Bioinformatics and Genomics

Integrated bioinformatics analysis of As, Au, Cd, Pb and Cu heavy metal responsive marker genes through Arabidopsis thaliana GEO datasets
Elena Papaleo –– The study used analyses of transcriptomics data to infer signatures associated with metal toxicity, which could help in the understanding of the mechanisms and marker of environmental exposure to heavy metals.
cRegulome: an R package for accessing microRNA and transcription factor-gene expression correlations in cancer
Elena Papaleo –– A nice, comfortable to use R package to infer and visualize the relationship between important regulatory biomolecules, such as transcription factors and microRNAs
An assessment for health education and health promotion in chronic disease demonstration districts: a comparative study from Hunan Province, China
Gregory Gilbert –– This study was designed to establish a framework of indicators for outcome evaluation of health education and promotion efforts in Chinese districts, and explore the factors involved to promote the effort. It concluded chronic disease demonstration districts performed better on the work of health education and health promotion than the non-demonstration districts.
Genome-wide analysis of long non-coding RNA expression profile in porcine circovirus 2-infected intestinal porcine epithelial cell line by RNA sequencing
Fernando Spilki –– The study provides new insights into the mechanisms of PCV-2 replication and the virus-cell relationship.
The draft genome of strain cCpun from biting midges confirms insect Cardinium are not a monophyletic group and reveals a novel gene family expansion in a symbiont
Joseph Gillespie –– Important taxonomic implications revealed by phylogeny estimation, and also a novel expansion of a nuclease family
Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics
Chris Creevey –– This is a comprehensive review of the state of the field of coalescence-based phylogenomics, with key recommendations for the future development of this area.
Discordant financial conflicts of interest disclosures between clinical trial conference abstract and subsequent publication
Andrew Gray –– With increasing scrutiny of clinical trials, it is imperative that FCOIs be accurately and completely described. The authors here find concerning evidence that this was not the case for their data.
Splitting on categorical predictors in random forests
Andrew Gray –– This article provides very useful practical guidance for those of us who use random forests with nominal variables.
Sleeping mattress determinants and evaluation: a biomechanical review and critique
Shi-Cong Tao –– Sleeping mattress, the topic of this manuscript, is closely related to human life. And this review gives a very good summary. Such a good article will move its field in the future.
Analysis of cause-effect inference by comparing regression errors
Charles Elkan –– This paper provides a very simple method to determine the direction of causation between two correlated variables that do not have a common cause. While the general idea was known before, this paper makes the idea precise, with solid mathematical and experimental justification.
Bioinformatics and Genomics

Section discussions

Identification of prognostic risk factors for pancreatic cancer using bioinformatics analysis @thePeerJ

Deep learning can be used to find gene start sites in genomic sequences. Two lessons: 1) Be careful about imbalanced datasets. 2) You can use well annotated species to annotated related species. #Bioinformatics #ComputationalBiology

Analysis of bone morphometrics and finite-element modelling of the weird Australian mekosuchine crocodylomorphs, supporting that they were more terrestrial than extant crocs tend to be:

Aggregation pathways of human γ D crystallin induced by metal ions revealed by time dependent methods @thePeerJ

Historical museum collections and contemporary population studies implicate roads and introduced predatory bullfrogs in the decline of western pond turtles @thePeerJ

Conservation implications of using an imitation carnivore to assess rarely used refuges as critical habitat features in an alpine ungulate @thePeerJ

A little late for the #Biodiversity themed #WorldEnvironmentDay but our article on 'Identifying potential threats to #soil biodiversity' has been published today in @thePeerJ #Ecology #SoilScience #WorldEnvironmentDay2020