Extrapolation of urn models via Poissonization: Accurate measurements of the microbial unknown

PLoS ONE

Volumn 6, Issue 6, 2011, Pages

  Lladser, Manuel E ^a   Gouet, Raúl ^b   Reeder, Jens ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b UNIVERSITY OF CHILE   (Chile)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANALYTICAL PARAMETERS; ARTICLE; CONTROLLED STUDY; EMBEDDING; HIGH THROUGHPUT SEQUENCING; MATHEMATICAL COMPUTING; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; POISSON DISTRIBUTION; PROCESS MODEL; SPECIES DIVERSITY; MICROBIOLOGY;

ALGORITHMS; ENVIRONMENTAL MICROBIOLOGY;

EID: 79959587000     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0021105     Document Type: Article

References (32)

1. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, et al. (2006) Microbial diversity in the deep sea and the underexplored \rare biosphere". Proc Natl Acad Sci USA 103: 12115-12120.
2. Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJ, (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67: 4399-4406.
3. Schloss PD, Handelsman J, (2004) Status of the microbial census. Microbiol Mol Biol Rev 68: 686-691.
4. Curtis TP, Head IM, Lunn M, Woodcock S, Schloss PD, et al. (2006) What is the extent of prokaryotic diversity? Phil Trans R Soc Lond 361: 2023-2037.
5. Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AK, et al. (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. Isme J 1: 283-290.
6. Hong SH, Bunge J, Jeon SO, Epstein SS, (2006) Predicting microbial species richness. Proc Natl Acad Sci USA 103: 117-122.
7. Quince C, Curtis TP, Sloan WT, (2008) The rational exploration of microbial diversity. Isme J 2: 997-1006.
8. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, et al. (2007) A core gut microbiome in obese and lean twins. Nature 457: 480-484.
9. Fierer N, Lauber CL, Zhou N, McDonald D, Costello EK, et al. (2010) Forensic identi_cation using skin bacterial communities and/or references within. Proc Natl Acad Sci USA 107: 6477-6481.
10. Magurran AE, (2004) Measuring Biological Diversity Oxford- Blackwell.
11. Burnham KP, Overton WS, (1978) Estimation of the size of a closed population when capture probabilities vary among animals. Biometrika 65: 625-633.
12. Chao A, (1984) Nonparametric estimation of the number of classes in a population. Scand J Stat 11: 265-270.
13. Chao A, (1897) Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43: 783-791.
14. Mao CX, Lindsay BG, (2007) Estimating the number of classes. Ann Stat 35: 917-930.
15. Bunge J, Fitzpatrick M, (1993) Estimating the number of species: A review. J Am Stat Assoc 88: 364-373.
16. Hinsley F, Stripp A, (1993) Codebreakers: The Inside Story of Bletchley Park Oxford Univ. Press.
17. Finch SJ, Mendell NR, Thode HC Jr, (1989) Probabilistic measures of adequacy of a numerical search for a global maximum. J Am Stat Assoc 84: 1020-1023.
18. Mao CX, (2004) Predicting the conditional probability of discovering a new class. J Am Stat Assoc 99: 1108-1118.
19. Good IJ, (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40: 237-264.
20. Robbins HE, (1968) On estimating the total probability of the unobserved outcomes of an experiment. Ann Math Stat 39: 256-257.
21. Starr N, (1979) Linear estimation of the probability of discovering a new species. Ann Stat 7: 644-652.
22. Clayton MK, Frees EW, (1987) Nonparametric estimation of the probability of discovering a new species. J Am Stat Assoc 82: 305-311.
23. Esty WW, (1983) A Normal limit law for a nonparametric estimator of the coverage of a random sample. Ann Statist 11: 905-912.
24. Aldous D, (1988) Probability Approximations via the Poisson Clumping Heuristic Springer-Verlag.
25. Mahmoud HM, (2000) Sorting: A Distribution Theory Wiley-Interscience.
26. Hwang HK, Janson S, (2008) Local limit theorems for _nite and in_nite urn models. Ann Probab 36: 992-1022.
27. Mao CX, Lindsay BG, (2002) A poisson model for the coverage problem with a genomic application. Biometrika 89: 669-681.
28. Durrett R, (1999) Essentials of stochastic processes Springer Texts in Statistics.
29. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, et al. (2009) The e_ect of diet on the human gut microbiome: A metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 1: 6ra14.
30. Fierer N, Hamady M, Lauber CL, Knight R, (2008) The inuence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci USA 105: 17994-17999.
31. Ross SM, (2002) Simulation Academic Press, third edition.
32. Abramowitz M, Stegun IA, (1964) Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables New York Dover, ninth Dover printing, tenth GPO printing edition.