iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology

[1]  E. Mosley‐Thompson,et al.  Glacier ice archives nearly 15,000-year-old microbes and phages , 2021, Microbiome.

[2]  Natalia N. Ivanova,et al.  Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome , 2021, Nature Microbiology.

[3]  Jiarong Guo,et al.  Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation , 2021, PeerJ.

[4]  P. Turner,et al.  Community context matters for bacteria-phage ecology and evolution , 2021, The ISME Journal.

[5]  J. Weitz,et al.  Revisiting the rules of life for viruses of microorganisms , 2021, Nature Reviews Microbiology.

[6]  Tom O. Delmont,et al.  VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses , 2021, Microbiome.

[7]  Mercè Llabrés,et al.  VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families , 2021, Bioinform..

[8]  N. Kyrpides,et al.  CheckV assesses the quality and completeness of metagenome-assembled viral genomes , 2020, Nature Biotechnology.

[9]  S. Hallam,et al.  Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters , 2020, The ISME Journal.

[10]  K. Konstantinidis,et al.  MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations , 2020, Microbiome.

[11]  I-Min A. Chen,et al.  IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses , 2020, Nucleic Acids Res..

[12]  Matthew B. Sullivan,et al.  Cenote-Taker 2 Democratizes Virus Discovery and Sequence Annotation , 2020, bioRxiv.

[13]  M. Sullivan,et al.  The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut , 2020, Cell Host & Microbe.

[14]  Christine L. Sun,et al.  Genome-resolved viral ecology in a marine oxygen minimum zone (OMZ) , 2020, bioRxiv.

[15]  Agnieszka Onisko,et al.  PhageAI - Bacteriophage Life Cycle Recognition with Machine Learning and Natural Language Processing , 2020, bioRxiv.

[16]  A. Kropinski,et al.  VIRIDIC—A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses , 2020, bioRxiv.

[17]  M. Sullivan,et al.  DRAM for distilling microbial metabolism to automate the curation of microbiome function , 2020, bioRxiv.

[18]  M. Sullivan,et al.  Viral Ecogenomics of Arctic Cryopeg Brine and Sea Ice , 2020, mSystems.

[19]  Yaxing Wei,et al.  The National Microbiome Data Collaborative: enabling microbiome science , 2020, Nature Reviews Microbiology.

[20]  Karthik Anantharaman,et al.  VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences , 2020, Microbiome.

[21]  Chao Deng,et al.  Identifying viruses from metagenomic data using deep learning , 2020, Quantitative Biology.

[22]  B. Andreopoulos,et al.  Phage-specific metabolic reprogramming of virocells , 2020, The ISME Journal.

[23]  J. Matthijnssens,et al.  Metagenomics in Virology , 2019, Reference Module in Life Sciences.

[24]  W. Shu,et al.  Depth-related variability in viral communities in highly stratified sulfidic mine tailings , 2019, Microbiome.

[25]  Robert D. Finn,et al.  MGnify: the microbiome analysis resource in 2020 , 2019, Nucleic Acids Res..

[26]  Maureen L. Coleman,et al.  Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems , 2019, Nature Reviews Microbiology.

[27]  Evelien M. Adriaenssens,et al.  Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks , 2019, Nature Biotechnology.

[28]  G. Cochrane,et al.  Marine DNA Viral Macro- and Microdiversity from Pole to Pole , 2019, Cell.

[29]  Matthew B. Sullivan,et al.  Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands , 2019 .

[30]  Michael J. Tisza,et al.  Discovery of several thousand highly diverse circular DNA viruses , 2019, bioRxiv.

[31]  Edian F. Franco,et al.  PhageWeb – Web Interface for Rapid Identification and Characterization of Prophages in Bacterial Genomes , 2018, Front. Genet..

[32]  Natalia N. Ivanova,et al.  Minimum Information about an Uncultivated Virus Genome (MIUViG) , 2018, Nature Biotechnology.

[33]  João C. Setubal,et al.  MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins , 2018, Front. Genet..

