Bioinformatics and Genomics

Article commentary

Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition in Trypanosoma cruzi

Editor rating: 8 / 10

Tomas Perez-Acle –– A parsimoniously executed research and well written article about transcriptomic studies on T. cruzi that may shed lights on novel targets for the treatment of the chronic disease produced by this parasite.
Facilitating permeability of landscapes impacted by roads for protected amphibians: patterns of movement for the great crested newt

Editor rating: 7 / 10

Stephen Wratten –– vital work on amphibian movement dynamics
Development and validation of a 36-gene sequencing assay for hereditary cancer risk assessment

Editor rating: 8 / 10

D. Gareth Evans –– Panel tests are becoming the bespoke test for cancer predisposition
­Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis

Editor rating: 8 / 10

Valeria Souza –– Streptomyces is a very interesting genera with wide metabolic capabilities, the genome is a confirmation of this interesting metabolism
Finding melanoma drugs through a probabilistic knowledge graph

Editor rating: 7 / 10

Yonghong Peng –– Interesting work.
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.

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

308 days ago
Counsyl's 'Development and validation of a 36-gene sequencing assay for hereditary cancer risk assessment' was one of the top 5 most viewed #MedicalGenetics and #Oncology articles published in @thePeerJ journal in 2017! https://t.co/kmdUy2YD1b

Great! 1st citation of my 'Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition in Trypanosoma cruzi' article published in #OpenAccess journal @thePeerJ https://t.co/uEbwtUndKm

401 days ago
New #roadecology research describes tunnel-fencing system for mitigating road impacts on newts https://t.co/LdNRfEgful

#WebSci17 work presented is based on paper "Finding melanoma drugs through a probabilistic knowledge graph" at https://t.co/lON8fI8vTU

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