Preprints (not yet peer-reviewed)

61 downloads
218 views

Cellular heterogeneity is important to biological processes, including cancer and development. However, proteome heterogeneity is largely unexplored because of the limitations of existing methods for quantifying protein levels in single cells. To alleviate these...

["Biochemistry","Cell Biology","Computational Biology","Developmental Biology","Molecular Biology"]
doi:10.7287/peerj.preprints.2767v1
45 downloads
420 views

Background. Opsin proteins are seven transmembrane receptor proteins which detect light. Opsins can be classified into two types and share little sequence identity: type 1, typically found in bacteria, and type 2, primarily characterized in metazoa. The type 2...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics","Mycology"]
doi:10.7287/peerj.preprints.2397v2
47 downloads
204 views

The scientific literature contains an historic record of the changing ways in which we describe the world. Shifts in understanding of scientific concepts are reflected in the introduction of new terms and the changing usage and context of existing ones. We conducted...

["Biodiversity","Bioinformatics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.2747v1
89 downloads
251 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
53 downloads
79 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
165 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
146 downloads
390 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
33 downloads
116 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
67 downloads
244 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
101 downloads
483 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
33 downloads
326 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
21 downloads
171 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
94 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
24 downloads
91 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
29 downloads
63 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
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