A two-way multi-dimensional mixture model for clustering metagenomic sequences

2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011

Volumn , Issue , 2011, Pages 191-200

  Prabhakara, Shruthi ^a   Acharya, Raj ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Clustering; Metagenomics; Mixture model

Indexed keywords

CLUSTERING; CLUSTERING METHODS; COMPOSITIONAL HETEROGENEITY; DATA SETS; EXPECTATION-MAXIMIZATION ALGORITHMS; GAUSSIANS; METAGENOMES; METAGENOMICS; MICROBIAL COMMUNITIES; MIXTURE MODEL; MIXTURE OF GAUSSIANS; MULTI-SPECIES; NAIVE BAYES; RELATIVE ABUNDANCE; SPECIES ABUNDANCE; STATISTICAL FRAMEWORK; TWO-WAY MIXTURE MODELS;

GENES; IMAGE SEGMENTATION; MIXTURES; PARAMETER ESTIMATION; POISSON DISTRIBUTION;

BIOINFORMATICS;

EID: 84858964274     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/2147805.2147826     Document Type: Conference Paper

References (36)

1. S. F. Altschul,W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. Basic local alignment search tool. Journal of molecular biology, 215(3):403-410, October 1990.
2. M. Bailly-Bechet, A. Danchin, M. Iqbal, M. Marsili, and M. Vergassola. Codon Usage Domains over Bacterial Chromosomes. PLoS Comput Biol, 2(4):e37+, April 2006.
3. S. D. Bentley and J. Parkhill. Comparative genomic structure of prokaryotes. Annual Review of Genetics, 38(1):771-791, 2004.
4. A. Brady and S. L. Salzberg. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nature methods, 6(9):673-676, September 2009.
5. V. Brendel, J. S. Beckmann, and E. N. Trifonov. Linguistics of nucleotide sequences: morphology and comparison of vocabularies. Journal of biomolecular structure & dynamics, 4(1):11, 1986.
6. A. Campbell, J. Mrázek, and S. Karlin. Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA. Proceedings of the National Academy of Sciences of the United States of America, 96(16):9184-9189, August 1999. (Pubitemid 29374729)
7. C.-K. Chan, A. Hsu, S. Halgamuge, and S.-L. Tang. Binning sequences using very sparse labels within a metagenome. BMC Bioinformatics, 9(1):215, 2008.
8. S. Chatterji, I. Yamazaki, Z. Bai, and J. Eisen. CompostBin: A DNA composition-based algorithm for binning environmental shotgun reads. ArXiv e-prints, 708, Aug 2007.
9. K. Chen and L. Pachter. Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput Biol, 1(2):e24, 07 2005.
10. J. R. Cole, B. Chai, R. J. Farris, Q. Wang, S. A. Kulam, D. M. McGarrell, G. M. Garrity, and J. M. Tiedje. The ribosomal database project (rdp-ii): sequences and tools for high-throughput rrna analysis. Nucleic Acids Research, 33(suppl 1):D294-D296, 2005. (Pubitemid 40207881)
11. D. Dalevi, N. N. Ivanova, K. Mavromatis, S. D. Hooper, E. Szeto, P. Hugenholtz, N. C. Kyrpides, and V. M. Markowitz. Annotation of metagenome short reads using proxygenes. Bioinformatics, 24(16):i7-i13, 2008.
12. P. J. Deschavanne, A. Giron, J. Vilain, G. Fagot, and B. Fertil. Genomic signature: characterization and classification of species assessed by chaos game representation of sequences. Mol Biol Evol, 16(10):1391-1399, October 1999. (Pubitemid 29473232)
13. G. Folino, F. Gori, M. Jetten, and E. Marchiori. Clustering Metagenome Short Reads Using Weighted Proteins. In C. Pizzuti, M. Ritchie, and M. Giacobini, editors, Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, volume 5483 of Lecture Notes in Computer Science, chapter 14, pages 152-163. Springer Berlin / Heidelberg, Berlin, Heidelberg, 2009.
14. D. H. Huson, A. F. Auch, J. Qi, and S. C. Schuster. MEGAN analysis of metagenomic data. Genome research, 17(3):377-386, March 2007. (Pubitemid 46376747)
15. J. Josse, A. D. Kaiser, and A. Kornberg. Enzymatic Synthesis of Deoxyribonucleic Acid. Journal of Biological Chemistry, 236(3):864-875, 1961.
16. S. Karlin, I. Ladunga, and B. E. Blaisdell. Heterogeneity of genomes: measures and values. Proceedings of the National Academy of Sciences of the United States of America, 91(26):12837-12841, 1994.
