Peer-reviewed Articles - General

22 downloads
189 views

Supertree methods enable the reconstruction of large phylogenies. The supertree problem can be formalized in different ways in order to cope with contradictory information in the input. Some supertree methods are based on encoding the input trees in a matrix; other...

["Bioinformatics","Computational Biology","Evolutionary Studies","Taxonomy","Computational Science"]
doi:10.7717/peerj.4987
58 downloads
297 views

Quantitative analysis of shape and form is critical in many biological disciplines, as context-dependent morphotypes reflect changes in gene expression and physiology, e.g., in comparisons of environment-dependent phenotypes, forward/reverse genetic assays or shape...

["Computational Biology","Ecology","Computational Science"]
doi:10.7717/peerj.4861
47 downloads
511 views

Dot plots are widely used to quickly compare sequence sets. They provide a synthetic similarity overview, highlighting repetitions, breaks and inversions. Different tools have been developed to easily generated genomic alignment dot plots, but they are often limited...

["Bioinformatics","Genomics","Computational Science"]
doi:10.7717/peerj.4958
44 downloads
238 views

Transcutaneous spinal cord stimulation (tSCS) has been extensively studied due to its promising application in motor function restoration. Many previous studies have explored both the essential mechanism of action and the methods for determining optimal stimulation...

["Bioengineering","Neuroscience","Computational Science"]
doi:10.7717/peerj.4921
53 downloads
247 views

When the task is reading nonwords aloud, skilled adult readers are very variable in the responses they produce: a nonword can evoke as many as 24 different responses in a group of such readers. Why is nonword reading so variable? We analysed a large database of...

["Cognitive Disorders","Psychiatry and Psychology","Computational Science"]
doi:10.7717/peerj.4879
77 downloads
185 views

Estimating the depth of anaesthesia (DoA) in operations has always been a challenging issue due to the underlying complexity of the brain mechanisms. Electroencephalogram (EEG) signals are undoubtedly the most widely used signals for measuring DoA. In this paper,...

["Anesthesiology and Pain Management","Statistics","Computational Science"]
doi:10.7717/peerj.4817
62 downloads
275 views

Proteins that modify the activity of transcription factors (TFs) are often called modulators and play a vital role in gene transcriptional regulation. Alternative splicing is a critical step of gene processing, and differentially spliced isoforms may have different...

["Bioengineering","Bioinformatics","Biotechnology","Genetics","Computational Science"]
doi:10.7717/peerj.4686
118 downloads
536 views

During the past decade, with the significant progress of computational power as well as ever-rising data availability, deep learning techniques became increasingly popular due to their excellent performance on computer vision problems. The size of the Protein Data...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7717/peerj.4750
74 downloads
285 views

Many individuals with posttraumatic stress disorder (PTSD) report experiencing frequent intrusive memories of the original traumatic event (e.g., flashbacks). These memories can be triggered by situations or stimuli that reflect aspects of the trauma and may reflect...

["Neuroscience","Psychiatry and Psychology","Computational Science"]
doi:10.7717/peerj.4701
1 citation
102 downloads
574 views

Malaria is a blood disease caused by the Plasmodium parasites transmitted through the bite of female Anopheles mosquito. Microscopists commonly examine thick and thin blood smears to diagnose disease and compute parasitemia. However, their accuracy depends on smear...

["Infectious Diseases","Computational Science","Data Mining and Machine Learning","Data Science"]
doi:10.7717/peerj.4568
1 citation
365 downloads
737 views

There is fundamental knowledge that during the resting state cerebral activity recorded by electroencephalography (EEG) is strongly modulated by the eyes-closed condition compared to the eyes-open condition, especially in the occipital lobe. However, little research...

["Neuroscience","Human\u2013Computer Interaction","Computational Science"]
doi:10.7717/peerj.4492
77 downloads
624 views

Identifying the separate parts in ultrasound images such as bone and skin plays a crucial role in the synovitis detection task. This paper presents a detector of bone and skin regions in the form of a classifier which is trained on a set of annotated images. Selected...

["Orthopedics","Radiology and Medical Imaging","Rheumatology","Human\u2013Computer Interaction","Computational Science"]
doi:10.7717/peerj.4411
124 downloads
1,162 views

RNA editing modifies transcripts and may alter their regulation or function. In humans, the most common modification is adenosine to inosine (A-to-I). We examined the global characteristics of RNA editing in 4,301 human tissue samples. More than 1.6 million A-to-I...

["Computational Biology","Genetics","Genomics","Cardiology","Computational Science"]
doi:10.7717/peerj.4466
1 citation
164 downloads
958 views

Background EEG may be affected by artefacts hindering the analysis of brain signals. Data-driven methods like independent component analysis (ICA) are successful approaches to remove artefacts from the EEG. However, the ICA-based methods developed so far are often...

["Neuroscience","Neurology","Computational Science"]
doi:10.7717/peerj.4380
152 downloads
592 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

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