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
133 downloads
358 views

"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" is still...

["Bioinformatics","Computer Education","Digital Libraries","Social Computing","World Wide Web and Web Science"]
doi:10.7287/peerj.preprints.1568v10
47 views

Background. Opsin proteins are seven transmembrane receptor proteins which detect light. Opsins can be classified into two types and share little sequence identity: type 1, typically found in bacteria, and type 2, primarily characterized in metazoa. The type 2...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics","Mycology"]
doi:10.7287/peerj.preprints.2397v1
2 downloads
36 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
37 downloads
125 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.2345v3
52 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
4 downloads
77 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
5 downloads
124 views

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
37 downloads
271 views

Background Dengue is one of the most common arboviral diseases prevalent worldwide and is caused by Dengue viruses (genus Flavivirus, family Flaviviridae). There are four serotypes of Dengue Virus (DENV-1 to DENV-4), each of which is further subdivided into distinct...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics","Virology"]
doi:10.7717/peerj.2326
46 downloads
509 views

We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7717/peerj.2359
28 downloads
673 views

Background: Information on cardiovascular gene transcription is fragmented and far behind the present requirements of the systems biology field. To create a comprehensive source of data for cardiovascular gene regulation and to facilitate a deeper understanding...

["Bioinformatics","Computational Biology","Cardiology","Computational Science"]
doi:10.7717/peerj.2339
12 downloads
79 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
3 downloads
60 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
229 downloads
118 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
96 downloads
274 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

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