Bioinformatics and Genomics

Editors' Picks

BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains
Jun Chen –– The tool is a nice contribution to the field and is useful in studying the phage lifestyle based on genome sequence only.
TCF7L2 rs7903146 polymorphism association with diabetes and obesity in an elderly cohort from Brazil
Antonio Palazón-Bru –– It is important to know the role of TCF7L2 rs7903146 in diabetes and obesity.
HiCEnterprise: identifying long range chromosomal contacts in Hi-C data
Jun Chen –– The authors provided a new software package for HiC data analysis. It is a nice contribution to the field.
Identification and comparison of circular RNAs in preeclampsia
Yuriy Orlov –– This study provides useful information for analysis circular RNAs in preeclampsia based on original experimental data and modern bioinformatics tools.
Improving the gnomonic approach with the gnomonicM R-package to estimate natural mortality throughout different life stages
Matteo Zucchetta –– The article presents the approach behind the gnomonicM R-package, making easy to understand the potential application of the method and to test the available tools.
NGScloud2: optimized bioinformatic analysis using Amazon Web Services
Yuriy Orlov –– Novel update for NGS cloud computing would be widely used for RNA-sequencing data analysis in model organisms.
Bioinformatics analysis for the identification of differentially expressed genes and related signaling pathways in H. pylori-CagA transfected gastric cancer cells
Alexander Bolshoy –– H. pylori is a very important interesting organism and all new knowledge is valuable.
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.
Multi-schema computational prediction of the comprehensive SARS-CoV-2 vs. human interactome
Shawn Gomez –– This manuscript describes the identification of a set of predicted protein-protein interactions between SARS-CoV-2 and its human host. This work is relevant on its own, as well as being highly complementary to other efforts focused on accelerating our understanding of this virus and potential mechanisms of pathogenesis.
Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager
Alexander Schliep –– A great community-wide framework to reproducibly, efficiently and robustly analyze ancient DNA.
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