Preprints (not yet peer-reviewed)

78 downloads
372 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
27 downloads
272 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
50 downloads
111 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
17 downloads
145 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
4 downloads
79 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
16 downloads
73 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
25 downloads
48 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
97 downloads
505 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
24 downloads
88 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
8 downloads
72 views

Data mining is one of the main activities in bioinformatics, specifically to extract knowledge from massive data sets related with gene expression measurement, CNV, DNA strings, and others. A long array of methods are used to perform such task, ranging from the...

["Bioinformatics","Computational Biology","Algorithms and Analysis of Algorithms","Data Mining and Machine Learning","Optimization Theory and Computation"]
doi:10.7287/peerj.preprints.2635v1
94 downloads
143 views

Synthetic biology is often misunderstood as creation of artificial life or new biology using principles different from those of extant organisms around us. But, fundamentally, the field is about engineering biology in a more efficient and effective way, and endowing...

["Biochemistry","Bioengineering","Biotechnology","Computational Biology","Molecular Biology"]
doi:10.7287/peerj.preprints.2634v1
34 downloads
150 views

There are a lot of algorithms and programs for reconstruction of phylogeny of a set of proteins basing on multiple sequence alignment. Many programs allow users to choose a number of parameters, for example, a model for maximum likelihood programs. Different programs...

["Bioinformatics","Computational Biology","Evolutionary Studies"]
doi:10.7287/peerj.preprints.2628v1
191 downloads
432 views

Metastatic cutaneous melanoma is an aggressive skin cancer with some progression-slowing treatments but no known cure. The omics data explosion has created many possible drug candidates, however filtering criteria remain challenging, and systems biology approaches...

["Bioinformatics","Computational Biology","Data Science","World Wide Web and Web Science"]
doi:10.7287/peerj.preprints.2007v2
148 downloads
473 views

Rapid yet accurate pKa prediction for drug-like molecules is a key challenge in computational chemistry. This study uses PM6-DH+/COSMO, PM6/COSMO, PM7/COSMO, PM3/COSMO, AM1/COSMO, PM3/SMD, AM1/SMD, and DFTB3/SMD to predict the pKa values of 53 amine groups in 48...

["Biophysics","Computational Biology"]
doi:10.7287/peerj.preprints.2564v2
49 downloads
138 views

Non-systematically collected, a.k.a. opportunistic, species observations are accumulating at a high rate in biodiversity databases. Occupancy models have arisen as the main tool to reduce effects of limited knowledge about effort in analyses of opportunistic data....

["Computational Biology","Conservation Biology","Ecology"]
doi:10.7287/peerj.preprints.2612v1
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