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

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
35 downloads
338 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
14 downloads
71 views

Statistical and biochemical studies of the standard genetic code (SGC) have found evidence that the impact of mistranslations is minimized in a way that erroneous codes are either synonymous or code for an amino acid with similar polarity as the originally coded...

["Bioinformatics","Evolutionary Studies","Genetics"]
doi:10.7287/peerj.preprints.3270v1
4 downloads
29 views

Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.3271v1
29 downloads
280 views

DNA metabarcoding provides species composition data for entire communities, yet information on intraspecific diversity is usually lost during data analysis. The capacity to infer intraspecific genetic diversity within whole communities would, however, represent...

["Biogeography","Bioinformatics","Molecular Biology","Freshwater Biology"]
doi:10.7287/peerj.preprints.3269v1
19 downloads
164 views

Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.3266v3
31 downloads
188 views

The annual German Conference on Bioinformatics (GCB) has brought together renowned international scientists in bioinformatics, computational biology, biostatistics, biology and medicine since 1993. The 25th GCB was held in Tübingen from 18th to 21st of September...

["Bioinformatics"]
doi:10.7287/peerj.preprints.3268v1
25 downloads
258 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
37 downloads
218 views

Aquaporins (AQPs) are essential channel proteins that execute multi-functions throughout plant growth and development, including water transport, uncharged solutes uptake, stress response, and so on. Here, we report the first genome-wide identification and characterization...

["Agricultural Science","Bioinformatics","Genomics","Plant Science"]
doi:10.7717/peerj.3747
51 downloads
197 views

Cinnamomum camphora, a member of the Lauraceae family, is a valuable aromatic and timber tree that is indigenous to the south of China and Japan. All parts of Cinnamomum camphora have secretory cells containing different volatile chemical compounds that are utilized...

["Bioinformatics","Conservation Biology","Genetics","Molecular Biology","Plant Science"]
doi:10.7717/peerj.3820
3 downloads
29 views

Background. Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease primarily affecting upper and lower motor neurons in the brain and spinal cord. The heterogeneity in the course of ALS clinical progression and ultimately survival, coupled...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning","Scientific Computing and Simulation"]
doi:10.7287/peerj.preprints.3262v1
3 downloads
103 views

Melanoma is a highly immunogenic tumor. Therefore, in recent years physicians have incorporated drugs that alter the immune system into their therapeutic arsenal against this disease, revolutionizing in the treatment of patients in an advanced stage of the disease....

["Bioinformatics","Algorithms and Analysis of Algorithms","Databases","Visual Analytics"]
doi:10.7287/peerj.preprints.3260v1
11 downloads
66 views

The mutational processes responsible for the somatic mutations observed in tumor samples can significantly vary not only between tumor types but also among the individual cancers within a tumor class. Mutational processes can be represented by so called “mutational...

["Bioinformatics","Computational Biology","Genomics","Oncology"]
doi:10.7287/peerj.preprints.3257v1
16 downloads
163 views

Bacterial surfaces are complex, built of from membranes, peptide-glycans and, importantly, proteins. The proteins play crucial roles as the key regulator of how the bacterium interacts with its environment. A full catalog of the motifs in coiled-coil proteins and...

["Bioinformatics","Infectious Diseases","Data Science"]
doi:10.7287/peerj.preprints.3118v2

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