Bioinformatics and Genomics

Circular RNAs as potential biomarkers and therapeutics for cardiovascular disease
Yuriy Orlov –– Circular RNA discussion is an emerging trend in biomedicine. Review of circRNA application as novel biomarkers brings attention of the readers.
Genome-wide identification and expression profile analysis of the Hsp20 gene family in Barley (Hordeum vulgare L.)
Axel Tiessen –– Comprehensive bioinformatic description of the heat shock protein family 20 (HSP20) in several plants (Arabidopsis, rice and barley)
Integrated analysis reveals five potential ceRNA biomarkers in human lung adenocarcinoma
Shi-Cong Tao –– Very valuable research
Risk factors for repeat percutaneous coronary intervention in young patients (≤45 years of age) with acute coronary syndrome
Cheng-Chia Yu –– routinely screening for disorders of glucose metabolism and a risk stratification of premature ACS patients
Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands
Keith Crandall –– Metagenomics is a powerful approach to survey microbial communities and here these authors demonstrate the added utility of long-read metagenomics focused on viral populations.
The synergistic effect of concatenation in phylogenomics: the case in Pantoea
Mikhail Gelfand –– The authors have done a very good job in evaluating he commonly used phylogenomics techniques and comparing it with alternative approaches. In a particular application to Pantoea, they've studied possible sources of noise, like homologous recombination. Hence, this paper is interesting from both methodological and evolutionary perspective.
virMine: automated detection of viral sequences from complex metagenomic samples
Gerard Lazo –– The authors have provided a diverse set of test examples, have provided the software to the public, and have developed containerized test environments. This tools should allow someone working with metagenomes to easily determine if this tool is right for their use-case environment.
Salivary LDOC1 is a gender-difference biomarker of oral squamous cell carcinoma
Cheng-Chia Yu –– Salivary LDOC1 is a gender-difference biomarker of oral cancer patients
Ozymandias: a biodiversity knowledge graph
Keith Crandall –– Knowledge graphs for biodiversity studies is a novel concept that will hopefully provide unique insights!
Complete plastome sequence of Iodes cirrhosa Turcz., the first in the Icacinaceae, comparative genomic analyses and possible split of Idoes species in response to climate changes
Axel Tiessen –– The plastidial genomic sequence of Iodes cirrhosa (Icacinaceae family) was determined and characterized in detail. The plastome contained 134 genes in total, corresponding to 112 unique genes encoding 80 proteins, 28 tRNAs, and 4 rRNAs. The genome also had 21 intron-containing genes, most of them had only one intron in each of them. A phylogeny was reconstructed with the plastomes of the five Iodes species. Positive evolutionary selection was detected for 52 amino acid sites from 27 genes. The divergence time of the six Iodes species was found to be 34.40 Mya.
Bioinformatics and Genomics

Section discussions

fRNAkenseq: a fully powered-by-CyVerse cloud integrated RNA-sequencing analysis tool @thePeerJ

Full-length transcriptome and targeted metabolome analyses provide insights into defense mechanisms of Malus sieversii against Agrilus mali @thePeerJ

Individual #behavioral type captured by a Bayesian model comparison of cap making by sponge crabs @thePeerJ

Our paper about transcriptomic changes in Trypanosoma cruzi is now published in @thePeerJ #Genomics #Microbiology #Parasitology

Drivers of beta diversity in ancient (Cassian Fm.) versus modern #reef-associated soft-bottom environments @VanessaJBeta via @thePeerJ #paleobiology #evolution #biodiversity

Another KUENM Group publication is out. This contribution points out and examines a problem with the traditional biodiversity inventory completeness statistics when applied to truly big data. @thePeerJ #Biodiversity