Peer-reviewed Articles

28 downloads
198 views

Background RNA-seq is a useful tool for analysis of gene expression. However, its robustness is greatly affected by a number of artifacts. One of them is the presence of duplicated reads. Results To infer the influence of different methods of removal of duplicated...

["Genomics"]
doi:10.7717/peerj.3091
1 citation
68 downloads
488 views

Degeneracy in the genetic code implies that different codons can encode the same amino acid. Usage preference of synonymous codons has been observed in all domains of life. There is much evidence suggesting that this bias has a major role on protein elongation...

["Bioinformatics","Genetics","Genomics","Molecular Biology","Statistics"]
doi:10.7717/peerj.3081
64 downloads
214 views

Trees in the Morus genera belong to the Moraceae family. To better understand the species status of genus Morus and to provide information for studies on evolutionary biology within the genus, the complete chloroplast (cp) genomes of M. cathayana and M. multicaulis...

["Genomics","Plant Science"]
doi:10.7717/peerj.3037
83 downloads
660 views

Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is...

["Computational Biology","Genomics"]
doi:10.7717/peerj.3035
62 downloads
299 views

American trypanosomiasis is a chronic and endemic disease which affects millions of people. Trypanosoma cruzi, its causative agent, has a life cycle that involves complex morphological and functional transitions, as well as a variety of environmental conditions....

["Biochemistry","Genomics","Molecular Biology","Parasitology","Infectious Diseases"]
doi:10.7717/peerj.3017
184 downloads
7,321 views

Background Much of the recent research in companion animal nutrition has focussed on understanding the role of diet on faecal microbiota composition. To date, diet-induced changes in faecal microbiota observed in humans and rodents have been extrapolated to pets...

["Genomics","Microbiology","Veterinary Medicine"]
doi:10.7717/peerj.3019
94 downloads
249 views

Background Whole mitochondrial DNA is being increasingly utilized for comparative genomic and phylogenetic studies at deep and shallow evolutionary levels for a range of taxonomic groups. Although mitogenome sequences are deposited at an increasing rate into public...

["Aquaculture","Fisheries and Fish Science","Biodiversity","Evolutionary Studies","Genomics","Marine Biology"]
doi:10.7717/peerj.2982
67 downloads
630 views

One of the main challenges of the post-genomic era is the understanding of how gene expression is controlled. Changes in gene expression lay behind diverse biological phenomena such as development, disease and the adaptation to different environmental conditions....

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.3052
58 downloads
300 views

Background The emergence and evolution of community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strains in Africa is poorly understood. However, one particular MRSA lineage called ST88, appears to be rapidly establishing itself as an “African”...

["Bioinformatics","Evolutionary Studies","Genomics","Microbiology"]
doi:10.7717/peerj.3047
199 downloads
1,554 views

The 16S rRNA gene has been used as master key for studying prokaryotic diversity in almost every environment. Despite the claim of several researchers to have the best universal primers, the reality is that no primer has been demonstrated to be truly universal....

["Biodiversity","Computational Biology","Genomics"]
doi:10.7717/peerj.3036
60 downloads
200 views

Background Polygonum minus is an herbal plant in the Polygonaceae family which is rich in ethnomedicinal plants. The chemical composition and characteristic pungent fragrance of Polygonum minus have been extensively studied due to its culinary and medicinal properties....

["Bioinformatics","Biotechnology","Genomics"]
doi:10.7717/peerj.2938
96 downloads
289 views

Circular RNAs (circRNAs) belong to a recently re-discovered species of RNA that emerge during RNA maturation through a process called back-splicing. A downstream 5′ splice site is linked to an upstream 3′ splice site to form a circular transcript instead of a canonical...

["Bioinformatics","Computational Biology","Genomics","Molecular Biology"]
doi:10.7717/peerj.2934
99 downloads
709 views

The past two decades have brought many important advances in our understanding of the hereditary susceptibility to cancer. Numerous studies have provided convincing evidence that identification of germline mutations associated with hereditary cancer syndromes can...

["Genomics","Oncology","Medical Genetics"]
doi:10.7717/peerj.3046
195 downloads
912 views

Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7717/peerj.2988
99 downloads
733 views

Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and 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:10.7717/peerj.2997

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