Preprints (not yet peer-reviewed)

17 downloads
89 views

The immune system protects a host from foreign pathogens. In rare cases, the immune system can attack the cells of the host organism causing autoimmune diseases. We outline a computational framework that combines bioinformatics and network analysis with an emerging...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3217v3
17 downloads
106 views

Network diffusion approaches are frequently used for identifying the relevant disease genes and for prioritizing the genes for drug sensitivity predictions. Majority of these studies rely on networks representing a single type of information. However, using multiplex...

["Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.3339v1
6 downloads
31 views

Personalized medicine is in great part enabled by the progress in data acquisition technologies for modern biology, such as next-generation sequencing (NGS). Conventional NGS processing workflows are composed by independent tools implementing shared-memory parallelism...

["Bioinformatics","Computational Biology","Distributed and Parallel Computing"]
doi:10.7287/peerj.preprints.3338v1
10 downloads
101 views

MicroRNAs (miRNAs) are small non-coding RNA molecules mediating the translational repression and degradation of target mRNAs in the cell. Mature miRNAs are used as a template by the RNA-induced silencing complex (RISC) to recognize the complementary mRNAs to be...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.3337v1
174 downloads
445 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.1479v3
14 downloads
151 views

As the costs of high-throughput measurement technologies continue to fall, experimental approaches in biomedicine are increasingly data intensive and the advent of big data is justifiably seen as holding the promise to transform medicine. However, as data volumes...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.3328v1
13 downloads
126 views

Systems Biology is a holistic approach, based on the integration of multiscale models and different kinds of data, aimed at studying the underlying mechanisms of complex biological systems. A GEnome-scale metabolic Model (GEM) is the representation of the metabolic...

["Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.3323v1
20 downloads
74 views

Celiac disease is a chronic condition, which can be described as inflammatory and autoimmune. The well-known treatment is a lifelong gluten-free diet, but it can be not totally effective for a high percentage of the patients. The aim of this work is to approach...

["Bioinformatics","Biotechnology","Computational Biology","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.3315v1
32 downloads
154 views

Network Diffusion has been proposed in several applications, thanks to its ability of amplifying biological signals and prioritizing genes that may be associated with a disease. Not surprising, the success of Network Diffusion on a “single layer” led to the first...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.3310v1
216 downloads
425 views

Landscape genetics combines population genetics, landscape ecology, and spatial analysis to identify landscape and genetic factors that influence genetic and genomic variation. Progress in the field depends on a strong conceptual foundation and the means of identifying...

["Computational Biology","Scientific Computing and Simulation","Spatial and Geographic Information Systems"]
doi:10.7287/peerj.preprints.2225v5
31 downloads
91 views

Coarse-grained simulations enable the study of membrane proteins in the context of their native environment but require reliable parameters. The CgProt force field is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to...

["Biophysics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.3306v1
43 downloads
91 views

Bertalanffy proposed the differential equation m´(t) = p × m (t) a –q × m (t) for the description of the mass growth of animals as a function m(t) of time t. He suggested that the solution using the metabolic scaling exponent a = 2/3 (von Bertalanffy growth function...

["Agricultural Science","Aquaculture, Fisheries and Fish Science","Computational Biology","Mathematical Biology"]
doi:10.7287/peerj.preprints.3303v1
26 downloads
58 views

We present GenotypeAnalytics (GA), a RESTFul service that makes it possible to mine association rules from Single Nucleotide Polymorphism (SNP) datasets using standard web browsers. GA can speed up and simplify the analysis of this massive amount of data, highlighting...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning","Data Science","World Wide Web and Web Science"]
doi:10.7287/peerj.preprints.3299v1
41 downloads
179 views

It is now becoming feasible to determine the composition of an individual gut microbiota (gut microflora), as well as the individual genome. In addition, whole genome scale metabolic models (GEMs) exist for a range of bacteria, and also for human. In principle...

["Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.3267v2
22 downloads
93 views

The immune system is a distributed decentralized system that functions without any centralized control. The immune system has millions of cells that function somewhat independently and can detect and respond to pathogens with considerable speed and efficiency....

["Computational Biology","Adaptive and Self-Organizing Systems","Agents and Multi-Agent Systems","Autonomous Systems"]
doi:10.7287/peerj.preprints.3150v2
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