Bioinformatics and Genomics

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.
Genetic characteristics of non-familial epilepsy
Jafri Abdullah –– This epilepsy type does not have enough data about it and is important.
Significance of TP53 mutation in bladder cancer disease progression and drug selection
Walter de Azevedo Jr. –– In this paper, the authors carried out a study focused on TP53 and discovered 50 % mutation in bladder cancer patients. Another exciting feature of this study is the identification of the sensibility to bladder cancer with TP53 mutation of three drugs, mitomycin-C, doxorubicin, and gemcitabine. In summary, their results have suggested the importance of TP53 mutation in disease development and drug choice in bladder cancer, which offers a new foundation for bladder cancer personalized treatment.
Algorithms for efficiently collapsing reads with Unique Molecular Identifiers
Sven Rahmann –– A well written article that examines UMI collapsing from a new point of view.
consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction
Elena Papaleo –– The paper describes a useful new package, consensusDE to perform differential expression analysis with three popular methods and compare the results. COnsensusDE also includes integration of RUV into the DE workflow.
Identification of key genes in non-small cell lung cancer by bioinformatics analysis
Vasco Azevedo –– manuscript that has identified genes implicated in cancer and give excellent clues to the area.
TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model
Elena Papaleo –– The authors developed a R-based package to study the effects of transposable elements on gene expression using a linear regression model. This is an important aspect to address in genomics and the availability of packages to facilitate and standardize these analyses is of great value for the community.
Identification of key genes and pathways associated with cholangiocarcinoma development based on weighted gene correlation network analysis
Yezaz Ghouri –– The article expands upon some genetic pathogenesis and pathways involved with development of cholangiocarcinoma which is has a high mortality rate and limited curative options.
ncRNA2MetS: a manually curated database for non-coding RNAs associated with metabolic syndrome
Elena Papaleo –– A huge effort of manual curation for a database on noncoding RNAs associated with metabolic syndrome. This work is relevance since metabolic syndrome has become a global threat to human health.
Bioinformatics and Genomics

Section discussions

Richling and Proschwitz examine new exotic introductions to tropical greenhouses in #Sweden - Identification problems of travelling snail species Read the full @PeerJLife article @uniofgothenburg #Gastropoda #Achatinellidae #Strobilopsidae

An article I handled as editor has been published @thePeerJ Nice piece of work expanding our knowledge of potential human and SARS-CoV-2 protein interactions #Bioinformatics #ComputationalBiology #MolecularBiology #DataMiningandMachineLearning #DataScience

My paper on tarantula biogeography was released today! Though I hesitate to speak in absolutes, we suggest some answers towards when and where the group emerged: #tarantula #evolution

Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture [PeerJ]

An article I handled as editor "The role of the isolation of the marginal seas during the Pleistocene in the genetic structure of black sea bream Acanthopagrus schlegelii (Bleeker, 1854) in the coastal waters of Japan" has been published today @thePeerJ

Just published in @PeerJCompSci - A deep learning algorithm to detect coronavirus (COVID-19) disease using CT images Read the full article #ArtificialIntelligence #DataMining #MachineLearning