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Applications of species accumulation curves in large-scale biological data analysis

Quantitative Biology 2015年第3期3卷 135-144页

作者： Chao Deng timothy daley Andrew Smith Molecular and Computational Biology University of Southern California

The species accumulation curve,or collector's curve,of a population gives the expected number of observed species or distinct classes as a function of sampling *** accumulation curves allow researchers to assess and compare diversity across populations or to evaluate the benefits of additional *** applications have focused on ecological populations but emerging large-scale applications,for example in DNA sequencing,are orders of magnitude larger and present new *** developed a method to estimate accumulation curves for predicting the complexity of DNA sequencing *** method uses rational function approximations to a classical nonparametric empirical Bayes estimator due to Good and Toulmin [Biometrika,1956,43,45–63].Here we demonstrate how the same approach can be highly effective in other large-scale applications involving biological data *** include estimating microbial species richness,immune repertoire size,and k-mer diversity for genome assembly *** show how the method can be modified to address populations containing an effectively infinite number of species where saturation cannot practically be *** also introduce a flexible suite of tools implemented as an R package that make these methods broadly accessible.

关键词： species accumulation curve accumulation region rational function approximation immune repertoire microbiome diversity species richness

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Fulminant Clostridium difficile infection: An association with prior appendectomy?

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World Journal of Gastrointestinal Surgery 2013年第8期5卷 233-238页

作者： Jesse Clanton Michael Subichin Katherine Drolshagen timothy daley Michael S Firstenberg Department of Surgery Northeast Ohio Medical University Summa Akron City Hospital Department of Pathology Northeast Ohio Medical University Summa Akron City Hospital Department of Mathematics University of Southern California

AIM: To examine if fulminant Clostridium difficile infections(CDI) resulting in colectomy was associated with a prior appendectomy and whether any association affected the severity of the ***: A retrospective chart review was performed on patients who underwent colectomy for CDI between 2001 and *** appendectomy rate was calculated based on the absence of an appendix on the surgical pathology *** was compared to an established lifetime risk of appendectomy in the general population.A chart review was performed for mortality and traditional markers of CDI disease ***’s exact test was used to calculate the likelihood of association between prior appendectomy,mortality,and clinical markers of severity of ***: Fifty-five specimens were identified with pseudomembranous colitis consistent with *** patients had a clinical history consistent with CDI and 45 of 55(81.8%) specimens also had microbiological confirmation of *** was observed in 24 of 55 specimens(0.436,99%CI: 0.280-0.606).This was compared to the lifetime incidence of appendectomy of 17.6%.The rate of appendectomy in our sample was significantly higher than would be expected in the general population(43.6% vs 17.6%,P < 0.01).Disease severity did not differ based on presence or absence of an appendix and no association was detected between prior appendectomy and mortality(OR = 0.588,95%CI: 0.174-1.970).CONCLUSION: The rate of appendectomy in the patients whose CDI led to colectomy,was significantly higher than the calculated lifetime risk,suggesting an association of appendectomy and severe CDI resulting in *** prospective studies are needed to assess any potential causal relationships affecting fulminant CDI.

关键词： Appendectomy Fulminant colitis Clostridium difficile

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