Preprints (not yet peer-reviewed)

306 downloads
598 views

Robust multi-array average (RMA) is a highly successful method for processing raw data from Affymetrix expression microarrays. However, most of the work on microarray data processing predates the widespread use of Python in scientific computing. Here, I describe...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.1790v1
434 downloads
239 views

This study combines experimental and modeling approaches in order to investigate the temporal dynamics of the human brain at rest. The dynamics of the neuronal activity is modeled with FitzHugh-Nagumo oscillators and the blood-oxygen-level-dependent (BOLD) time...

["Computational Biology","Neuroscience","Computational Science"]
doi:10.7287/peerj.preprints.1784v1
99 downloads
314 views

The fight against the emergence of mutant influenza strains has led to the screening of an increasing number of compounds for inhibitory activity against influenza neuraminidase. This study explores the chemical space of neuraminidase inhibitors (NAIs), which provides...

["Bioinformatics","Computational Biology","Drugs and Devices","Computational Science"]
doi:10.7287/peerj.preprints.1554v2
1,343 downloads
436 views

The natural sciences, such as ecology and earth science, study complex interactions between biotic and abiotic systems in order to infer understanding and make predictions. Machine-learning-based methods have an advantage over traditional statistical methods in...

["Bioinformatics","Ecology","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.1720v1
220 downloads
465 views

Recent studies have shown that International medical graduates (IMG) comprise a substantial and increasingly larger share of the medical workforce, internationally. IMGs wishing to work in English-speaking countries face many challenges. And overcoming such challenges...

["Translational Medicine","Science and Medical Education","Computational Science"]
doi:10.7287/peerj.preprints.1711v2
215 downloads
396 views

Background. In recent years, artificial intelligence (AI) has become an important issue, in which, how to make computers understand the thinking of human being is one of critical topics. If computer could perceive and respond to person's non-verbal language such...

["Kinesiology","Psychiatry and Psychology","Computational Science"]
doi:10.7287/peerj.preprints.1650v1
418 downloads
410 views

The present contribution reports direct numerical simulations of pulsatile flow through a 75% eccentric stenosis using the Lattice Boltzmann Method (LBM). The stenosis was previously studied by Varghese, Frankel, and Fischer in a benchmark computation, and the...

["Computational Biology","Neurology","Computational Science"]
doi:10.7287/peerj.preprints.1548v3
161 downloads
570 views

Background. Fish species may be identified based on their unique otolith shape or contour. Several pattern recognition methods have been proposed to classify fish species through morphological features of the otolith contours. However, there has been no fully-automated...

["Aquaculture, Fisheries and Fish Science","Bioinformatics","Marine Biology","Taxonomy","Computational Science"]
doi:10.7287/peerj.preprints.1517v1
149 downloads
311 views

Background: Ketamine has been reported to have efficacy as an antidepressant in several studies of treatment-resistant depression. In this study, we investigate whether an acute administration of ketamine leads to reductions in the functional connectivity of subgenual...

["Neuroscience","Psychiatry and Psychology","Radiology and Medical Imaging","Computational Science"]
doi:10.7287/peerj.preprints.1436v1
151 downloads
665 views

Current research and development approaches to drug discovery have become less fruitful and more costly. One alternative paradigm is that of drug repositioning. Many marketed examples of repositioned drugs have been identified through serendipitous or rational...

["Bioinformatics","Computational Biology","Drugs and Devices","Pharmacology","Computational Science"]
doi:10.7287/peerj.preprints.1427v1
419 downloads
289 views

Software design and its engineering is essential for bioinformatics software impact. We propose a new approach ‘Butterfly’, for the betterment of modeling of scientific software solutions by targeting key developmental points: intuitive, graphical user interface...

["Bioinformatics","Human-Computer Interaction","Computational Science"]
doi:10.7287/peerj.preprints.1423v1
396 downloads
921 views

Cellular homeostasis involves transmembrane molecular transport mediated by membrane-spanning proteins. Such proteins either carry the molecules across the membrane, or facilitate their diffusion. A generic formulation that describes transmembrane fluxes, derived...

["Biophysics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.1312v6
652 downloads
630 views

Motivation: The third generation sequencing (3GS) technology generates long sequences of thousands of bases. However, its error rates are estimated in the range of 15-40%, much higher than the previous generation (approximately 1%). Fundamental tasks such as genome...

["Bioinformatics","Biotechnology","Computational Biology","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.1401v1
515 downloads
469 views

Smallholder farms dominate in many parts of the world, particularly Sub-Saharan Africa. These systems are characterized by small, heterogeneous, and often indistinct field patterns, requiring a specialized methodology to map agricultural land cover. Using a variety...

["Agricultural Science","Environmental Sciences","Human-Computer Interaction","Computational Science"]
doi:10.7287/peerj.preprints.1367v1
307 downloads
452 views

Computational modelling of cardiac cellular electrophysiology has a long history, with many models now available for different species, cell types, and experimental preparations. This success brings with it a challenge: how do we assess and compare the underlying...

["Biophysics","Computational Biology","Cardiology","Computational Science"]
doi:10.7287/peerj.preprints.1338v1
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