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genomics

Across indepedent cancer genomes it has been observed that some sites have been recurrently hit by single nucleotide variants (SNVs). Such recurrently hit sites might be either i) drivers of cancer that are postively selected during oncogenesis, ii) due to mutation...

["Bioinformatics","Computational Biology","Genetics","Genomics"]
doi:10.7287/peerj.preprints.2089v1
20 downloads
265 views

Genome-wide association studies (GWAS) have uncovered thousands of associations between genetic variants and diseases. Using the same datasets, prediction of disease risk can be attempted. Phase information is an important biological structure that has seldom been...

["Bioinformatics","Computational Biology","Genomics","Epidemiology","Statistics"]
doi:10.7287/peerj.preprints.2074v1
4 downloads
57 views

Environmental stresses select for suitably adapted genes. These stresses will promote the propagation of certain mutations, and the loss of others, throughout the evolution of a species. For organisms living two thousand meters below the ocean’s surface, one of...

["Genetics","Genomics","Marine Biology","Microbiology","Molecular Biology"]
doi:10.7287/peerj.preprints.2071v1
26 downloads
847 views

Background. Massively parallel sequencing technology is being used to sequence highly diverse populations of DNA such as that derived from heterogeneous cell mixtures containing both wild-type and disease-related states. At the core of such molecule tagging techniques...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.2074
51 downloads
190 views

Mauremys reevesii (Geoemydidae) is one of the most common and widespread semi-aquatic turtles in East Asia. The unusually long lifespan of some individuals makes this turtle species a potentially useful model organism for studying the molecular basis of longevity....

["Genetics","Genomics","Zoology"]
doi:10.7717/peerj.2062
59 downloads
277 views

The majority of bacterial genome annotations are currently automated and based on a ‘gene by gene’ approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here...

["Bioinformatics","Genomics","Microbiology"]
doi:10.7717/peerj.2056
38 downloads
194 views

Background. Xylella fastidiosa, the causative agent of various plant diseases including Pierce’s disease in the US, and Citrus Variegated Chlorosis in Brazil, remains a continual source of concern and economic losses, especially since almost all commercial varieties...

["Biochemistry","Bioinformatics","Genomics","Plant Science"]
doi:10.7717/peerj.2007
9 downloads
75 views

Aeromonas salmonicida subsp. salmonicida, the causative agent of furunculosis in salmonids, is an issue especially because many isolates of this bacterium display antibiotic resistances, which limit treatments against the disease. Recent results suggested the possible...

["Aquaculture, Fisheries and Fish Science","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2067v1
36 downloads
214 views

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:10.7717/peerj.2019
58 downloads
273 views

Physcion and chrysophanol induce defense responses against powdery mildew in cucumbers. The combination of these two compounds has synergistic interaction against the disease. We performed RNA-seq on cucumber leaf samples treated with physcion and chrysophanol...

["Agricultural Science","Bioinformatics","Genetics","Genomics","Plant Science"]
doi:10.7717/peerj.1991
81 downloads
404 views

Background. Chromosome conformation capture, coupled with high throughput DNA sequencing in protocols like Hi-C and 3C-seq, has been proposed as viable means to generate data to resolve the genomes of microorganisms living in naturally occuring environments. Metagenomic...

["Bioinformatics","Computational Biology","Genomics","Microbiology","Computational Science"]
doi:10.7287/peerj.preprints.1974v2
440 downloads
717 views

The Phalaenopsis orchid is an important potted flower of 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:10.7717/peerj.2017
79 downloads
524 views

Biological control agents (BCA) are beneficial organisms that are applied to protect plants from pests. Many fungi of the genus Trichoderma are successful BCAs but the underlying mechanisms are not yet fully understood. Trichoderma cf. atroviride strain LU132 is...

["Genetics","Genomics","Microbiology","Molecular Biology","Mycology"]
doi:10.7717/peerj.2023
97 downloads
541 views

Daphnia are key model organisms for mechanistic studies of phenotypic plasticity, adaptation and microevolution, which have led to an increasing demand for genomics resources. A key step in any genomics analysis, such as high-throughput sequencing, is the availability...

["Aquaculture, Fisheries and Fish Science","Evolutionary Studies","Genomics","Marine Biology","Molecular Biology"]
doi:10.7717/peerj.2004
68 downloads
294 views

The HSF (heat shock factor) gene family contains highly conserved plant-specific transcription factors that play an important role in plant high-temperature stress responses. The present study aimed to characterize the HSF transcription factor genes in tomato (Solanum...

["Bioinformatics","Genomics","Plant Science"]
doi:10.7717/peerj.1961

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