Preprints (not yet peer-reviewed)

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The widespread availability of high resolution digital elevation models (DEM) opens the possibility of applying physically based models of landslide initiation to large areas. With increasing size of the study area and resolution of the DEM, the required computing...

["Distributed and Parallel Computing","Scientific Computing and Simulation","Spatial and Geographic Information Systems"]
doi:10.7287/peerj.preprints.2206v1

Kamus Dewan is the authoritative dictionary for Bahasa Malaysia, containing a wealth of linguistic and cultural information about Bahasa Malaysia. It is currently available in print, as well as a searchable online dictionary. However, the online dictionary lacks...

["Computational Linguistics","Natural Language and Speech"]
doi:10.7287/peerj.preprints.2205v1

The growing popularity of Free and Open Source (FOSS) GIS software is without doubts due to the possibility to build and customize geospatial applications to meet specific requirements for any users. From this point of view, QGIS is one of the most flexible as...

["Data Science","Spatial and Geographic Information Systems"]
doi:10.7287/peerj.preprints.2204v1

Background. Artificial enrichment of lakes has posed serious management problems for water supply. In results many European lakes had already undergone significant eutrophication. It seems that a good tool to determine the influence of catchment use on the trophic...

["Data Science","Spatial and Geographic Information Systems"]
doi:10.7287/peerj.preprints.2203v1

Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA samples—and their quantifiable metadata—preserved in large institutional biorepositories that are discoverable to the scientific community. Improvements in sequencing...

["Biodiversity","Bioinformatics","Genomics","Molecular Biology","Zoology"]
doi:10.7287/peerj.preprints.2202v1

We propose here a working unit for teaching basic concepts of protein folding and evolution centred around the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding. In our experience, developed at a...

["Bioinformatics","Computational Biology","Computer Education"]
doi:10.7287/peerj.preprints.2201v1

Background: Multivariate statistical approaches (MSA), such as principal components analysis and multidimensional scaling, seek to uncover meaningful patterns within datasets by considering multiple response variables in a concerted fashion. Although these techniques...

["Environmental Sciences","Genomics","Marine Biology","Molecular Biology","Statistics"]
doi:10.7287/peerj.preprints.2200v1

Motivation Molecular docking is an efficient method to predict the conformations adopted by the ligand within the target binding site. Usually, standard docking protocol involves only one structure to represent the receptor, overlooking the changes in the binding...

["Bioinformatics","Computational Science"]
doi:10.7287/peerj.preprints.2199v1

Background. Names for ”substances” used in food products are rarely precise. The term bamboo (Bambusoideae, Poaceae) comprises over 1600 distinct species of which only few are well established sources for food products on the European market (i.e. bamboo sprouts)....

["Food Science and Technology","Molecular Biology","Plant Science","Taxonomy"]
doi:10.7287/peerj.preprints.2198v1

Predicting protein structure from sequence remains a major open problem in protein biochemistry. One component of predicting complete structures is the prediction of inter-residue contact patterns (contact maps). Here, we discuss protein contact map prediction...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.2197v1

Diversity of complex microbial communities can be rapidly assessed by community amplicon sequencing of marker genes (e.g., 16S), often yielding many thousands of DNA sequences per sample. However, analysis of community amplicon sequencing data requires multiple...

["Biodiversity","Bioinformatics","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.2196v1

Motivation One of the fundamental issues in both chemistry and biology is the identification of the structural determinants that dictate protein folding and stability. The decoding of the folding code of protein structures would have a major impact on native structure...

["Biochemistry","Computational Biology"]
doi:10.7287/peerj.preprints.2195v1

Cross-contamination of human and animal cell lines is a frequent event. For this reason, the results obtained with the same cell lines by different research groups are often not fully comparable, this leading to main reproducibility issues. The short tandem repeat...

["Bioinformatics","Cell Biology","Molecular Biology","Oncology"]
doi:10.7287/peerj.preprints.2194v1

The material collected during a Spanish, multi-year expedition to the Neotropics in the 1860s was described by J.G. Hidalgo in the ‘Moluscos del Viaje al Pacifico’. Correspondence between Hidalgo and H. Crosse reveals how part of the material collected by the ‘Comisión...

["Taxonomy","Zoology"]
doi:10.7287/peerj.preprints.2193v1
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High throughput sequencing techniques have opened up the world of microbial diversity to scientists, and a flurry of studies in the most remote and extreme habitats on earth have begun to elucidate the key roles of microbes in ecosystems with extreme conditions....

["Biodiversity","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.1874v2
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