Peer-reviewed Articles

19 downloads
113 views

Shotgun metagenomics of microbial communities reveal information about strains of relevance for applications in medicine, biotechnology and ecology. Recovering their genomes is a crucial but very challenging step due to the complexity of the underlying biological...

["Bioinformatics","Computational Biology","Data Science"]
doi:10.7717/peerj-cs.117
92 downloads
554 views

Background Fast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide...

["Bioinformatics","Computational Biology","Microbiology"]
doi:10.7717/peerj.3353
33 downloads
212 views

The dynamics and conformational landscape of proteins in organic solvents are events of potential interest in nonaqueous process catalysis. Conformational changes, folding transitions, and stability often correspond to structural rearrangements that alter contacts...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.3341
31 downloads
125 views

Coptis chinensis Franch., the Chinese goldthread (‘Weilian’ in Chinese), one of the most important medicinal plants from the family Ranunculaceae, and its rhizome has been widely used in Traditional Chinese Medicine for centuries. Here, we analyzed the chemical...

["Biochemistry","Bioinformatics","Computational Biology","Plant Science"]
doi:10.7717/peerj.3303
48 downloads
281 views

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran...

["Computational Biology","Mathematical Biology","Computational Science"]
doi:10.7717/peerj.3327
58 downloads
607 views

Obstructive sleep apnea syndrome (OSAS) is a common clinical condition. The way that OSAS risk factors associate and converge is not a random process. As such, defining OSAS phenotypes fosters personalized patient management and population screening. In this paper,...

["Bioinformatics","Computational Biology","Health Policy","Respiratory Medicine","Computational Science"]
doi:10.7717/peerj.3289
77 downloads
597 views

Metagenomics-based studies have provided insight into many of the complex microbial communities responsible for maintaining life on this planet. Sequencing efforts often uncover novel genetic content; this is most evident for phage communities, in which upwards...

["Bioinformatics","Computational Biology","Microbiology","Virology"]
doi:10.7717/peerj.3281
47 downloads
254 views

Protein post-translational modification (PTM) is an important mechanism that is involved in the regulation of protein function. Considering the high-cost and labor-intensive of experimental identification, many computational prediction methods are currently available...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.3261
81 downloads
383 views

Genomes evolve through a combination of mutation, drift, and selection, all of which act heterogeneously across genes and lineages. This leads to differences in branch-length patterns among gene trees. Genes that yield trees with the same branch-length patterns...

["Computational Biology","Evolutionary Studies","Genomics"]
doi:10.7717/peerj.3241
39 downloads
324 views

Background Opsin proteins are seven transmembrane receptor proteins which detect light. Opsins can be classified into two types and share little sequence identity: type 1, typically found in bacteria, and type 2, primarily characterized in metazoa. The type 2 opsins...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics","Mycology"]
doi:10.7717/peerj.3206
72 downloads
404 views

CRISPRs (clustered regularly interspaced short palindromic repeats) are particular repeat sequences found in wide range of bacteria and archaea genomes. Several tools are available for detecting CRISPR arrays in the genomes of both domains. Here we developed a...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.3219
48 downloads
583 views

We developed a web-based cloud-hosted system that allow users to archive, listen, visualize, and annotate recordings. The system also provides tools to convert these annotations into datasets that can be used to train a computer to detect the presence or absence...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning"]
doi:10.7717/peerj-cs.113
80 downloads
509 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
62 downloads
380 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
131 downloads
649 views

D. suzukii is a relatively recent and destructive pest species to the North American soft-skinned fruit industry. Understanding this species’ potential to shift in abundance and range due to changing climate is an important part of an effective mitigation and management...

["Agricultural Science","Computational Biology","Ecology","Environmental Sciences","Mathematical Biology"]
doi:10.7717/peerj.3192

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