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genomics

Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacle Chelonibia testudinaria (Linnaeus,...

["Ecology","Evolutionary Studies","Genomics","Molecular Biology","Zoology"]
doi:10.7287/peerj.preprints.1715v1
12 downloads
98 views

Next generation sequencing (NGS) technology is a widely accepted tool used by microbial ecologists to explore complex microbial communities in different ecosystems. As new NGS platforms continue to become available, it becomes imperative to compare data obtained...

["Bioinformatics","Genomics","Microbiology","Taxonomy","Statistics"]
doi:10.7717/peerj.1599
8 downloads
55 views

Phalaenopsis orchid is an important potted flower with high economic value around the world. We report the 3.1 Gb draft genome assembly of an important winter flowering Phalaenopsis ‘KHM190’ cultivar. We generated 89.5 Gb RNA-seq and 113 million sRNA-seq reads...

["Genomics","Plant Science"]
doi:10.7287/peerj.preprints.1707v1
257 downloads
2,332 views

An ever expanding body of research investigates the human microbiome in general and the skin microbiome in particular. Microbiomes vary greatly from individual to individual. Understanding the factors that account for this variation, however, has proven challenging,...

["Ecology","Evolutionary Studies","Genomics","Microbiology","Dermatology"]
doi:10.7717/peerj.1605
253 downloads
740 views

High throughput sequencing has changed many aspects of population genetics, molecular ecology, and related fields, affecting both experimental design and data analysis. The software package ANGSD allows users to perform a number of population genetic analyses on...

["Bioinformatics","Evolutionary Studies","Genetics","Genomics"]
doi:10.7287/peerj.preprints.1472v2
88 downloads
441 views

High-throughput sequencing provides a fast and cost effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target organisms requires advanced bioinformatics...

["Bioinformatics","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.1695v1
59 downloads
388 views

The amount of data used in phylogenetics has grown explosively in the recent years and many phylogenies are inferred with hundreds or even thousands of loci and many taxa. These modern phylogenomic studies often entail separate analyses of each of the loci in addition...

["Computational Biology","Genomics","Statistics"]
doi:10.7717/peerj.1660
76 downloads
536 views

Five closely related populations of bacteria from the Candidate Phylum (CP) Peregrinibacteria, part of the bacterial Candidate Phyla Radiation (CPR), were sampled from filtered groundwater obtained from an aquifer adjacent to the Colorado River near the town of...

["Bioinformatics","Environmental sciences","Genomics","Microbiology"]
doi:10.7717/peerj.1607
82 downloads
382 views

Genetic analyses can identify the scale at which wildlife species are impacted by human activities, and provide demographic information useful for management. Here, we use thousands of nuclear DNA genetic loci to assess whether genetic structure occurs within Lasiurus...

["Conservation biology","Ecology","Genetics","Genomics"]
doi:10.7717/peerj.1647
57 downloads
113 views

Sentieon DNAseq Software is a suite of tools for running DNA sequencing secondary analyses. The Sentieon DNAseq Software produces identical results to the Genome Analysis Toolkit (GATK) Best Practice Workflow using HaplotypeCaller, with more than a 20-fold increase...

["Bioinformatics","Genomics"]
doi:10.7287/peerj.preprints.1672v2
19 downloads
58 views

Geosmithia morbida is a filamentous ascomycete that causes Thousand Cankers Disease in the eastern black walnut tree. This pathogen is commonly found in the western U.S.; however, recently the disease was also detected in several eastern states where the black...

["Genomics","Mycology"]
doi:10.7287/peerj.preprints.1671v1
110 downloads
1,062 views

Large, publicly available gene expression datasets are often analyzed with the aid of machine learning algorithms. Although RNA-seq is increasingly the technology of choice, a wealth of expression data already exist in the form of microarray data. If machine learning...

["Bioinformatics","Computational biology","Genomics"]
doi:10.7717/peerj.1621
54 downloads
270 views

The Zingiberales are an iconic order of monocotyledonous plants comprising eight families with distinctive and diverse floral morphologies and representing an important ecological element of tropical and subtropical forests. While the eight families are demonstrated...

["Evolutionary studies","Genomics","Plant science","Taxonomy"]
doi:10.7717/peerj.1584
102 downloads
664 views

Baltic Sea deep water and sediments hold one of the largest anthropogenically induced hypoxic areas in the world. High nutrient input and low water exchange result in eutrophication and oxygen depletion below the halocline. As a consequence at Landsort Deep, the...

["Ecology","Genomics","Marine Biology","Microbiology"]
doi:10.7717/peerj.1593
58 downloads
299 views

The red flour beetle, Tribolium castaneum, is a major agricultural pest responsible for considerable loss of stored grain and cereal products worldwide. T. castaneum larvae have a highly compartmentalized gut, with cysteine peptidases mostly in the acidic anterior...

["Agricultural Science","Genomics"]
doi:10.7717/peerj.1581

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