Preprints (not yet peer-reviewed)

18 downloads
71 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
64 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
86 downloads
135 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
29 downloads
134 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
182 downloads
421 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
27 downloads
75 views

Emerging viruses cause a lot of fatalities as they jump to humans from other species. Here we develop a novel technique to computationally estimate an important parameter of within-host viral infection: the lifespan of infected cells. Our approach is general and...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.2621v1
142 downloads
445 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
48 downloads
126 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
48 downloads
164 views

Worldwide concern about the impacts of endocrine disrupting compounds on both human and environmental health has led to implementation of multiple screening and testing programs. In most cases these programs have focused on impacts to the estrogen, androgen and...

["Computational Biology","Toxicology","Science Policy"]
doi:10.7287/peerj.preprints.2605v1
48 downloads
267 views

Simulating development of fish stocks may be as complex as calculation of the development of the atmosphere, which is treated in meteorology as an initial value problem in physics. This approach was first proposed by Abbe and Bjerknes in the beginning of the 20...

["Aquaculture, Fisheries and Fish Science","Computational Biology","Mathematical Biology"]
doi:10.7287/peerj.preprints.2604v1
293 downloads
792 views

The dynamics of ecological communities can be described by two contrasting models: the first assumes that individuals of all species are identical and do not have interactions. The second assumes that species are different, adapted to particular habitat conditions,...

["Biodiversity","Computational Biology","Ecology","Mathematical Biology"]
doi:10.7287/peerj.preprints.1589v3
31 downloads
196 views

Sparse coding is an effective operating principle for the brain, one that can guide the discovery of features and support the learning of assocations. Here we show how spiking neurons with discrete dendrites can learn sparse codes via an online, nonlinear Hebbian...

["Computational Biology","Adaptive and Self-Organizing Systems","Artificial Intelligence","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.2595v1
9 downloads
110 views

Identification of DNA markers associated with mealiness trait is an important tool to agricultural industry. Many peach breeding initiatives have as aim to improve early selection of varieties with better postharvest performance. We present a family-based approach...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.2565v1
166 downloads
442 views

For this initial work, we shall focus on introducing a biological model for utilization [mainly] as a descriptive framework on which future analyses will be based. The model includes a definition of a biological system as a composite of properties that occupy defined...

["Bioengineering","Computational Biology","Mathematical Biology"]
doi:10.7287/peerj.preprints.1148v4
33 downloads
172 views

Benign prostatic hyperplasia is a common disease in men aged over 50 years old, with an incidence increasing to more than 80% over the age of 70, that is increasingly going to attract pharmaceutical interest. Within conventional therapies, such as α-adrenoreceptor...

["Computational Biology","Pharmacology"]
doi:10.7287/peerj.preprints.2543v1
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