Bioinformatics and Genomics

Article commentary

Non-H3 CDR template selection in antibody modeling through machine learning

Editor rating: 8 / 10

Elena Papaleo –– This work reports a new method for template selection in antibody modeling using the RosettaAntibody framework. It has the potential to improve the accuracy of antibody structure prediction.
A direct approach to estimating false discovery rates conditional on covariates

Editor rating: 8 / 10

Jun Chen –– Multiple testing is a fundamental statistical problem in the big data era. Current practices do not consider the auxilary information accompanying the hypotheses, leading to less powerful mutliple testing precedures. This new procedure provides a novel, principled way to use the covariates in the framework of false discovery control, and is expected to be more powerful than the classic procedures when the covariate is informative.
RIP-MD: a tool to study residue interaction networks in protein molecular dynamics

Section Editor rating: 9 / 10

Elena Papaleo –– Network theory applied to protein structural ensembles is a powerful paradigm to understand structure-function relationship. This work offers a new solid plugin to explore structures from simulations with graph analysis.
SLiMEnrich: 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.
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.
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.
Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus

Editor rating: 8 / 10

Sven Rahmann –– This work presents the first bioinformatic solution for multi-locus sequence typing from long reads.
Integrated analysis of differentially expressed profiles and construction of a competing endogenous long non-coding RNA network in renal cell carcinoma

Editor rating: 9 / 10

Min Zhao –– This is a good example to integrate data for lncRNAs in a specific cancer type.
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.
Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining

Editor rating: 9 / 10

Hugo Sarmento –– Litterature text-mining to discover gene-gene interaction.

Discussing these articles

Non-H3 CDR template selection in antibody modeling through machine learning @thePeerJ

So happy to see this work with @jtleek on false discovery rates conditional on covariates published in @thePeerJ! #bioinformatics #statistics #rstats.

RIP-MD: a tool to study residue interaction networks in protein molecular dynamics @thePeerJ

Hooray! Latest lab publication now out in @thePeerJ #Bioinformatics #ComputationalBiology #MolecularBiology

93 days ago
It was a pleasure to publish with @thePeerJ, they are very professional. #Bioinformatics #ComputationalBiology #Bayesian #Networks

Study constructs a competitive endogenous RNA network, suggests several lncRNAs of prognostic value in renal cell #kidneyCancer

Krocus for uncorrected long read MLST has been published today in @thePeerJ #Bioinformatics #Microbiology #Epidemiology

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

Well done Sanna, Suwisa and Filip