Bioinformatics and Genomics

A multi-task pipeline with specialized streams for classification and segmentation of infection manifestations in COVID-19 scans
Sebastian Ventura –– Interesting approach to automatically diagnose COVID infections, including the comparison of several previous methods.
Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function
Jun Chen –– This work is timely. It elucidates the evolution and host adaptation of SARS-CoV-2. It is a valuable contribution to the understanding of the coronavirus pandemic.
Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load
Alexander Bolshoy –– The public interest in everything related to the ongoing pandemic is very high. This literature review may help to navigate in the sea of publications.
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.
Adaptive Metropolis-coupled MCMC for BEAST 2
Jun Chen –– The author proposed an adaptive Metropolis-coupled MCMC algorithm for Bayesian phylogenetics and implemented in their software package BEAST 2. It is a significant methodological contribution to the field.
Anti-COVID-19 multi-epitope vaccine designs employing global viral genome sequences
Jun Chen –– The topic is highly significant since the only solution to the pandemic seems to be an effective vaccine. The manuscript will surely attract numerous readers.
Identification and validation of prognostic signature for breast cancer based on genes potentially involved in autophagy
Philip Coates –– The work provides new information into the role of autophagy in breast cancer progression. The identification of a gene signature will improve prognostic indicators in the clinic and may lead to application of available drugs that target autophagy for therapy.
The regulatory genome constrains protein sequence evolution: implications for the search for disease-associated genes
Hossein Khiabanian –– The paper present a novel approach in assessing tissue-specific impact of gene expression on protein sequence evolution.
Detecting the outbreak of influenza based on the shortest path of dynamic city network
Yong Wang –– Forecasting flu outbreak based on data science is promising, challenging, and urgently needed. This manuscript proposed a new metric based on the shortest path in dynamic city network.
Bioinformatics and Genomics

Section discussions

Evaluation of pro-apoptotic potential of taxifolin against liver cancer @thePeerJ

Huckstep et al. @WEHI_research @UniMelbMDHS present new research; measuring pathway database coverage of the phosphoproteome Read the full @PeerJLife article #Bioinformatics #ComputationalBiology #MolecularBiology #DataScience

Ocasio and Duong @EinsteinMed use deep learning prediction of mild cognitive impairment conversion to Alzheimer’s disease at 3 years after diagnosis Read the full @PeerJCompSci article #AI #DataMining #MachineLearning

Week 104: Partition your variance! How much variation does this predictor or a set of predictors explain in a mixed-effects model? And more! Easy with the R package packagepartR2: Paper: With wonderful @m_a_sto & @sogohae

An article I handled as editor has been published today @thePeerJ #Aquaculture,FisheriesandFishScience #FoodScienceandTechnology #Genomics #Microbiology

Pavlovikj et al. @UNLincoln present #ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses Read the full @PeerJLife article #Genomics #Microbiology #MolecularBiology #Bacteria

My article has been published today in @thePeerJ #Bioinformatics #PlantScience

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

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