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.
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.
PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads

Section Editor rating: 8 / 10

Elena Papaleo –– The authors present a novel tool, PlasmidSeeker, which could be useful for genomic research and also help the time-consuming and tedious assembly steps.
Out of Asia: mitochondrial evolutionary history of the globally introduced supralittoral isopod Ligia exotica

Editor rating: 8 / 10

Curtis Daehler –– This work provides genetic evidence suggesting the native range of a widely distributed animal that was accidentally spread by humans starting hundreds of years ago.
The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages

Editor rating: 8 / 10

Xavier Pochon –– This study provides the first range-wide phylogeographic study of the banded coral shrimp S. hispidus, extending across more than 27,000 km of the globe. Coalescence analysis brings evidence that an isolated Indo-Pacific lineage evolved from a rare dispersal event from the Atlantic around South Africa via the Benguela Current, thereby colonizing the Indian and Pacific Oceans, followed by dispersal across the Indo-Pacific in the last 200,000 years. Surprisingly, this benthic coral reef associated shrimp shows a single haplotype dominating the largest continuous tropical oceanic expanse on the planet.

Discussing these articles

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

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

Study constructs a competitive endogenous RNA network, suggests several lncRNAs of prognostic value in renal cell #kidneyCancer https://t.co/00othpy2X5 https://t.co/f0vg7PIoRR

Krocus for uncorrected long read MLST has been published today in @thePeerJ https://t.co/zlZchJRjM6 #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 https://t.co/LZhz1F2vbm

Well done Sanna, Suwisa and Filip

PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads https://t.co/ltYMfY300w via @thePeerJ

The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages https://t.co/TXOB7dyxro https://t.co/QkZN9Zfxz0