Peer-reviewed Articles

65 downloads
491 views

Background Differential expression analysis on the basis of RNA-Seq count data has become a standard tool in transcriptomics. Several studies have shown that prior normalization of the data is crucial for a reliable detection of transcriptional differences. Until...

["Bioinformatics","Statistics"]
doi:10.7717/peerj.3859
34 downloads
184 views

Background The emergence of functions in biological systems is a long-standing issue that can now be addressed at the cell level with the emergence of high throughput technologies for genome sequencing and phenotyping. The reconstruction of complete metabolic networks...

["Bioinformatics","Computational Biology","Artificial Intelligence"]
doi:10.7717/peerj.3860
49 downloads
363 views

Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response...

["Biodiversity","Biogeography","Bioinformatics","Microbiology"]
doi:10.7717/peerj.3827
27 downloads
217 views

Cataloging mutated driver genes that confer a selective growth advantage for tumor cells from sporadic passenger mutations is a critical problem in cancer genomic research. Previous studies have reported that some driver genes are not highly frequently mutated...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj-cs.133
92 downloads
955 views

Background As next generation sequence technology has advanced, there have been parallel advances in genome-scale analysis programs for determining evolutionary relationships as proxies for epidemiological relationship in public health. Most new programs skip traditional...

["Bioinformatics","Evolutionary Studies","Food Science and Technology","Genomics","Epidemiology"]
doi:10.7717/peerj.3893
77 downloads
451 views

RNA-Seq is a recent and efficient technique that uses the capabilities of next-generation sequencing technology for characterizing and quantifying transcriptomes. One important task using gene-expression data is to identify a small subset of genes that can be used...

["Bioinformatics","Computational Biology","Statistics","Medical Genetics","Computational Science"]
doi:10.7717/peerj.3890
47 downloads
231 views

Background The honey bee (Apis mellifera) is a highly diverse species commonly used for honey production and pollination services. The oviposition of the honey bee queen affects the development and overall performance of the colony. To investigate the ovary activation...

["Agricultural Science","Bioinformatics","Entomology","Genetics"]
doi:10.7717/peerj.3881
44 downloads
299 views

Background The current first line drugs for treating uncomplicated malaria are artemisinin (ART) combination therapies. However, Plasmodium falciparum parasites resistant to ART and partner drugs are spreading, which threatens malaria control efforts. Rodent malaria...

["Bioinformatics","Genetics","Genomics","Microbiology","Parasitology"]
doi:10.7717/peerj.3766
675 downloads
7,089 views

Next-generation sequencing of 16S ribosomal RNA is widely used to survey microbial communities. Sequences are typically assigned to Operational Taxonomic Units (OTUs). Closed- and open-reference OTU assignment matches reads to a reference database at 97% identity...

["Bioinformatics","Computational Biology","Microbiology"]
doi:10.7717/peerj.3889
68 downloads
458 views

We have developed a machine learning approach to predict stimulation-dependent enhancer-promoter interactions using evidence from changes in genomic protein occupancy over time. The occupancy of estrogen receptor alpha (ERα), RNA polymerase (Pol II) and histone...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.3742
70 downloads
1,047 views

Mating behaviour and predation avoidance in Heliconius involve visual colour signals; however, there is considerable inter-individual phenotypic variation in the appearance of colours. In particular, the red pigment varies from bright crimson to faded red. It has...

["Animal Behavior","Bioinformatics","Ecology","Entomology","Zoology"]
doi:10.7717/peerj.3821
59 downloads
250 views

Many bacterial effector proteins that are delivered to host cells during infection are enzymes targeting host cell signalling. Recently, Legionella pneumophila effector Lpg1137 was experimentally characterised as a serine protease that cleaves human syntaxin 17....

["Bioinformatics","Molecular Biology"]
doi:10.7717/peerj.3849
133 downloads
975 views

Taxonomic markers such as the 16S ribosomal RNA gene are widely used in microbial community analysis. A common first step in marker-gene analysis is grouping genes into clusters to reduce data sets to a more manageable size and potentially mitigate the effects...

["Bioinformatics","Ecology","Microbiology","Computational Science"]
doi:10.7717/peerj.3812
157 downloads
692 views

Background Viral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community,...

["Bioinformatics","Ecology","Genomics","Microbiology"]
doi:10.7717/peerj.3817
70 downloads
382 views

Background The rapid increase in antibiotic resistance by various bacterial pathogens underlies the significance of developing new therapies and exploring different drug targets. A fraction of bacterial pathogens abbreviated as ESKAPE by the European Center for...

["Bioinformatics","Computational Biology","Microbiology","Pharmacology"]
doi:10.7717/peerj.3765

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