Preprints (not yet peer-reviewed)

33 downloads
157 views

Sigmoidal and double-sigmoidal dynamics are commonly observed in many areas of biology. Here we present sicegar, an R package for the automated fitting and classification of sigmoidal and double-sigmodial data. The package categorizes data into one of three categories,...

["Bioinformatics","Computational Biology","Mathematical Biology","Statistics","Data Science"]
doi:10.7287/peerj.preprints.3116v1
54 downloads
200 views

Extinction models vary in the information they require, the simplest considering the rate of certain sightings only. More complicated methods include uncertain sightings and allow for variation in the reliability of uncertain sightings. Generally extinction models...

["Conservation Biology","Ecology","Mathematical Biology"]
doi:10.7287/peerj.preprints.3095v1
19 downloads
101 views

The classical way of defining enzyme inhibition has obscured the distinction between inhibitory effect and the inhibitor binding constant. This article examines the relationship between the simple binding curve used to define biomolecular interactions and the standard...

["Biochemistry","Computational Biology","Mathematical Biology","Drugs and Devices","Pharmacology"]
doi:10.7287/peerj.preprints.3094v1
59 downloads
292 views

There is currently unprecedented interest in quantifying variation in thermal physiology among organisms in order to understand and predict the biological impacts of climate change. A key parameter in this quantification of thermal physiology is the performance...

["Ecology","Environmental Sciences","Mathematical Biology"]
doi:10.7287/peerj.preprints.3068v1
14 downloads
109 views

While theory offers clear predictions for when recombination will evolve in changing environments, it is unclear what natural scenarios can generate the necessary conditions. The Red Queen hypothesis provides one such scenario in natural populations, but it requires...

["Evolutionary Studies","Genetics","Mathematical Biology"]
doi:10.7287/peerj.preprints.3047v1
55 downloads
175 views

Many applications require the calculation of site-specific evolutionary rates from alignments of amino-acid sequences. For example, catalytic residues in enzymes and interface regions in protein complexes can be inferred from observed relative rates. While numerous...

["Bioinformatics","Evolutionary Studies","Mathematical Biology"]
doi:10.7287/peerj.preprints.3002v1
27 downloads
368 views

Pedigrees, though straightforward and versatile, lack the ability to tell us information about many individuals. Though numerical systems have been developed, there is currently no system to quantify the probability of a pedigree following certain inheritance systems....

["Bioinformatics","Genetics","Mathematical Biology","Statistics"]
doi:10.7287/peerj.preprints.2871v5
331 downloads
1,157 views

The dynamics of ecological communities have been described by neutral and niche theories that are now increasingly integrated into unified models. It is known that a critical transition exists between these two states, but the spatial aspect of this transition...

["Biodiversity","Computational Biology","Ecology","Mathematical Biology"]
doi:10.7287/peerj.preprints.1589v4
33 downloads
185 views

Locusts are famous for its excellent jumping performance. Jumping helps locusts avoid predators and initiate flight. In this paper, high-speed videos are recorded to analyze the jumping performance of Locusta migratoria Linnaeus from ground with different roughness....

["Animal Behavior","Mathematical Biology","Zoology"]
doi:10.7287/peerj.preprints.2877v1
83 downloads
218 views

Given the rapid population decline and recent petition for listing of the monarch butterfly (Danaus plexippus L.) under the Endangered Species Act, an accurate estimate of the Eastern, migratory population size is needed. Because of difficulty in counting individual...

["Conservation Biology","Ecology","Entomology","Mathematical Biology"]
doi:10.7287/peerj.preprints.2832v1
36 downloads
189 views

We studied the effect of linearization on the repeatability of the Tofts and reference region models (RRM) for Dynamic Contrast-Enhanced MRI (DCE MRI). We compared the repeatabilities of these two linearized models, the standard non-linear version, and semi-quantitative...

["Mathematical Biology","Radiology and Medical Imaging","Statistics"]
doi:10.7287/peerj.preprints.2824v1
80 downloads
276 views

This document is my attempt at distilling some of the information in two papers published by Anthony Nicholls (J. Comput. Aided Mol. Des. 2014, 28, 887; ibid 2016, 30, 103). Anthony also very kindly provided some new equations, not found in the papers, in response...

["Biophysics","Computational Biology","Mathematical Biology","Computational Science"]
doi:10.7287/peerj.preprints.2693v1
37 downloads
380 views

Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunities to...

["Computational Biology","Ecology","Mathematical Biology","Microbiology","Statistics"]
doi:10.7287/peerj.preprints.2685v1
120 downloads
600 views

Knowledge on how functional responses (a measurement of feeding interaction strength) are affected by patch size and habitat complexity (represented by refuge availability) is crucial for understanding food-web stability and subsequently biodiversity. Due to their...

["Ecology","Mathematical Biology","Zoology"]
doi:10.7287/peerj.preprints.2190v2
75 downloads
358 views

Simulating development of fish stocks may be as complex as calculation of the development of the atmosphere, which is treated in meteorology as an initial value problem in physics. This approach was first proposed by Abbe and Bjerknes in the beginning of the 20...

["Aquaculture, Fisheries and Fish Science","Computational Biology","Mathematical Biology"]
doi:10.7287/peerj.preprints.2604v1
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