Bioinformatics and Genomics

PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks

Editor rating: 9 / 10

Walter de Azevedo Jr. –– The authors report the development and application of a suite of tools, called PBxplore. This computational tool can be used to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). It is an interesting development for scientists interesting in molecular dynamics simulations of protein structures.
Coral-associated viral communities show high levels of diversity and host auxiliary functions

Editor rating: 7 / 10

Fabiano Thompson –– addresses virus diversity in reef systems, and roles in genome plasticity.
Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion

Editor rating: 8 / 10

Peter Prentis –– This article is the first comparative analysis of marsupial microbiomes.
The intervals method: a new approach to analyse finite element outputs using multivariate statistics

Editor rating: 7 / 10

Philip Cox –– This article describes a new technique for analysing the results of FEA. It has the potential to be used widely in the discipline.
voomDDA: discovery of diagnostic biomarkers and classification of RNA-seq data

Editor rating: 7 / 10

Zemin Ning –– RNA-seq analysis is very useful and popular and we should expect general interests from the community.
Trichoplax adhaerens reveals a network of nuclear receptors sensitive to 9-cis-retinoic acid at the base of metazoan evolution

Editor rating: 7 / 10

Christopher Cooper –– One of very few articles on Trichoplax, an emerging model organism of increasing importance in evo-devo biology.
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.

Discussing these articles

My article has been published today in @thePeerJ https://t.co/jHwNBx4ZGb #Bioinformatics #ComputationalBiology #MolecularBiology

New #GBR coral virome article published in @thePeerJ https://t.co/ijZU4k7qwM #Genomics #MarineBiology #Microbiology #MolecularBiology #Virology

246 days ago
Doing our bit to fill the knowledge gap on iconic Australian marsupials @thePeerJ https://t.co/GSQMAk2Hfu #Genomics #Microbiology

Our new paper in @thePeerJ presents a new method to merge #FEA outputs with multivariate statistics. #biomechanics https://t.co/ozapJDmSKt https://t.co/cTgEw6xs4H

Trichoplax adhaerens reveals a network of nuclear receptors sensitive to 9-cis-retinoic acid at the base of... https://t.co/EpbPqCZ0Qh

295 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