Learning to classify species with barcodes

BMC Bioinformatics

Volumn 10, Issue SUPPL.14, 2009, Pages

  Bertolazzi, Paola ^a   Felici, Giovanni ^a   Weitschek, Emanuel ^a  

^a CNR   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER CIRCUITS; MINING; OPTIMIZATION;

AUTOMATED TECHNIQUES; COMPACT FORMULAS; CYTOCHROME C OXIDASE; DNA FRAGMENT; LOGIC MINING; MITOCHONDRIAL DNA; OPTIMIZATION MODELS;

BAR CODES;

CYTOCHROME C OXIDASE; CYTOCHROME C OXIDASE SUBUNIT 1; DNA FRAGMENT; UNCLASSIFIED DRUG;

ARTICLE; BIOINFORMATICS; CLINICAL EFFECTIVENESS; COMPUTER PROGRAM; DNA BARCODING; GENETIC DATABASE; GENETIC SIMILARITY; INFORMATION TECHNOLOGY; LOGIC MINING METHOD; MATHEMATICAL ANALYSIS; NUCLEOTIDE SEQUENCE; RECOGNITION; SPECIES DIFFERENCE; SPECIES IDENTIFICATION; TAXONOMY; TRAINING;

EID: 70749116135     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S14-S7     Document Type: Article

References (31)

1. Rach J, DeSalle R, Sarkar I, Schierwater B, Hadrys H. Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata. Proc R Soc B 2008, 275:237-247. 10.1098/rspb.2007.1290, 2212734, 17999953.
2. Woese C, Fox G. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. PNAS 1977, 74:5088-5090. 10.1073/pnas.74.11.5088, 432104, 270744.
3. Nanney D. DGenes and phenes in Tetrahymena. Bioscience 1982, 32:783-740.
4. Pace N. A molecular view of microbial diversity and the biosphere. Bioscience 1997, 276:734-740.
5. Brown B, Emberson R, Paterson A. Mitochondrial COI and II provide useful markers for Weiseana (Lepidoptera, Hepialidae) species identification. Bull Entomol 1999, 89:287-294.
6. Bucklin A, Guarnieri M, Hill R, Bentley A, Kaartvedt S. Taxonomic and systematic assessment of planktonic copepods using mitochondrial COI sequence variation and competitive species-specific PCR. Hydrobiology 1999, 401:239-254.
7. Hebert P, Cywinska A, Ball S, de Waard J. Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences 2003, 270:313-321.
8. Saccone C, DeCarla G, Gissi C, Pesole G, Reynes A. Evolutionary genomics in the Metazoa: the mito-chondrial DNA as a model system. Bioscience 1999, 238:195-210.
9. Min X, Hickey D. DNA barcodes provide a quick preview of mitochondrial genome composition. PLoS ONE 2007, 2:325.
10. Hebert P, Penton E, Burns J, Janzen D, Hallwachs W. Ten species in one: DNA barcoding reveals cryptic species in the Neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci USA 2004, 101:14812-14817. 10.1073/pnas.0406166101, 522015, 15465915.
11. Hebert P, Stoeckle M, Zemlak T, Francis C. Identification of birds through COI DNA barcodes. PLOS Biol 2004, 2:1-7.
12. Smith A, Woodley N, Janzen D, Hallwachs W, Hebert P. DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae). PNAS 2006, 103:3657-3662. 10.1073/pnas.0511318103, 1383497, 16505365.
13. Hajibabaei M, Singer G, Clare E, Hebert P. Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring. BMC Biology 2007, 5:24. 10.1186/1741-7007-5-24, 1906742, 17567898.
14. Felici G, Truemper K. A Minsat approach for learning in logic domains. INFORMS Journal on computing 2002, 14.
15. Felici G, Truemper K. The Lsquare System for Mining Logic Data. Encyclopedia of Data Warehousing and Mining 2005, 693-697. Idea Group Publishing, JW.
16. Felici G, Sun F, Truemper K. Learning Logic Formulas and Related Error Distributions. Data Mining and Knowledge Discovery Approaches Based on Rule Induction Techniques 2006, Springer, Felici G, ET.
17. Bertolazzi P, Felici G, Festa P, Lancia G. Logic classification and feature selection for biomedical data. Comput Math Appl 2008, 55:889-899.
18. Meusnier I, Singer G, Landry J, Hickey D, Hebert P, Hajibabaei M. A universal DNA mini-barcode for biodiversity analysis. BMC Genomics 2008, 9:214. doi:10.1186/1471-2164-9-214., 10.1186/1471-2164-9-214, 2396642, 18474098.
19. Jia Min X, Hickey D. Assessing the effect of varying sequence length on DNA barcoding of fungi. Mol Ecol Notes 2007, 7:365-373. 10.1111/j.1471-8286.2007.01698.x, 1890918, 18784789.
20. Saitou N, Nei M. The Neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4:406-425.
21. Abdo Z, Golding G. A Step Toward Barcoding Life: A Model-Based, Decision-Theoretic Method to Assign Genes to Preexisting Species Groups. Systematic Biology 2007, 56:44-56. 10.1080/10635150601167005, 17366136.
22. Howard A, Sumathi M, Wai Lok S. Testing the Reliability of Genetic Methods of Species Identification via Simulation. Systematic Biology 2008, 57:216-230. 10.1080/10635150802032990, 18398767.
23. Kuksa P, Pavlovic V. Fast Kernel Methods for SVM Sequence Classifiers. Algorithms in Bioinformatics 2007, 4645:228-239.
24. Sarkar I, Planet P, Bael TE, Stanley S, Siddall M, DeSalle R, Figurski D. Characteristic Attributes in Cancer Microarrays. Journal of Biomedical Informatics 2002, 35:111-122. 10.1016/S1532-0464(02)00504-X, 12474425.
25. Sarkar I, Thornton J, Planet P, Schierwater B, DeSalle R. A systematic method for classification of novel homeoboxes. Molecular Phylogenetics and Evolution 2002, 24:388-399. 10.1016/S1055-7903(02)00259-2, 12220982.
26. Zhang A, Sikes D, Muster C, Li S. Inferring Species Membership Using DNA Sequences with Back-Propagation Neural Networks. Systematic Biology 2008, 57:202-215. 10.1080/10635150802032982, 18398766.
27. Nielsen R, Matz M. Statistical Approaches for DNA Barcoding. Systematic Biology 2006, 55:162-169. 10.1080/10635150500431239, 16507534.
28. Chia-Jung C, Yao-Ting H, Kun-Mao C. A greedier approach for finding tag SNPs. Bioinformatics 2006, 22:685-691. 10.1093/bioinformatics/btk035, 16403792.
29. Garey M, Johnson D. Computers and Intractability: A Guide to the Theory of NP-Completeness (Series of Books in the Mathematical Sciences) 1979, W H Freeman.
30. Truemper K. Design of Logic-based Intelligent Systems 2004, Wiley-Interscience.
31. Buschmann F, Henney K, Schmidt D. Pattern-Oriented Software Architecture: A Pattern Language for Distributed Computing 2007, 4. Wiley.