4.7 Article

Systematic identification and characterization of viral small RNAs from small RNA-Seq data

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates

Andrew D. Yates et al.

Summary: Ensembl Genomes provides access to non-vertebrate genomes complementing the vertebrate resources developed by the Ensembl project, creating one of the most comprehensive genomic resources globally. They are focused on reducing genome redundancy and improving gene annotation, pangenome analysis, data dissemination speed, and support for the microbial research community.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemistry & Molecular Biology

Ensembl 2022

Fiona Cunningham et al.

Summary: Ensembl is unique in its flexible infrastructure for access to genomic data and annotation. They have focused on expediting annotation of new assemblies via the Ensembl Rapid Release platform, with the greatest annual number of newly annotated genomes released. They also developed a new method for comparative analyses and annotated non-vertebrate eukaryotes for the first time.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemical Research Methods

vsRNAfinder: a novel method for identifying high-confidence viral small RNAs from small RNA-Seq data

Zena Cai et al.

Summary: vsRNAfinder is a de novo method for identifying high-confidence vsRNAs from sRNA-Seq data, which outperforms widely used methods in identifying viral miRNAs and shows similar performance in animal and plant sRNAs identification. It greatly facilitates the effective identification of vsRNAs from sRNA-Seq data.

BRIEFINGS IN BIOINFORMATICS (2022)

Article Biochemical Research Methods

VirusCircBase: a database of virus circular RNAs

Zena Cai et al.

Summary: A systematic survey identified numerous viral circRNAs from 23 viral species, including both double-stranded DNA viruses and single-stranded RNA viruses. These viral circRNAs exhibit diverse characteristics and are involved in various cellular activities and diseases.

BRIEFINGS IN BIOINFORMATICS (2021)

Review Microbiology

RNA Virus-Encoded miRNAs: Current Insights and Future Challenges

Asuka Nanbo et al.

Summary: The article provides an overview of the roles of microRNAs in regulating gene expression and the impact of virus-encoded miRNAs on viral replication and immune evasion. It also discusses the persistence of RNA virus-encoded miRNAs in hosts, as well as the potential applications of miRNAs in diagnosis and therapeutics.

FRONTIERS IN MICROBIOLOGY (2021)

Article Biochemistry & Molecular Biology

SEAweb: the small RNA Expression Atlas web application

Raza-Ur Rahman et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Plant Sciences

An Online Database for Exploring Over 2,000 Arabidopsis Small RNA Libraries

Li Feng et al.

PLANT PHYSIOLOGY (2020)

Article Biochemistry & Molecular Biology

miRBase: from microRNA sequences to function

Ana Kozomara et al.

NUCLEIC ACIDS RESEARCH (2019)

Review Oncology

Small non-coding RNA and cancer

Giulia Romano et al.

CARCINOGENESIS (2017)

Article Microbiology

SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology

Lucia Morales et al.

CELL HOST & MICROBE (2017)

Review Cell Biology

The expanding world of small RNAs in plants

Filipe Borges et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2015)

Article Biochemistry & Molecular Biology

A cytoplasmic RNA virus generates functional viral small RNAs and regulates viral IRES activity in mammalian cells

Kuo-Feng Weng et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Multidisciplinary Sciences

MicroRNA-like viral small RNA from Dengue virus 2 autoregulates its replication in mosquito cells

Mazhar Hussain et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Biochemistry & Molecular Biology

NCBI GEO: archive for functional genomics data sets-update

Tanya Barrett et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biochemistry & Molecular Biology

The sequence read archive: explosive growth of sequencing data

Yuichi Kodama et al.

NUCLEIC ACIDS RESEARCH (2012)

Review Microbiology

Virus-Encoded microRNAs: An Overview and a Look to the Future

Rodney P. Kincaid et al.

PLOS PATHOGENS (2012)