Applications of artificial intelligence in bioinformatics: A review

Expert Systems with Applications

Volumn 30, Issue 1, 2006, Pages 2-10

  Ezziane, Zoheir ^a  

^a Information Technology BMA International   (United Arab Emirates)

Author keywords

AI tools in bioinformatics; Intelligent bioinformatics systems; Intelligent DNA sequencing

Indexed keywords

ALGORITHMS; BIOTECHNOLOGY; COMPUTATIONAL COMPLEXITY; DATABASE SYSTEMS; DNA SEQUENCES; ERROR ANALYSIS; INFORMATION SCIENCE; MOLECULAR BIOLOGY;

AI TOOLS IN BIOINFORMATICS; INTELLIGENT BIOINFORMATICS SYSTEM; INTELLIGENT DNA SEQUENCING; OFF-SHELF SYSTEMS;

ARTIFICIAL INTELLIGENCE;

EID: 27844603905     PISSN: 09574174     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.eswa.2005.09.042     Document Type: Article

References (75)

1. Adleman, L. M. (1998). Location sensitive sequencing of DNA. Technical report, University of Southern California.
2. R.B. Altman Challenges for intelligent systems in biology IEEE Intelligent Systems 16 6 2001 14 18
3. S.F. Altschul, W. Gish, W. Miller, E.W. Meyers, and D.J. Lipman Basic local alignment search tool Journal of Molecular Biology 215 3 1990 403 410
4. T.L. Bailey, and C. Elkan Fitting a mixture model by expectation maximization to discover motifs in biopolymers Proceedings of the second international conference on intelligent systems for molecular biology 1994 (pp. 28-36)
5. W. Bains Hybridization methods for DNA sequencing Genomics 11 1991 294 301
6. W. Bains, and G.C. Smith A novel method for nucleic acid sequence determination Journal of Theoretical Biology 135 1988 303 307
7. V.B. Bajic, V. Brusic, J. Li, S.K. Ng, and L. Wong From informatics to bioinformatics Proceedings of the first Asia-Pacific bioinformatics conference on bioinformatics, Adelaide, Australia 2003 (pp. 3-12)
8. J. Barker, and J. Thornton Software engineering challenges in bioinformatics Proceedings of the 26th international conference on software engineering (ICSE'04), Edinburgh, Scotland, UK 2004 (pp. 12-15)
9. A. Bendor, I. Pe'er, R. Shamir, and R. Sharan On the complexity of positional sequencing by hybridization Journal of Computational Biology 8 4 2001 361 371
10. B. Bergeron Bioinformatics computing 2003 Prentice-Hall Upper Saddle River, NJ
11. C. Bertelle, A. Dutot, F. Guinand, and D. Olivier DNA sequencing hybridization based on multi-castes ant system Proceedings of agents in bioinformatics (NETTAB'02), Bologna, Italy 2002 (pp. 1-7)
12. J. Blazewicz, P. Formanowicz, M. Kasprzak, J. Markiewicz, and J. Welglarz DNA sequencing with positive and negative errors Journal of Computational Biology 6 1999 113 123
13. J. Blazewicz, and M. Kasprzak Hybrid genetic algorithm for DNA sequencing with errors Journal of Heuristics 8 2002 495 502
14. J. Blazewicz, and M. Kasprzak Complexity of DNA sequencing by hybridization Theoretical Computer Science 290 2003 1459 1473
15. P. Boufounos, S. El-Difrawy, and D. Ehrlich Basecalling using hidden Markov models Journal of the Franklin Institute 341 1-2 2004 23 36
16. P. Bresciani, P. Fontana, and P. Busetta A knowledge based interface for distributed biological databases Proceedings of the international workshop on agents in bioinformatics (NETTAB-02), Bologna, Italy 2002 http://sra.itc.it/ people/bresciani/publications/nettab-2002.pdf
17. S.D. Broude, T. Sano, C.S. Smith, and C.R. Cantor Enhanced DNA sequencing by hybridization Proceedings of the National Academy of Sciences USA 91 1994 3072 3076
