Preprints (not yet peer-reviewed)

829 downloads
3,909 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
79 downloads
370 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
35 downloads
226 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
76 downloads
216 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
37 downloads
152 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
48 downloads
276 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
37 downloads
259 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
39 downloads
137 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
35 downloads
384 views

Recent years have witnessed the discovery of protein–coding genes which appear to have evolved de novo from previously non-coding sequences. This has changed the long-standing view that coding sequences can only evolve from other coding sequences. However, there...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genetics","Genomics"]
doi:10.7287/peerj.preprints.3031v2
35 downloads
387 views

Motion detection and position tracking of animal behavior over a period of time produce massive amount of information, but analysis and interpretation of such huge datasets are challenging. Here we describe statistical methods to extract major movement structures...

["Animal Behavior","Computational Biology"]
doi:10.7287/peerj.preprints.2908v2
31 downloads
229 views

Cancer development as an ecological and evolutionary process is poorly understood, which includes early cancer evolution, malignancy and metastasis. It was hypothesised that the tumour microenvironment (TME) plays a critical role in this process. Unfortunately,...

["Computational Biology","Ecology","Evolutionary Studies","Genetics","Oncology"]
doi:10.7287/peerj.preprints.3052v1
51 downloads
140 views

Understanding how structural and functional alterations of individual tissues impact on whole-joint function is challenging, particularly in humans where direct invasive experimentation is difficult. Finite element computational models produce quantitative predictions...

["Bioengineering","Biotechnology","Computational Biology"]
doi:10.7287/peerj.preprints.3050v1
22 downloads
110 views

Aminoacyl-tRNA synthetases (aaRS) are enzymes that catalyze the ligation of tRNAs to their cognate amino acids. There are aaRSs specific to each of the 20 standard amino acids. These enzymes are divided into two classes, class I and class II, which are unrelated...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics"]
doi:10.7287/peerj.preprints.3045v1
60 downloads
207 views

Hermaphroditic plants experience inbreeding through both self-fertilization and bi-parental inbreeding. Therefore, many plant species have evolved either heteromorphic (morphology-based) or homomorphic (molecular-based) self-incompatibility (SI) systems. These...

["Biogeography","Computational Biology","Evolutionary Studies","Genetics","Plant Science"]
doi:10.7287/peerj.preprints.3042v1
545 downloads
2,419 views

This essay proposes mathematical answers to meta-scientific questions including "how much knowledge is produced by research?", "how rapidly is a field making progress?", "what is the expected reproducibility of a result?", "what do we mean by soft science?", "what...

["Computational Biology","Evolutionary Studies","Science Policy","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.1968v3
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