Showing papers in "Genomics in 2020"

TL;DR: In this paper, a method for genotyping SARS-CoV-2 viruses using complete genomes is presented, which employs the multiple sequence alignments of the genome isolates with the SARS CoV-1 reference genome.

TL;DR: Evaluating the infiltration of immune cells in 1109 breast cancer samples obtained from TCGA by applying the ssGSEA to the transcriptome of these samples revealed that this 11-lncRNA signature was a novel and important prognostic factor independent of multiple clinicopathological parameters.

TL;DR: It is shown that SARS-CoV-2 has the most mutations on the targets of various nucleocapsid gene primers and probes, which have been widely used around the world to diagnose COVID-19, and that due to human immune response induced APOBEC mRNA (C >T) editing, diagnostic targets should also be selected to avoid cytidines.

TL;DR: The results on five medical datasets indicate that the proposed PSO-based multi objective feature selection method improves previous related methods in terms of efficiency and effectiveness.

TL;DR: Analyses of codon usage, amino acid frequency, putative RNA editing sites, and repeats showed a great extent of similarities between Hibiscus rosa-sinensis and HibiscUS syriacus.

TL;DR: It was identified blood-cell derived molecular signatures that might be useful as candidate peripheral biomarkers in AD and potential drugs and epigenetic data associated with these molecules that may be useful in designing therapeutic approaches to ameliorate AD.

TL;DR: The emerging roles of circRNA-miRNA-mRNA axis in cardiovascular pathophysiology and regulation were discussed, with a novel focus on cardioprotective network activities of the circRNA.

TL;DR: This first pan-cancer study offers a relatively comprehensive understanding of the oncogenic roles of SND1 across different tumors and observed an enhanced phosphorylation level of S426 in several tumors.

TL;DR: Codon usage, amino acid frequencies, oligonucleotide repeats, GC contents, and gene features revealed similarities among the 13 species, and Phylogenetic analyses corroborated the monophyly of Aroideae but were unable to resolve the positions of Calla and Schismatoglottis.

TL;DR: Comparison of chloroplast genomes of Withania somnifera with four other Solanaceae species revealed similarities in genomic features, including structure, nucleotide content, codon usage, RNA editing sites, simple sequence repeats (SSRs), oligonucleotide repeats, and tandem repeats.

TL;DR: Chloroplast genome sequences of two further Artemisia species showed high similarities in genome sizes, gene synteny, GC content, synonymous and non-synonymous substitutions, codon usage, amino acids frequencies, RNA editing sites, microsatellites, and oligonucleotide repeats, and maximum likelihood tree showed Artemisia a monophyletic genus.

TL;DR: iBitter-SCM is a computational model that can predict the bitterness of peptides directly from their amino acid sequence without any dependence on their functional domain or structural information and can serve as an important tool to facilitate the high-throughput prediction and de novo design of bitter peptides.

TL;DR: In this review, drug databases are classified into several groups based on data content and different classes can be applied to find a new application of the existing drugs.

TL;DR: This is the first study exhibiting the expression profiles of SlPR-1 genes under an abiotic stress, drought, in tomato, and the results indicate that the SlPR -1 genes play active roles in response to drought.

TL;DR: This study highlights the accumulation of mutation on ORF3a in Indian SARS-CoV2 genomes which may provide the designing therapeutic approach against SAR's virulence property in Indian patients.

TL;DR: A novel bioinformatics tool named CKSAAP_FormSite is proposed to predict lysine formylation sites, and feature analysis shows that some amino acid pairs around formylated sites may play an important role in the prediction.

TL;DR: KEGG pathways analysis revealed the top two pathways of the Human T cell Lymphotropic Virus-1 infection and the mTOR signaling pathway might influence the progress of IS.

TL;DR: It is found that methylation is not a random process and that closer neighboring CpG sites are more likely to share the same methylation status, and if the distance between CpGs increases, the degree of co-methylation decreases.

TL;DR: It is confirmed that lnc RNA SNHG16 was highly expressed in glioma and may exert oncogenic function as a competing endogenous RNA (ceRNA) to regulate EGFR by sponging of miR-373-3p through activating PI3K/AKT pathway, which providing a new insight of the regulatory network of lncRNA SNHg16 in the development of gliomas.

TL;DR: It is demonstrated that alterations in circulating miRNAs are associated with the response and outcome in NSCLC patients treated with anti-PD1 drugs.

TL;DR: The proposed rMRMR-MBA method is able to produce very promising results with high classification accuracy which can be considered a promising contribution for gene selection domain.

TL;DR: The C-terminus motif DLLV has been changed to DFLV and YLLV in the proteins QJR88103 and QKI36831 respectively, which might affect the binding of this motif with the host protein PALS1.

TL;DR: This paper proposed two heuristic methods for gene selection, namely, Xvariance against Mutual Congestion, which tries to classify labels using internal attributes of features however MutualCongestion is frequency based.

TL;DR: Evidence is presented to show that the proposed hybrid approach is superior to the state-of-the-art methods on the same benchmark dataset, and represents a further step towards developing the prediction models for DNA replication in particular and DNA sequences in general.

TL;DR: An overview of circRNA expression in the ovine MG and the interaction between some key circRNAs and their target miRNAs is provided, which improves the knowledge of the role of circ RNA in sheep milk synthesis.

TL;DR: A two-level new computational model "iNR-2 L" is developed and it is anticipated that the proposed computational model might be a practical and effective tool for academia and research community.

TL;DR: This is the first study to generate a hybrid of IonTorrent and MinION reads to obtain single chromosomal genomes, which would enable to precisely infer both structural arrangement of genes and SNP based analysis for phylogenetic information.

TL;DR: The present study reported numerous features of these genes, and may provide a platform for their detailed functional characterization in future studies.

TL;DR: The flavonoid-related key enzyme genes were identified, and their expression patterns in different tissues were further analyzed using quantitative real-time PCR, which will be useful in understanding the molecular mechanisms of different tissues in Dendrobium officinale.

TL;DR: Clinico-pathological analysis found Indian CACX patients with alterations of H19 by deletion or, promoter methylation with concomitant low expression have poor prognosis, and Ingenuity® Pathway analysis with deregulated DEncGs identified functionally important gene, H19.