Preprints (not yet peer-reviewed)

52 downloads
321 views

Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms...

["Bioinformatics","Environmental Sciences","Genomics","Microbiology","Soil Science"]
doi:10.7287/peerj.preprints.2473v1
113 downloads
332 views

Unique Molecular Identifiers (UMIs) have been incorporated into RNA-Seq experiments to overcome issues with abundance estimation from samples that may have many PCR amplification cycles. However, the use of UMIs in many different types of sequencing experiments...

["Bioinformatics","Genetics","Genomics"]
doi:10.7287/peerj.preprints.2465v1
92 downloads
303 views

Forest trees cover just over 30% of the earth's surface and are studied by researchers around the world for both their conservation and economic value. With the onset of high throughput technologies, tremendous phenotypic and genomic data sets have been generated...

["Bioinformatics","Data Mining and Machine Learning","Databases"]
doi:10.7287/peerj.preprints.2345v4
59 downloads
291 views

Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments, clinical diagnostics and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2449v1
44 downloads
257 views

Background. The capacity of species to respond and perceive visual signal is integral to their evolutionary success. Giraffe is closely related to okapi, but the two species have broad range of phenotypic differences including their visual capacities. Vision studies...

["Bioinformatics","Evolutionary Studies","Genomics"]
doi:10.7287/peerj.preprints.2444v1
62 downloads
168 views

Arranging a heterogeneous collection of entities into a hierarchy of linearly ordered levels (layers or strata) is a general ordering scheme that is a widely used notion for organizing knowledge. On the basis of four specific examples, all of which are relevant...

["Bioinformatics","Computational Biology","Zoology","Computational Science"]
doi:10.7287/peerj.preprints.2429v1
46 downloads
193 views

microRNAs are small, non-coding RNAs involved in post-transcriptional gene regulation. Since the dysregulation of only a few miRNAs can affect many biological pathways, miRNAs are thought to play a key role in cancer development and can be used as biomarkers for...

["Bioinformatics","Genomics","Molecular Biology"]
doi:10.7287/peerj.preprints.2423v1
224 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
312 downloads
381 views

Circular RNAs (circRNAs) belong to a recently re-discovered species of RNA that emerge during RNA maturation through a process called back-splicing. A downstream 5’ splice site is linked to an upstream 3’ splice site to form a circular transcript instead of a canonical...

["Bioinformatics","Computational Biology","Genomics","Molecular Biology"]
doi:10.7287/peerj.preprints.2418v1
166 downloads
598 views

ABSTRACT "Publication forms the core structure supporting the development and transmission of scientific knowledge" (Galbraith2015). Yet, with the WorldWideWeb a dominant part of current scientific publication and information-dissemination, internet "publication"...

["Bioinformatics","Computer Education","Digital Libraries","Social Computing","World Wide Web and Web Science"]
doi:10.7287/peerj.preprints.1568v12
269 downloads
2,072 views

Background. VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing metagenomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar 2010) for which the source code is not publicly available,...

["Biodiversity","Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2409v1
54 downloads
411 views

As the generation and use of genomic datasets is becoming increasingly common in all areas of biology, the need for resources to collate, analyse and present data from one or more genome projects is becoming more pressing. The Ensembl platform is a powerful tool...

["Bioinformatics","Genomics"]
doi:10.7287/peerj.preprints.2401v1
104 downloads
227 views

The late detection of non-genotoxic carcinogens in the drug development process can delay drug candidates for unmet medical needs from reaching the market despite considerable investments in their development. To enable faster, safer, and less expensive development...

["Bioinformatics","Computational Biology","Molecular Biology","Oncology","Pharmacology"]
doi:10.7287/peerj.preprints.2393v1
67 downloads
149 views

Background: Amoebiasis is the third most common parasitic cause of morbidity and mortality particularly in countries with poor hygienic settings. There exists an ambiguity in the diagnosis of amoebiasis, and hence arises a necessity for a better diagnostic approach....

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.2392v1
63 downloads
259 views

Amyloids are proteins associated with the number of clinical disorders (e.g., Alzheimer's, Creutzfeldt-Jakob's and Huntington's diseases). Despite their diversity, all amyloid proteins can undergo aggregation initiated by 6- to 15-residue segments, called hot spots....

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.2390v1
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