Preprints (not yet peer-reviewed)

589 downloads
658 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
97 downloads
311 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
331 downloads
642 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
309 downloads
770 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
133 downloads
294 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
570 downloads
1,059 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
18 downloads
88 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
249 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
300 downloads
2,283 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
76 downloads
197 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
1,174 downloads
3,202 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
135 downloads
301 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
616 downloads
1,236 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
70 downloads
157 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
101 downloads
199 views

Cervical cancer is the fourth most common cancer in women worldwide with human papillomavirus (HPV) being the main cause of disease. Chromosomal amplifications have been identified as a source of upregulation of cervical cancer driver genes but cannot fully explain...

["Computational Biology","Microbiology","Oncology"]
doi:10.7287/peerj.preprints.26957v1
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