17. D. R. Kelley and S. L. Salzberg. Clustering metagenomic sequences with interpolated Markov models. BMC bioinformatics, 11(1):544+, Nov. 2010.
18. A. Kislyuk, S. Bhatnagar, J. Dushoff, and J. S. Weitz. Unsupervised statistical clustering of environmental shotgun sequences. BMC bioinformatics, 10(1):316+, 2009.
19. J. Li and H. Zha. Two-way poisson mixture models for simultaneous document classification and word clustering. Comput. Stat. Data Anal., 50:163-180, January 2006. (Pubitemid 41277017)
20. B. Liu, T. Gibbons, M. Ghodsi, and M. Pop. Metaphyler: Taxonomic profiling for metagenomic sequences. In T. Park, S. K.-W. Tsui, L. Chen, M. K. Ng, L. Wong, and X. Hu, editors, BIBM, pages 95-100. IEEE Computer Society, 2010.
21. K. Mavromatis, N. Ivanova, K. Barry, H. Shapiro, E. Goltsman, A. C. McHardy, I. Rigoutsos, A. Salamov, F. Korzeniewski, M. Land, A. Lapidus, I. Grigoriev, P. Richardson, P. Hugenholtz, and N. C. Kyrpides. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature Methods, 4(6):495-500, April 2007. (Pubitemid 46852075)
22. A. C. C. McHardy, H. G. G. Martín, A. Tsirigos, P. Hugenholtz, and I. Rigoutsos. Accurate phylogenetic classification of variable-length DNA fragments. Nature methods, 4(1):63-72, January 2007. (Pubitemid 46029478)
23. S. Nasser, A. Breland, F. Harris, and M. Nicolescu. A fuzzy classifier to taxonomically group dna fragments within a metagenome. In Fuzzy Information Processing Society, 2008. NAFIPS 2008. Annual Meeting of the North American, pages 1 -6, May 2008.
24. J. Pearl. Probabilistic reasoning in intelligent systems : networks of plausible inference. Morgan Kaufmann, September 1988.
25. M. S. RappÃl' and S. J. Giovannoni. The uncultured microbial majority. Annual Review of Microbiology, 57(1):369-394, 2003. (Pubitemid 37392948)
26. G. Reinert, S. Schbath, and M. S. Waterman. Probabilistic and Statistical Properties of Words: An Overview. Journal of Computational Biology, 7(1-2):1-46, February 2000. (Pubitemid 30412159)
27. S. Robin, F. Rodolphe, and S. Schbath. DNA, Words and Models: Statistics of Exceptional Words. Cambridge University Press, November 2005.
28. G. Rosen, E. Garbarine, D. Caseiro, R. Polikar, and B. Sokhansanj. Metagenome fragment classification using n-mer frequency profiles. Advances in Bioinformatics, 2008.
29. G. Russell, P. Walker, R. Elton, and J. Subak-Sharpe. Doublet frequency analysis of fractionated vertebrate nuclear dna. Journal of Molecular Biology, 108(1):1 -20, 1976.
30. F. Schreiber, P. Gumrich, R. Daniel, and P. Meinicke. Treephyler: fast taxonomic profiling of metagenomes. Bioinformatics, 26(7):960-961, Apr. 2010.
31. Y. Song, Z. Zhuang, H. Li, Q. Zhao, J. Li, W.-C. Lee, and C. L. Giles. Real-time automatic tag recommendation. In Proceedings of the 31st annual international ACM SIGIR conference on Research and development in information retrieval, SIGIR '08, pages 515-522, New York, NY, USA, 2008. ACM.
32. H. Teeling, A. Meyerdierks, M. Bauer, R. Amann, and F. O. Glöckner. Application of tetranucleotide frequencies for the assignment of genomic fragments. Environmental Microbiology, 6(9):938-947, September 2004. (Pubitemid 39123248)
33. H. Teeling, J. Waldmann, T. Lombardot, M. Bauer, and F. Glockner. TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. BMC Bioinformatics, 5(1):163+, October 2004.
34. R. Tibshirani and G. Walther. Cluster Validation by Prediction Strength. Journal of Computational & Graphical Statistics, 14(3):511-528, September 2005. (Pubitemid 41442147)
35. G. W. Tyson, J. Chapman, P. Hugenholtz, E. E. Allen, R. J. Ram, P. M. Richardson, V. V. Solovyev, E. M. Rubin, D. S. Rokhsar, and J. F. Banfield. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature, 428(6978):37-43, March 2004. (Pubitemid 38332350)
36. Y.-W. Wu and Y. Ye. A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-Tuples. Research in Computational Molecular Biology, 2010.