Bioinformatics and Genomics

Editors' Picks

Predictive models for stage and risk classification in head and neck squamous cell carcinoma (HNSCC)
Mitchell Stark –– A comprehensive approach to a complex issue.
Adaptive Metropolis-coupled MCMC for BEAST 2
Jun Chen –– The author proposed an adaptive Metropolis-coupled MCMC algorithm for Bayesian phylogenetics and implemented in their software package BEAST 2. It is a significant methodological contribution to the field.
Anti-COVID-19 multi-epitope vaccine designs employing global viral genome sequences
Jun Chen –– The topic is highly significant since the only solution to the pandemic seems to be an effective vaccine. The manuscript will surely attract numerous readers.
Identification and validation of prognostic signature for breast cancer based on genes potentially involved in autophagy
Philip Coates –– The work provides new information into the role of autophagy in breast cancer progression. The identification of a gene signature will improve prognostic indicators in the clinic and may lead to application of available drugs that target autophagy for therapy.
The regulatory genome constrains protein sequence evolution: implications for the search for disease-associated genes
Hossein Khiabanian –– The paper present a novel approach in assessing tissue-specific impact of gene expression on protein sequence evolution.
Detecting the outbreak of influenza based on the shortest path of dynamic city network
Yong Wang –– Forecasting flu outbreak based on data science is promising, challenging, and urgently needed. This manuscript proposed a new metric based on the shortest path in dynamic city network.
Very few sites can reshape the inferred phylogenetic tree
James Procter –– Reproducible phylogenetic studies remain relatively scarce, despite the ready availability of informatics tools to enable reproducible studies to be published. This paper focuses on the impact on one critical aspect of phylogenetic methodology: 'filtering of phylogenetically informative sites' - they provide both an elegant demonstration of the how phylogenetic signals can be removed or enhanced by selecting sites according to one or another hypothesis, and useful procedures for identifying additional taxa to increase the potential information in a phylogenetic dataset, and identifying phylogenetically informative sites without the application of arbitrary thresholds to omit columns in multiple sequence alignments.
Transcriptome analysis reveals a reprogramming energy metabolism-related signature to improve prognosis in colon cancer
Michael Hallett –– Energy metabolism is a key prognostic marker in colon cancer; good biomarker panels are therefore important for polling the state of this process in tumors.
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.
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.
Bioinformatics and Genomics

Section discussions

Predictive models for stage and risk classification in head and neck squamous cell carcinoma (HNSCC) @thePeerJ

Analysis of dynamic and widespread lncRNA and miRNA expression in fetal sheep skeletal muscle @thePeerJ

Our article "The reuse of public datasets in the life sciences: potential risks and rewards" has been published in @thePeerJ #Bioinformatics #ComputationalBiology #Genomics #ComputationalScience #DataScience #100DaysOfCode

Genetic diversity and structure of the critically endangered Artocarpus annulatus, a crop wild relative of jackfruit (A. heterophyllus) @thePeerJ

Identification of NUF2 and FAM83D as potential biomarkers in triple-negative breast cancer @thePeerJ

Our article has been published today in @PeerJCompSci  To learn more about FAIR workflows: #DataScience #WorldWideWebandWebScience #SoftwareEngineering