Bioinformatics and Genomics

Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets

Editor rating: 8 / 10

Ugo Bastolla –– The method presented in this paper may be very useful to identify which taxonomic groups are driving the differences in the composition of microbial communities detected in different environmental samples with varying properties, thus facilitating the analysis of metagenomic experiments and large microbial communities.
Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy

Editor rating: 7 / 10

Marina Kalyuzhnaya –– The article provides first insides into microbial communities of an unusual sub-terrestrial ecosystem.
RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing

Editor rating: 7 / 10

Alexander Mikheyev –– This is a useful tool, which may be of use to many scientists studying TE insertions.
The DNA methylation level against the background of the genome size and t-heterochromatin content in some species of the genus Secale L

Editor rating: 7 / 10

Gerard Lazo –– With reference genomes taking shape and becoming ready; background experiments to build hypotheses on genome structure are still relevant. Though a clear answer may not have been presented here, a negative result is not necessarily unhelpful; another approach should be contemplated.
Three new karst-dwelling Cnemaspis Strauch, 1887 (Squamata; Gekkoniade) from Peninsular Thailand and the phylogenetic placement of C. punctatonuchalis and C. vandeventeri

Editor rating: 8 / 10

Keith Crandall –– As biodiversity is continuously threatened and negatively impacted, studies like this that not only describe the basic taxonomic units of biodiversity, but place that information in a rich, phylogenetic, ecological, morphological, and geographic setting are essential.
Osmolyte regulation by TonEBP/NFAT5 during anoxia-recovery and dehydration–rehydration stresses in the freeze-tolerant wood frog (Rana sylvatica)

Editor rating: 8 / 10

Dunxian Tan –– This observation provides novel information in the field of ischemia/reperfusion protection
Resources available for autism research in the big data era: a systematic review

Editor rating: 7 / 10

Jon Brock –– Autism research is increasingly moving towards a "big data" approach. This review of the available databases will be an invaluable resource for researchers in the field.
Optimizing the use of a sensor resource for opponent polarization coding

Editor rating: 9 / 10

Mario Negrello –– This article contains an insighful and thorough analysis of the physical constraints for encoding and the processing of information in polarized vision, and more specifically, in polarization opponency. This article is exemplary for the field of neural coding in that it covers multiple angles in the analysis with solid logics and deep appreciation for the biological phenomenon under study.
Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons

Editor rating: 8 / 10

Blanca Landa –– The new pipeline will be a valuable tool for people woorking in NGS of 16S amplicons
Hydrogel scaffolds promote neural gene expression and structural reorganization in human astrocyte cultures

Editor rating: 7 / 10

Luciano Fadiga –– technically sound, it addresses a relevant topic

Discussing these articles

@methanoJen @JasonDewees @SoutheastGeobio @mousquemere The photo on the first slide, opposite the Lost City photo, is of an ultrabasic spring at the Voltri Massif in Italy. https://t.co/aHHHd2J7e4

@mason_lab Also a problem for microbiome data! Useful alternatives: https://t.co/tJ2eQwuZeW https://t.co/pvBA5jm9ys https://t.co/OvgkUIB0CL