Benchmarking of s ingle‐virus genomics: a new tool for uncovering the virosphere

Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems

(2019) M. E. Sieracki et al.   Scientific Reports

Droplet Digital PCR for Estimating Absolute Abundances of Widespread Pelagibacter Viruses

(2019) Francisco Martinez-Hernandez et al.   Frontiers in Microbiology

Viral Communities in the Global Deep Ocean Conveyor Belt Assessed by Targeted Viromics

(2019) Daniele De Corte et al.   Frontiers in Microbiology

Trends of Microdiversity Reveal Depth-Dependent Evolutionary Strategies of Viruses in the Mediterranean

(2019) Felipe Hernandes Coutinho et al.   mSystems

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Deciphering the Human Virome with Single-Virus Genomics and Metagenomics

(2018) Maria de la Cruz Peña et al.   Viruses-Basel

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

(2018) Yoann Seeleuthner et al.   Nature Communications

Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

(2018) DaYang Chen et al.   Scientific Reports

Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean

(2018) Francisco Martinez-Hernandez et al.   ISME Journal

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Genomic exploration of individual giant ocean viruses

(2017) William H Wilson et al.   ISME Journal

Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans

(2017) Felipe H. Coutinho et al.   Nature Communications

Single-virus genomics reveals hidden cosmopolitan and abundant viruses

(2017) Francisco Martinez-Hernandez et al.   Nature Communications

Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles

(2017) Ramunas Stepanauskas et al.   Nature Communications

Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters

(2017) Mario López-Pérez et al.   PLoS Genetics

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells

(2017) Jean-François Mangot et al.   Scientific Reports

Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis

(2017) David López-Escardó et al.   Scientific Reports

Membrane vesicles in sea water: heterogeneous DNA content and implications for viral abundance estimates

(2016) Steven J Biller et al.   ISME Journal

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

TruePrime is a novel method for whole-genome amplification from single cells based on TthPrimPol

(2016) Ángel J. Picher et al.   Nature Communications

INC-Seq: accurate single molecule reads using nanopore sequencing

(2016) Chenhao Li et al.   GigaScience

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

(2015) Jessica M Labonté et al.   ISME Journal

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Effects of sample treatments on genome recovery via single-cell genomics

(2014) Scott Clingenpeel et al.   ISME Journal

Depth-Specific Distribution of the SAR116 Phages Revealed by Virome Binning

(2014) Ilnam Kang et al.   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

Obtaining genomes from uncultivated environmental microorganisms using FACS–based single-cell genomics

(2014) Christian Rinke et al.   Nature Protocols

A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods

(2014) Charles F. A. de Bourcy et al.   PLoS One

Bacterial Vesicles in Marine Ecosystems

(2014) S. J. Biller et al.   SCIENCE

Effects of a novel cell stabilizing reagent on DNA amplification by PCR as compared to traditional stabilizing reagents

(2013) Kausik Das et al.   ACTA HISTOCHEMICA

Marine viruses, a genetic reservoir revealed by targeted viromics

(2013) Joaquín Martínez Martínez et al.   ISME Journal

Expanding the Marine Virosphere Using Metagenomics

(2013) Carolina Megumi Mizuno et al.   PLoS Genetics

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Single cell genomics: an individual look at microbes

(2012) Ramunas Stepanauskas   CURRENT OPINION IN MICROBIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Genomic sequencing of uncultured microorganisms from single cells

(2012) Roger S. Lasken   NATURE REVIEWS MICROBIOLOGY

High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton

(2011) Manuel Martinez-Garcia et al.   ISME Journal

Single Virus Genomics: A New Tool for Virus Discovery

(2011) Lisa Zeigler Allen et al.   PLoS One

Decontamination of MDA Reagents for Single Cell Whole Genome Amplification

(2011) Tanja Woyke et al.   PLoS One

Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists

(2011) H. S. Yoon et al.   SCIENCE