Preprints (not yet peer-reviewed)

4 downloads
30 views

Predicting disease status for a complex human disease using genomic data is an important, yet challenging, step in personalized medicine. Among many challenges, the so-called curse of dimensionality problem results in unsatisfied performances of many state-of-art...

["Bioinformatics","Computational Biology","Genomics","Data Mining and Machine Learning","Data Science"]
doi:10.7287/peerj.preprints.27123v1
615 downloads
725 views

Phylogenetic comparative methods (PCMs), especially ones based on linear models, have played a central role in understanding species’ trait evolution. These methods, however, usually assume that phylogenetic trees are known without error or uncertainty, but this...

["Computational Biology","Evolutionary Studies","Genetics","Taxonomy","Statistics"]
doi:10.7287/peerj.preprints.1216v2
103 downloads
322 views

The ability of vertebrates to generate rhythm within their spinal neural networks is essential for walking, running, and other rhythmic behaviors. The central pattern generator (CPG) network responsible for these behaviors is well-characterized with experimental...

["Animal Behavior","Bioinformatics","Computational Biology","Neuroscience","Computational Science"]
doi:10.7287/peerj.preprints.26734v2
338 downloads
654 views

The classical way of defining enzyme inhibition has obscured the distinction between inhibitory effect and the inhibitor binding constant. This article examines the relationship between the simple binding curve used to define biomolecular interactions and the standard...

["Biochemistry","Computational Biology","Mathematical Biology","Drugs and Devices","Pharmacology"]
doi:10.7287/peerj.preprints.3094v2
312 downloads
776 views

Computational models in biology encode molecular and cell biological processes. These models often can be represented as biochemical reaction networks. Studying such networks, one is mostly interested in systems that share similar reactions and mechanisms. Typical...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning","Data Science"]
doi:10.7287/peerj.preprints.1479v4
136 downloads
296 views

Analysing the relationships between biomolecules and the genetic diseases is a highly active area of research, where the aim is to identify the genes and their products that cause a particular disease due to functional changes originated from mutations. Biological...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.26663v2
593 downloads
1,079 views

Potential Natural Vegetation (PNV) is the vegetation cover in equilibrium with climate, that would exist at a given location non-impacted by human activities. PNV is useful for raising public awareness about land degradation and for estimating land potential. This...

["Biogeography","Computational Biology","Plant Science","Data Mining and Machine Learning","Spatial and Geographic Information Science"]
doi:10.7287/peerj.preprints.26811v2
19 downloads
89 views

Background. DNA methylation, an important epigenetic mark, is well known for its regulatory role in gene expression, especially the negative regulation in the promoter region. However, its correlation with gene expression at population level has not been well studied....

["Bioinformatics","Computational Biology","Genomics","Epidemiology","Statistics"]
doi:10.7287/peerj.preprints.27055v1
105 downloads
251 views

The rhizobium-legume symbiosis is a major source of fixed nitrogen (ammonia) in the biosphere. The potential for this process to increase agricultural yield while reducing the reliance on nitrogen-based fertilizers has generated interest in understanding and manipulating...

["Computational Biology","Genetics","Genomics","Microbiology","Synthetic Biology"]
doi:10.7287/peerj.preprints.27033v2
301 downloads
2,285 views

Because the shapes and forms of many coral reefs resemble karst (erosion landforms created by dissolution of limestone), it is widely believed that those reefs have grown on karst foundations, and that Holocene growth perpetuates the underlying topography. However,...

["Computational Biology","Marine Biology","Biosphere Interactions"]
doi:10.7287/peerj.preprints.963v2
80 downloads
201 views

A simulation based study on model fitting for sensory neurons from stimulus/response data is presented. The employed model is a continuous time recurrent neural network (CTRNN) which is a member of models with known universal approximation features. This feature...

["Computational Biology","Neuroscience"]
doi:10.7287/peerj.preprints.27015v1
1,185 downloads
3,212 views

This article proposes quantitative answers to meta-scientific questions including "how much knowledge is attained by a research field?","how rapidly is a field making progress?", "what is the expected reproducibility of a result?", "how much knowledge is lost from...

["Computational Biology","Ethical Issues","Science Policy","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.1968v4
140 downloads
306 views

Antibodies are proteins generated by the adaptive immune system to recognize and counteract a plethora of pathogens through specific binding. This adaptive binding is mediated by structural diversity in the six complementary determining region (CDR) loops (H1,...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.26996v1
622 downloads
1,251 views

Many pressing medical challenges - such as diagnosing disease, enhancing directed stem cell differentiation, and classifying cancers - have long been hindered by limitations in our ability to quantify proteins in single cells. Mass-spectrometry (MS) is poised to...

["Bioengineering","Biotechnology","Cell Biology","Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.26821v2
74 downloads
162 views

The study of how the observable features of organisms, i.e., their phenotypes, result from the complex interplay between genetics, development, and the environment, is central to much research in biology. The varied language used in the description of phenotypes,...

["Biodiversity","Computational Biology","Evolutionary Studies"]
doi:10.7287/peerj.preprints.26988v1
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