Peer-reviewed Articles - Computer sci

66 downloads
409 views

Forested areas are increasing across Europe, driven by both reforestation programs and farmland abandonment. While tree planting remains the standard reforestation strategy, there is increased interest in spontaneous regeneration as a cost-effective method with...

["Computational Biology","Conservation Biology","Ecology","Forestry","Spatial and Geographic Information Science"]
doi:10.7717/peerj.6219
35 downloads
236 views

Antibodies are proteins generated by the adaptive immune system to recognize and counteract a plethora of pathogens through specific binding. This adaptive binding is mediated by structural diversity in the six complementary determining region (CDR) loops (H1,...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.6179
21 downloads
170 views

In polyploid genomes, homoeologs are a specific subtype of homologs, and can be thought of as orthologs between subgenomes. In Orthologous MAtrix, we infer homoeologs in three polyploid plant species: upland cotton (Gossypium hirsutum), rapeseed (Brassica napus),...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.6231
257 downloads
1,011 views

Metagenomic and meta-barcode DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.6160
58 downloads
173 views

Background Solanum nigrum (black nightshade; S. nigrum), a member of family Solanaceae, has been endowed with a heterogeneous array of secondary metabolites of which the steroidal glycoalkaloids (SGAs) and steroidal saponins (SS) have vast potential to serve as...

["Biochemistry","Bioinformatics","Cell Biology","Computational Biology","Plant Science"]
doi:10.7717/peerj.6012
57 downloads
353 views

Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning"]
doi:10.7717/peerj.6142
71 downloads
477 views

Background Rhamnolipids, biosurfactants with a wide range of biomedical applications, are amphiphilic molecules produced on the surfaces of or excreted extracellularly by bacteria including Pseudomonas aeruginosa. However, Pseudomonas putida is a non-pathogenic...

["Bioinformatics","Computational Biology","Synthetic Biology","Computational Science","Data Mining and Machine Learning"]
doi:10.7717/peerj.6046
40 downloads
344 views

The classical way of defining enzyme inhibition has obscured the distinction between inhibitory effect and the inhibitor binding constant. This article examines the relationship between the simple binding curve used to define biomolecular interactions and the standard...

["Biochemistry","Computational Biology","Mathematical Biology","Drugs and Devices","Pharmacology"]
doi:10.7717/peerj.6082
64 downloads
333 views

Background The human hand can perform a range of manipulation tasks, from holding a pen to holding a hammer. The central nervous system (CNS) uses different strategies in different manipulation tasks based on task requirements. Attempts to compare postures of the...

["Bioengineering","Computational Biology","Neuroscience","Kinesiology","Computational Science"]
doi:10.7717/peerj.6078
174 downloads
718 views

Protein structure is not static; residues undergo conformational rearrangements and, in doing so, create, stabilize or break non-covalent interactions. Molecular dynamics (MD) is a technique used to simulate these movements with atomic resolution. However, given...

["Bioinformatics","Biophysics","Computational Biology"]
doi:10.7717/peerj.5998
52 downloads
382 views

Reverse engineering metabolome data to infer metabolic interactions is a challenging research topic. Here we introduce JacLy, a Jacobian-based method to infer metabolic interactions of small networks (<20 metabolites) from the covariance of steady-state metabolome...

["Bioengineering","Bioinformatics","Biotechnology","Computational Biology","Computational Science"]
doi:10.7717/peerj.6034
57 downloads
266 views

Axonal stimulation with electric currents is an effective method for controlling neural activity. An electric field parallel to the axon is widely accepted as the predominant component in the activation of an axon. However, recent studies indicate that the transverse...

["Biophysics","Computational Biology","Mathematical Biology","Neurology"]
doi:10.7717/peerj.6020
71 downloads
440 views

Ecological communities are composed of a combination of core species that maintain local viable populations and transient species that occur infrequently due to dispersal from surrounding regions. Preliminary work indicates that while core and transient species...

["Computational Biology","Ecology"]
doi:10.7717/peerj.6019
86 downloads
421 views

Gammatones have had a long history in auditory studies, and recent theoretical work suggests they may play an important role in cochlear mechanics as well. Following this lead, the present paper takes five examples of basilar membrane impulse responses and uses...

["Biophysics","Computational Biology","Mathematical Biology","Neuroscience","Otorhinolaryngology"]
doi:10.7717/peerj.6016
63 downloads
244 views

The Bertalanffy–Pütter growth model describes mass m at age t by means of the differential equation dm/dt = p * ma − q * mb. The special case using the von Bertalanffy exponent-pair a = 2/3 and b = 1 is most common (it corresponds to the von Bertalanffy growth...

["Aquaculture, Fisheries and Fish Science","Computational Biology","Mathematical Biology","Computational Science","Natural Resource Management"]
doi:10.7717/peerj.5973

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