PeerJ – Bioinformatics and Genomics section

11 July 2018

MIRU-profiler: a rapid tool for determination of 24-loci MIRU-VNTR profiles from assembled genomes of Mycobacterium tuberculosis

Rahim Rajwani, Sheeba Shehzad, Gilman Kit Hang Siu

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.

3 July 2018

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.

28 June 2018

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.

25 June 2018

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

15 June 2018

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.

15 June 2018

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.

6 June 2018

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.

29 May 2018

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.

29 May 2018

Exosomes in cancer: small vesicular transporters for cancer progression and metastasis, biomarkers in cancer therapeutics

Editor rating: 7 / 10