Preprints (not yet peer-reviewed)

9 downloads
78 views

Background. The globally abundant coccolithophore, Emiliania huxleyi, plays an important ecological role in oceanic carbon biogeochemistry by forming a cellular covering of plate-like CaCO3 crystals (coccoliths) and fixing CO2. It is unknown how the cells arrange...

["Mathematical Biology"]
doi:10.7287/peerj.preprints.3457v1
73 downloads
208 views

This work aims for modeling and simulating the metastasis of cancer, via the analogy between the cancer process and the board game Go. In the game of Go, black stones play first, could correspond to metastasis of cancer. Moreover, playing white stones on the second...

["Bioinformatics","Biophysics","Computational Biology","Mathematical Biology","Computational Science"]
doi:10.7287/peerj.preprints.3434v1
41 downloads
230 views

The sixth mass extinction poses an unparalleled quantitative challenge to conservation biologists. Mathematicians and ecologists alike face the problem of developing models that can scale predictions of extinction rates from populations to the level of a species,...

["Conservation Biology","Ecology","Mathematical Biology","Statistics","Climate Change Biology"]
doi:10.7287/peerj.preprints.3367v1
118 downloads
136 views

Bertalanffy proposed the differential equation m´(t) = p × m (t) a –q × m (t) for the description of the mass growth of animals as a function m(t) of time t. He suggested that the solution using the metabolic scaling exponent a = 2/3 (von Bertalanffy growth function...

["Agricultural Science","Aquaculture, Fisheries and Fish Science","Computational Biology","Mathematical Biology"]
doi:10.7287/peerj.preprints.3303v1
40 downloads
240 views

Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports...

["Bioinformatics","Genomics","Mathematical Biology"]
doi:10.7287/peerj.preprints.3223v1
23 downloads
114 views

Algal blooms have been the subject of considerable research as they occur over various spatial and temporal scales and can produce toxins that disrupt their ecosystem. Algal blooms are often governed by nutrient availability however other limitations exist. Algae...

["Biodiversity","Computational Biology","Ecology","Marine Biology","Mathematical Biology"]
doi:10.7287/peerj.preprints.3218v1
23 downloads
133 views

Models and the process of modeling are fundamental to the discipline of biology, and therefore should be incorporated into undergraduate biology courses. In this essay, we draw upon the literature and our own teaching experiences to provide practical suggestions...

["Evolutionary Studies","Genetics","Mathematical Biology","Science and Medical Education"]
doi:10.7287/peerj.preprints.3215v1
128 downloads
255 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
64 downloads
265 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
73 downloads
190 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
100 downloads
429 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
26 downloads
147 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
69 downloads
221 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
36 downloads
493 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
372 downloads
1,271 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
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