Bioinformatics and Genomics

Understanding the spread of de novo and transmitted macrolide-resistance in Mycoplasma genitalium
Hiroshi Nishiura –– AMR modeling elucidated an appropriate STD treatment strategy.
Prediction of antiviral drugs against African swine fever viruses based on protein–protein interaction analysis
Walter de Azevedo Jr. –– In this work, Zhu et al. describe a study that brings an up-to-date set of protein-protein interactions between African swine fever virus and swine. This manuscript may contribute not only to deepen our understanding of the African swine fever virus-swine protein-protein interactions but also help in the development of novel antiviral drugs against this virus.
Identification of key genes and pathways affected in epicardial adipose tissue from patients with coronary artery disease by integrated bioinformatics analysis
Burcu Bakir-Gungor –– The association between epicardial fat and coronary artery disease is an important research field since obesity is increasing world-wide and it is one of the main risk factors associated with cardiovascular disease.
PigLeg: prediction of swine phenotype using machine learning
Walter de Azevedo Jr. –– This paper describes an application of machine learning techniques to assess the state of limbs in pigs based on growth rate and meat characteristics. It might be of interest to those involved in the development of machine learning models and also for researchers working in the study of industrial pig farming.
Discovery of potential targets of Triptolide through inverse docking in ovarian cancer cells
Walter de Azevedo Jr. –– In this manuscript by We et al., the authors applied inverse docking simulations to search for potential targets for Triptolide. This drug is a key component of traditional Chinese medicine “Tripterygiumwilfordii Hook F.” and has shown potent anticancer activities. Here, We et al. indicated potential protein-ligand interactions involving Triptolide and four target genes, Annexin A5, ATP synthase, β-tubulin, and HSP90. The authors highlighted that further work will focus on the signaling pathways involved in ovarian cancer and focused on the potential targets of Triptolide.
FGL2 is positively correlated with enhanced antitumor responses mediated by T cells in lung adenocarcinoma
Walter de Azevedo Jr. –– In this manuscript by Yuan et al., the authors investigated the expression profile and potential functions of fibrinogen-like protein 2 in lung adenocarcinoma. They used bioinformatics tools to determine the potential roles of this protein in lung adenocarcinoma. After an analysis of their results, the authors proposed that fibrinogen-like protein 2 is a beneficial marker for lung adenocarcinoma treatment outcomes.
Iroki: automatic customization and visualization of phylogenetic trees
Thiago Venancio –– Important for visualization phylogenetic trees with customized settings.
A comparative study of machine learning algorithms for predicting acute kidney injury after liver cancer resection
Walter de Azevedo Jr. –– In this work, Lei et al., applied machine learning techniques to assess the likelihood of acute kidney injury after liver cancer resection. Among the machine learning methods used in this study, LightGBM and random forest showed the best overall predictive performance. Their results indicate that features such as age, cholesterol, tumor size, and surgery duration influence the likelihood and development of postoperative acute kidney injury.
The complete mitogenome of Arion vulgaris Moquin-Tandon, 1855 (Gastropoda: Stylommatophora): mitochondrial genome architecture, evolution and phylogenetic considerations within Stylommatophora
Walter de Azevedo Jr. –– In the study conducted by Doğan et al., the authors sequenced and annotated the complete mitogenome of "Arion vulgaris" Moquin-Tandon, 1855 (Gastropoda: Stylommatophora). This species is considered as a serious invasive pest both in agriculture and private gardens. Among their conclusions, the authors highlighted that their sequence analysis revealed that several codons or different branches have experienced diversifying selection suggesting adaptation to new environmental conditions.
Upregulated expression of pyruvate kinase M2 mRNA predicts poor prognosis in lung adenocarcinoma
Cheng Zhan –– This manuscript identified the relationship between PKM2 expression and the clinicopathological characteristics in lung adenocarcinoma.
Bioinformatics and Genomics

Section discussions

Habitat association in the critically endangered Mangshan pit viper (Protobothrops mangshanensis), a species endemic to China @thePeerJ

Investigation of microbial community interactions between Lake Washington methanotrophs using ­­­­­­­genome-scale metabolic modeling @thePeerJ

New paper alert: I am happy to announce that my latest descriptive paper on the cranial osteology of the pleurosternid turtle Pleurosternon bullockii is published today in @thePeerJ, together with @RollotYann & W. Joyce: 1/4

Our new paper on the #endangered #Africanpenguin foraging using benthic environments #novel. Follow the link for some pics/videos of penguins foraging with #sharks #whales #seabird

Bite force data suggests relationship between acrodont tooth implantation and strong bite force @thePeerJ

For all of the tree canker pathogen fans out there, our Oc-j genome paper is out! via @thePeerJ