Bioinformatics and Genomics

Article commentary

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.
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.
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.
Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales

Editor rating: 7 / 10

Peter Dunfield –– Will specificaly interest those working on methanogenesis, but more broadly the technical novelty may appeal to many microbial ecologists interested in mining metagenomic datases.
Exome sequencing study of 20 patients with high myopia

Editor rating: 7 / 10

Yong Wang –– This paper performed exom sequencing to study high myopia and identified several potential disease genes. The data and analysis provides a valuable resources for the field.
Plant data visualisation using network graphs

Editor rating: 7 / 10

Massimiliano Zanin –– An interesting demonstration on how data can be represented using new web-based technologies.
A minimal set of internal control genes for gene expression studies in head and neck squamous cell carcinoma

Section Editor rating: 7 / 10

Elena Papaleo –– An interesting solution to identify a subset of reference genes for qualitative qPCR of cancer samples
Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches

Editor rating: 7 / 10

Jun Chen –– The article provides a timely and informative comparison of the state-of-the-art error-correction pipelines. The presented results can guide the selection of appropriate pipelines that suit the research needs.

Discussing these articles

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

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

Nice approach for using large-scale mining of specific genes to identify novel lineages of important metabolic genes https://t.co/Edf2AMrCCh via @thePeerJ

Plant data visualisation using network graphs https://t.co/jNhxh3QGUR @thePeerJ https://t.co/WtIvd7p08x

our recent paper on a minimal set of internal control genes for gene expression studies in head and neck squamous cell carcinoma busts old myths on housekeeping genes in hnscc gene expression studies https://t.co/vf1rBZuUl9 #openscience

Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches https://t.co/gdqfcA3Qhd w @BetaScience