18. K. Bryson, M. Luck, M. Joy, and D.T. Jones Applying agents to bioinformatics in GeneWeaver Lecture notes in artificial intelligence (pp. 60-71) Vol. 1860 2000
19. S.M. Chou, T.S. Lee, Y.E. Shao, and I.F. Chen Mining the breast cancer pattern using artificial neural networks and multivariate adaptive regression splines Expert Systems with Applications 27 1 2004 133 142
20. J. Cohen Bioinformatics - An introduction for computer scientist ACM Computing Surveys 36 2 2004 122 158
21. K. Decker, S. Zheng, and C. Schmidt A multi-agent system for automated genomic annotation Proceedings of the fifth international conference on autonomous agents, Montreal, Canada 2001 (pp. 433-440)
22. M. Delgado, W. Fajardo, E. Gibaja, and R. Pérez-Pérez BioMen: An information system to herbarium Expert Systems with Applications 28 3 2005 507 518
23. H. Douzono, S. Hara, and Y. Noguchi An application of genetic algorithm to DNA sequencing by oligonucleotide hybridization Proceedings of the IEEE international joint symposia on intelligence and systems, Rockville, Maryland, USA 1998 (pp. 92-98)
24. R. Drmanac, L. Hood, and R. Crkvenjakov DNA sequence determination by hybridization: A strategy for efficient large scale sequencing Science 260 1993 1649 1652
25. R. Drmanac, I. Labat, I. Brunker, and R. Crkvenjakov Sequencing of megabase plus DNA by hybridization: Theory of the method Genomics 4 1989 114 128
26. M.E. Dyer, A.M. Frieze, and S. Suen The probability of unique solutions of sequencing by hybridization Journal of Computational Biology 1 1994 105 110
27. S.P.A. Fodor, J.L. Read, M.C. Pirrung, L. Stryer, A.T. Lu, and D. Solas Light-directed, spatially addressable parallel chemical synthesis Science 251 1991 767 773
28. G.B. Fogel, and K. Chellapilla Simulated sequencing by hybridization using evolutionary programming Proceedings of the congress on evolutionary computation, Washington DC, USA 1999 (pp. 463-469)
29. G.B. Fogel, K. Chellapilla, and D.B. Fogel Reconstruction of DNA sequence information from simulated DNA chip using evolutionary programming Proceedings of the seventh annual conference on evolutionary programming, San Diego, CA, USA 1998 (pp. 429-436)
30. A. Frieze, and B.V. Hallorsson Optimal sequencing by hybridization Proceedings of the fifth annual international conference on computational molecular biology (RECOMB'01), Montreal, Canada 2001 (pp. 141-148)
31. L. Fu An expert network for DNA sequence analysis IEEE Intelligent Systems 14 1 1999 65 71
32. J.R. Graham, and K. Decker Towards a distributed, environment-centered agent framework Lecture notes in computer science Vol. 1757 1999 (pp. 290-304)
33. D. Gusfield Introduction to the IEEE/ACM transactions on computational biology and bioinformatics IEEE/ACM Transactions on Computational Biology and Bioinformatics 1 1 2004 2 3
34. D. Gusfield, R. Karp, L. Wang, and P. Stelling Graph traversals, genes and matroids: An efficient case of the traveling salesman problem Discrete Applied Mathematics 88 1998 167 180
35. E. Halperin, S. Halperin, T. Hartman, and R. Shamir Handling long targets and errors in sequencing by hybridization Proceedings of the sixth annual international conference on computational molecular biology (RECOMB'02), Washington, DC, USA 2002 (pp. 176-185)
36. S. Hannenhalli, P. Pevzner, H. Lewis, and S. Skiena Positional sequencing by hybridization Computer Applications in the Biosciences 12 1996 19 24
37. A.G. Hatzigeorgiou, N. Mache, and M. Reczko Functional site prediction on the DNA sequence by artificial neural networks Proceedings of the IEEE international joint symposia in intelligence and systems (IJSIS'96), Rockville, MD, USA 1996 (pp. 12-17)
