Preprints (not yet peer-reviewed)

5 downloads
75 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
44 downloads
119 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
21 downloads
334 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
322 downloads
1,097 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
29 downloads
174 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
82 downloads
194 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
27 downloads
175 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
73 downloads
262 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
35 downloads
348 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
108 downloads
564 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
69 downloads
337 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
106 downloads
667 views

Wildlife collision data are ubiquitous, though challenging for making ecological inference due to typically irreducible uncertainty relating to the sampling process. We illustrate a new approach that is useful for generating inference from predator data arising...

["Conservation Biology","Ecology","Mathematical Biology","Statistics"]
doi:10.7287/peerj.preprints.2572v1
173 downloads
496 views

For this initial work, we shall focus on introducing a biological model for utilization [mainly] as a descriptive framework on which future analyses will be based. The model includes a definition of a biological system as a composite of properties that occupy defined...

["Bioengineering","Computational Biology","Mathematical Biology"]
doi:10.7287/peerj.preprints.1148v4
90 downloads
138 views

Here we shall apply the approach presented in the paper Dynamics of resource allocation in biological systems in considering resource allocation in cancer cell metabolism, specifically, aerobic glycolysis (Warburg effect). Aerobic glycolysis, the metabolic phenomenon...

["Biochemistry","Cell Biology","Mathematical Biology","Molecular Biology","Oncology"]
doi:10.7287/peerj.preprints.2533v1
130 downloads
265 views

‘Big Data’ and a surge in quantitative methodologies increasingly urge bioresearchers to train and improve their mathematical and computational skills. In response to this challenge the Biotechnology and Biological Sciences Research Council in the United Kingdom...

["Computational Biology","Mathematical Biology","Science and Medical Education","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.2523v1
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