Bioinformatics and Genomics

Article commentary

Application of EST-SSR markers developed from the transcriptome of Torreya grandis (Taxaceae), a threatened nut-yielding conifer tree

Editor rating: 9 / 10

Pankaj Jaiswal –– This article on Torreya grandis (Taxaceae) an ancient conifer species that is endemic to southeast China provides an important insight into the population structure and distribution of the species. It also generated the genomic resources necessary to move forward the research on Torreya grandis.
Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales

Editor rating: 7 / 10

Peter Dunfield –– Will specificaly interest those working on methanogenesis, but more broadly the technical novelty may appeal to many microbial ecologists interested in mining metagenomic datases.
Exome sequencing study of 20 patients with high myopia

Editor rating: 7 / 10

Yong Wang –– This paper performed exom sequencing to study high myopia and identified several potential disease genes. The data and analysis provides a valuable resources for the field.
Plant data visualisation using network graphs

Editor rating: 7 / 10

Massimiliano Zanin –– An interesting demonstration on how data can be represented using new web-based technologies.
A minimal set of internal control genes for gene expression studies in head and neck squamous cell carcinoma

Section Editor rating: 7 / 10

Elena Papaleo –– An interesting solution to identify a subset of reference genes for qualitative qPCR of cancer samples
Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches

Section Editor rating: 6 / 10

Keith Crandall –– Error correction in microbiome studies is essential and this paper offers some great insights on approaches.
Profile and clinical implication of circular RNAs in human papillary thyroid carcinoma

Editor rating: 6 / 10

Paula Soares –– The article adds new data in the area of non coding DNA
piRNN: deep learning algorithm for piRNA prediction

Editor rating: 6 / 10

Lourdes Peña-Castillo –– It introduces a piRNA predictor that outperforms previous available tools.
The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly

Section Editor rating: 7 / 10

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

Editor rating: 7 / 10

Elena Papaleo –– An interesting read for the cancer biology and computational biology community on the usage of RNASeq to study somatic mutations.

Discussing these articles

Nice approach for using large-scale mining of specific genes to identify novel lineages of important metabolic genes https://t.co/Edf2AMrCCh via @thePeerJ

Plant data visualisation using network graphs https://t.co/jNhxh3QGUR @thePeerJ https://t.co/WtIvd7p08x

our recent paper on a minimal set of internal control genes for gene expression studies in head and neck squamous cell carcinoma busts old myths on housekeeping genes in hnscc gene expression studies https://t.co/vf1rBZuUl9 #openscience

Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches https://t.co/gdqfcA3Qhd w @BetaScience

Profile and clinical implication of circular RNAs in human papillary thyroid carcinoma https://t.co/l63IAW6C83 @thePeerJ https://t.co/sQnKcphie5

Finally Published! The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly. https://t.co/6Ss7TULCKQ

piRNN: deep learning algorithm for piRNA prediction https://t.co/89HxjfRbzb @thePeerJ https://t.co/XLv0RlKL5Q