Bioinformatics and Genomics

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.
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
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.
Restriction digest screening facilitates efficient detection of site-directed mutations introduced by CRISPR in C. albicans UME6

Editor rating: 7 / 10

Bettina Böttcher –– Nice method.
MIPhy: identify and quantify rapidly evolving members of large gene families

Editor rating: 7 / 10

Daniel Lahr –– There really are very few pieces of software that focus on analyses of large gene families. The issue is a complicated one, and the scarcity of software actually represents the attitude of researchers to shy away from such questions. If well accepted, this has the potential to spur new ways of looking at old questions.
Exosomes in cancer: small vesicular transporters for cancer progression and metastasis, biomarkers in cancer therapeutics

Editor rating: 7 / 10

J. Thomas Sanderson –– Good, solid and timely review of the entitled topic.
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.

Discussing these articles

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

21 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

Trying to understand large gene family? Try MIPhy by @DaveAScientist, @johngilleard and me. Published today in @thePeerJ https://t.co/Ecll4Xj17v #Bioinformatics #ComputationalBiology #EvolutionaryStudies

48 days ago
Exosomes and cancer https://t.co/eWbFB5K3po #exosomes #microvesicle #cancer #tumor

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 https://t.co/LZhz1F2vbm