Preprints (not yet peer-reviewed)

8 downloads
76 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
52 downloads
204 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
42 downloads
195 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
23 downloads
149 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
225 downloads
348 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
142 downloads
266 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
124 downloads
764 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
51 downloads
180 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
56 downloads
214 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
37 downloads
184 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
63 downloads
491 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
36 downloads
157 views

Background. In the early and late stages of cell reprogramming to induced pluripotent stem cells (iPSCs) ectopic expression of Oct4, Sox2, Klf4 and Myc (OSKM) aroused two peaks of transcriptional and epigenetic change respectively. However, it was relatively quiet...

["Bioinformatics","Cell Biology","Mathematical Biology","Molecular Biology","Statistics"]
doi:10.7287/peerj.preprints.1991v1
43 downloads
77 views

Multiple metrics have been developed to detect causality relations between data describing the elements constituting complex systems, all of them considering their evolution through time. Here we propose a metric able to detect causality within static data sets,...

["Bioinformatics","Neuroscience","Statistics"]
doi:10.7287/peerj.preprints.1827v1
71 downloads
227 views

The genome–wide study of epigenetic states requires the integrative analysis of histone modification ChIP–seq data. Here, we introduce an easy–to–use analytic framework to compare profiles of enrichment in histone modifications around classes of genomic elements,...

["Bioinformatics","Computational Biology","Genomics","Statistics"]
doi:10.7287/peerj.preprints.1723v2
649 downloads
363 views

The natural sciences, such as ecology and earth science, study complex interactions between biotic and abiotic systems in order to infer understanding and make predictions. Machine-learning-based methods have an advantage over traditional statistical methods in...

["Bioinformatics","Ecology","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.1720v1
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