Preprints (not yet peer-reviewed)

29 downloads
97 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
25 downloads
102 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
31 downloads
238 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
12 downloads
121 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
19 downloads
82 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
14 downloads
92 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
20 downloads
145 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
394 downloads
600 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
29 downloads
132 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
30 downloads
292 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
5,092 downloads
28,061 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
21 downloads
138 views

Personalized medicine is in great part enabled by the progress in data acquisition technologies for modern biology, such as next-generation sequencing (NGS). Conventional NGS processing workflows are composed by independent tools implementing shared-memory parallelism...

["Bioinformatics","Computational Biology","Distributed and Parallel Computing"]
doi:10.7287/peerj.preprints.3338v1
18 downloads
130 views

MicroRNAs (miRNAs) are small non-coding RNA molecules mediating the translational repression and degradation of target mRNAs in the cell. Mature miRNAs are used as a template by the RNA-induced silencing complex (RISC) to recognize the complementary mRNAs to be...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.3337v1
185 downloads
540 views

Computational models in biology encode molecular and cell biological processes. These models often can be represented as biochemical reaction networks. Studying such networks, one is mostly interested in systems that share similar reactions and mechanisms. Typical...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning","Data Science"]
doi:10.7287/peerj.preprints.1479v3
28 downloads
189 views

As the costs of high-throughput measurement technologies continue to fall, experimental approaches in biomedicine are increasingly data intensive and the advent of big data is justifiably seen as holding the promise to transform medicine. However, as data volumes...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.3328v1
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