9 papers · ranked by Valyu relevance
Carlos P. Carmona, Robert Szava-Kovats, Meelis Pärtel
The biodiversity of a site includes the absent species from the region that are theoretically able to live in the site’s particular ecological conditions. These species constitute the dark diversity of the site. Unlike present species, dark diversity is unobservable and can only be estimated. Most existing methods to…
Dmitriy G. Seleznev, Alexander A. Prokin, Ekaterina M. Kurina
A methodology for identifying pairs of mutually associated and mutually incompatible species pairs based on qualitative ecological data in the ‘species-samples’ format is described. Statistical criteria for assessing the direction and strength of species associations using discrete hypergeometric and binomial…
Sean K. Martin, John P. Aggleton, Shane M. O’Mara
Large-scale simultaneous in vivo recordings of neurons in multiple brain regions raises the question of the probability of recording direct interactions of neurons within, and between, multiple brain regions. In turn, identifying inter-regional communication rules between neurons during behavioural tasks might be…
Rui Fan, Qinghua Cui
Gene functional enrichment analysis represents one of the most popular bioinformatics methods for annotating the pathways and function categories of a given gene list. Current algorithms for enrichment computation such as Fisher’s exact test and hypergeometric test totally depend on the category count numbers of the…
Jeffrey P. Spence, Tony Zeng, Hakhamanesh Mostafavi, Jonathan K. Pritchard
The Discrete-Time Wright Fisher (DTWF) model and its large population diffusion limit are central to population genetics. These models describe the forward-in-time evolution of the frequency of an allele in a population and can include the fundamental forces of genetic drift, mutation, and selection. Computing…
Vladimir A. Kuznetsov, Andre Grageda, Davood Farbod
Modern high-throughput biological systems detection methods generate empirical frequency distributions (EFD) which exhibit complex forms and have long right-side tails. Such EFD are often observed in normal and pathological processes, of which the probabilistic properties are essential, but the underlying probability…
Konstantinos Zagganas, Thanasis Vergoulis, Georgios K. Georgakilas, Theodore Dalamagas
miRNA functional enrichment is a type of analysis that is used to predict which biological functions may be affected by a group of miRNAs or validate whether a list of dysregulated miRNAs are linked to a diseased state. The standard method for functional enrichment analysis uses the hypergeometric distribution to…
Lore Hostens, Koenraad Van Meerbeek, Dymphna Wiegmans, Keith Larson + 6 more
Dark diversity refers to the set of species that are not observed in an area but could potentially occur based on suitable local environmental conditions. In this paper, we applied both niche-based and co-occurrence-based methods to estimate the dark diversity of vascular plant species in the subarctic tundra. We then…
Patrick Vallet
The influence of environmental factors on the dynamics of tree species can imply non-linear relationships. Some of them exhibit threshold effects. Hyperbolic functions effectively represent ecological processes that display threshold behaviours. However, the mathematical formulation of the hyperbola is complex, which…