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.
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.
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.
Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak

Editor rating: 9 / 10

Nicholas Loman –– This is a really well worked example of how whole genome sequencing is transforming public health surveillance of infectious diseases.
Genome-wide identification of ABA receptor PYL family and expression analysis of PYLs in response to ABA and osmotic stress in Gossypium

Editor rating: 10 / 10

Pankaj Jaiswal –– It contributes to PYL gene family annotation in cotton.
A microbial survey of the International Space Station (ISS)

Editor rating: 9 / 10

Joël Mossong –– This is an interesting article on the microbial contamination of an unusual habitat in space, the international space station.
Uncovering the relationship and mechanisms of Tartary buckwheat (Fagopyrum tataricum) and Type II diabetes, hypertension, and hyperlipidemia using a network pharmacology approach

Editor rating: 9 / 10

Juan Rodriguez-Flores –– While many different studies compare diets on a broad level in terms of their impact on T2D, this study takes a unique approach and looks at a particular food (buckwheat) in terms of its biochemical composition and the medicinal value of each compound. This is a valuable approach that should be conducted extensively for other foods with presumable medicinal value, i.e. non-pharmaceutical risk reduction or treatment of disease.
PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks

Editor rating: 9 / 10

Walter de Azevedo Jr. –– The authors report the development and application of a suite of tools, called PBxplore. This computational tool can be used to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). It is an interesting development for scientists interesting in molecular dynamics simulations of protein structures.
BioFuelDB: a database and prediction server of enzymes involved in biofuels production

Editor rating: 9 / 10

Walter de Azevedo Jr. –– This work may be of interest for researchers who work on the development of databases for proteins related to biofuel development.
Distinct patterns in the gut microbiota after surgical or medical therapy in obese patients

Editor rating: 9 / 10

Jie Liu –– This is a hot topic addressing an important question.

Discussing these articles

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

Well done Sanna, Suwisa and Filip

315 days ago
Our paper on WGS to inform the public health response to a complex state-wide KPC outbreak in @thePeerJ with @BenjaminHowden @tstinear @torstenseemann and many others

A microbial survey of the ISS. via @thePeerJ

357 days ago
Four way #VennDiagram caught my eye in @thePeerJ email, expected #DataViz disaster, but turns out it not that bad a choice as the set overlaps here are relatively small

My article has been published today in @thePeerJ #Bioinformatics #ComputationalBiology #MolecularBiology

BioFuelDB: a database and prediction server of enzymes involved in biofuels production…

#microbiota #Obesity @thePeerJ #Genomics #Microbiology #GastroenterologyandHepatology

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