Accurate profiling of microbial communities from massively parallel sequencing using convex optimization

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 8214 LNCS, Issue , 2013, Pages 279-297

  Zuk, Or ^a,b   Amir, Amnon ^c   Zeisel, Amit ^c   Shamir, Ohad ^d   Shental, Noam ^e  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b TOYOTA TECHNOLOGICAL INSTITUTE AT CHICAGO   (United States)

^c WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^d MICROSOFT RESEARCH   (United States)

^e OPEN UNIVERSITY OF ISRAEL   (Israel)

Author keywords

Convex optimization; Massively Parallel Sequencing; Microbial Community Reconstruction; Short reads

Indexed keywords

ALGORITHMS; CONVEX OPTIMIZATION; INFORMATION RETRIEVAL;

CONVEX OPTIMIZATION PROBLEMS; DIVIDE-AND-CONQUER ALGORITHM; MAHALANOBIS DISTANCES; MASSIVELY PARALLEL SEQUENCING; MICROBIAL COMMUNITIES; REALISTIC SCENARIO; RECONSTRUCTION ERROR; SHORT READS;

MICROORGANISMS;

EID: 84890412464     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-319-02432-5_31     Document Type: Conference Paper

References (25)

1. Amir, A., Zeisel, A., Zuk, O., Elgart, M., Stern, S., Shamir, O., Turnbaugh, P.J., Soen, Y., Shental, N.: High resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions. In Revision (2013)
2. Amir, A., Zuk, O.: Bacterial community reconstruction using compressed sensing. Journal of Computational Biology 18(11), 1723-1741 (2011)
3. Cole, J.R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R.J., Kulam-Syed-Mohideen, A.S., McGarrell, D.M., Marsh, T., Garrity, G.M., et al.: The ribosomal database project: improved alignments and new tools for rrna analysis. Nucleic Acids Research 37(suppl. 1), D141-D145 (2009)
4. DeSantis, T.Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E.L., Keller, K., Huber, T., Dalevi, D., Hu, P., Andersen, G.L.: Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with arb. Applied and environmental microbiology 72(7), 5069-5072 (2006)
5. Eckburg, P.B., Bik, E.M., Bernstein, C.N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S.R., Nelson, K.E., Relman, D.A.: Diversity of the human intestinal microbial flora. Science 308(5728), 1635-1638 (2005)
6. Eskin, I., Hormozdiari, F., Conde, L., Riby, J., Skibola, C., Eskin, E., Halperin, E.: eALPS: Estimating abundance levels in pooled sequencing using available genotyping data. In: Deng, M., Jiang, R., Sun, F., Zhang, X. (eds.) RECOMB 2013. LNCS, vol. 7821, pp. 32-44. Springer, Heidelberg (2013)
7. Gentry, T.J., Wickham, G.S., Schadt, C.W., He, Z., Zhou, J.: Microarray applications in microbial ecology research. Microbial Ecology 52(2), 159-175 (2006)
8. Grant, M., Boyd, S.: Graph implementations for nonsmooth convex programs. In: Blondel, V., Boyd, S., Kimura, H. (eds.) Recent Advances in Learning and Control. LNCIS, vol. 371, pp. 95-110. Springer, Heidelberg (2008), http://stanford.edu/~boyd/graph-dcp.html
9. Haft, D.H., Tovchigrechko, A.: High-speed microbial community profiling. Nature Methods 9(8), 793-794 (2012)
10. Hamady, M., Knight, R.: Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Research 19(7), 1141-1152 (2009)
11. Hiller, D., Jiang, H., Xu, W., Wong, W.H.: Identifiability of isoform deconvolution from junction arrays and rna-seq. Bioinformatics 25(23), 3056-3059 (2009)
12. Huse, S.M., Dethlefsen, L., Huber, J.A., Welch, D.M., Relman, D.A., Sogin, M.L.: Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genetics 4(11), e1000255 (2008)
13. Kessner, D., Turner, T., Novembre, J.: Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data. Molecular Biology and Evolution 30(5), 1145-1158 (2013)
14. Lozupone, C., Knight, R.: UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology 71(12), 8228-8235 (2005)
15. Lozupone, C.A., Hamady, M., Kelley, S.T., Knight, R.: Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities. Applied and Environmental Microbiology 73(5), 1576-1585 (2007)
16. Mardis, E.R.: The impact of next-generation sequencing technology on genetics. Trends in Genetics 24(3), 133-141 (2008)
17. Meinicke, P., Aßhauer, K.P., Lingner, T.: Mixture models for analysis of the taxonomic composition of metagenomes. Bioinformatics 27(12), 1618-1624 (2011)
18. Paster, B.J., Boches, S.K., Galvin, J.L., Ericson, R.E., Lau, C.N., Levanos, V.A., Sahasrabudhe, A., Dewhirst, F.E.: Bacterial diversity in human subgingival plaque. Journal of Bacteriology 183(12), 3770-3783 (2001)
19. Pavoine, S., Dufour, A.B., Chessel, D.: From dissimilarities among species to dissimilarities among communities: a double principal coordinate analysis. Journal of Theoretical Biology 228(4), 523-537 (2004)
20. Pilanci, M., El Ghaoui, L., Chandrasekaran, V.: Recovery of sparse probability measures via convex programming. In: NIPS (2012)
21. CVX Research. CVX: Matlab software for disciplined convex programming, ver. 2.0 (2012), http://cvxr.com/cvx
22. Rockafellar, R.T.: Convex Analysis. Princeton Mathematics Series, vol. 28. Princeton University Press (1970)
23. Segata, N., Waldron, L., Ballarini, A., Narasimhan, V., Jousson, O., Huttenhower, C.: Metagenomic microbial community profiling using unique clade-specific marker genes. Nature Methods 9(8), 811-814 (2012)
24. Shawe-Taylor, J., Cristianini, N.: Kernel methods for pattern analysis. Cambridge University Press (2004)
25. Xia, L.C., Cram, J.A., Chen, T., Fuhrman, J.A., Sun, F.: Accurate genome relative abundance estimation based on shotgun metagenomic reads. PloS One 6(12), e27992 (2011)