Bioinformatics and Genomics

Article commentary

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.
A simple molecular technique for distinguishing species reveals frequent misidentification of Hawaiian corals in the genus Pocillopora

Editor rating: 8 / 10

Xavier Pochon –– This study developed a simple and cost-effective assay that quickly allows for discrimination amongst coral species in the genus Pocillopora using simple PCR amplification followed by digestion with widely available restriction enzymes. Pocilloporid corals exhibit extreme phenotypic plasticity, making morphological identification of species very challenging. The assay was tested on 691 coral samples collected from across the Hawaiian Archipelago and successfully characterised all six Pocillopora species occurring in Hawaii. Compared to sequence-based identification, this method is simple, rapid and represents a cost saving of nearly 95%. This work will benefit future studies of population structure, ecology, biodiversity, evolution and conservation in this challenging coral genus.
Complex versus simple models: ion-channel cardiac toxicity prediction

Editor rating: 8 / 10

Heiko Enderling –– This article discusses the contributions of quantitative models in predicting biology, and makes an important point about the balance of simplicity/complexity/accuracy/usefulness of biophysical models. If simple models capture biological complexity, the use of more detailed models must be properly justified.

Discussing these articles

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

PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads via @thePeerJ

The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages

New paper to ID Pocillopora corals

new publication: a comprehensive analysis on how a well-defined simple heuristic is as good (if not better) than complex mathematical models, used by FDA and bloated pharma companies, in ion-channel safety pharmacology #mathbiology