Bioinformatics and Genomics

Article commentary

A novel genus and cryptic species harboured within the monotypic freshwater crayfish genus Tenuibranchiurus Riek, 1951 (Decapoda: Parastacidae)

Editor rating: 7 / 10

Keith Crandall –– This paper demonstrates that there is significant hidden diversity still to be discovered and described in this interesting group of Australian freshwater crayfish.
Whole genome sequencing of group A Streptococcus: development and evaluation of an automated pipeline for emmgene typing

Editor rating: 7 / 10

Keith Crandall –– This study presents a novel bioinformatics pipeline for emm gene typing from whole genome sequence data from Streptococcus, the most common etiological agent of throat infections.
CRF: detection of CRISPR arrays using random forest

Editor rating: 9 / 10

Gian Tartaglia –– The identification if CRISPR arrays is crucial to understand how the system works and can be manipulated in applications
Floral pathway integrator gene expression mediates gradual transmission of environmental and endogenous cues to flowering time

Editor rating: 8 / 10

Gerrit Beemster –– The approach integrates a large amount of data on flowering time regulation and provides a new method for this incorporating modelling with expression and phenotypic data.
gb4gv: a genome browser for geminivirus

Editor rating: 8 / 10

Ana Grande-Pérez –– A comprehensive and useful tool that will aid plant science community in the study of geminivirus genomics
Comparative proteomics of Rhizopus delemar ATCC 20344 unravels the role of amino acid catabolism in fumarate accumulation

Editor rating: 8 / 10

Vladimir Uversky –– Interesting and important data are provided on the peculiarities and mechanisms of fumarate accumulation in Rhizopus delemar ATCC 20344
Systematic drug repositioning through mining adverse event data in

Editor rating: 8 / 10

Walter de Azevedo Jr. –– Drug repositioning is a hot topic in drug development and application of computational tools to improve the chances of success of this methodology is of great interest for a broad spectrum of researchers. The present manuscript reports an interesting analysis of drug repositioning using data from randomized clinical trials available at The authors used text mining tools to extract serious adverse event data and their results indicate new uses of existing drugs. In my view, the most important contribution of the present work is the method itself, which could be used for drug repositioning not only for cancer but also for other diseases.
Curvature reduces bending strains in the quokka femur

Editor rating: 7 / 10

Philip Cox –– Because, although the focus of the article is one particular bone in one species of mammal, the results have implications for understanding the biomechanics of bones much more widely.
Effect of method of deduplication on estimation of differential gene expression using RNA-seq

Editor rating: 7 / 10

Vsevolod Makeev –– It contains a valuable know-how, the important part of bioinformatics practice that is seldom become explained in detail in publications.
BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation

Editor rating: 8 / 10

Ugo Bastolla –– I think that the new method will make a useful contribution in the fast developing field of microbiota analysis

Discussing these articles

153 days ago
@USCDornsife has done a great rundown on our most recent work! Here are the papers discussed - | |

Novel genus/species in Tenuibranchiurus via @thePeerJ

CRF(CRISPR Finder by Random Forest)ランダムフォレストで〜2,000以上の微生物ゲノムのCRISPRアレイ同定 PeerJ 0425

My article has been published today in @thePeerJ #Bioinformatics #Genomics #Microbiology #InfectiousDiseases

Floral pathway integrator gene expression mediates gradual transmission of environmental and endogenous… @thePeerJ

Systematic drug repositioning through mining adverse event data in