Species in the genus Ganoderma include several ecologically important and pathogenic fungal species whose medicinal and economic value is substantial. Due to the highly similar morphological features within the Ganoderma, identification of species has relied heavily...

["Bioinformatics","Mycology","Taxonomy"]
doi:10.7717/peerj.3596

Analysis of DNA microarray data has been very useful for experimental molecular biology, as it provides unprecedented opportunities to study a wide variety of biological processes. As a part of this analysis, biclustering has been consolidated as one of the first...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.3110v1
21 downloads
121 views

Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations....

["Bioinformatics","Evolutionary Studies","Plant Science"]
doi:10.7717/peerj.3569
32 downloads
254 views

Background This paper is a comment on the idea of matrix-free Cladistics. Demonstration of this idea’s efficiency is a major goal of the study. Within the proposed framework, the ordinary (phenetic) matrix is necessary only as “source” of Hennigian trees, not as...

["Bioinformatics","Taxonomy","Computational Science"]
doi:10.7717/peerj.3578
321 downloads
4,524 views

The website Sci-Hub provides access to scholarly literature via full text PDF downloads. The site enables users to access articles that would otherwise be paywalled. Since its creation in 2011, Sci-Hub has grown rapidly in popularity. However, until now, the extent...

["Bioinformatics","Legal Issues","Science and Medical Education","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.3100v1
48 downloads
567 views

Newly emerging influenza viruses continue to threaten public health. A rapid determination of the host range of newly discovered influenza viruses would assist in early assessment of their risk. Here, we attempted to predict the host of influenza viruses using...

["Bioinformatics","Computational Biology","Virology"]
doi:10.7717/peerj.3579
27 downloads
204 views

Background As the fifth most common cancer worldwide, Hepatocellular carcinoma (HCC) is also the third most common cause of cancer-related death in China. Several lncRNAs have been demonstrated to be associated with occurrence and prognosis of HCC. However, identification...

["Bioinformatics","Molecular Biology","Gastroenterology and Hepatology","Oncology"]
doi:10.7717/peerj.3575
31 downloads
359 views

The major virulence factor of the pneumococcus, and target for conjugate vaccines, is the polysaccharide capsule, which is usually encoded by the highly variable cps locus. Serotype 37 is an unusual pneumococcal type in which the single β-glucosyltransferase gene...

["Bioinformatics","Genomics","Microbiology","Infectious Diseases"]
doi:10.7717/peerj.3571
8 downloads
93 views

We have developed a machine learning approach to predict context specific 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 marks...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.3093v1
296 downloads
574 views

Oxford Nanopore Technologies' MinION sequencer was launched in pre-release form in 2014 and represents an exciting new sequencing paradigm. The device offers multi-kilobase reads and a streamed mode of operation that allows processing of reads as they are generated....

["Bioinformatics","Genomics"]
doi:10.7287/peerj.preprints.3090v1
43 downloads
210 views

Background The availability of large databases containing high resolution three-dimensional (3D) models of proteins in conjunction with functional annotation allows the exploitation of advanced supervised machine learning techniques for automatic protein function...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning"]
doi:10.7717/peerj-cs.124
23 downloads
351 views

Background The ferric uptake regulator (Fur) is a transcription factor and the main regulator of iron acquisition in prokaryotes. When bound to ferric iron, Fur recognizes its DNA binding site and generally executes its function by repressing transcription of its...

["Bioinformatics","Genetics","Marine Biology","Microbiology","Molecular Biology"]
doi:10.7717/peerj.3461
135 downloads
671 views

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of...

["Bioinformatics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.2452v4
211 downloads
1,638 views

The Tara Oceans Expedition has provided large, publicly-accessible microbial metagenomic datasets from a circumnavigation of the globe. Utilizing several size fractions from the samples originating in the Mediterranean Sea, we have used current assembly and binning...

["Bioinformatics","Marine Biology","Microbiology"]
doi:10.7717/peerj.3558

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