Preprints (not yet peer-reviewed)

35 downloads
313 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
27 downloads
111 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
51 downloads
227 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
346 downloads
692 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
26 downloads
172 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
46 downloads
179 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
37 downloads
851 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
67 downloads
374 views

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide potential defenses against invading pathogens. However, we have little to no understanding of the external bacterial microbiome on bats,...

["Biogeography","Bioinformatics","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.2493v1
273 downloads
1,354 views

The high cost of library preparation remains a major obstacle to sequencing large numbers of individual genomes. Illumina’s proprietary tagmentation technology allows for rapid and easy preparation of sequencing libraries, but remains prohibitively expensive for...

["Bioinformatics","Genomics","Molecular Biology"]
doi:10.7287/peerj.preprints.2475v1
260 downloads
507 views

To microbiologists, the term macroecology may conjure iconic images of wildebeests grazing in African savannahs or hummingbirds pollinating flowers in a tropical rain forest. Contrary to what the name implies, macroecology is not the ecological study of macroscopic...

["Biodiversity","Biogeography","Bioinformatics","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.2478v1
112 downloads
297 views

Biomineralization is the process by which living organisms construct hard skeletons creating complex structures that range from specialized tissues such as bone or teeth to ecosystems such as coral reefs. Biominerals are composed of both inorganic minerals and...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics"]
doi:10.7287/peerj.preprints.1983v2
72 downloads
255 views

Sharing and reusing data in research is a welcome and encouraged practice since it maximises the scientific outcomes given limited financial, material and human resources. Interdisciplinary research is considered to benefit from this practice, uniting researchers...

["Bioinformatics","Computational Biology","Data Science","Spatial and Geographic Information Systems"]
doi:10.7287/peerj.preprints.2248v3
66 downloads
351 views

Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms...

["Bioinformatics","Environmental Sciences","Genomics","Microbiology","Soil Science"]
doi:10.7287/peerj.preprints.2473v1
127 downloads
350 views

Unique Molecular Identifiers (UMIs) have been incorporated into RNA-Seq experiments to overcome issues with abundance estimation from samples that may have many PCR amplification cycles. However, the use of UMIs in many different types of sequencing experiments...

["Bioinformatics","Genetics","Genomics"]
doi:10.7287/peerj.preprints.2465v1
97 downloads
312 views

Forest trees cover just over 30% of the earth's surface and are studied by researchers around the world for both their conservation and economic value. With the onset of high throughput technologies, tremendous phenotypic and genomic data sets have been generated...

["Bioinformatics","Data Mining and Machine Learning","Databases"]
doi:10.7287/peerj.preprints.2345v4
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