iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria
Lawrence Berkeley National Laboratory · Joint Genome Institute · +4 more institutions
Abstract
The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied through metagenomics. While metagenomes enable high-throughput exploration of the viral sequence space, metagenome-derived sequences lack key information compared to isolated viruses, in particular host association. Different computational approaches are available to predict the host(s) of uncultivated viruses based on their genome sequences, but thus far individual approaches are limited either in precision or in recall, i.e., for a number of viruses they yield erroneous predictions or no prediction at all. Here, we describe iPHoP, a two-step framework that integrates multiple methods to reliably predict host…
Citation impact
- FWCI
- 103.49
- Percentile
- 100%
- References
- 79
Authors
7- SRSimon RouxCorresponding
Lawrence Berkeley National Laboratory, Joint Genome Institute
- APAntônio Pedro CamargoCorresponding
Lawrence Berkeley National Laboratory, Joint Genome Institute
- FHFelipe H. CoutinhoCorresponding
Institut de Ciències del Mar
- SMShareef M. DabdoubCorresponding
University of Iowa
- BEBas E. DutilhCorresponding
Utrecht University, Friedrich Schiller University Jena
Topics & keywords
- Metagenomics
- Biology
- Archaea
- Genome
- Human virome
- Computational biology
- Host (biology)
- Bacteria
Funding
- UDU.S. Department of EnergyAwards: -AC02-05CH11231, Contract No. DE-AC02-05CH11231, 05CH11231, Contract DE-AC02-05CH11231, No. DE-AC02-05CH11231, AC02-05CH11231, DE-AC02, DE-AC02-05CH11231, DE-AC02-
- AVAlexander von Humboldt-StiftungAward: DE-AC02-05CH11231
- JGJoint Genome InstituteAwards: DE-AC02-05CH11231, AC02-05CH11231
- ECEuropean CommissionAwards: 865694, 955974, DE-AC02-05CH11231, CEX2019-000928-S
- DFDeutsche ForschungsgemeinschaftAwards: Project-ID 390713860, DE-AC02-05CH11231, ID 390713860, 390713860, EXC 2051
- BFBundesministerium für Bildung und ForschungAwards: CEX2019-000928-S, 390713860
- OOOffice of ScienceAwards: Contract DE-AC02-05CH11231, AC02-05CH11231, -AC02-05CH11231, DE-AC02, No. DE-AC02-05CH11231, Contract No. DE-AC02-05CH11231
- EREuropean Research CouncilAward: 865694
- BABiological and Environmental ResearchAwards: 05CH11231, No. DE-AC02-05CH11231, Contract No. DE-AC02-05CH11231, DE-AC02-05CH11231, AC02-05CH11231
- LBLawrence Berkeley National LaboratoryAwards: DE-AC02-05CH11231, No. DE-AC02-05CH11231, Contract No. DE-AC02-05CH11231, 05CH11231, AC02-05CH11231
- HMH2020 Marie Skłodowska-Curie ActionsAwards: 955974, Horizon 2020, CEX2019-000928-S
- HEHORIZON EUROPE Marie Sklodowska-Curie ActionsAward: 955974