Peer-reviewed Articles - Biology

37 downloads
333 views

The appropriate timing of flowering is crucial for the reproductive success of plants. Hence, intricate genetic networks integrate various environmental and endogenous cues such as temperature or hormonal statues. These signals integrate into a network of floral...

["Bioinformatics","Computational Biology","Developmental Biology","Plant Science"]
doi:10.7717/peerj.3197
56 downloads
720 views

We report the genome sequence of Exiguobacterium chiriqhucha str. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of the Exiguobacterium genomes available suggest that our strain belongs to the same species as the previously reported...

["Biochemistry","Biodiversity","Bioinformatics","Genomics","Microbiology"]
doi:10.7717/peerj.3162
49 downloads
231 views

Prebiotics are selectively fermentable dietary compounds that result in changes in the composition and/or activity of the intestinal microbiota, thus conferring benefits upon host health. In veterinary medicine, commercially available products containing prebiotics...

["Bioinformatics","Microbiology","Veterinary Medicine","Gastroenterology and Hepatology","Nutrition"]
doi:10.7717/peerj.3184
22 downloads
231 views

Predicting protein structure from sequence remains a major open problem in protein biochemistry. One component of predicting complete structures is the prediction of inter-residue contact patterns (contact maps). Here, we discuss protein contact map prediction...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.3139
44 downloads
385 views

Background Geminiviruses (family Geminiviridae) are prevalent plant viruses that imperil agriculture globally, causing serious damage to the livelihood of farmers, particularly in developing countries. The virus evolves rapidly, attributing to its single-stranded...

["Agricultural Science","Bioinformatics","Genomics","Virology"]
doi:10.7717/peerj.3165
58 downloads
400 views

Background The capacity of visually oriented species to perceive and respond to visual signal is integral to their evolutionary success. Giraffes are closely related to okapi, but the two species have broad range of phenotypic differences including their visual...

["Bioinformatics","Evolutionary Studies","Genomics"]
doi:10.7717/peerj.3145
52 downloads
524 views

Background Maleic acid is a multi-functional chemical widely used in the field of industrial chemistry for producing food additives and food contact materials. As maleic acid may contaminate food by the release from food packages or intentional addition, it raises...

["Bioinformatics","Computational Biology","Food Science and Technology","Genomics"]
doi:10.7717/peerj.3175
95 downloads
693 views

Most reconstruction methods for genomes of ancient origin that are used today require a closely related reference. In order to identify genomic rearrangements or the deletion of whole genes, de novo assembly has to be used. However, because of inherent problems...

["Bioinformatics","Paleontology","Computational Science"]
doi:10.7717/peerj.3126
43 downloads
457 views

Sensitivity of short read DNA-sequencing for gene fusion detection is improving, but is hampered by the significant amount of noise composed of uninteresting or false positive hits in the data. In this paper we describe a tiered prioritisation approach to extract...

["Bioinformatics","Genomics","Oncology","Translational Medicine"]
doi:10.7717/peerj.3166
81 downloads
378 views

The Clustered Regularly Interspaced Short Palindromic Repeats associated (CRISPR-Cas) systems consist of RNA-protein complexes that provide bacteria and archaea with sequence-specific immunity against bacteriophages, plasmids, and other mobile genetic elements....

["Biochemistry","Bioinformatics","Evolutionary Studies","Microbiology"]
doi:10.7717/peerj.3161
43 downloads
348 views

The filamentous fungus Rhizopus delemar naturally accumulates relatively high amounts of fumarate. Although the culture conditions that increase fumarate yields are well established, the network underlying the accumulation of fumarate is not yet fully understood....

["Biochemistry","Bioinformatics","Biotechnology","Microbiology"]
doi:10.7717/peerj.3133
84 downloads
365 views

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
54 downloads
472 views

Gene regulation modulates RNA expression via transcription factors. Post-transcriptional gene regulation in turn influences the amount of protein product through, for example, microRNAs (miRNAs). Experimental establishment of miRNAs and their effects is complicated...

["Bioinformatics","Computational Biology","Computational Science"]
doi:10.7717/peerj.3131
54 downloads
302 views

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
193 downloads
1,375 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

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