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Total of 376 results See all subject areas
genomics

Evolutionary studies of clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated (cas) genes can provide insights into host-pathogen co-evolutionary dynamics and the frequency at which different genomic events (e.g., horizontal vs....

["Evolutionary Studies","Genomics","Microbiology","Infectious Diseases"]
doi:10.7717/peerj.340

In ChIP-Seq and DNase-Seq experiments the density of background reads can vary from sample to sample. Differences in background read densities between samples do not necessarily correspond to proportional changes of read densities in true ChIP-Seq peaks. Therefore,...

["Bioinformatics","Genomics","Neuroscience","Statistics"]
doi:10.7287/peerj.preprints.175v2

Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly...

["Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7717/peerj.332

Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls,...

["Bioinformatics","Genomics","Marine Biology","Molecular Biology"]
doi:10.7287/peerj.preprints.314v1

Bacteria were long assumed to be monoploid, maintaining one copy of a circular chromosome. In recent years it became obvious that the majority of species in several phylogenetic groups of prokaryotes are oligoploid or polyploid, e.g. in halophilic and methanogenic...

["Biochemistry","Genetics","Genomics","Microbiology","Molecular Biology"]
doi:10.7287/peerj.preprints.306v1

Emberizid sparrows (emberizidae) have played a prominent role in the study of avian vocal communication and social behavior. We present here brain transcriptomes for three emberizid model systems, song sparrow Melospiza melodia, white-throated sparrow Zonotrichia...

["Animal Behavior","Evolutionary Studies","Genomics","Neuroscience"]
doi:10.7287/peerj.preprints.297v3

Molecular surveys of aphotic habitats have indicated the presence of major uncultured lineages phylogenetically classified as members of the Cyanobacteria. One of these lineages has recently been proposed as a non-photosynthetic sister phylum to the Cyanobacteria,...

["Genomics","Microbiology"]
doi:10.7287/peerj.preprints.204v2

While numerous effective peak finders have been developed for eukaryotic systems, we have found that the approaches used can be error prone when run on high coverage bacterial and archaeal ChIP-Seq datasets. We have developed Pique, an easy to use ChIP-Seq peak...

["Bioinformatics","Genomics"]
doi:10.7287/peerj.preprints.290v2

Background: The phylogeny of birds which are adapted to aquatic environments is controversial because of convergent evolution. Methods: To understand water bird evolution in more detail, we sequenced the majority of mitochondrial protein coding genes (6699 nucleotides...

["Biodiversity","Evolutionary Studies","Genetics","Genomics","Zoology"]
doi:10.7287/peerj.preprints.272v1

Metagenomics is a valuable tool for the study of microbial communities but has been limited by the difficulty of “binning” the resulting sequences into groups corresponding to the individual species and strains that constitute the community. Moreover, there are...

["Bioengineering","Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.260v1

The characterization of complex diseases remains a great challenge for biomedical researchers due to the myriad interactions of genetic and environmental factors. Adaptation of phylogenomic techniques to increasingly available genomic data provides an evolutionary...

["Bioinformatics","Evolutionary Studies","Genomics"]
doi:10.7287/peerj.preprints.230v1

Zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) comprise a powerful class of tools that are redefining the boundaries of biological research. Although these technologies have begun to enable targeted genome modifications,...

["Biotechnology","Genetics","Genomics"]
doi:10.7287/peerj.preprints.229v1

The dramatic increase in genome sequencing during the last years has changed our ideas about bacterial diversity, from single gene to whole community DNA surveys; we have learned that nature's lagest gene repository resides in bacteria resides in bacteria. Comparison...

["Evolutionary Studies","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.113v2

Assembling the Tree Of Life (TOL) faces the pressing challenge of incorporating a rapidly growing number of sequenced genomes. This problem is exacerbated by the fact that different sets of genes are informative at different evolutionary scales. Here, we present...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics"]
doi:10.7287/peerj.preprints.223v1

Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly...

["Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.220v1

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