Bioinformatics and Genomics

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.
Staphylococcus aureus viewed from the perspective of 40,000+ genomes

Section Editor rating: 6 / 10

Keith Crandall –– Looks like a great platform for exploring variation across bacterial genomes.
MIRU-profiler: a rapid tool for determination of 24-loci MIRU-VNTR profiles from assembled genomes of Mycobacterium tuberculosis

Editor rating: 7 / 10

Joël Mossong –– Provides interesting insights on extract traditional typing data from WGS. Similar tools are likely to be useful also for other bacterial species, e.g. MLVA for Salmonella and VTEC.
Genetic polymorphisms and forensic efficiency of 19 X-chromosomal STR loci for Xinjiang Mongolian population

Editor rating: 7 / 10

Xuhua Xia –– Human populations develop different traditions, cultures and social systems, and it is important to know how much of these variations is due to genetic isolation. When we see social system A practiced by population 1 in region X, and social system B practiced by population 2 in region Y, we would like to know whether historical and environmental factors favor social system A in population 1 and social system B in population 2, or social system A is in fact better than social system B in both populations, but population 2, due to isolation, have never had a chance to practice social system A. Genetic differentiation helps us to understand if the populations are indeed isolated. This paper provides good documentation on genetic differentiation among Chinese populations and can serve as a basis for biogeographic inferences for future studies.
Gene buddies: linked balanced polymorphisms reinforce each other even in the absence of epistasis

Editor rating: 7 / 10

Antonio Amorim –– Useful approach (and clarification) to the epistatic and linkage interactions in evolution.
Distinctive facial features in idiopathic Moyamoya disease in Caucasians: a first systematic analysis

Editor rating: 6 / 10

Jeanette Erdmann –– Interesting approach to defining patients very early in disease progression. Needs validation in an independent patient sample.
Specalyzer—an interactive online tool to analyze spectral reflectance measurements

Editor rating: 7 / 10

Budiman Minasny –– An online tool for snalaysing spectra data maybe of interest to plant scientists
GEsture: an online hand-drawing tool for gene expression pattern search

Editor rating: 6 / 10

Gerard Lazo –– This may be an easier approach toward generalizing and discovering significant data without a formal scientific approach; however, this fact needs to be expressly recognized before an hypothesis would be developed.
Horizontally transferred genes in the ctenophore Mnemiopsis leidyi

Editor rating: 7 / 10

Daniel Lahr –– HGT is a process that happens in all domains of life and is very poorly understood form both a patterns point of view, as well as mechanisms. Using such model organisms to address the issue is likely to be appreciated by a wide variety of evolutionary biologists.
Comprehensive circular RNA expression profile in radiation-treated HeLa cells and analysis of radioresistance-related circRNAs

Editor rating: 7 / 10

Alfonso Valencia –– The article is study of the potential functional importance of differentially expressed Circular RNAs in a particular biological system, i.e response to radiation in HeLa cells. Function is investigated in terms of enrichment in Gene Ontology and KEGG pathways. The study is representative of a general class of functional studies of biological systems combining experimental determination and functional enrichment.

Discussing these articles

GEsture: an online hand-drawing tool for gene expression pattern search https://t.co/TEk9ZxsjVZ https://t.co/Yc5qlK6M2r

Happy to see this published today in @thePeerJ https://t.co/9BQaO0Tb7D #Bioinformatics #Genomics #InfectiousDiseases #PublicHealth. Staphopia started as a Masters project for @rpetit3 in 2010!

MIRU-profiler: a rapid tool for determination of 24-loci MIRU-VNTR profiles from assembled genomes of Mycobacterium tuberculosis https://t.co/9HtPxcKHJD @thePeerJ https://t.co/0aXCISKCeK

It's here. The blog post that became a preprint that became a @thePeerJ paper. Gene buddies: linked balanced polymorphisms reinforce each other even in the absence of epistasis https://t.co/cyYABXiD6x #BalancingSelection #Evolution #Simulation #Linkage #GeneticDiversity #Buddies

An article I handled as editor has been published today @thePeerJ https://t.co/AO4X8JRzfX #Genetics #Neurology

22 days ago
An article I handled as editor has been published today @thePeerJ https://t.co/M2RlWCneOq #AgriculturalScience #Bioinformatics #DataScience

Comprehensive circular RNA expression profile in radiation-treated HeLa cells and analysis of radioresistance-related circRNAs https://t.co/NU196QuLYC @thePeerJ https://t.co/PVoYwRK8ge

Ryan Lab published "Horizontally transferred genes in the ctenophore Mnemiopsis leidyi" today in @thePeerJ https://t.co/oUnhLPcY8d #EvolutionaryStudies #Genomics https://t.co/q8FRQyNnHi