Preprints (not yet peer-reviewed)

10 downloads
147 views

Shotgun metagenomics of microbial communities reveals information about strains of relevance for applications in medicine, biotechnology and ecology. Recovering their genomes is a crucial, but very challenging step, due to the complexity of the underlying biological...

["Bioinformatics","Computational Biology","Data Science"]
doi:10.7287/peerj.preprints.2626v2
7 downloads
56 views

There are a lot of algorithms and programs for reconstruction of phylogeny of a set of proteins basing on multiple sequence alignment. Many programs allow users to choose a number of parameters, for example, a model for maximum likelihood programs. Different programs...

["Bioinformatics","Computational Biology","Evolutionary Studies"]
doi:10.7287/peerj.preprints.2628v1
128 downloads
302 views

Metastatic cutaneous melanoma is an aggressive skin cancer with some progression-slowing treatments but no known cure. The omics data explosion has created many possible drug candidates, however filtering criteria remain challenging, and systems biology approaches...

["Bioinformatics","Computational Biology","Data Science","World Wide Web and Web Science"]
doi:10.7287/peerj.preprints.2007v2
6 downloads
45 views

Emerging viruses cause a lot of fatalities as they jump to humans from other species. Here we develop a novel technique to computationally estimate an important parameter of within-host viral infection: the lifespan of infected cells. Our approach is general and...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.2621v1
10 downloads
74 views

Acidithiobacillus ferrooxidans ( A. ferrooxidans ) is a gram-negative, extremely acidophilic, mesophilic, chemolithotrophic bacterium and the most well-studied acidophilic organism which is usually found in acid environments such as acid mine drainage. The draft...

["Bioinformatics","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2620v1
25 downloads
272 views

To answer many of the major questions in comparative botany, ecology, and global change biology it is necessary to extrapolate across enormous geographic, temporal and taxonomic scales. Yet much ecological knowledge is still based on observations conducted within...

["Biodiversity","Biogeography","Bioinformatics","Ecology","Computational Science"]
doi:10.7287/peerj.preprints.2615v2
83 downloads
289 views

The global deep subsurface biosphere is thought to be one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to...

["Bioinformatics","Environmental Sciences","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2613v1
9 downloads
78 views

The need of an approach for the definition of a platform-independent medical digital library, using only open-source tools, will be described. To test the need and the success of such an approach, a library will be created, which can later be used in a larger scale...

["Bioinformatics","Computer Vision","Digital Libraries","Software Engineering"]
doi:10.7287/peerj.preprints.2599v1
80 downloads
318 views

Mutation processes differ between types of point mutation, genomic locations, cells, and biological species. For some point mutations, specific neighbouring bases are known to be mechanistically influential. Beyond these cases, numerous questions remain unresolved...

["Bioinformatics","Evolutionary Studies","Genetics","Medical Genetics"]
doi:10.7287/peerj.preprints.2236v3
19 downloads
85 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
34 downloads
124 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
49 downloads
464 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
430 downloads
313 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
7 downloads
54 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
97 downloads
79 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
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