Bioinformatics and Genomics

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.
CRF: detection of CRISPR arrays using random forest

Editor rating: 9 / 10

Gian Tartaglia –– The identification if CRISPR arrays is crucial to understand how the system works and can be manipulated in applications
Optimizing the use of a sensor resource for opponent polarization coding

Editor rating: 9 / 10

Mario Negrello –– This article contains an insighful and thorough analysis of the physical constraints for encoding and the processing of information in polarized vision, and more specifically, in polarization opponency. This article is exemplary for the field of neural coding in that it covers multiple angles in the analysis with solid logics and deep appreciation for the biological phenomenon under study.

Discussing these articles

Well done Sanna, Suwisa and Filip

143 days ago
Our paper on WGS to inform the public health response to a complex state-wide KPC outbreak in @thePeerJ https://t.co/AGHHHEJcCz with @BenjaminHowden @tstinear @torstenseemann and many others

A microbial survey of the ISS. https://t.co/DMdgTYuwLi via @thePeerJ

185 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 https://t.co/KPy3hJ63JF

My article has been published today in @thePeerJ https://t.co/jHwNBx4ZGb #Bioinformatics #ComputationalBiology #MolecularBiology

BioFuelDB: a database and prediction server of enzymes involved in biofuels production https://t.co/0QDMHoJRW0… https://t.co/7EdgdJAJ6G

#microbiota #Obesity @thePeerJ https://t.co/rOb2y9McAp #Genomics #Microbiology #GastroenterologyandHepatology

CRF(CRISPR Finder by Random Forest)ランダムフォレストで〜2,000以上の微生物ゲノムのCRISPRアレイ同定 PeerJ 0425 https://t.co/gExc9M5pe9

Popular Science: "Scientists are trying to figure out which bacteria have colonized our space station"
https://www.popsci.com/ISS-microbiome

The space station is about as sanitary as your run-of-the-mill bachelor pad
https://www.digitaltrends.com/cool-tech/space-station-is-chock-full-of-germs/

The International Space Station is super germy
https://www.washingtonpost.com/news/speaking-of-science/wp/2017/12/05/the-international-space-station-is-super-germy/

The International Space Station is swarming with bacteria
https://cosmosmagazine.com/biology/the-international-space-station-is-swarming-with-bacteria

Just Like Home: Space Station Has Same Microbes As Your House
https://www.space.com/38980-space-station-bacteria-similar-human-homes-study.html

The ISS Bacterial Community Resembles What You'd Find in Your Home
https://www.seeker.com/space/the-iss-bacterial-community-resembles-what-youd-find-in-your-home

International Space Station colonised by mysterious bugs – including ‘alien’ bacteria
http://metro.co.uk/2017/12/05/international-space-station-colonised-mysterious-bugs-including-alien-bacteria-7134669/

'Diverse' bacteria found on International Space Station like that on Earth, scientists reveal
http://www.independent.co.uk/news/science/nasa-international-space-station-bacteria-found-earth-home-humans-study-iss-a8092756.html

The bacterial community on the International Space Station resembles homes
https://phys.org/news/2017-12-bacterial-international-space-station-resembles.html

BACTERIA IN SPACE: INTERNATIONAL SPACE STATION HAS LOTS OF THE SAME MICROBES AS ANY OTHER HOME
http://www.newsweek.com/bacteria-space-international-space-station-has-same-microbes-any-other-home-735208