38. A.G. Hatzigeorgiou, H. Papanikolaou, and M. Reczko Finding the reading frame in protein coding regions on DNA sequences: A combination of statistical and neural network methods M. Mohammadian Computational intelligence for modeling, control and automation 1999 IOS Press Vienna, OH 148 153
39. T. Hernandez, and S. Kambhampati Integration of biological sources: Current systems and challenges ahead ACM SIGMOD Record 33 3 2004 51 60
40. S. Ji Molecular information theory: Solving the mysteries of DNA G. Ciobanu G. Rozenberg Modeling in molecular biology Natural computing series 2004 Springer Berlin 141 150
41. I. Jonassen Efficient discovery of conserved patterns using a pattern graph Computer Applications in the Biosciences 13 1997 509 522
42. I. Jonassen, J.F. Collins, and D.G. Higgins Finding flexible patterns in unaligned protein sequences Protein Science 4 1995 1587 1595
43. K. Karasawas, R. Baldock, and A. Burger A multi-agent bioinformatics integration system with adjustable autonomy: An overview Proceedings of the first international joint conference on autonomous agents and multiagent systems: Part 1, Bologna, Italy 2002 (pp. 302-303)
44. J. Kasturi, and R. Acharya Clustering of diverse genomic data using information fusion Proceedings of the 2004 ACM symposium on applied computing, Nicosia, Cyprus 2004 (pp. 116-120)
45. S. Khan, R. Makkena, F. McGeary, K. Decker, W. Gillis, and C. Schmidt A multi-agent system for the quantitative simulation of biological networks Proceedings of the second international joint conference on autonomous agents and multiagent systems, Melbourne, Australia 2003 (pp. 385-392)
46. K.R. Khrapko, Y.P. Lysov, A.A. Khorlyn, V.V. Shick, V.L. Florentieve, and A.D. Mirzabekov An oligonucleotide hybridization approach to DNA sequencing FEBS Letters 256 1989 118 122
47. A. Krogh An introduction to hidden Markov models for biological sequences S.L. Salzberg D.B. Searls S. Kasif Computional methods in molecular biology 1998 Elsevier Amsterdam 45 63
48. T. Kulikova, P. Aldebert, N. Althorpe, W. Baker, K. Bates, and P. Browne The EMBL nucleotide sequence database Nucleic Acids Research 32 2004 27 30
49. K. Kumar, M. Palakal, S. Mukhopashyay, M. Stephens, and H. Li BioMap: Toward the development of a knowledge base of biomedical literature Proceedings of the 2004 ACM symposium on applied computing, Nicosia, Cyprus 2004 (pp. 121-127)
50. R. Laskowski PDBsum: Summaries and analyses of PDB structures Nucleic Acids Research 29 2001 221 222
51. L. Lo Conte, B. Ailey, T. Hubbard, S. Brenner, A. Murzin, and C. Chothia SCOP: A structural classification of proteins database Nucleic Acids Research 28 1 2000 257 259
52. C. Majje, and G. Sahoo DNA sequencing by oligonucleotide hybridization: A genetic algorithm approach Proceedings of the international conference on genetics and evolutionary computation (GECCO), Seattle, Washington, USA 2004 http://www.cs.bham.ac.uk/~wbl/biblio/gecco2004/WSOE001.pdf
53. L. Moreau, S. Miles, C. Goble, M. Greenwood, V. Dialani, and M. Addis On the use of agents in a bioinformatics grid Proceedings of the third international symposium on cluster computing and the grid, Tokyo, Japan 2003 (pp. 653-660)
54. D. Noble DNA sequencing on a chip Analytical Chemistry 67 5 1995 201A 204A
55. D. Page, and M. Craven Biological applications of multi-relational data mining ACM SIGKDD Explorations Newsletter 5 1 2003 69 79
