Preprints (not yet peer-reviewed)

33 downloads
166 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
1,913 downloads
19,358 views

The website Sci-Hub provides access to scholarly literature via full text PDF downloads. The site enables users to access articles that would otherwise be paywalled. Since its creation in 2011, Sci-Hub has grown rapidly in popularity. However, until now, the extent...

["Bioinformatics","Legal Issues","Science and Medical Education","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.3100v1
28 downloads
368 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
70 downloads
235 views

A measure of statistical evidence should permit the sample size determination so that the probability M of obtaining (strong) misleading evidence can be held as low as desired. On this desideratum the p-value fails completely, as it leads either to an arbitrary...

["Bioinformatics","Epidemiology","Statistics"]
doi:10.7287/peerj.preprints.2869v1
18 downloads
165 views

Basic idea of science is reproducibility of phenomena and experiments. Reproducibility of data analyses and reports is becoming more and more important. It requires structured organization of data, augmented with enought metadata for future re-use of data. Our...

["Bioinformatics","Genomics","Plant Science","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.2791v1
182 downloads
428 views

Background RNA sequencing (RNA-Seq) is a powerful technique for transcriptome profiling of the organisms that uses the capabilities of next-generation sequencing (NGS) technologies. Recent advances in NGS let to measure the expression levels of tens to thousands...

["Bioinformatics","Genomics","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.2761v1
107 downloads
269 views

Site-specific evolutionary rates can be estimated from codon sequences or from amino-acid sequences. For codon sequences, the most popular methods use some variation of the dN/dS ratio. For amino-acid sequences, one widely-used method is called Rate4Site, and it...

["Bioinformatics","Computational Biology","Evolutionary Studies","Statistics"]
doi:10.7287/peerj.preprints.2739v1
35 downloads
267 views

Identifying the pathways that control a cellular phenotype is the first step to building a mechanistic model. Recent examples in developmental biology, cancer genomics, and neurological disease have demonstrated how changes in the variability of gene expression...

["Bioinformatics","Cell Biology","Statistics"]
doi:10.7287/peerj.preprints.2585v1
350 downloads
557 views

“Omics” studies generate long lists of genes, proteins, metabolites or other features which can be difficult to decipher. Feature set enrichment analysis utilizing annotated groups/classes of features (such as pathways, gene ontology terms or gene/metabolic modules)...

["Bioinformatics","Immunology","Statistics","Metabolic Sciences","Computational Science"]
doi:10.7287/peerj.preprints.2420v1
204 downloads
351 views

The reliable detection of novel bacterial pathogens from next generation sequencing data is a key challenge for microbial diagnostics. Current computational tools usually rely on sequence similarity and often fail to detect novel species when closely related genomes...

["Bioinformatics","Genomics","Microbiology","Statistics"]
doi:10.7287/peerj.preprints.2379v1
136 downloads
870 views

Recent years have brought about the realisation of an irreproducibility crisis in science, which may have numerous causes, including common standards of statistical analysis. For decades, the methodological paradigm of null hypothesis significance testing (NHST)...

["Bioinformatics","Science and Medical Education","Statistics"]
doi:10.7287/peerj.preprints.2249v1
68 downloads
217 views

Estimation of natural selection on protein-coding sequences is a key comparative genomics approach for de novo prediction of lineage specific adaptations. Selective pressure is measured on a per-gene basis by comparing the rate of non-synonymous substitutions to...

["Bioinformatics","Computational Biology","Evolutionary Studies","Mathematical Biology","Statistics"]
doi:10.7287/peerj.preprints.2218v1
68 downloads
292 views

Motivation Nowadays, advances in technology has arisen in a huge amount of data in both biomedical research and healthcare systems. This growing amount of data gives rise to the need for new research methods and analysis techniques. Analysis of these data offers...

["Bioinformatics","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.2186v1
42 downloads
274 views

MOTIVATION Alkaptonuria (AKU) is a rare and genetic disease which causes discoloration of bone (a process called ‘ochronosis’) and induces early-onset osteoarthritis. AKU data have not been organized yet and the disease has no approved biomarkers. The ability to...

["Bioinformatics","Computational Biology","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.2174v1
85 downloads
598 views

Genome-wide association studies (GWAS) have uncovered thousands of associations between genetic variants and diseases. Using the same datasets, prediction of disease risk can be attempted. Phase information is an important biological structure that has seldom been...

["Bioinformatics","Computational Biology","Genomics","Epidemiology","Statistics"]
doi:10.7287/peerj.preprints.2074v1
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