Peer-reviewed Articles

23 downloads
96 views

Microbial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains only vaguely understood....

["Bioinformatics","Ecology","Microbiology"]
doi:10.7717/peerj.4395
18 downloads
76 views

We present Skan (Skeleton analysis), a Python library for the analysis of the skeleton structures of objects. It was inspired by the “analyse skeletons” plugin for the Fiji image analysis software, but its extensive Application Programming Interface (API) allows...

["Biochemistry","Bioinformatics","Parasitology","Computational Science"]
doi:10.7717/peerj.4312
58 downloads
469 views

Complex networks have been successfully applied to the characterization and modeling of complex systems in several distinct areas of Biological Sciences. Nevertheless, their utilization in phylogenetic analysis still needs to be widely tested, using different molecular...

["Bioinformatics","Computational Biology","Evolutionary Studies"]
doi:10.7717/peerj.4349
117 downloads
718 views

Microbes in the gut microbiome form sub-communities based on shared niche specialisations and specific interactions between individual taxa. The inter-microbial relationships that define these communities can be inferred from the co-occurrence of taxa across multiple...

["Bioinformatics","Ecology","Microbiology"]
doi:10.7717/peerj.4303
1 citation
51 downloads
439 views

We introduce LEISR (Likehood Estimation of Individual Site Rates, pronounced “laser”), a tool to infer relative evolutionary rates from protein and nucleotide data, implemented in HyPhy. LEISR is based on the popular Rate4Site (Pupko et al., 2002) approach for...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics"]
doi:10.7717/peerj.4339
77 downloads
508 views

The ubiquitous daily rhythms in mammalian physiology are guided by progression of the circadian clock. In mice, systemic disruption of the clock can promote tumor growth. In vitro, multiple oncogenes can disrupt the clock. However, due to the difficulties of studying...

["Bioinformatics","Computational Biology","Genomics","Oncology"]
doi:10.7717/peerj.4327
85 downloads
828 views

Carnivorous plants are striking examples of evolutionary convergence, displaying complex and often highly similar adaptations despite lack of shared ancestry. Using available carnivorous plant genomes along with non-carnivorous reference taxa, this study examines...

["Bioinformatics","Evolutionary Studies","Genomics","Plant Science"]
doi:10.7717/peerj.4322
297 downloads
2,030 views

Pangenomes offer detailed characterizations of core and accessory genes found in a set of closely related microbial genomes, generally by clustering genes based on sequence homology. In comparison, metagenomes facilitate highly resolved investigations of the relative...

["Bioinformatics","Ecology","Genomics","Microbiology"]
doi:10.7717/peerj.4320
106 downloads
642 views

Genomic signal processing (GSP) methods which convert DNA data to numerical values have recently been proposed, which would offer the opportunity of employing existing digital signal processing methods for genomic data. One of the most used methods for exploring...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.4264
135 downloads
1,065 views

Background The recent proliferation of large amounts of biodiversity transcriptomic data has resulted in an ever-expanding need for scalable and user-friendly tools capable of answering large scale molecular evolution questions. FUSTr identifies gene families involved...

["Bioinformatics","Evolutionary Studies","Genomics"]
doi:10.7717/peerj.4234
78 downloads
448 views

Sigmoidal and double-sigmoidal dynamics are commonly observed in many areas of biology. Here we present sicegar, an R package for the automated fitting and classification of sigmoidal and double-sigmoidal data. The package categorizes data into one of three categories,...

["Bioinformatics","Computational Biology","Mathematical Biology","Statistics","Data Science"]
doi:10.7717/peerj.4251
58 downloads
284 views

Background With the continuous discovery of microRNA’s (miRNA) association with a wide range of biological and cellular processes, expression profile-based functional characterization of such post-transcriptional regulation is crucial for revealing its significance...

["Biochemistry","Bioinformatics","Computational Biology","Molecular Biology","Data Mining and Machine Learning"]
doi:10.7717/peerj.4262
81 downloads
302 views

The etiology of cancer includes aberrant cellular homeostasis where a compromised RNA regulatory network is a prominent contributing factor. In particular, noncoding RNAs including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) were recently shown to play...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.4254
44 downloads
250 views

Background Minimal change disease (MCD) is a kind of nephrotic syndrome (NS). In this study, we aimed to establish a mathematical diagnostic model based on biological parameters to classify MCD. Methods A total of 798 NS patients were divided into MCD group and...

["Bioinformatics","Epidemiology","Nephrology"]
doi:10.7717/peerj.4237
208 downloads
1,591 views

With the increase in the availability of metagenomic data generated by next generation sequencing, there is an urgent need for fast and accurate tools for identifying viruses in host-associated and environmental samples. In this paper, we developed a stand-alone...

["Bioinformatics","Genomics","Microbiology","Virology"]
doi:10.7717/peerj.4227

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