Bioinformatics and Genomics

Article commentary

Comprehensive circular RNA expression profile in radiation-treated HeLa cells and analysis of radioresistance-related circRNAs

Editor rating: 7 / 10

Alfonso Valencia –– The article is study of the potential functional importance of differentially expressed Circular RNAs in a particular biological system, i.e response to radiation in HeLa cells. Function is investigated in terms of enrichment in Gene Ontology and KEGG pathways. The study is representative of a general class of functional studies of biological systems combining experimental determination and functional enrichment.
Restriction digest screening facilitates efficient detection of site-directed mutations introduced by CRISPR in C. albicans UME6

Editor rating: 7 / 10

Bettina Böttcher –– Nice method.
MIPhy: identify and quantify rapidly evolving members of large gene families

Editor rating: 7 / 10

Daniel Lahr –– There really are very few pieces of software that focus on analyses of large gene families. The issue is a complicated one, and the scarcity of software actually represents the attitude of researchers to shy away from such questions. If well accepted, this has the potential to spur new ways of looking at old questions.
Exosomes in cancer: small vesicular transporters for cancer progression and metastasis, biomarkers in cancer therapeutics

Editor rating: 7 / 10

J. Thomas Sanderson –– Good, solid and timely review of the entitled topic.
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.

Discussing these articles

Comprehensive circular RNA expression profile in radiation-treated HeLa cells and analysis of radioresistance-related circRNAs https://t.co/NU196QuLYC @thePeerJ https://t.co/PVoYwRK8ge

Trying to understand large gene family? Try MIPhy by @DaveAScientist, @johngilleard and me. Published today in @thePeerJ https://t.co/Ecll4Xj17v #Bioinformatics #ComputationalBiology #EvolutionaryStudies

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

169 days ago
Exosomes and cancer https://t.co/eWbFB5K3po #exosomes #microvesicle #cancer #tumor

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