Bioinformatics and Genomics

Editors' Picks

Analysis of deubiquitinase OTUD5 as a biomarker and therapeutic target for cervical cancer by bioinformatic analysis
Walter de Azevedo Jr. –– In this research paper, the authors analyzed the expression of (ovarian tumor protease) deubiquitinase 5 (OTUD5) in cervical cancer and its relationship with clinical characteristics. This study provided new insights for further research on its regulatory mechanism in tumors.
A game-theoretic model of Monkeypox to assess vaccination strategies
Hiroshi Nishiura –– Excellent application study
Identification of SPRR3 as a novel diagnostic/prognostic biomarker for oral squamous cell carcinoma via RNA sequencing and bioinformatic analyses
Xuehui Huang –– The work may provide important biomarkers in clinical test.
GISA: using Gauss Integrals to identify rare conformations in protein structures
Elena Papaleo –– The identification of rare conformations in protein structures is a challenging and important task. These conformations are often critical for protein function. This work provide an interesting different way to tackle this problem.
DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics
Tomas Hrbek –– A rapid, efficient and robust tool for analyzing RADseq and other related data. Has the potential to be widely used by the scientific community.
Contributions of Latin American researchers in the understanding of the novel coronavirus outbreak: a literature review
Robert Winkler –– The review demonstrates the general performance of scientific research in Latin America in response to a critical threat. Thus, it might influence political decision-makers.
The mitochondrial genome of Acrobeloides varius (Cephalobomorpha) confirms non-monophyly of Tylenchina (Nematoda)
Jia-Yong Zhang –– This research provide the complete mitochondrial genome of Acrobeloides varius.
The spindle assembly checkpoint and speciation
Ugo Bastolla –– This paper is important in the context of sympatric speciation, where it supports a speciation mechanism based on the variation of the number of chromosomes through sound molecular biology reasoning and mathematical modelling.
Integrated analysis of lymphocyte infiltration-associated lncRNA for ovarian cancer via TCGA, GTEx and GEO datasets
Walter de Azevedo Jr. –– In this study, Wu et al identified long non-coding RNA-associated competing endogenous RNA (ceRNA) axes that could delineate more reliable prognostic parameters of high-grade serous ovarian cancer, and to examine the long non-coding RNAs’ possible mechanism of in lymphocyte infiltration. The authors were able to define numerous prognostic biomarkers for the incidence and development of high-grade serous ovarian cancer and constructed a network for ceRNA axes.
Identification of key miRNAs in the progression of hepatocellular carcinoma using an integrated bioinformatics approach
Walter de Azevedo Jr. –– Previously studies indicated the association of aberrant expression of microRNAs (miRNAs) and transcriptional factors (TFs) with the development of hepatocellular carcinoma. In work conducted by Zheng et al., the authors investigated potential transcriptomic markers of hepatocellular carcinoma using the analysis of microarray datasets. They used datasets available in the GEO database. Their analysis indicated that two miRNAs—hsa-mir-106b and hsa-mir-195 are identified as potential classifiers of hepatocellular carcinoma.
Bioinformatics and Genomics

Section discussions

New in @thePeerJ Universality vs experience: a cross-cultural pilot study on the consonance effect in music at different altitudes Spoiler - No effect of altitude :)

Rodents’ responses to manipulated plant litter and seed densities: implications for restoration @thePeerJ

Predicting the effect of variants on splicing using Convolutional Neural Networks @thePeerJ