Preprints (not yet peer-reviewed)

7 downloads
162 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
21 downloads
301 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
14 downloads
74 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
7 downloads
78 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
7 downloads
63 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
15 downloads
128 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
424 downloads
1,931 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
28 downloads
74 views

Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists, and thus its application in biological research has been limited. In order to popularize...

["Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.3040v1
87 downloads
352 views

Background: For more than 25 years the golden mussel Limnoperna fortunei has been an aggressive invader in South America freshwaters, having travelled more than 5,000 km upstream across 5 countries. The mussel has outcompeted native species in the invaded environments...

["Bioinformatics","Computational Biology","Conservation Biology","Genetics","Genomics"]
doi:10.7287/peerj.preprints.2995v1
84 downloads
329 views

Sharing and reusing data in research is a welcome and encouraged practice since it maximises the scientific outcomes given limited financial, material and human resources. Interdisciplinary research is considered to benefit from this practice, uniting researchers...

["Bioinformatics","Computational Biology","Data Science","Spatial and Geographic Information Systems"]
doi:10.7287/peerj.preprints.2248v4
164 downloads
310 views

Landscape genetics combines population genetics, landscape ecology, and spatial analysis to identify landscape and genetic factors that influence genetic and genomic variation. Progress in the field depends on a strong conceptual foundation and the means of identifying...

["Computational Biology","Scientific Computing and Simulation","Spatial and Geographic Information Systems"]
doi:10.7287/peerj.preprints.2225v4
78 downloads
212 views

Digital repositories bring direct impact and influence on the research community and society but measuring their value using formal metrics remains challenging. their value. It is challenging to define a single perfect metric that covers all quality aspects. Here,...

["Bioinformatics","Computational Biology","Digital Libraries","World Wide Web and Web Science"]
doi:10.7287/peerj.preprints.2688v2
15 downloads
118 views

Movement in proteins requires energy. To this end, natural selection has selected phosphate as the principal energy currency in cells. On the other hand, depicting the state of transcription could come in the form of epigenetic markers, which are modifications...

["Biochemistry","Cell Biology","Computational Biology","Genetics","Molecular Biology"]
doi:10.7287/peerj.preprints.2966v1
15 downloads
109 views

Most biological processes within a cell are carried out by protein-protein interaction (PPI) networks, or so called interactomics. Therefore, identification of PPIs is crucial to elucidating protein functions and further understanding of various cellular biological...

["Bioinformatics","Biotechnology","Computational Biology"]
doi:10.7287/peerj.preprints.2964v1
50 downloads
285 views

Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.2942v1
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