Bioinformatics and Genomics

Article commentary

Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs

Editor rating: 7 / 10

Marc Robinson-Rechavi –– This study allows to link natural variation in morphology with genetic divergence in expression patterns, thus helping link ecology to molecular genomics.
An Indo-Pacific damselfish (Neopomacentrus cyanomos) in the Gulf of Mexico: origin and mode of introduction

Editor rating: 7 / 10

Donald Kramer –– Although only dealing with a single invasive species, it is a very thorough and interesting analysis of the potential for oil rigs to move fish (and potentially other marine species) around the world.
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.
Evaluating the adaptive evolutionary convergence of carnivorous plant taxa through functional genomics

Editor rating: 8 / 10

Todd Vision –– This is a novel and innovative approach to studying the genomic correlates of convergent evolution. It is likely to inspire similar studies in other systems and for other kinds of genomic changes, as well as bioinformatic work to refine and extend the methods.
Gene-based association study for lipid traits in diverse cohorts implicates BACE1 and SIDT2 regulation in triglyceride levels

Editor rating: 7 / 10

Steven Buyske –– The article shows genetics associations of lipid traits in populations (cohorts from Nigeria and the Philippines) not previously studied. Besides confirming some associations already found in Europeans, the authors found novel associations in BACE1 and SIDT2.
Tissue material properties and computational modelling of the human tibiofemoral joint: a critical review

Editor rating: 7 / 10

Jun Pang –– It is a very interesting literature review.
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.
A gene expression-based risk model reveals prognosis of gastric cancer

Editor rating: 7 / 10

Yong Wang –– The authors provide a potential useful diagnostic model for gastric cancer by using omics data
Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise

Editor rating: 7 / 10

Juan Riesgo-Escovar –– It addresses methodological problems that hinder comparison of these type of results from different publications.
Simulations indicate that scores of lionfish (Pterois volitans) colonized the Atlantic Ocean

Editor rating: 7 / 10

Mark Hixon –– This study provides insight on the size of the founding introduced population that gave rise to one of the worst marine invasions in history.

Discussing these articles

Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs Good job @vonStadarhraun https://t.co/SKVXoWQ3Ix via @thePeerJ

new publication: https://t.co/MONo6omrX3 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

287 days ago
Evaluating the adaptive evolutionary convergence of carnivorous plant taxa through functional genomics https://t.co/z1sFqYaSeP

Our @NIHR15 funded article on cholesterol traits in diverse populations, led by @LoyolaBioinfo BS/MS student Angela Andaleon, has been published today in @thePeerJ https://t.co/3Ulwm5nvDD

Our article has been published today in @thePeerJ https://t.co/xsVSirvY3c. Well done Abby Peters - another PhD output! @livuniAgeing @livunieng #Bioengineering #Biotechnology #ComputationalBiology

315 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

Ever wonder how many lionfish spawned the invasion in the Atlantic? Probably over 100! https://t.co/XHpPpH52ud

Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise https://t.co/7Yb3oztKOm

Discover Magazine: Dozens—Perhaps Even Hundreds—of Lionfish Likely Launched the Atlantic Invasion
http://blogs.discovermagazine.com/science-sushi/2017/12/27/dozens-perhaps-even-hundreds-of-lionfish-likely-launched-the-atlantic-invasion/