Bioinformatics and Genomics
Article commentary
18 December 2018
Local persistence of Mann’s soft-haired mouse Abrothrix manni (Rodentia, Sigmodontinae) during Quaternary glaciations in southern Chile
Editor rating: 7 / 10
Juan J. Morrone –– Interesting contribution on the natural history of a poorly known species.
10 December 2018
A direct approach to estimating false discovery rates conditional on covariates
Editor rating: 8 / 10
Jun Chen –– Multiple testing is a fundamental statistical problem in the big data era. Current practices do not consider the auxilary information accompanying the hypotheses, leading to less powerful mutliple testing precedures. This new procedure provides a novel, principled way to use the covariates in the framework of false discovery control, and is expected to be more powerful than the classic procedures when the covariate is informative.
7 December 2018
RIP-MD: a tool to study residue interaction networks in protein molecular dynamics
Section Editor rating: 9 / 10
Elena Papaleo –– Network theory applied to protein structural ensembles is a powerful paradigm to understand structure-function relationship. This work offers a new solid plugin to explore structures from simulations with graph analysis.
6 December 2018
Development and internal validation of a nine-lncRNA prognostic signature for prediction of overall survival in colorectal cancer patients
Editor rating: 7 / 10
Amanda Toland –– This article identified microRNAs whose expression may be useful for prognosis in colorectal cancer. Findings from this study may help to drive prospective clinical studies to evaluate the utility of these microRNAs.
30 November 2018
Analyses of long non-coding RNA and mRNA profiling in the spleen of diarrheic piglets caused by Clostridium perfringens type C
Editor rating: 7 / 10
Jürg Bähler –– This study explores the involvement of both long non-coding and messenger RNAs in host immune and inflammatory responses of piglets to a pathogenic infection with Clostridium.
14 November 2018
Integration of phylogenomics and molecular modeling reveals lineage-specific diversification of toxins in scorpions
Editor rating: 7 / 10
Keith Crandall –– Really nice venom study on scorpions using transcriptomic data in a phylogenetic context.
31 October 2018
SLiMEnrich: computational assessment of protein–protein interaction data as a source of domain-motif interactions
Section Editor rating: 8 / 10
Elena Papaleo –– To experimentally identify functional short linear motifs (SLiMs) is challenged by their very low affinities. This paper introduces a new computational pipeline to assess how useful a certain protein-protein interaction dataset can be to capture SLiMs. I believe that it will be a very nice tool for many researchers working with protein-protein interactions with in-vitro and cellular assays, as well as for computational biologists.
29 October 2018
Ensemble learning for detecting gene-gene interactions in colorectal cancer
Editor rating: 7 / 10
Jin-Kao Hao –– The work tackles an important topic with an interesting approach and advances the state of the art in the field.
19 October 2018
Distributed Bayesian networks reconstruction on the whole genome scale
Editor rating: 8 / 10
Jürg Bähler –– A new method for reconstructing large transcriptional networks that removes some of the computational bottlenecks of such genome-scale analyses.
19 October 2018
BdBG: a bucket-based method for compressing genome sequencing data with dynamic de Bruijn graphs
Section Editor rating: 7 / 10
Elena Papaleo –– A new and interesting approach to improve compression of sequencing data to tackle the related issues in NGS data processing. 
Academic Editors
Average h-index of Editorial Board: 35
Discussing these articles
PLOS Paleo Community @PLOSPaleo
2 days ago
Local persistence of Mann’s soft-haired mouse Abrothrix manni (Rodentia, Sigmodontinae) during Quaternary glaciations in southern Chile https://t.co/xKTKmupwAg
Simina Boca @siminaboca
10 days ago
So happy to see this work with @jtleek on false discovery rates conditional on covariates published in @thePeerJ! https://t.co/Z2uL1cfmp1 #bioinformatics #statistics #rstats.
Behav Ecol Papers @BehavEcolPapers
13 days ago
RIP-MD: a tool to study residue interaction networks in protein molecular dynamics https://t.co/DtDX8WvyPK @thePeerJ https://t.co/U7Cn3IZgPA
Kevin Arbuckle @phylophile
36 days ago
A rare 'proper' (phylogenetic) comparative analysis of venom evolution, in this case of scorpions with a cool use of morphometrics of toxin molecules: https://t.co/jie9MjsN7U
Richard Edwards @cabbagesofdoom
49 days ago
Hooray! Latest lab publication now out in @thePeerJ https://t.co/PZKtIYTmwJ #Bioinformatics #ComputationalBiology #MolecularBiology
Behav Ecol Papers @BehavEcolPapers
52 days ago
Ensemble learning for detecting gene-gene interactions in colorectal cancer https://t.co/8RP8WSXaFo @thePeerJ https://t.co/nJnoU69bq8
aln @systemnaBio
62 days ago
It was a pleasure to publish with @thePeerJ, they are very professional. https://t.co/j6zKi376tJ #Bioinformatics #ComputationalBiology #Bayesian #Networks