[34]  Changsheng Li,et al.  Host-linked soil viral ecology along a permafrost thaw gradient , 2018, Nature Microbiology.

[35]  Rick L. Stevens,et al.  KBase: The United States Department of Energy Systems Biology Knowledgebase , 2018, Nature Biotechnology.

[36]  S. Saleska,et al.  Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing , 2018, mSystems.

[37]  M. Bradford,et al.  Understanding how microbiomes influence the systems they inhabit , 2018, bioRxiv.

[38]  Rob Knight,et al.  Current understanding of the human microbiome , 2018, Nature Medicine.

[39]  Takashi Yoshida,et al.  ViPTree: the viral proteomic tree server , 2017, Bioinform..

[40]  Jonathan Vincent,et al.  WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs , 2017, Bioinform..

[41]  M. Sullivan,et al.  Putative archaeal viruses from the mesopelagic ocean , 2017, PeerJ.

[42]  Matthew B. Sullivan,et al.  vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria , 2017, PeerJ.

[43]  Andrew J. Davison,et al.  Consensus statement: Virus taxonomy in the age of metagenomics , 2017, Nature Reviews Microbiology.

[44]  Dawn B. Goldsmith,et al.  Towards quantitative viromics for both double-stranded and single-stranded DNA viruses , 2016, PeerJ.

[45]  J. Weitz,et al.  Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer , 2016, BMC Genomics.

[46]  A. Vardi,et al.  Virocell Metabolism: Metabolic Innovations During Host-Virus Interactions in the Ocean. , 2016, Trends in microbiology.

[47]  B. Hurwitz,et al.  Protocols.io: Virtual Communities for Protocol Development and Discussion , 2016, PLoS biology.

[48]  Ken Youens-Clark,et al.  iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure , 2016, The ISME Journal.

[49]  David S. Wishart,et al.  PHASTER: a better, faster version of the PHAST phage search tool , 2016, Nucleic Acids Res..

[50]  B. Hurwitz,et al.  VERVENet: the viral ecology research and virtual exchange network , 2016 .

[51]  Doreen Ware,et al.  The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences , 2016, PLoS biology.

[52]  Bas E. Dutilh,et al.  Computational approaches to predict bacteriophage–host relationships , 2015, FEMS microbiology reviews.

[53]  Tom O. Delmont,et al.  Anvi’o: an advanced analysis and visualization platform for ‘omics data , 2015, PeerJ.

[54]  Matthew B. Sullivan,et al.  VirSorter: mining viral signal from microbial genomic data , 2015, PeerJ.

[55]  Matthew B. Sullivan,et al.  Rising to the challenge: accelerated pace of discovery transforms marine virology , 2015, Nature Reviews Microbiology.

[56]  Bonnie L Hurwitz,et al.  Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses , 2014, Proceedings of the National Academy of Sciences.

[57]  Karthik Anantharaman,et al.  Sulfur Oxidation Genes in Diverse Deep-Sea Viruses , 2014, Science.

[58]  S. Hallam,et al.  Metabolic reprogramming by viruses in the sunlit and dark ocean , 2013, Genome Biology.

[59]  S. Hallam,et al.  Sequencing platform and library preparation choices impact viral metagenomes , 2013, BMC Genomics.

[60]  Daniel J. Nasko,et al.  VIROME: a standard operating procedure for analysis of viral metagenome sequences , 2012, Standards in genomic sciences.

[61]  François Enault,et al.  Metavir: a web server dedicated to virome analysis , 2011, Bioinform..

[62]  Katherine H. Huang,et al.  Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism. , 2011, Proceedings of the National Academy of Sciences of the United States of America.

[63]  C. Suttle.  Marine viruses — major players in the global ecosystem , 2007, Nature Reviews Microbiology.

[64]  Luke R. Thompson,et al.  Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts , 2006, PLoS biology.

[65]  Sallie W. Chisholm,et al.  Photosynthesis genes in marine viruses yield proteins during host infection , 2005, Nature.

[66]  E. Delong,et al.  Archaeal dominance in the mesopelagic zone of the Pacific Ocean , 2001, Nature.