Preprints (not yet peer-reviewed)

25 downloads
126 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
7 downloads
93 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
55 downloads
381 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
39 downloads
229 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
291 downloads
755 views

The dynamics of ecological communities can be described by two contrasting models: the first assumes that individuals of all species are identical and do not have interactions. The second assumes that species are different, adapted to particular habitat conditions,...

["Biodiversity","Computational Biology","Ecology","Mathematical Biology"]
doi:10.7287/peerj.preprints.1589v3
80 downloads
302 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
166 downloads
429 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
18 downloads
92 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
89 downloads
161 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
23 downloads
150 views

The Simulation Experiment Description Markup Language (SED-ML) is a standardized format for exchanging simulation studies independently of software tools. We present the SED-ML Web Tools, a software that supports SED-ML Level 1 Version 2, including complex modifications...

["Bioinformatics","Computational Biology","Mathematical Biology","Molecular Biology","Computational Science"]
doi:10.7287/peerj.preprints.2515v1
12 downloads
101 views

Here we present a single working model that attempts at reconciliation of biological systems. To do this we recognize and emphasize a universal theme of all biological systems: a need for resources. That is, we consider the dynamics of resource allocation as a...

["Biochemistry","Cell Biology","Mathematical Biology","Anatomy and Physiology","Metabolic Sciences"]
doi:10.7287/peerj.preprints.2503v1
28 downloads
222 views

Complex physiological dynamics have been argued to be a signature of healthy physiological function. Here we test whether the complexity of metabolic rate fluctuations in small endotherms decreases with lower environmental temperatures. To do so we examine the...

["Computational Biology","Ecology","Mathematical Biology","Statistics"]
doi:10.7287/peerj.preprints.2404v1
618 downloads
520 views

Background: The dengue fever is a mosquito-borne viral disease and a regular epidemic in Thailand. The peak of the dengue epidemic period is around June to August during the rainy season. It is believed that the climate is an important factor for dengue transmission.Method:...

["Computational Biology","Mathematical Biology","Infectious Diseases"]
doi:10.7287/peerj.preprints.756v5
53 downloads
483 views

Despite high success rate in treating human Strongyloides infection with ivermectin, there is no consensus about the treatment of hyperinfection by helminths of the genus Strongyloides in immunocompromised people. Chances of survival of patients suffering from...

["Computational Biology","Mathematical Biology","Parasitology","Infectious Diseases","Public Health"]
doi:10.7287/peerj.preprints.2399v1
76 downloads
253 views

We study the glycosylation processes that convert initially toxic substrates to nutritionally valuable metabolites in the flavonoid biosynthesis pathway of tomato (Solanum lycopersicum) seedlings. To estimate the reaction rates we use ordinary differential equations...

["Agricultural Science","Computational Biology","Food Science and Technology","Mathematical Biology","Plant Science"]
doi:10.7287/peerj.preprints.2077v2
What is a PeerJ Preprint?

A PeerJ Preprint is a draft of an article, abstract, or poster that has not yet been peer-reviewed for formal publication. Submit a draft, incomplete, or final version of your work for free.

Submissions today can be approved by Editorial Staff and online in 24 hours.

Establish precedent. Solicit feedback. Publish updates.

Top subject areas - Preprints

Top subject areas - People

View all subject areas