Peer-reviewed Articles - Biology

This paper describes the development and application of a suite of tools, called PBxplore, to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). Proteins are highly dynamic macromolecules, and a classical way to analyze their...

["Bioinformatics","Computational Biology","Molecular Biology"]
doi:10.7717/peerj.4013
13 downloads
107 views

Background Oral tongue squamous cell carcinoma (OTSCC) is the most common subtype of oral cancer. A predictive gene signature is necessary for prognosis of OTSCC. Methods Five microarray data sets of OTSCC from the Gene Expression Omnibus (GEO) and one data set...

["Bioinformatics","Computational Biology","Genetics","Genomics","Oncology"]
doi:10.7717/peerj.4062
43 downloads
233 views

Peripheral nerves are extremely complex biological structures. The knowledge of their response to stretch is crucial to better understand physiological and pathological states (e.g., due to overstretch). Since their mechanical response is deterministically related...

["Bioengineering","Computational Biology","Neurology"]
doi:10.7717/peerj.4005
70 downloads
280 views

Background The emergence of functions in biological systems is a long-standing issue that can now be addressed at the cell level with the emergence of high throughput technologies for genome sequencing and phenotyping. The reconstruction of complete metabolic networks...

["Bioinformatics","Computational Biology","Artificial Intelligence"]
doi:10.7717/peerj.3860
52 downloads
371 views

Cataloging mutated driver genes that confer a selective growth advantage for tumor cells from sporadic passenger mutations is a critical problem in cancer genomic research. Previous studies have reported that some driver genes are not highly frequently mutated...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj-cs.133
112 downloads
587 views

RNA-Seq is a recent and efficient technique that uses the capabilities of next-generation sequencing technology for characterizing and quantifying transcriptomes. One important task using gene-expression data is to identify a small subset of genes that can be used...

["Bioinformatics","Computational Biology","Statistics","Medical Genetics","Computational Science"]
doi:10.7717/peerj.3890
870 downloads
8,270 views

Next-generation sequencing of 16S ribosomal RNA is widely used to survey microbial communities. Sequences are typically assigned to Operational Taxonomic Units (OTUs). Closed- and open-reference OTU assignment matches reads to a reference database at 97% identity...

["Bioinformatics","Computational Biology","Microbiology"]
doi:10.7717/peerj.3889
67 downloads
353 views

Objective The objective of this study is to conduct a systematic review of multi-scale HIV immunoepidemiological models to improve our understanding of the synergistic impact between the HIV viral-immune dynamics at the individual level and HIV transmission dynamics...

["Computational Biology","Mathematical Biology","Epidemiology","HIV","Immunology"]
doi:10.7717/peerj.3877
93 downloads
639 views

We have developed a machine learning approach to predict stimulation-dependent enhancer-promoter interactions using evidence from changes in genomic protein occupancy over time. The occupancy of estrogen receptor alpha (ERα), RNA polymerase (Pol II) and histone...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.3742
104 downloads
580 views

The crustacean order Stomatopoda comprises seven superfamilies of mantis shrimps, found in coastal waters of the tropics and subtropics. These marine carnivores bear notable raptorial appendages for smashing or spearing prey. We investigated the evolutionary relationships...

["Computational Biology","Evolutionary Studies"]
doi:10.7717/peerj.3844
87 downloads
444 views

Background The rapid increase in antibiotic resistance by various bacterial pathogens underlies the significance of developing new therapies and exploring different drug targets. A fraction of bacterial pathogens abbreviated as ESKAPE by the European Center for...

["Bioinformatics","Computational Biology","Microbiology","Pharmacology"]
doi:10.7717/peerj.3765
80 downloads
376 views

Background C-X-C chemokine ligand 12 (CXCL12) has important implications in breast cancer (BC) pathogenesis. It is selectively expressed on B and T lymphocytes and is involved in hematopoiesis, thymocyte trafficking, stem cell motility, neovascularization, and...

["Bioinformatics","Computational Biology","Genetics","Epidemiology"]
doi:10.7717/peerj.3822
207 downloads
1,052 views

Plants play a crucial role in foodstuff, medicine, industry, and environmental protection. The skill of recognising plants is very important in some applications, including conservation of endangered species and rehabilitation of lands after mining activities....

["Bioinformatics","Computational Biology","Plant Science"]
doi:10.7717/peerj.3792
105 downloads
988 views

Clustered regularly interspaced short palindromic repeat (CRISPR) systems are the adaptive immune systems of bacteria and archaea against viral infection. While CRISPRs have been exploited as a tool for genetic engineering, their spacer sequences can also provide...

["Bioinformatics","Computational Biology","Ecology","Genomics","Microbiology"]
doi:10.7717/peerj.3788
98 downloads
373 views

Background The endoplasmic reticulum plays an important role in many cellular processes, which includes protein synthesis, folding and post-translational processing of newly synthesized proteins. It is also the site for quality control of misfolded proteins and...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.3561

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