Preprints (not yet peer-reviewed)

22 downloads
98 views

Housekeeping genes are ubiquitously expressed and maintain basic cellular function across tissue/cell types conditions. The present study aimed to develop a set of pig housekeeping genes and compare characteristics of structure, evolution and function of housekeeping...

["Bioinformatics","Evolutionary Studies","Genetics"]
doi:10.7287/peerj.preprints.3450v1
127 downloads
349 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.2688v3
69 downloads
205 views

This work aims for modeling and simulating the metastasis of cancer, via the analogy between the cancer process and the board game Go. In the game of Go, black stones play first, could correspond to metastasis of cancer. Moreover, playing white stones on the second...

["Bioinformatics","Biophysics","Computational Biology","Mathematical Biology","Computational Science"]
doi:10.7287/peerj.preprints.3434v1
72 downloads
176 views

Currently the National Center of Biotechnology Information (NCBI) assigns individual taxonomy identifiers to each distinct influenza virus isolate submitted to GenBank. To support this practice, individual flu isolates must be manually added to the NCBI taxonomy...

["Bioinformatics","Computational Biology","Taxonomy","Virology","Science Policy"]
doi:10.7287/peerj.preprints.3428v1
79 downloads
185 views

Normalization is the first critical step in microbiome sequencing data analysis used to account for variable library sizes. Current RNA-Seq based normalization methods that have been adapted for microbiome data fail to consider the unique characteristics of microbiome...

["Bioinformatics","Genomics","Statistics"]
doi:10.7287/peerj.preprints.3417v2
32 downloads
126 views

The hemagglutinin subtypes from Influenza A can be divided into distinct lineages. This is important for tracing the evolutionary history of the gene. It allows regional lineages to be identified and studied. The process of lineage identification depends on phylogenetic...

["Bioinformatics","Virology","Computational Science"]
doi:10.7287/peerj.preprints.3396v1
48 downloads
327 views

In translational medicine, the technology of RNA sequencing (RNA-seq) continues to prove powerful, and transforming the RNA-seq data into biological insights has become increasingly imperative. We present the Transcriptomics profiler for Easy Discovery (TED) toolkit,...

["Bioinformatics","Genomics","Translational Medicine","Computational Science","Data Science"]
doi:10.7287/peerj.preprints.3385v1
15 downloads
130 views

Most evolutionary analyses or structure modeling are based upon pre-estimated multiple sequence alignment (MSA) models. From a computational point of view, it is too complex to estimate a correct alignment. Hence, increasing or identifying signal inside sequence...

["Bioinformatics"]
doi:10.7287/peerj.preprints.3376v1
34 downloads
117 views

The analysis of large numbers of sequences requires the reduction of ambiguities during the analytical work to ensure that the effort will focus only on confirmed sequences. Performing this work automatically may help to minimize potential errors associated with...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.3364v1
21 downloads
117 views

In plant mitochondria an essential mechanism for gene expression is RNA editing, often influencing the synthesis of functional proteins. RNA editing alters the linearity of genetic information transfer, intro- ducing differences between RNAs and their coding DNA...

["Bioinformatics"]
doi:10.7287/peerj.preprints.3362v1
29 downloads
170 views

The immune system protects a host from foreign pathogens. In rare cases, the immune system can attack the cells of the host organism causing autoimmune diseases. We outline a computational framework that combines bioinformatics and network analysis with an emerging...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3217v3
404 downloads
617 views

Pattern recognition is commonly used for identifying an unknown entity from a set of known objects curated in a database, and find use in various applications such as fingerprint matching and microbial identification. Mass spectrometry is increasingly used in identifying...

["Biodiversity","Bioinformatics","Ecology","Microbiology","Science and Medical Education"]
doi:10.7287/peerj.preprints.580v3
37 downloads
141 views

Ecological niche modeling (ENM) is increasingly being used in studying the relationship between species distributions and environmental conditions. The development of ENM software/algorithms is heading toward open-source programming, for the advantage of efficiency...

["Biogeography","Bioinformatics","Ecology","Zoology","Data Science"]
doi:10.7287/peerj.preprints.3346v1
40 downloads
302 views

Current research posits that all multicellular organisms live in symbioses with associated microorganisms and form so-called metaorganisms or holobionts. Cnidarian metaorganisms are of specific interest given that stony corals provide the foundation of the globally...

["Bioinformatics","Genomics","Virology","Biosphere Interactions"]
doi:10.7287/peerj.preprints.3343v1
8,854 downloads
34,685 views

The website Sci-Hub provides access to scholarly literature via full text PDF downloads. The site enables users to access articles that would otherwise be paywalled. Since its creation in 2011, Sci-Hub has grown rapidly in popularity. However, until now, the extent...

["Bioinformatics","Legal Issues","Science and Medical Education","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.3100v2
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