Bioinformatics and Genomics

Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches
Jun Chen –– The article provides a timely and informative comparison of the state-of-the-art error-correction pipelines. The presented results can guide the selection of appropriate pipelines that suit the research needs.
The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly
Keith Crandall –– De novo transcriptome assembly is a complex and difficult problem without a solid solution that works well across species. This helps move the needle in the right direction.
Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data
Elena Papaleo –– An interesting read for the cancer biology and computational biology community on the usage of RNASeq to study somatic mutations.
Venomix: a simple bioinformatic pipeline for identifying and characterizing toxin gene candidates from transcriptomic data
Keith Crandall –– This is a novel bioinformatic pipeline to find toxin genes from transcriptome data that looks to be broadly applicable across organisms.
Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus
Keith Crandall –– Krocus looks like a great piece of software now extended for long-read sequencing technology to identify MLST schemes.
Perceived user preferences and usability evaluation of mainstream wearable devices for health monitoring
Jie Liu –– Health care
Integrated analysis of differentially expressed profiles and construction of a competing endogenous long non-coding RNA network in renal cell carcinoma
Min Zhao –– This is a good example to integrate data for lncRNAs in a specific cancer type.
MIRU-profiler: a rapid tool for determination of 24-loci MIRU-VNTR profiles from assembled genomes of Mycobacterium tuberculosis
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
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
Antonio Amorim –– Useful approach (and clarification) to the epistatic and linkage interactions in evolution.
Bioinformatics and Genomics

Section discussions

A great article I helped peer review published today in @PeerJCompSci #DataMiningandMachineLearning #ScientificComputingandSimulation #SoftwareEngineering

An interesting article about Genome-wide analysis of the SOD gene family in Zostera marina under temperature stress, I handled as an editor has been published today @thePeerJ #Ecology #MolecularBiology #PlantScience

Origin identification of migratory pests (European Starling) using geochemical fingerprinting @thePeerJ

Just published! Although my contribution was minimal, I now have a darter paper. Check it out: Phylogeography of the Yazoo Darter via @thePeerJ

Transcriptional profiling to identify the key genes and pathways of pterygium @thePeerJ