Bioinformatics and Genomics

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data

Editor rating: 8 / 10

Anthony Amend –– This paper highlights the use of a synthetic mock community as a standard to filter out bad quality data.
BLAST-based validation of metagenomic sequence assignments

Section Editor rating: 7 / 10

Elena Papaleo –– A nice tool to improve taxonomic classifications
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.
PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads

Section Editor rating: 8 / 10

Elena Papaleo –– The authors present a novel tool, PlasmidSeeker, which could be useful for genomic research and also help the time-consuming and tedious assembly steps.

Discussing these articles

“BLAST-based validation of metagenomic sequence assignments” is published in @thePeerJ: https://t.co/DcQqQttg5J @BrianOndov @dan_sommer @ShashiRatnayake

If you want use next gen sequencing for microbial communities, this is how you need to do it. The new paradigm. @MAJusino @jonpalmer2013 #fungi #microbiome #ecology https://t.co/LZhz1F2vbm

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

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

PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads https://t.co/ltYMfY300w via @thePeerJ