5 downloads
65 views

Site-specific evolutionary rates can be estimated from codon sequences or from amino-acid sequences. For codon sequences, the most popular methods use some variation of the dN/dS ratio. For amino-acid sequences, one widely-used method is called Rate4Site, and it...

["Bioinformatics","Computational Biology","Evolutionary Studies","Statistics"]
doi:10.7287/peerj.preprints.2739v1
15 downloads
121 views

Single-cell RNA-Sequencing (scRNA-Seq) is a fast-evolving technology that enables the understanding of biological processes at an unprecedentedly high resolution. However, well-suited bioinformatics tools to analyze the data generated from this new technology are...

["Bioinformatics","Genomics"]
doi:10.7717/peerj.2888
36 downloads
370 views

Autophagy serves as a turnover mechanism for the recycling of redundant and/or damaged macromolecules present in eukaryotic cells to re-use them under starvation conditions via a double-membrane structure known as autophagosome. A set of eukaryotic genes called...

["Bioinformatics","Cell Biology","Computational Biology"]
doi:10.7717/peerj.2878
471 downloads
1,643 views

A central challenge in the present era of biodiversity loss is to assess and manage human impacts on freshwater ecosystems. Macroinvertebrates are an ideal group for Environmental Impacts Assessment (EIA). However, generating accurate macroinvertebrate inventories...

["Biodiversity","Bioinformatics","Ecology","Genetics","Molecular Biology"]
doi:10.7287/peerj.preprints.2044v4
5 downloads
8 views

Drug discovery process plays an important role in identifying new investigational drug-likes and developing new potential inhibitors related to a determinate target, in biopharmaceutical field [1]. An alternative promising and efficient used to identify new active...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.2721v1
12 downloads
51 views

The appropriate timing of flowering is crucial for the reproductive success of plants. Hence, intricate genetic networks integrate various environmental and endogenous cues such as temperature or hormonal statues. These signals integrate into a network of floral...

["Bioinformatics","Computational Biology","Developmental Biology","Plant Science"]
doi:10.7287/peerj.preprints.2724v1
2 downloads
55 views

Structure informs function, and this may be the evolutionary reason why alternative splicing, which is capable of generating different variants of the same protein, arise. But, given the energetic cost of generating different splice variants for testing their capability...

["Biochemistry","Bioinformatics","Genomics","Molecular Biology","Anatomy and Physiology"]
doi:10.7287/peerj.preprints.2717v1
118 downloads
687 views

Recently, there has been a move encouraged by many stakeholders towards generating big, open data in many areas of research. One area where big, open data is particularly valuable is in research relating to complex heterogeneous disorders such as Autism Spectrum...

["Bioinformatics","Neuroscience","Psychiatry and Psychology"]
doi:10.7717/peerj.2880
147 downloads
529 views

The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. The expanding crowd of scientists and...

["Bioinformatics","Ecology","Microbiology"]
doi:10.7717/peerj.2836
49 downloads
240 views

Biomaterial scaffolds have the potential to enhance neuronal development and regeneration. Understanding the genetic responses of astrocytes and neurons to biomaterials could facilitate the development of synthetic environments that enable the specification of...

["Bioengineering","Bioinformatics","Cell Biology","Genomics","Neuroscience"]
doi:10.7717/peerj.2829
8 downloads
152 views

Background In the era of semantic web, life science ontologies play an important role in tasks such as annotating biological objects, linking relevant data pieces, and verifying data consistency. Understanding ontology structures and overlapping ontologies is essential...

["Bioinformatics","Computational Science"]
doi:10.7287/peerj.preprints.2715v1
3 downloads
25 views

We developed a web-based cloud-hosted system that allow users to archive, listen, visualize, and annotate recordings. The system also provides tools to convert these annotations into datasets that can be used to train a computer to detect the presence or absence...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.2713v1
23 downloads
271 views

Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we...

["Bioinformatics","Computational Biology","Ecology","Genomics","Microbiology"]
doi:10.7717/peerj.2844
55 downloads
358 views

Background Chrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in detail at the molecular level, and no genomic and only little...

["Biodiversity","Bioinformatics","Ecology","Evolutionary Studies","Genomics"]
doi:10.7717/peerj.2832
97 downloads
539 views

Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents...

["Bioinformatics","Taxonomy","Computational Science"]
doi:10.7287/peerj.preprints.1982v2

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