Preprints (not yet peer-reviewed)

396 downloads
1,008 views

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed...

["Agricultural Science","Bioinformatics","Computational Biology","Plant Science","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3225v1
33 downloads
368 views

Epigenetic research focuses on understanding non-inheritable factors influencing gene regulation and covers various cellular mechanisms such as DNA methylation, histone modification, miRNA function and transcription factor binding sites. Recent advances in high-throughput...

["Bioinformatics","Computational Biology","Genetics","Molecular Biology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3224v1
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
120 downloads
439 views

The development of methods to estimate rates of speciation and extinction from time-calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal ecological factors. We use rigorous simulations...

["Bioinformatics","Computational Biology","Evolutionary Studies"]
doi:10.7287/peerj.preprints.3206v1
13 downloads
78 views

We propose a series of ODE systems to model the various dynamics of human-Borg interaction during a Borg invasion. These models, progressively developed one after the other, could provide humanity and other peace-loving intergalactic species the necessary mathematical...

["Computational Biology","Adaptive and Self-Organizing Systems","Scientific Computing and Simulation"]
doi:10.7287/peerj.preprints.3198v1
701 downloads
2,501 views

Computers are a central tool in the research process, enabling complex and large scale data analysis. As computer-based research has increased in complexity, so have the challenges of ensuring that this research is reproducible. To address this challenge, we review...

["Anthropology","Computational Biology","Science and Medical Education","Computational Science","Data Science"]
doi:10.7287/peerj.preprints.3192v1
79 downloads
230 views

The regulatory code that determines whether and how a given genetic variant affects the function of a regulatory element remains poorly understood for most classes of regulatory variation. Indeed the large majority of bioinformatics tools have been developed to...

["Bioinformatics","Computational Biology","Computational Science","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3185v1
1,340 downloads
4,938 views

Spreadsheets are widely used software tools for data entry, storage, analysis, and visualization. Focusing on the data entry and storage aspects, this paper offers practical recommendations for organizing spreadsheet data to reduce errors and ease later analyses....

["Computational Biology","Science and Medical Education","Statistics","Computational Science","Data Science"]
doi:10.7287/peerj.preprints.3183v1
91 downloads
401 views

An immune system inspired Artificial Immune System (AIS) algorithm is presented, and is used for the purposes of automated program verification. Relevant immunological concepts are discussed and the field of AIS is briefly reviewed. It is proposed to use this AIS...

["Computational Biology","Adaptive and Self-Organizing Systems","Theory and Formal Methods"]
doi:10.7287/peerj.preprints.2690v3
39 downloads
277 views

Analysis of DNA microarray data has been very useful for experimental molecular biology, as it provides unprecedented opportunities to study a wide variety of biological processes. As a part of this analysis, biclustering has been consolidated as one of the first...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.3110v2
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
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
69 downloads
334 views

We have developed a machine learning approach to predict context specific enhancer-promoter interactions using evidence from changes in genomic protein occupancy over time. The occupancy of estrogen receptor alpha (ERα), RNA polymerase (Pol II) and histone marks...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.3093v1
62 downloads
306 views

Introduction: Increasingly, the emergence and evolution of our species is being tied to genetic exchange between divergent lineages within ~1Ma (e.g., Neanderthals, Denisovans). However, little is known about genetic exchange during earlier (pre-1Ma) human evolution...

["Anthropology","Computational Biology","Evolutionary Studies","Genetics","Paleontology"]
doi:10.7287/peerj.preprints.3071v1
65 downloads
167 views

The osmotic pressure of chondroitin sulfate glycosaminoglycans (CS-GAGs) in a simulated physiological environment of articular cartilage is thoroughly examined in silico using full atomistic models. The effects of chemical and physical properties were investigated...

["Biochemistry","Biophysics","Computational Biology","Anatomy and Physiology","Rheumatology"]
doi:10.7287/peerj.preprints.3063v1
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