Bioinformatics and Genomics

Editors' Picks

ZebraShare: a new venue for rapid dissemination of zebrafish mutant data
Mason Posner –– Zebrashare will be a valuable resource for the large and growing zebrafish research community to share gene edited mutants and collaborate on follow up studies. This crowdsourcing of mutants, built right into ZFIN, will help prevent redundant work and facilitate sharing of data.
Syncmers are more sensitive than minimizers for selecting conserved k‑mers in biological sequences
Joseph Gillespie –– In this novel work, Dr. Edgar makes a significant advance on using k-mer selection for sequence analysis: selected k-mers act as seeds for sequence matching, with generated "syncmers" having attractive properties of minimizers without having to depend on neighboring sequence.
Identification of significant genes signatures and prognostic biomarkers in cervical squamous carcinoma via bioinformatic data
Jianye Ge –– Excellent and very responsive reviewer
Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function
Yuriy Orlov –– This work discusses the evolution of coronavirus genomes.
Comparing local ancestry inference models in populations of two- and three-way admixture
Jianye Ge –– Excellent scientist and reviewer!
Predictive models for stage and risk classification in head and neck squamous cell carcinoma (HNSCC)
Mitchell Stark –– A comprehensive approach to a complex issue.
Identification of SPRR3 as a novel diagnostic/prognostic biomarker for oral squamous cell carcinoma via RNA sequencing and bioinformatic analyses
Xuehui Huang –– The work may provide important biomarkers in clinical test.
Toward insights on determining factors for high activity in antimicrobial peptides via machine learning
Robert Winkler –– Peptides are part of the natural defense of humans against pathogenic microbes and relatively easy to synthesize chemically in a huge diversity. The presented computational strategy facilitates the rational design of antimicrobial drugs.
The complete mitochondrial genome of stag beetle Lucanus cervus (Coleoptera: Lucanidae) and phylogenetic analysis
Jia-Yong Zhang –– This study reported the mitochondrial genome of the stag beetle Lucanus cervus.
Identification of microRNA signatures in umbilical cord blood associated with maternal characteristics
Cheng-Chia Yu –– UCB miRNAs should be studied also as biomarkers for screening and diagnosis of 213 pregnancy-associated complications and pathologies.
Bioinformatics and Genomics

Section discussions

As promised a few weeks back, BACPHLIP is officially published! Thanks to @thePeerJ, a set of helpful reviewers, and users who have been submitting feedback Use it for all your phage lifestyle classification needs! (okay, with *some* minor caveats)

Hot off the press! Our article has been published today in @thePeerJ #Bioinformatics #ComputationalBiology #Genomics #Microbiology #ComputationalScience.

Just published in @PeerJCompSci - An effective classification framework for brain-computer interface system design based on combining of fNIRS and EEG signals Read the full article #Bioinformatics #ArtificialIntelligence #AI

TCF7L2 rs7903146 polymorphism association with diabetes and obesity in an elderly cohort from Brazil @thePeerJ

Léonard et al. @UniversiteLiege present #ToRQuEMaDA: tool for retrieving queried Eubacteria, metadata and dereplicating assemblies Read the full @PeerJLife article #Bioinformatics #Genomics #Microbiology #Taxonomy

Lin et al. present a public database-based retrospective study - Identification of P2RY13 as an immune-related prognostic biomarker in #lung adenocarcinoma Read the full @PeerJLife article #Bioinformatics #Immunology #Oncology

Duke researchers: Silent mutations may be how Covid-19 spreads before symptoms appear

Pinpointing the 'silent' mutations that gave the coronavirus an evolutionary edge