Peer-reviewed Articles - General

8 downloads
146 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
34 downloads
279 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
89 downloads
561 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
34 downloads
214 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
52 downloads
351 views

Dramatic increases in data produced by next-generation sequencing (NGS) technologies demand data compression tools for saving storage space. However, effective and efficient data compression for genome sequencing data has remained an unresolved challenge in NGS...

["Bioinformatics","Biotechnology","Computational Science","Data Science"]
doi:10.7717/peerj.5611
120 downloads
703 views

Background The amount of plant data such as taxonomical classification, morphological characteristics, ecological attributes and geological distribution in textual and image forms has increased rapidly due to emerging research and technologies. Therefore, it is...

["Bioinformatics","Human-Computer Interaction","Computational Science"]
doi:10.7717/peerj.5579
1 citation
168 downloads
584 views

Oral squamous cell carcinoma (OSCC) is a major malignant cancer of the head and neck. Long non-coding RNAs (lncRNAs) have emerged as critical regulators during the development and progression of cancers. This study aimed to identify a lncRNA-related signature with...

["Bioinformatics","Oncology","Computational Science"]
doi:10.7717/peerj.5307
225 downloads
952 views

Although most of the cervical cancer cases are reported to be closely related to the Human Papillomavirus (HPV) infection, there is a need to study genes that stand up differentially in the final actualization of cervical cancers following HPV infection. In this...

["Bioinformatics","Computational Biology","Pathology","Computational Science","Data Mining and Machine Learning"]
doi:10.7717/peerj.5285
112 downloads
361 views

Time-resolved phylogenetic methods use information about the time of sample collection to estimate the rate of evolution. Originally, the models used to estimate evolutionary rates were quite simple, assuming that all lineages evolve at the same rate, an assumption...

["Bioinformatics","Genetics","Computational Science"]
doi:10.7717/peerj.5140
64 downloads
460 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
211 downloads
2,097 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
110 downloads
528 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
1 citation
318 downloads
1,062 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
319 downloads
1,112 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
1 citation
619 downloads
2,122 views

Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical...

["Bioinformatics","Computational Biology","Genomics","Human-Computer Interaction","Computational Science"]
doi:10.7717/peerj.4040

Refine by manuscript type

Top subject areas - Articles

Top subject areas - People

View all subject areas