Bioinformatics and Genomics

Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining

Section Editor rating: 7 / 10

Elena Papaleo –– An interesting comprehensive text mining approach to annotate genes
On the efficiency of the genetic code after frameshift mutations

Editor rating: 7 / 10

Thomas Tullius –– This clearly written paper addresses an important issue in understanding the stability of the genetic code: how frameshift mutations are accommodated.
EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation

Section Editor rating: 7 / 10

Elena Papaleo –– An interesting machine learning application to enzyme classification at the structural level.
FluxPyt: a Python-based free and open-source software for 13C-metabolic flux analyses

Section Editor rating: 7 / 10

Elena Papaleo –– The program FluxPyt is user-friendly and help the analyses of metabolic flux.
phylopath: Easy phylogenetic path analysis in R

Section Editor rating: 7 / 10

Elena Papaleo –– A nice R-based tool to perform phylogenetic path analyses.
Gene characteristics of the complete mitochondrial genomes of Paratoxodera polyacantha and Toxodera hauseri (Mantodea: Toxoderidae)

Editor rating: 7 / 10

Antonio Amorim –– This paper contributes significantly to the knowledge of mitogenomes evolution.
Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences

Editor rating: 7 / 10

Donovan Parks –– Detailed study showing the limitations of using 16S rRNA and ITS sequences for establishing the taxonomic profiles of environmental samples.
Natural history bycatch: a pipeline for identifying metagenomic sequences in RADseq data

Section Editor rating: 6 / 10

Elena Papaleo –– It is a nice and meaningful methodological work for processing metagenomic data.
Pathways of topological rank analysis (PoTRA): a novel method to detect pathways involved in hepatocellular carcinoma

Editor rating: 6 / 10

Alfonso Valencia –– The analysis of cancer-related functions/pathways is interesting. The overall computational approach interesting and can be significant. In this context, the possible implications and biological interpretation of gene expression variability is relatively new.
GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data

Section Editor rating: 6 / 10

Elena Papaleo –– Careful normalization is a crucial step in handling data such as the ones from the microbiome and the method here presented is nicely convincing.

Discussing these articles

Well done Sanna, Suwisa and Filip

An article I handled as editor has been published today @thePeerJ: On the efficiency of the genetic code after frameshift mutations, by Regine Geyer​ and Amir Madany Mamlouk​​. https://t.co/qNRwGXvPbK #Bioinformatics #EvolutionaryStudies #Genetics

'EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation' article published in #OpenAccess journal @thePeerJ https://t.co/1TBCS7IW2f

FluxPyt: a Python-based free and open-source software for 13C-metabolic flux analyses https://t.co/gAFNlfjQGQ by @thePeerJ #bioinformatics

The paper for the phylopath package is now published in @PeerJ. It includes a worked example of a study by @AGonzalezVoyer, @MGS_tweets and others. PDF typesetting looks quite good! https://t.co/SGxRcVK4qx

@uribe_convers @hollybik Just saw this one which looks cool: https://t.co/wtgOsaxmev

38 days ago
Accuracy of taxonomy prediction https://t.co/f7MjLz3bKf via @thePeerJ

GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data https://t.co/knvDTifPoN