Bioinformatics and Genomics

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.
Identification of an eight-gene signature for survival prediction for patients with hepatocellular carcinoma based on integrated bioinformatics analysis
Maria Cristina Albertini –– Important information related to hepatocellular carcinoma prediction has been discovered.
Bioinformatics and Genomics

Section discussions

#AmazingBeetles Barcoding Australian Cetoniinae via @thePeerJ

Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L. @thePeerJ #EvolutionaryStudies #Genomics #PlantScience @WVUBiology

Check out our latest devil paper where we show inbreeding depression in a disease free population. Strong impetus for genetic rescue as part of Wild Devil Recovery program. One of ⁦@DrBeckyMae⁩‘s PhD chapters. ⁦@HoggCarolyn⁩ ⁦@CEGrueber⁩

ということで、論文が公開されました。 Modeling of plant cover class data

Comprehensive assessment of the coupling coordination degree between urbanization and ecological environment in the Siberian and Far East Federal Districts, Russia from 2005 to 2017 @thePeerJ