Preprints (not yet peer-reviewed)

16 downloads
45 views

Effective approaches for assessing mitochondrial DNA (mtDNA) variation are important to multiple scientific disciplines. Mitochondrial haplogroups characterize branch points in the phylogeny of mtDNA. Several tools exist for mitochondrial haplogroup classification....

["Genetics","Genomics"]
doi:10.7287/peerj.preprints.3420v1
37 downloads
134 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
34 downloads
89 views

Brucellosis is a commonly diagnosed zoonosis that causes infertility and abortion in cattle, it is acquired from handling of infected animals or consuming contaminated milk or milk products. In Colombia, it is classified as prevention and control disease, despite...

["Agricultural Science","Genomics"]
doi:10.7287/peerj.preprints.3416v1
49 downloads
176 views

Although recent advances in molecular methods have facilitated understanding the evolution of fungal symbiosis, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae...

["Biodiversity","Ecology","Genomics","Microbiology","Mycology"]
doi:10.7287/peerj.preprints.3408v1
31 downloads
252 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
47 downloads
136 views

Similar to natural rivers, manmade inlets connect inland runoff to the ocean. Port Everglades Inlet (PEI) is a busy cargo and cruise ship port in South Florida, which can act as a source of pollution and nutrients to surrounding beaches and offshore coral reefs....

["Environmental Sciences","Genomics","Marine Biology","Microbiology"]
doi:10.7287/peerj.preprints.3369v1
45 downloads
97 views

The herbal medicinal genus Aconitum L., belonging to the Ranunculaceae family, represents the earliest diverging lineage within the eudicots. It currently comprises of two subgenera, A. subgenus Lycoctonum and A. subg. Aconitum. The complete chloroplast (cp) genome...

["Biodiversity","Evolutionary Studies","Genomics","Plant Science"]
doi:10.7287/peerj.preprints.3360v1
29 downloads
192 views

Venom has been associated with the ecological success of many groups of organisms, most notably reptiles, gastropods, and arachnids. In some cases, diversification has been directly linked to tailoring of venoms for dietary specialization. Spiders in particular...

["Biodiversity","Entomology","Genomics"]
doi:10.7287/peerj.preprints.3358v1
31 downloads
293 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
18 downloads
131 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
23 downloads
167 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
73 downloads
312 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
40 downloads
186 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
75 downloads
334 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
28 downloads
127 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
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