Preprints (not yet peer-reviewed)

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
94 downloads
329 views

In 2007 the Independent Scientific Group (ISG) reported to the UK government the impact on bovine tuberculosis (TB) in cattle of a trial where badgers were culled between 1998 and 2005. This trial, known as the Randomised Badger Culling Trial (RBCT), was performed...

["Epidemiology","Infectious Diseases","Statistics"]
doi:10.7287/peerj.preprints.2336v3

By screening sequence reads from the chloroplast (cp) genome of S. suchowensis that generated by the next generation sequencing platforms, we built the complete circular pseudomolecule for its cp genome. This pseudomolecule is 155,508 bp in length, which has a...

["Bioinformatics","Genomics","Plant Science"]
doi:10.7287/peerj.preprints.2388v1
38 downloads
76 views

In a report issued to the UK government in 2007 on the Randomised Badger Culling Trial (RBCT), it was stated that the incidence of bovine tuberculosis (TB) in cattle increased in areas surrounding where badgers were removed. It is known that badger culling perturbs...

["Epidemiology","Infectious Diseases","Statistics"]
doi:10.7287/peerj.preprints.2376v2

The coral reefs around Praia do Tofo, southern Mozambique, are known for their aggregations of marine megafauna but as yet few studies have comprehensively examined their broader biodiversity. This study is the first to assess the ichthyofaunal diversity of this...

["Biodiversity","Conservation Biology","Marine Biology"]
doi:10.7287/peerj.preprints.2389v1
1 download
40 views

Urban habitats are characterized by a number of unique environmental variables, including modified vegetative structure, fragmentation, small patch size, invasive species, and higher levels of anthropogenic noise. Many songbird species are found less frequently...

["Animal Behavior","Biodiversity","Ecology","Coupled Natural and Human Systems"]
doi:10.7287/peerj.preprints.2387v1
51 downloads
192 views

Biodiversity-ecosystem function (BEF) experiments routinely employ common garden designs, drawing samples from a local biota. The communities from which taxa are sampled may not, however, be at equilibrium. To test for temporal changes in BEF relationships, I assembled...

["Biodiversity","Ecology","Ecosystem Science","Environmental Sciences","Microbiology"]
doi:10.7287/peerj.preprints.1897v2
39 views

Longitudinal studies focusing on lifetime reproductive success (LRS) have been used to measure individual breeding performance and identify commonalities among successful breeders. By extending the focus to subsequent generations we identify a proportion of high-quality...

["Conservation Biology","Ecology","Marine Biology","Zoology"]
doi:10.7287/peerj.preprints.2386v1
5 downloads
55 views

In aggressive solid tumors like melanoma, a strategy for therapy personalization can be achieved by combining high-throughput data on the patient’s specific tumor mutation and expression profiles. A remarkable case is dendritic cell-based immunotherapy, where tumor...

["Bioinformatics","Dermatology","Immunology"]
doi:10.7287/peerj.preprints.2385v1
2 downloads
40 views

Deregulation of miRNAs is implicated in many diseases in particular cancer, where miRNAs can act as tumour suppressors or oncogenes. As sequence-based miRNA target predictions do not provide condition-specific information, many algorithms combine expression data...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.2384v1
15 downloads
34 views

Most reconstruction methods for genomes of ancient origin that are used today require a closely related reference. In order to identify genomic rearrangements or the deletion of whole genes, de novo assembly has to be used. However, because of inherent problems...

["Bioinformatics","Paleontology","Computational Science"]
doi:10.7287/peerj.preprints.2383v1
4 downloads
44 views

The “Graphical Fragment Assembly” (GFA) is an emerging format for the representation of sequence assembly graphs, which can be adopted by both de Bruijn graph- and string graph-based assemblers. Here we present RGFA, an implementation of the proposed GFA specification...

["Bioinformatics","Genomics"]
doi:10.7287/peerj.preprints.2381v1
188 downloads
135 views

The Tübiom project is a community-based project aimed at constructing a large, representative reference database of human gut microbiome profiles. The goal is to collect 10 000 profiles, along with detailed metadata on each participants health and lifestyle. All...

["Bioinformatics","Computational Biology","Science and Medical Education"]
doi:10.7287/peerj.preprints.2382v1
35 downloads
119 views

Mutation processes differ between types of point mutation, genomic locations, cells, and biological species. For some point mutations, specific neighbouring bases are known to be mechanistically influential. Beyond these cases, numerous questions remain unresolved...

["Bioinformatics","Evolutionary Studies","Genetics","Medical Genetics"]
doi:10.7287/peerj.preprints.2236v2
253 downloads
1,045 views

Software is a critical part of modern research and yet there is little support across the scholarly ecosystem for its acknowledgement and citation. Inspired by the activities of the FORCE11 working group focused on data citation, this document summarizes the recommendations...

["Digital Libraries","Software Engineering"]
doi:10.7287/peerj.preprints.2169v4
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