56. M. Palakal, S. Mukhopashyay, and J. Mostafa An intelligent biological information management system Proceedings of the 2002 ACM symposium on applied computing, Madrid, Spain 2002 (pp. 159-163)
57. I. Pe'er, and R. Shamir Spectrum alignment: Efficient resequencing by hybridization Proceedings of the eighth international conference on intelligent systems in molecular biology (ISMB'00), La Jolla, California, USA 2000 (pp. 260-268)
58. P.C. Pendharkar, J.A. Rodger, G.J. Yaverbaum, N. Herman, and M. Benner Association, statistical, mathematical and neural approaches for mining breast cancer patterns Expert Systems with Applications 17 3 1999 223 232
59. P.A. Pevzner l-Tuple DNA sequencing Journal of Biomolecular Structure and Dynamics 7 1989 63 73
60. P.A. Pevzner, and R. Lipshutz Towards DNA sequencing chips Proceedings of the international conference on mathematical foundations of computer science Lecture notes in computer science Vol. 841 1994 (pp. 143-158)
61. P.A. Pevzner, Y.P. Lysov, K.R. Khrapko, A.V. Belyavsky, V.L. Florentiev, and A.D. Mirzabekov Improved chips for sequencing by hybridization Journal of Biomolecular Structure and Dynamics 9 1991 399 410
62. F. Preparata, A. Frieze, and E. Upfal On the power of universal bases in sequencing by hybridization Proceedings of the third annual international conference on computational molecular biology (RECOMB'99), Lyon, France 1999 (pp. 295-301)
63. F. Preparata, and E. Upfal Sequencing-by-hybridization at the information- theory bound: An optima algorithm Proceedings of the fourth annual international conference on computational molecular biology (RECOMB'00), Tokyo, Japan 2000 (pp. 245-253)
64. D. Rocco, and T. Critchlow Automatic discovery and classification of bioinformatics web sources Bioinformatics 19 15 2003 1927 1933
65. R. Shamir, and D. Tsur Large scale sequencing by hybridization Proceedings of the fifth annual international conference on computational molecular biology (RECOMB'01), Montreal, Canada 2001 (pp. 269-277)
66. J. Shavlik, L. Hunter, and D. Searls Introduction Machine Learning 21 1995 5 10
67. S.S. Skiena, and G. Sunaram Reconstructing strings from substrings Journal of Computational Biology 2 1995 333 353
68. R.D. Smith, and T.F. Smith Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative modelling Protein Engineering 5 1 1992 35 41
69. P. Srinivasan, J. Mitchell, O. Bodenreider, G. Pant, and F. Menczer Web crawling agents for retrieving biomedical information Proceedings of the international workshop on agents in bioinformatics (NETTAB-02). Bologna, Italy 2002
70. A.C. Tan, and D. Gilbert An empirical comparison of supervised machine learning techniques in bioinformatics Proceedings first Asia-Pacific bioinformatics conference (APBC2003), Adelaide, Australia 2003 (pp. 219-222)
71. C. Tang, and A. Zhang Mining multiple phenotype structures underlying gene expression profiles Proceedings of the 12th international conference on information and knowledge management, New Orleans, LA, USA 2003 pp. 418-425
72. Vilo, J. (1998). Discovering frequent patterns from strings. Technical report C-1998-9. Department of Computer Science, University of Helsinki.
73. H.C. Wang, H.C. Kuo, H.H. Chen, Y.Y. Hsiao, and W.C. Tsai KSPF: Using gene sequence patterns and data mining for biological knowledge management Expert Systems with Applications 28 3 2005 537 545
74. M.S. Waterman Introduction to computational biology 1995 Chapman & Hall London
75. P.J. Woolf, and Y. Wang A fuzzy logic approach to analyzing gene expression data Physiological Genomics 3 2000 9 15