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.
Local persistence of Mann’s soft-haired mouse Abrothrix manni (Rodentia, Sigmodontinae) during Quaternary glaciations in southern Chile

Editor rating: 7 / 10

Juan J. Morrone –– Interesting contribution on the natural history of a poorly known species.
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.
Development and internal validation of a nine-lncRNA prognostic signature for prediction of overall survival in colorectal cancer patients

Editor rating: 7 / 10

Amanda Toland –– This article identified microRNAs whose expression may be useful for prognosis in colorectal cancer. Findings from this study may help to drive prospective clinical studies to evaluate the utility of these microRNAs.
Analyses of long non-coding RNA and mRNA profiling in the spleen of diarrheic piglets caused by Clostridium perfringens type C

Editor rating: 7 / 10

Jürg Bähler –– This study explores the involvement of both long non-coding and messenger RNAs in host immune and inflammatory responses of piglets to a pathogenic infection with Clostridium.
Integration of phylogenomics and molecular modeling reveals lineage-specific diversification of toxins in scorpions

Editor rating: 7 / 10

Keith Crandall –– Really nice venom study on scorpions using transcriptomic data in a phylogenetic context.
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.
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.

Discussing these articles

Non-H3 CDR template selection in antibody modeling through machine learning https://t.co/CM4Jv2ZPwX @thePeerJ https://t.co/eJwun02qIO

Local persistence of Mann’s soft-haired mouse Abrothrix manni (Rodentia, Sigmodontinae) during Quaternary glaciations in southern Chile https://t.co/xKTKmupwAg

So happy to see this work with @jtleek on false discovery rates conditional on covariates published in @thePeerJ! https://t.co/Z2uL1cfmp1 #bioinformatics #statistics #rstats.

RIP-MD: a tool to study residue interaction networks in protein molecular dynamics https://t.co/DtDX8WvyPK @thePeerJ https://t.co/U7Cn3IZgPA

A rare 'proper' (phylogenetic) comparative analysis of venom evolution, in this case of scorpions with a cool use of morphometrics of toxin molecules: https://t.co/jie9MjsN7U

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

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