Bioinformatics and Genomics

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.
cRegulome: an R package for accessing microRNA and transcription factor-gene expression correlations in cancer
Elena Papaleo –– A nice, comfortable to use R package to infer and visualize the relationship between important regulatory biomolecules, such as transcription factors and microRNAs
Genome-wide analysis of long non-coding RNA expression profile in porcine circovirus 2-infected intestinal porcine epithelial cell line by RNA sequencing
Fernando Spilki –– The study provides new insights into the mechanisms of PCV-2 replication and the virus-cell relationship.
The draft genome of strain cCpun from biting midges confirms insect Cardinium are not a monophyletic group and reveals a novel gene family expansion in a symbiont
Joseph Gillespie –– Important taxonomic implications revealed by phylogeny estimation, and also a novel expansion of a nuclease family
Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics
Chris Creevey –– This is a comprehensive review of the state of the field of coalescence-based phylogenomics, with key recommendations for the future development of this area.
Bioinformatics and Genomics

Section discussions

My article has been published today in @thePeerJ #Genomics #Microbiology #MolecularBiology #Virology #InfectiousDiseases Genomic characterization and phylogenetic analysis of the first SARS-CoV-2 variants introduced in Lebanon

Beyond gene ontology: using #biocuration approach to improve the gene nomenclature and functional annotation of #rice S-domain kinase subfamily Research from @naithani_s et al. @osubpp published in @PeerJLife #Bioinformatics #Genomics #PlantScience

Zhang et al. examine high throughput microRNAs sequencing profile of serum exosomes in women with and without polycystic ovarian syndrome Read the full @PeerJLife article #MolecularBiology #Gynecology

Schoenbachler and Hughey @VUMChealth @BiomedVandy present #pmparser and #PMDB: resources for large-scale, open studies of the biomedical literature Read the full @PeerJLife article #Bioinformatics #DataScience

My article has been published today in @thePeerJ #Bioinformatics #Genetics #Genomics #Zoology

Wyżewski et al. @UniWarszawski @UTSWNews present a novel predicted ADP-ribosyltransferase-like family conserved in eukaryotic evolution Read the full @PeerJLife article #Biochemistry #Bioinformatics #Biophysics #Evolution

My article has been published today in @thePeerJ #Biodiversity #EvolutionaryStudies #Genomics #Taxonomy #Zoology #artemia