Bioinformatics and Genomics

Article commentary

Multi-scale immunoepidemiological modeling of within-host and between-host HIV dynamics: systematic review of mathematical models

Editor rating: 7 / 10

Antonio Palazón-Bru –– A methodological approach to be taken into account to assess the quality of predictive models.
Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data

Editor rating: 7 / 10

Kenta Nakai –– I believe that the manuscript deals with a very new and important topic and might be cited well.
Ananke: temporal clustering reveals ecological dynamics of microbial communities

Editor rating: 7 / 10

A. Murat Eren –– Ananke provides a framework to investigate temporal sampling efforts by organizing marker gene sequences into clusters of ecological patterns. While Hall et al. reports improvement over the current marker gene workflows with this approach, they demonstrate how clustering data based on sequence identity may obscure detailed investigations of ecological patterns in time-series data.
Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

Editor rating: 8 / 10

Michael Hallett –– The paper addresses the potential of viral metagenomics in a general fashion that could impact the design of many studies.
Fish Ontology framework for taxonomy-based fish recognition

Editor rating: 7 / 10

Mohammad Shamsur Rahman –– In the past, taxonomy was not a lucrative branch of science but due to the development of web based taxonomy, now, it's rather attractive to do fish taxonomy!
Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine

Editor rating: 8 / 10

Vincent Thomas –– First description of the genome of a new, dominant bacterial species that is fund in rat's ileum. Can have significant impact on our understanding of this ecosystem.
BioFuelDB: a database and prediction server of enzymes involved in biofuels production

Editor rating: 9 / 10

Walter de Azevedo Jr. –– This work may be of interest for researchers who work on the development of databases for proteins related to biofuel development.
RNA helicase domains of viral origin in proteins of insect retrotransposons: possible source for evolutionary advantages

Editor rating: 7 / 10

Yegor Vassetzky –– The MS describes the transfer of viral helicases to insect retrotransposons.
Targeted NGS for species level phylogenomics: “made to measure” or “one size fits all”?

Editor rating: 8 / 10

Keith Crandall –– This paper effectively demonstrates the utility of designing clade specific markers from hybrid-enrichment compared to more global approaches and provides custom scripts to analyze transcriptome and whole genome data to identify such markers.
A laid-back trip through the Hennigian Forests

Editor rating: 7 / 10

Zemin Ning –– The paper has some new ideas and people who are working in the same area should be interested.

Discussing these articles

412 days ago
My article has been published today in @thePeerJ https://t.co/TEBQq1Zmr8 #Bioinformatics #ComputationalBiology #Genomics

Ananke: temporal clustering reveals ecological dynamics of microbial communities https://t.co/pP3Xxt2Err w @mikehall_dal @rob_beiko @quendi

Benchmarking viromics: in silico evaluation of metagenome-enabled estim of viral community composition & diversity https://t.co/lfkbrIeFdz

Genomic and functional analysis of <i>romboutsia ilealis</i> crib<sup>t</s... - Gerritsen J et al. - https://t.co/LGlx3joeOR #microbiome

Fish Ontology framework for taxonomy-based fish recognition https://t.co/saBKWguklj via @thePeerJ

I find report controversial, have to read more carefully though - [viral] RNA helicase in insect retrotransposons https://t.co/Lh6DIE97T8

BioFuelDB: a database and prediction server of enzymes involved in biofuels production https://t.co/0QDMHoJRW0… https://t.co/7EdgdJAJ6G

Challenging phylogeny? You need "made to measure" hyb-seq markers. Paper & Kadlec's new tools out at @thePeerJ https://t.co/LPhEsYLEQZ https://t.co/kZwho1xThj