Research graph
References from Codon-aware multi-scale feature fusion for metagenomic sequence classification. Local targets link to admitted publications; unresolved targets remain external evidence.
The microbial engines that drive Earth’s biogeochemical cycles
10.1126/science.1153213 · 2008 · External reference
Oceanography. Microbes, molecules, and marine ecosystems
10.1126/science.1093892 · 2004 · External reference
Redefining viruses: Lessons from Mimivirus
10.1038/nrmicro1858 · 2008 · External reference
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
10.1073/pnas.74.11.5088 · 1977 · External reference
The Analysis of Natural Microbial Populations by Ribosomal RNA Sequences.
10.1007/978-1-4757-0611-6_1 · 1986 · External reference
Microbial ecology and evolution: A ribosomal RNA approach
10.1146/annurev.mi.40.100186.002005 · 1986 · External reference
Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing
10.1128/jb.173.14.4371-4378.1991 · 1991 · External reference
Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon
10.1128/jb.178.3.591-599.1996 · 1996 · External reference
Screening of a fosmid library of marine environmental genomic DNA fragments reveals four clones related to members of the order Planctomycetales
10.1128/aem.64.8.3075-3078.1998 · 1998 · External reference
Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms
10.1128/aem.66.6.2541-2547.2000 · 2000 · External reference
Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage
10.1046/j.1462-2920.2000.00133.x · 2000 · External reference
Environmental genomics of “Haloquadratum walsbyi” in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species
10.1186/1471-2164-7-171 · 2006 · External reference
Environmental genome shotgun sequencing of the Sargasso Sea
10.1126/science.1093857 · 2004 · External reference
Metagenomics: Application of genomics to uncultured microorganisms
10.1128/mmbr.68.4.669-685.2004 · 2004 · External reference
Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates
2011 · External reference
Genomic variation landscape of the human gut microbiome
10.1038/nature11711 · 2013 · External reference
Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics
10.1016/j.csbj.2016.11.005 · 2016 · External reference
Viruses in the sea
10.1038/nature04160 · 2005 · External reference
Marine viruses--major players in the global ecosystem
10.1038/nrmicro1750 · 2007 · External reference
Marine viruses and their biogeochemical and ecological effects
10.1038/21119 · 1999 · External reference
Viruses and nutrient cycles in the sea: viruses play critical roles in the structure and function of aquatic food webs
10.2307/1313569 · 1999 · External reference
VirSorter: Mining viral signal from microbial genomic data
10.7717/peerj.985 · 2015 · External reference
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
10.1186/s40168-017-0283-5 · 2017 · External reference
Identifying viruses from metagenomic data using deep learning
10.1007/s40484-019-0187-4 · 2020 · External reference
PPR-Meta: A tool for identifying phages and plasmids from metagenomic fragments using deep learning
10.1093/gigascience/giz066 · 2019 · External reference
VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences
10.1186/s40168-020-00867-0 · 2020 · External reference
VirSorter2: A multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses
10.1186/s40168-020-00990-y · 2021 · External reference
Source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities
10.1073/pnas.1600974113 · 2016 · External reference
Identification of mobile genetic elements with geNomad
10.1038/s41587-023-01953-y · 2024 · External reference
cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data
10.1093/bioinformatics/btq299 · 2010 · External reference
PlasFlow: Predicting plasmid sequences in metagenomic data using genome signatures
10.1093/nar/gkx1321 · 2018 · External reference
PlaScope: A targeted approach to assess the plasmidome from genome assemblies at the species level
2018 · External reference
PlasClass improves plasmid sequence classification
10.1371/journal.pcbi.1007781 · 2020 · External reference
Microbial eukaryotes in the human microbiome: Ecology, evolution, and future directions
10.3389/fmicb.2011.00153 · 2011 · External reference
Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments
10.1111/j.1365-294x.2011.05297.x · 2012 · External reference
The ecology and diversity of microbial eukaryotes in geothermal springs
10.1038/s41396-018-0104-2 · 2018 · External reference
CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms
10.1371/journal.pbio.1001419 · 2012 · External reference
A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes
2009 · External reference
A global ocean atlas of eukaryotic genes
10.1038/s41467-017-02342-1 · 2018 · External reference
Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems
10.1038/s41598-019-42487-1 · 2019 · External reference
The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing
10.1371/journal.pbio.1001889 · 2014 · External reference
Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics
10.1101/gr.253070.119 · 2020 · External reference
The new tree of eukaryotes
10.1016/j.tree.2019.08.008 · 2020 · External reference
Fast and sensitive taxonomic classification for metagenomics with Kaiju
10.1038/ncomms11257 · 2016 · External reference
MetaEuk-sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics
10.1186/s40168-020-00808-x · 2020 · External reference
Genome-reconstruction for eukaryotes from complex natural microbial communities
10.1101/gr.228429.117 · 2018 · External reference
Tiara: deep learning-based classification system for eukaryotic sequences
10.1093/bioinformatics/btab672 · 2022 · External reference
Whokaryote: distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure
2022 · External reference
DeepMicroClass sorts metagenomic contigs into prokaryotes, eukaryotes and viruses
2024 · External reference
4CAC: 4-class classifier of metagenome contigs using machine learning and assembly graphs
2024 · External reference
The protist ribosomal reference database (PR2): A catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy
2013 · External reference
The PLSDB 2025 update: Enhanced annotations and improved functionality for comprehensive plasmid research
2025 · External reference
Linking virus genomes with host taxonomy
10.3390/v8030066 · 2016 · External reference
IMG/VR v3: An integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses
10.1093/nar/gkaa946 · 2021 · External reference
