Bioinformatics and Genomics

Article commentary

CMTCN: a web tool for investigating cancer-specific microRNA and transcription factor co-regulatory networks

Editor rating: 6 / 10

Elena Papaleo –– A new web tool to investigate the cooperative action of transcription factors and microRNAs in regulating gene expression with a focus on cancer.
PromoterPredict: sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence

Editor rating: 6 / 10

Yuriy Orlov –– This is classical bioinformatics work on promoter analysis.
imGLAD: accurate detection and quantification of target organisms in metagenomes

Editor rating: 6 / 10

Ian McDonald –– Adds new methodology which will uesful to other research groups
SLiM-Enrich: 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.
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.
The influence of Neanderthal alleles on cytotoxic response

Editor rating: 6 / 10

Chris Vulpe –– Neanderthal alleles may influence our response to toxic stress
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.
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.
What is an archaeon and are the Archaea really unique?

Editor rating: 6 / 10

Joseph Gillespie –– This study entertains an alternative (and rather contentious) hypothesis on the origin of Archaea.
Application of EST-SSR markers developed from the transcriptome of Torreya grandis (Taxaceae), a threatened nut-yielding conifer tree

Editor rating: 9 / 10

Pankaj Jaiswal –– This article on Torreya grandis (Taxaceae) an ancient conifer species that is endemic to southeast China provides an important insight into the population structure and distribution of the species. It also generated the genomic resources necessary to move forward the research on Torreya grandis.

Discussing these articles

CMTCN: a web tool for investigating cancer-specific microRNA and transcription factor co-regulatory networks https://t.co/9w5DKUxBHk @thePeerJ https://t.co/ugpGWL1T5V

PromoterPredict: sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence https://t.co/GuiWmQevZL @thePeerJ https://t.co/WyV5lE6wbp

Should you need to find a specific pathogen in your metagenomic data: https://t.co/i7f5ElPeDz

Hooray! Latest lab publication now out in @thePeerJ https://t.co/PZKtIYTmwJ #Bioinformatics #ComputationalBiology #MolecularBiology

Ensemble learning for detecting gene-gene interactions in colorectal cancer https://t.co/8RP8WSXaFo @thePeerJ https://t.co/nJnoU69bq8

The influence of Neanderthal alleles on cytotoxic response https://t.co/YGeTfKv3wk

26 days ago
It was a pleasure to publish with @thePeerJ, they are very professional. https://t.co/j6zKi376tJ #Bioinformatics #ComputationalBiology #Bayesian #Networks

What is an archaeon and are the Archaea really unique? https://t.co/WOusc9RwPN