Peer-reviewed Articles - Biology

9 downloads
73 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
44 downloads
224 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
92 downloads
202 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
33 downloads
266 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
37 downloads
192 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
62 downloads
380 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
65 downloads
343 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
53 downloads
204 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
45 downloads
217 views

T1 Lipase is a thermostable secretary protein of Geobacillus zalihae strain previously expressed in a prokaryotic system and purified using three-step purification: affinity 1, affinity 2, and ion exchange chromatography (IEX). This approach is time consuming and...

["Biochemistry","Computational Biology"]
doi:10.7717/peerj.5833
86 downloads
552 views

Transcription factors (TFs) and microRNAs (miRNAs) are well-characterized trans-acting essential players in gene expression regulation. Growing evidence indicates that TFs and miRNAs can work cooperatively, and their dysregulation has been associated with many...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7717/peerj.5951
70 downloads
353 views

Background A positive association between diabetes and breast cancer has been identified by various epidemiological and clinical studies. However, the possible molecular interactions between the two heterogeneous diseases have not been fully determined yet. There...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.5917
33 downloads
211 views

The ability of vertebrates to generate rhythm within their spinal neural networks is essential for walking, running, and other rhythmic behaviors. The central pattern generator (CPG) network responsible for these behaviors is well-characterized with experimental...

["Animal Behavior","Bioinformatics","Computational Biology","Neuroscience","Computational Science"]
doi:10.7717/peerj.5849
45 downloads
269 views

We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ70 factor of RNA polymerase. σ70 promoters are ubiquitously used in recombinant DNA technology, but characterizing their strength...

["Bioinformatics","Computational Biology","Genomics","Synthetic Biology","Data Mining and Machine Learning"]
doi:10.7717/peerj.5862
77 downloads
535 views

Many important cellular processes involve protein–protein interactions (PPIs) mediated by a Short Linear Motif (SLiM) in one protein interacting with a globular domain in another. Despite their significance, these domain-motif interactions (DMIs) are typically...

["Bioinformatics","Computational Biology","Molecular Biology"]
doi:10.7717/peerj.5858
57 downloads
340 views

Background The need for read-based phasing arises with advances in sequencing technologies. The minimum error correction (MEC) approach is the primary trend to resolve haplotypes by reducing conflicts in a single nucleotide polymorphism-fragment matrix. However,...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.5852

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