Preprints (not yet peer-reviewed)

67 downloads
451 views

The Drosophila melanogaster white-eyed w1118 line serves as a blank control, allowing genetic recombination of any gene of interest along with a readily recognizable marker. w1118 flies display behavioral susceptibility to environmental stimulation such as light....

["Animal Behavior","Computational Biology"]
doi:10.7287/peerj.preprints.2908v3
243 downloads
658 views

The sharing and re-use of data has become a cornerstone of modern science. Multiple platforms now allow quick and easy data sharing. So far, however, data publishing models have not accommodated on-going scientific improvements in data: for many problems, datasets...

["Computational Biology","Ecology","Computational Science","Data Science"]
doi:10.7287/peerj.preprints.3401v1
15 downloads
85 views

While biochemistry evidently affects the growth rate of cells, many biochemists routinely ignore population variation, just like population geneticists usually ignore causal details of biochemistry that underpin a change in growth rate caused by a mutation. A true...

["Biochemistry","Cell Biology","Computational Biology","Oncology","Computational Science"]
doi:10.7287/peerj.preprints.3371v1
19 downloads
83 views

The analysis of large numbers of sequences requires the reduction of ambiguities during the analytical work to ensure that the effort will focus only on confirmed sequences. Performing this work automatically may help to minimize potential errors associated with...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.3364v1
20 downloads
147 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
26 downloads
140 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
21 downloads
138 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
18 downloads
131 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
187 downloads
541 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
32 downloads
193 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
22 downloads
166 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
27 downloads
107 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
40 downloads
186 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
229 downloads
510 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
45 downloads
114 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
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