2 downloads
22 views

Chlamydia suis is a swine pathogen that also causes zoonotic infections. Many strains contain a tet(C) cassette conferring tetracycline resistance originally acquired by horizontal gene transfer from a Gram-negative donor. As we and others have described the capacity...

["Cell Biology","Genomics","Microbiology","Molecular Biology","Infectious Diseases"]
doi:10.7287/peerj.preprints.2489v1
21 downloads
260 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
74 downloads
186 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
14 downloads
121 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
137 downloads
890 views

High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental...

["Genomics","Microbiology","Molecular Biology"]
doi:10.7717/peerj.2486
62 downloads
261 views

Background Meningitis is a major cause of mortality in tuberculosis (TB). It is not clear what factors promote central nervous system invasion and pathology but it has been reported that certain strains of Mycobacterium tuberculosis (Mtb) might have genetic traits...

["Bioinformatics","Genomics","Microbiology"]
doi:10.7717/peerj.2484
21 downloads
207 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
33 downloads
234 views

Across independent 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","Computational Science"]
doi:10.7717/peerj.2391
16 downloads
111 views

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.2452v2
33 downloads
172 views

Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments, clinical diagnostics and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2449v1
77 downloads
496 views

Streptococcus pneumoniae typically express one of 92 serologically distinct capsule polysaccharide (cps) types (serotypes). Some of these serotypes are closely related to each other; using the commercially available typing antisera, these are assigned to common...

["Bioinformatics","Genomics","Microbiology","Infectious Diseases"]
doi:10.7717/peerj.2477
19 downloads
356 views

Background Transposable element (TE) polymorphisms are important components of population genetic variation. The functional impacts of TEs in gene regulation and generating genetic diversity have been observed in multiple species, but the frequency and magnitude...

["Bioinformatics","Genomics","Plant Science"]
doi:10.7287/peerj.preprints.2447v1
13 downloads
73 views

Background. The capacity of species to respond and perceive visual signal is integral to their evolutionary success. Giraffe is closely related to okapi, but the two species have broad range of phenotypic differences including their visual capacities. Vision studies...

["Bioinformatics","Evolutionary Studies","Genomics"]
doi:10.7287/peerj.preprints.2444v1
18 downloads
124 views

microRNAs are small, non-coding RNAs involved in post-transcriptional gene regulation. Since the dysregulation of only a few miRNAs can affect many biological pathways, miRNAs are thought to play a key role in cancer development and can be used as biomarkers for...

["Bioinformatics","Genomics","Molecular Biology"]
doi:10.7287/peerj.preprints.2423v1
12 downloads
91 views

Background: Reference genes serve an important role as an endogenous control/standard for data normalisation in gene expression studies. Although reference genes have recently been suggested for marsupials, independent analysis of reference genes on different immune...

["Genomics","Molecular Biology"]
doi:10.7287/peerj.preprints.2422v1

Top subject areas - Articles & Preprints

Top subject areas - People

View all subject areas