Preprints (not yet peer-reviewed)

30 downloads
186 views

Identifying the pathways that control a cellular phenotype is the first step to building a mechanistic model. Recent examples in developmental biology, cancer genomics, and neurological disease have demonstrated how changes in the variability of gene expression...

["Bioinformatics","Cell Biology","Statistics"]
doi:10.7287/peerj.preprints.2585v1
43 downloads
172 views

The lessons learned during six years of experience in design, development, and operation of four Science Gateway (SG) generations motivated us to develop yet another generation of platforms coined “Rosemary”. At the core of Rosemary the three fundamental SG functions,...

["Bioinformatics","Digital Libraries","Distributed and Parallel Computing"]
doi:10.7287/peerj.preprints.2576v1
146 downloads
1,498 views

OncoRank adopts a method for finding recurrent miRNA-target interactions to find genes with consistent relationships to patient survival across cancers. Genes are first ranked in each cancer by their Cox coefficients, and these ranks are then combined by applying...

["Bioinformatics","Genomics","Oncology"]
doi:10.7287/peerj.preprints.2574v1
446 downloads
396 views

“Open access” has become a central theme of journal reform in academic publishing. In this article, I examine the consequences of an important technological loophole in which publishers can claim to be adhering to the principles of open access by releasing articles...

["Bioinformatics","Evidence Based Medicine","Health Policy","Translational Medicine","Science Policy"]
doi:10.7287/peerj.preprints.2566v1
10 downloads
128 views

Identification of DNA markers associated with mealiness trait is an important tool to agricultural industry. Many peach breeding initiatives have as aim to improve early selection of varieties with better postharvest performance. We present a family-based approach...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.2565v1
121 downloads
134 views

We report the development and characterization of 13 novel microsatellite loci for the Caribbean queen conch, Lobatus gigas, an ecologically and commercially important marine gastropod. Paired-end sequencing was carried out on genomic DNA from a single queen conch...

["Bioengineering","Bioinformatics","Conservation Biology","Genetics","Genomics"]
doi:10.7287/peerj.preprints.2559v1
1,530 downloads
730 views

The diversity of complex microbial communities can be rapidly assessed by high-throughput DNA sequencing of marker gene (e.g., 16S) PCR amplicon pools, often yielding many thousands of DNA sequences per sample. However, analysis of such community amplicon sequencing...

["Biodiversity","Bioinformatics","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.2196v3
34 downloads
127 views

Walking velocity is an important control variable in gait disorders due to sensory or cerebellar disfunction. Non-preferred walking speeds are closely linked to a higher risk of falls. A compensation strategy of patients to avoid these speed sectors can be assumed....

["Bioinformatics","Anatomy and Physiology","Neurology"]
doi:10.7287/peerj.preprints.2545v1
39 downloads
338 views

We present a new supertree method that enables rapid estimation of a summary tree on the scale of millions of leaves. This supertree method summarizes a collection of input phylogenies and an input taxonomy. We introduce formal goals and criteria for such a supertree...

["Bioinformatics","Computational Biology","Evolutionary Studies","Taxonomy"]
doi:10.7287/peerj.preprints.2538v1
30 downloads
121 views

Practical experiences are reported about implementing a workflow for the prediction of mass spectra. QCEIMS is used to simulate the fragmentation trajectories consequently leading to predicted mass spectra for small molecules, such as metabolites. The individual...

["Bioinformatics","Scientific Computing and Simulation"]
doi:10.7287/peerj.preprints.2528v1
56 downloads
237 views

Binary matrix with a priori defined plesiomorphic character‐state may be re-­written as a simple set of branching diagrams (as a “Hennigian forest”). The last might be analyzed by the average consensus method. This procedure eventually avoids the taxon-­‐character...

["Bioinformatics","Computational Biology","Taxonomy"]
doi:10.7287/peerj.preprints.2487v4
362 downloads
709 views

Geographical Information Systems (GIS) are considered to be applications-led technology. Consequently, geographic information scientists commonly find themselves as guest in host disciplines in order to best exploit spatial analysis tools and methods, appropriately...

["Bioinformatics","Computational Biology","Spatial and Geographic Information Systems"]
doi:10.7287/peerj.preprints.1721v3
31 downloads
180 views

The Simulation Experiment Description Markup Language (SED-ML) is a standardized format for exchanging simulation studies independently of software tools. We present the SED-ML Web Tools, a software that supports SED-ML Level 1 Version 2, including complex modifications...

["Bioinformatics","Computational Biology","Mathematical Biology","Molecular Biology","Computational Science"]
doi:10.7287/peerj.preprints.2515v1
55 downloads
219 views

We report the genome sequence of Exiguobacterium pavilionensis str. N139, isolated from a high-altitude Andean lake. The 2,952,588-bp genome contains one chromosome and three megaplasmids. The genome analysis suggests the presence of enzymes that confer E. pavilionensis...

["Biochemistry","Biodiversity","Bioinformatics","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2512v1
43 downloads
886 views

The 1st Argentine Symposium of Young Bioinformatics Researchers took place on 9-10 May 2016 at Universidad de Buenos Aires, Buenos Aires, Argentina. This event evolved from a previous meeting series known as Argentine Student Council Symposium that have been successfully...

["Bioinformatics","Computational Biology","Science and Medical Education"]
doi:10.7287/peerj.preprints.2494v1
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