Preprints (not yet peer-reviewed)

7 downloads
165 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
7 downloads
90 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
12 downloads
120 views

Systems Biology is a holistic approach, based on the integration of multiscale models and different kinds of data, aimed at studying the underlying mechanisms of complex biological systems. A GEnome-scale metabolic Model (GEM) is the representation of the metabolic...

["Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.3323v1
44 downloads
214 views

Phenotypic differences between closely related taxa or populations can arise through genetic variation or be environmentally induced, in both cases leading to altered transcription of genes during the structural and functional development of the body. Comparative...

["Developmental Biology","Ecology","Evolutionary Studies","Genomics","Freshwater Biology"]
doi:10.7287/peerj.preprints.3318v1
31 downloads
147 views

Network Diffusion has been proposed in several applications, thanks to its ability of amplifying biological signals and prioritizing genes that may be associated with a disease. Not surprising, the success of Network Diffusion on a “single layer” led to the first...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.3310v1
58 downloads
278 views

In industry, the yeast Rhodotorula mucilaginosa is commonly used for the production of carotenoids. The production of carotenoids is important because they are used as natural colorants in food and some carotenoids are precursors of retinol (vitamin A). However,...

["Biotechnology","Genomics","Microbiology","Mycology","Plant Science"]
doi:10.7287/peerj.preprints.3219v2
21 downloads
112 views

Propensities for different amino acids within a protein site change in the course of evolution, so that an amino acid deleterious in a particular species may be acceptable at the same site in a different species. Here, we study the amino acid-changing variants...

["Evolutionary Studies","Genomics"]
doi:10.7287/peerj.preprints.3211v2
40 downloads
204 views

Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.3266v3
30 downloads
98 views

The mutational processes responsible for the somatic mutations observed in tumor samples can significantly vary not only between tumor types but also among the individual cancers within a tumor class. Mutational processes can be represented by so called “mutational...

["Bioinformatics","Computational Biology","Genomics","Oncology"]
doi:10.7287/peerj.preprints.3257v1
21 downloads
181 views

Background. Enteroviruses are small non-enveloped viruses with (+) ssRNA genome with one open reading frame. Enterovirus protein 3C (or 3CD for some species) binds the replicative element oriL to initiate replication. The replication of enteroviruses features low...

["Evolutionary Studies","Genomics","Virology"]
doi:10.7287/peerj.preprints.3153v2
18 downloads
173 views

Computational biology is rapidly advancing thanks to the many new tools developed and published each month. A systematic benchmarking practice would help biomedical researchers leverage this technological expansion to optimize their projects. Several aspects of...

["Computational Biology","Genetics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.3236v1
61 downloads
178 views

Standard procedures for NGS data analysis involve a pre-processing step of reads quality assessment, followed by the alignment of the filtered reads to a reference genome. Typically the amount of reads that correctly maps to the specific reference genome ranges...

["Bioinformatics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.3230v1
18 downloads
189 views

Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports...

["Bioinformatics","Genomics","Mathematical Biology"]
doi:10.7287/peerj.preprints.3223v1
234 downloads
635 views

RNA sequencing (RNA-Seq) is a powerful technique for thegene-expression profiling of organisms that uses the capabilities of next-generation sequencing technologies.Developing gene-expression-based classification algorithms is an emerging powerful method for diagnosis,...

["Bioinformatics","Genomics","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.2761v2
320 downloads
231 views

Emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring...

["Conservation Biology","Ecology","Genetics","Genomics","Zoology"]
doi:10.7287/peerj.preprints.3209v1
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