Diversity and evolution of the animal virome
The COVID-19 pandemic has given the study of virus evolution and ecology new relevance.
Although viruses were first identified more than a century ago, we likely know less about …
Although viruses were first identified more than a century ago, we likely know less about …
Glycoinformatics in the artificial intelligence era
Artificial intelligence (AI) methods have been and are now being increasingly integrated in
prediction software implemented in bioinformatics and its glycoscience branch known as …
prediction software implemented in bioinformatics and its glycoscience branch known as …
Identification of mobile genetic elements with geNomad
Identifying and characterizing mobile genetic elements in sequencing data is essential for
understanding their diversity, ecology, biotechnological applications and impact on public …
understanding their diversity, ecology, biotechnological applications and impact on public …
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata
AP Camargo, S Nayfach, IMA Chen… - Nucleic acids …, 2023 - academic.oup.com
Viruses are widely recognized as critical members of all microbiomes. Metagenomics
enables large-scale exploration of the global virosphere, progressively revealing the …
enables large-scale exploration of the global virosphere, progressively revealing the …
[HTML][HTML] Expansion of the global RNA virome reveals diverse clades of bacteriophages
High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA
virome. Mining 5,150 diverse metatranscriptomes uncovered> 2.5 million RNA virus contigs …
virome. Mining 5,150 diverse metatranscriptomes uncovered> 2.5 million RNA virus contigs …
Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v. 9
S Mukherjee, D Stamatis, CT Li… - Nucleic acids …, 2023 - academic.oup.com
Abstract The Genomes OnLine Database (GOLD)(https://gold. jgi. doe. gov/) at the
Department of Energy Joint Genome Institute (DOE-JGI) continues to maintain its role as one …
Department of Energy Joint Genome Institute (DOE-JGI) continues to maintain its role as one …
Hybrids of RNA viruses and viroid-like elements replicate in fungi
Earth's life may have originated as self-replicating RNA, and it has been argued that RNA
viruses and viroid-like elements are remnants of such pre-cellular RNA world. RNA viruses …
viruses and viroid-like elements are remnants of such pre-cellular RNA world. RNA viruses …
High-quality metagenome assembly from long accurate reads with metaMDBG
We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG
combines a de Bruijn graph assembly in a minimizer space with an iterative assembly over …
combines a de Bruijn graph assembly in a minimizer space with an iterative assembly over …
Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer
DNA sequencing data continue to progress toward longer reads with increasingly lower
sequencing error rates. Here, we define an algorithmic approach, mdBG, that makes use of …
sequencing error rates. Here, we define an algorithmic approach, mdBG, that makes use of …
Viruses defined by the position of the virosphere within the replicator space
Originally, viruses were defined as miniscule infectious agents that passed through filters
that retain even the smallest cells. Subsequently, viruses were considered obligate …
that retain even the smallest cells. Subsequently, viruses were considered obligate …