem BHaS, Ch.L., ed., Nova Science Publisher: NY 2009.
17. Randić M, Zupan J, Vikic-Topic D. On representation of proteins by star-like graphs. J Mol Graph Model 2007: 290-305.
18. Koutsofios E, North SC. Drawing Graphs with dot. AT&T Bell Laboratories, Murray Hill: NJ, USA 1993.
19. González-Díaz H, Molina-Ruiz R, Hernandez I. March-Inside version 3.0 (Markov Chains Invariants for Simulation & Design); Windows supported version under request to the main author contact email: gonzalezdiazh@yahoo.es. 3.0 ed 2007.
20. Koschützki D. CentiBiN Version 1.4.2. 2006: CentiBiN Version 1.4.2, Centralities in Biological Networks © 2004-6 Dirk Koschützki Research Group Network Analysis, IPK Gatersleben, Germany.
21. Batagelj V, Pajek M.A. Program for Large Network Analysis (ver. 1.15), http://vlado.fmf.uni-lj.si/pub/networks/pajek/. 1.15 ed 2006.
22. Harary F. Graph Theory. Westview Press: MA 1969.
23. StatSoft.Inc. STATISTICA, (data analysis software system), version 6.0, www.statsoft.com. 6.0 ed 2002.
24. Witten IH, Frank E. WEKA: Waikato Environment for Knowledge Analysis. 2000.
25. Munteanu CR, Gonzalez-Diaz H, Borges F, de Magalhaes AL. Natural/random protein classification models based on star network topological indices. J Theor Biol 2008; 254(4): 775-83.
26. Munteanu CR, Magalhaes AL, Uriarte E, Gonzalez-Diaz H. Multitarget QPDR classification model for human breast and colon cancer-related proteins using star graph topological indices. J Theor Biol 2009; 257(2): 303-11.
27. González-Díaz H, Ferino G, Munteanu CR, Vilar S, Uriarte E. Protein Graphs in Cancer Prediction. In: Oncoproteomics; Cho WK, ed., Springer 2009.
28. Perez-Bello A, Munteanu CR, Ubeira FM, De Magalhaes AL, Uriarte E, Gonzalez-Diaz H. Alignment-free prediction of mycobacterial DNA promoters based on pseudo-folding lattice network or star-graph topological indices. J Theor Biol 2009; 256(3): 458-66.
29. Cruz-Monteagudo M, Munteanu CR, Borges F, et al. Stochastic molecular descriptors for polymers. 4. Study of complex mixtures with topological indices of mass spectra spiral and star networks: The blood proteome case. Polymer 2008; 49: 5575-87.
30. Berman HM, Westbrook J, Feng Z, et al. The Protein Data Bank. Nucleic Acids Res 2000; 28: 235-42.
31. Griffiths AJF, Miller JH, Suzuki DT, Lewontin RC, Gelbart WM. Introduction to Genetic Analysis. 7th ed. W. H. Freeman & Co.: New York 1999.
32. Zubieta JK, Heitzeg MM, Smith YR, et al. COMT val158met genotype affects mu-opioid neurotransmitter responses to a pain stressor. Science 2003; 299(5610): 1240-3.
33. Wonodi I, Mitchell BD, Stine OC, et al. Lack of association between COMT gene and deficit/nondeficit schizophrenia. Behav Brain Funct 2006; 2: 42.
34. Breiger R. The Analysis of Social Networks. In: Handbook of Data Analysis; Hardy M, Bryman A, eds., Sage Publications: London 2004; 505-26.
35. Abercrombie N, Hill S, Turner BS. The Penguin Dictionary of Sociology. In: Social structure, Penguin: London 2000.
36. Craig C. Social Structure, Dictionary of the Social Sciences,. Oxford University Press: Oxford 2002.
37. Wellman B, Berkowitz SD. Social Structures: A Network Approach. Cambridge University Press: Cambridge 1988.
38. White H, Boorman S, Breiger R. Social Structure from Multiple Networks: Blockmodels of Roles and Positions. American Journal of Sociology 1976; 81(730-780).
39. Newman M. The structure and function of complex networks. SIAM Review 2003; 56: 167-256.
40. Moreno JL. Who Shall Survive?. Beacon House: New York 1934.
41. Padgett JF, Ansell CK. Robust Action and the Rise of the Medici, 1400-1434. Amer J Sociol 1993; 98(6): 1259-319.
42. Mariolis P. Interlocking directorates and control of corporations: The theory of bank control. Social Sci Quart 1975; 56: 425-39.
43. Mizruchi MS. The American Corporate Network, 1904-1974. Sage: Beverly Hills 1982.
44. Klovdahl AS, Potterat JJ, Woodhouse DE, Muth JB, Muth SQ, Darrow WW. Social networks and infectious disease: the Colorado Springs Study. Soc Sci Med 1994; 38(1): 79-88.
45. Liljeros F, Edling CR, Amaral LA, Stanley HE, Aberg Y. The web of human sexual contacts. Nature 2001; 411(6840): 907-8.