Inferring Regulatory Networks from Expression Data Using Tree-Based Methods
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September 2010 |
The size of the immune repertoire of bacteria
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February 2020 |
Bacteriophages isolated from Lake Michigan demonstrate broad host-range across several bacterial phyla
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October 2015 |
VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families
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January 2021 |
A continuous evolution system for contracting the host range of bacteriophage T7
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January 2020 |
Host-linked soil viral ecology along a permafrost thaw gradient
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July 2018 |
Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing
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October 2018 |
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome
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June 2021 |
Accurate viral genome reconstruction and host assignment with proximity-ligation sequencing
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preprint
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June 2021 |
Diversity in the soil virosphere: to infinity and beyond?
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November 2022 |
Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria
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April 2020 |
inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains
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January 2021 |
Viral abundance, community structure and correlation with bacterial community in soils of different cover plants
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December 2021 |
The ‘Neglected’ Soil Virome – Potential Role and Impact
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August 2018 |
Microbial community response to hydration-desiccation cycles in desert soil
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April 2017 |
Phage-Encoded Sigma Factors Alter Bacterial Dormancy
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August 2022 |
Piggyback-the-Winner in host-associated microbial communities
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July 2016 |
Active virus-host interactions at sub-freezing temperatures in Arctic peat soil
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October 2021 |
Network analysis methods for studying microbial communities: A mini review
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January 2021 |
Host diversity slows bacteriophage adaptation by selecting generalists over specialists
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January 2021 |
Ecology of viruses in soils: Past, present and future perspectives
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February 2008 |
Interactions between bacterial and phage communities in natural environments
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August 2021 |
Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations
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June 2019 |
Minimum Information about an Uncultivated Virus Genome (MIUViG)
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December 2018 |
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
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May 2015 |
Fast and accurate long-read alignment with Burrows–Wheeler transform
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January 2010 |
Virome Sequencing of the Human Intestinal Mucosal–Luminal Interface
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October 2020 |
Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay
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February 2017 |
MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut
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February 2021 |
Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists
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November 2013 |
Taxonomy of prokaryotic viruses: 2018-2019
update from the ICTV Bacterial and Archaeal Viruses Subcommittee
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journal
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March 2020 |
Pre-exposure to drought increases the resistance of tropical forest soil bacterial communities to extended drought
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November 2012 |
VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses
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February 2021 |
Uncovering Earth’s virome
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August 2016 |
Twelve years of SAMtools and BCFtools
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journal
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January 2021 |
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata
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journal
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November 2022 |
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
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October 2009 |
SAMBLASTER: fast duplicate marking and structural variant read extraction
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May 2014 |
Unified feature association networks through integration of transcriptomic and proteomic data
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journal
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September 2019 |
UniProt: the Universal Protein knowledgebase
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January 2004 |
Prokaryotic virus host predictor: a Gaussian model for host prediction of prokaryotic viruses in metagenomics
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January 2021 |
Bottlenecks and Hubs in Inferred Networks Are Important for Virulence in Salmonella typhimurium
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February 2009 |
VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences
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June 2020 |
Wisdom of crowds for robust gene network inference
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July 2012 |
Identifying viruses from metagenomic data using deep learning
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January 2020 |
Ecological speciation of bacteriophage lambda in allopatry and sympatry
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journal
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December 2016 |
Viral Regulation on Bacterial Community Impacted by Lysis-Lysogeny Switch: A Microcosm Experiment in Eutrophic Coastal Waters
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July 2019 |
Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen
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February 2018 |
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
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November 2003 |
Soil viruses: Understudied agents of soil ecology
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journal
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November 2022 |
WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs
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journal
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July 2017 |
dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
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July 2017 |
Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory
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September 2017 |
Moisture modulates soil reservoirs of active DNA and RNA viruses
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August 2021 |
ViPTree: the viral proteomic tree server
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March 2017 |
CheckV assesses the quality and completeness of metagenome-assembled viral genomes
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December 2020 |
Life in Dry Soils: Effects of Drought on Soil Microbial Communities and Processes
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journal
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November 2018 |
Prophage-mediated defence against viral attack and viral counter-defence
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journal
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January 2017 |
DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes
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December 2021 |
CRISPR-Cas immunity in prokaryotes
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October 2015 |
Metagenomic reconstructions of bacterial CRISPR loci constrain population histories
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journal
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September 2015 |
High-Throughput Chromosomal Conformation Capture (Hi-C) Metagenome Sequencing Reveals Soil Moisture Impacts on Phage-Host Interactions
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journalarticle
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January 2023 |
Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles
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journal
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January 2007 |
The Sequence Alignment/Map format and SAMtools
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journal
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June 2009 |
Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences
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journal
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November 2016 |
Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants
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journal
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September 2021 |
Soil microbiomes and climate change
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journal
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October 2019 |
bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes
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February 2019 |
Drought and host selection influence bacterial community dynamics in the grass root microbiome
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journal
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July 2017 |
fastp: an ultra-fast all-in-one FASTQ preprocessor
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September 2018 |
Enterovirus inactivation in soil
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journal
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October 1979 |