Bioinformatics and Genomics

Editors' Picks

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.
The methylation level of TFAP2A is a potential diagnostic biomarker for retinoblastoma: an analytical validation study
Jesus Vera –– This may help to the diagnosis of retinoblastoma and others eye conditions.
Characterization of the GRAS gene family reveals their contribution to the high adaptability of wheat
Alexander Bolshoy –– GRAS gene family is very important in plants. This study promotes research in the field.
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.
Development and clinical validation of a 3-miRNA signature to predict prognosis of gastric cancer
Cheng Zhan –– This manuscript constructed a 3-miRNA signature to predict prognosis of gastric cancer.
Assessing the effects of time-dependent restrictions and control actions to flatten the curve of COVID-19 in Kazakhstan
Antonio Palazón-Bru –– The authors assessed the spread of COVID-19 in central Asia, giving us relevant information about this new disease.
Bioinformatics and Genomics

Section discussions

My article with @jlvazpol and @fmoramarquez has been published today in thePeerJ #Bioinformatics #ComputationalBiology

A quantitative assessment of site-level factors in influencing Chukar (Alectoris chukar) introduction outcomes @thePeerJ

#Bioinformatics analysis for the identification of differentially expressed genes and related signaling pathways in H. pylori-CagA transfected gastric cancer cells Read the full @PeerJLife article #Biochemistry #Bioinformatics #CellBiology #Microbiology

New @PeerJLife article examines the identification and characterization of #melon circular RNAs involved in powdery mildew responses through comparative transcriptome analysis Read the full article #AgriculturalScience #Bioinformatics

The latest paper I handled @thePeerJ introduces a new mutant sharing resource for the #Zebrafish community - welcome ZebraShare! #Zebrafish