Preprints (not yet peer-reviewed)

77 downloads
234 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
35 downloads
63 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
47 downloads
143 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
132 downloads
349 views

A major goal of systems neuroscience is to understand how the brain represents information, and how those representations are used to drive behavior. Even though genetic model organisms like Drosophila grant unprecedented experimental access to the nervous system...

["Animal Behavior","Computational Biology","Neuroscience"]
doi:10.7287/peerj.preprints.2720v1
28 downloads
93 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
57 downloads
228 views

This document is my attempt at distilling some of the information in two papers published by Anthony Nicholls (J. Comput. Aided Mol. Des. 2014, 28, 887; ibid 2016, 30, 103). Anthony also very kindly provided some new equations, not found in the papers, in response...

["Biophysics","Computational Biology","Mathematical Biology","Computational Science"]
doi:10.7287/peerj.preprints.2693v1
93 downloads
398 views

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.2452v3
31 downloads
297 views

Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunities to...

["Computational Biology","Ecology","Mathematical Biology","Microbiology","Statistics"]
doi:10.7287/peerj.preprints.2685v1
68 downloads
124 views

Digital repositories bring direct impacts and influence to the research community and society but at the moment it is challenging to objectively measure their value. We distinguished the difference between impacts and influence and discussed measures and mentions...

["Bioinformatics","Computational Biology","Digital Libraries","World Wide Web and Web Science"]
doi:10.7287/peerj.preprints.2688v1
20 downloads
154 views

Type I restriction-modification enzymes are multisubunit, multifunctional molecular machines that recognize specific DNA target sequences, and their multisubunit organization underlies their multifunctionality. EcoR124I is the archetype of Type I restriction-modification...

["Biochemistry","Biophysics","Computational Biology","Molecular Biology"]
doi:10.7287/peerj.preprints.2680v1
6 downloads
83 views

The definition of the structural basis of the conformational preferences of the genetically encoded aminoacid residues is crucial to decipher the physical code of protein folding and would have a huge impact on our understanding of protein structure and function....

["Bioinformatics","Computational Biology","Databases"]
doi:10.7287/peerj.preprints.2665v1
23 downloads
80 views

Food components are object of many studies aimed to identify compounds responsible of positive effects in nutrition and food science. Compound categories include antioxidants, whose positive activity is commonly related to their activity in deactivating free radicals....

["Biochemistry","Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.2658v1
27 downloads
51 views

Evolutionary theory presents a number of conceptual hurdles for the undergraduate student. In addition, the extended timespan over which many evolutionary processes occur, coupled with the time constraints of the typical undergraduate laboratory, restricts the...

["Computational Biology","Science and Medical Education"]
doi:10.7287/peerj.preprints.2647v1
101 downloads
531 views

Shotgun metagenomics of microbial communities reveals information about strains of relevance for applications in medicine, biotechnology and ecology. Recovering their genomes is a crucial, but very challenging step, due to the complexity of the underlying biological...

["Bioinformatics","Computational Biology","Data Science"]
doi:10.7287/peerj.preprints.2626v3
28 downloads
97 views

Drug discovery is a step-by-step process very important in biopharmaceutical field. We are interested in identifying new investigational drug-likes as potential inhibitors of determinate biological-therapeutic targets, trying to decrease the side effects and to...

["Bioinformatics","Computational Biology","Drugs and Devices"]
doi:10.7287/peerj.preprints.2639v1
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