Peer-reviewed Articles - Biology

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Willow is a widely used dioecious woody plant of Salicaceae family in China. Due to their high biomass yields, willows are promising sources for bioenergy crops. In this study, we assembled the complete mitochondrial (mt) genome sequence of S. suchowensis with...

["Bioinformatics","Genomics","Plant Science"]
doi:10.7717/peerj.3148
1 download
1 view

The number of protein structures in the PDB database has been increasing more than 15-fold since 1999. The creation of computational models predicting enzymatic function is of major importance since such models provide the means to better understand the behavior...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7717/peerj.3095
18 downloads
199 views

Identification and quantification of microorganisms is a significant step in studying the alpha and beta diversities within and between microbial communities respectively. Both identification and quantification of a given microbial community can be carried out...

["Bioinformatics","Computational Biology","Genomics","Microbiology","Taxonomy"]
doi:10.7717/peerj.3138
36 downloads
221 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
75 downloads
512 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
68 downloads
221 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
94 downloads
719 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
66 downloads
316 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
201 downloads
7,955 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
98 downloads
261 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
74 downloads
642 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
64 downloads
321 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
202 downloads
1,577 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
63 downloads
212 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
107 downloads
320 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

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