Statistical normalization methods in microbiome data with application to microbiome cancer research

Y **a - Gut microbes, 2023 - Taylor & Francis
Mounting evidence has shown that gut microbiome is associated with various cancers,
including gastrointestinal (GI) tract and non-GI tract cancers. But microbiome data have …

Sampling networks of ecological interactions

P Jordano - Functional ecology, 2016 - Wiley Online Library
Sampling ecological interactions presents similar challenges, problems, potential biases
and constraints as sampling individuals and species in biodiversity inventories. Robust …

Waste not, want not: why rarefying microbiome data is inadmissible

PJ McMurdie, S Holmes - PLoS computational biology, 2014 - journals.plos.org
Current practice in the normalization of microbiome count data is inefficient in the statistical
sense. For apparently historical reasons, the common approach is either to use simple …

Hyperdominance in the Amazonian tree flora

H Ter Steege, NCA Pitman, D Sabatier, C Baraloto… - Science, 2013 - science.org
Introduction Recent decades have seen a major international effort to inventory tree
communities in the Amazon Basin and Guiana Shield (Amazonia), but the vast extent and …

Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages

RK Colwell, A Chao, NJ Gotelli, SY Lin… - Journal of plant …, 2012 - academic.oup.com
Aims In ecology and conservation biology, the number of species counted in a biodiversity
study is a key metric but is usually a biased underestimate of total species richness because …

Robust estimation of microbial diversity in theory and in practice

B Haegeman, J Hamelin, J Moriarty, P Neal… - The ISME …, 2013 - academic.oup.com
Quantifying diversity is of central importance for the study of structure, function and evolution
of microbial communities. The estimation of microbial diversity has received renewed …

The concepts of bias, precision and accuracy, and their use in testing the performance of species richness estimators, with a literature review of estimator performance

BA Walther, JL Moore - Ecography, 2005 - Wiley Online Library
The purpose of this review is to clarify the concepts of bias, precision and accuracy as they
are commonly defined in the biostatistical literature, with our focus on the use of these …

Detecting diversity: emerging methods to estimate species diversity

KJ Iknayan, MW Tingley, BJ Furnas… - Trends in ecology & …, 2014 - cell.com
Estimates of species richness and diversity are central to community and macroecology and
are frequently used in conservation planning. Commonly used diversity metrics account for …

Sufficient sampling for asymptotic minimum species richness estimators

A Chao, RK Colwell, CW Lin, NJ Gotelli - Ecology, 2009 - Wiley Online Library
Biodiversity sampling is labor intensive, and a substantial fraction of a biota is often
represented by species of very low abundance, which typically remain undetected by …

Estimating species richness and accumulation by modeling species occurrence and detectability

RM Dorazio, JA Royle, B Söderström, A Glimskär - Ecology, 2006 - Wiley Online Library
A statistical model is developed for estimating species richness and accumulation by
formulating these community‐level attributes as functions of model‐based estimators of …