Related references
Note: Only part of the references are listed.Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities
Derek M. Bickhart et al.
NATURE BIOTECHNOLOGY (2022)
Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED
Sam Kovaka et al.
NATURE BIOTECHNOLOGY (2021)
Readfish enables targeted nanopore sequencing of gigabase-sized genomes
Alexander Payne et al.
NATURE BIOTECHNOLOGY (2021)
Report of the Independent Panel for Pandemic Preparedness and Response: making COVID-19 the last pandemic
Ellen Johnson Sirleaf et al.
LANCET (2021)
New Approaches to Anticipate the Risk of Reverse Zoonosis
Peng Jia et al.
TRENDS IN ECOLOGY & EVOLUTION (2021)
A global metagenomic map of urban microbiomes and antimicrobial resistance
David Danko et al.
CELL (2021)
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities
I-Min A. Chen et al.
NUCLEIC ACIDS RESEARCH (2021)
Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids
Wei Gu et al.
NATURE MEDICINE (2021)
MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data
Enrique Doster et al.
NUCLEIC ACIDS RESEARCH (2020)
Optimizing DNA Extraction Methods for Nanopore Sequencing of Neisseria gonorrhoeae Directly from Urine Samples
Teresa L. Street et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2020)
STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies
Tehmina Bharucha et al.
LANCET INFECTIOUS DISEASES (2020)
Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
Kern Rei Chng et al.
NATURE MEDICINE (2020)
Long-read human genome sequencing and its applications
Glennis A. Logsdon et al.
NATURE REVIEWS GENETICS (2020)
Metagenomic characterisation of avian parvoviruses and picornaviruses from Australian wild ducks
Jessy Vibin et al.
SCIENTIFIC REPORTS (2020)
metaFlye: scalable long-read metagenome assembly using repeat graphs
Mikhail Kolmogorov et al.
NATURE METHODS (2020)
IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring
Katrina L. Kalantar et al.
GIGASCIENCE (2020)
iGenomics: Comprehensive DNA sequence analysis on your Smartphone
Aspyn Palatnick et al.
GIGASCIENCE (2020)
Highly accurate long-read HiFi sequencing data for five complex genomes
Ting Hon et al.
SCIENTIFIC DATA (2020)
Harnessing the MinION: An example of how to establish long-read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora
Miriam Schalamun et al.
MOLECULAR ECOLOGY RESOURCES (2019)
Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions
James Stimson et al.
MOLECULAR BIOLOGY AND EVOLUTION (2019)
A new genomic blueprint of the human gut microbiota
Alexandre Almeida et al.
NATURE (2019)
New insights from uncultivated genomes of the global human gut microbiome
Stephen Nayfach et al.
NATURE (2019)
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage
Rene S. Hendriksen et al.
NATURE COMMUNICATIONS (2019)
Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease
Timothy A. Blauwkamp et al.
NATURE MICROBIOLOGY (2019)
Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid
Steve Miller et al.
GENOME RESEARCH (2019)
Linking the resistome and plasmidome to the microbiome
Thibault Stalder et al.
ISME JOURNAL (2019)
Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes
Denis Bertrand et al.
NATURE BIOTECHNOLOGY (2019)
Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection
Themoula Charalampous et al.
NATURE BIOTECHNOLOGY (2019)
Microbiome analysis of Ixodes scapularis ticks from New York and Connecticut
Rafal Tokarz et al.
TICKS AND TICK-BORNE DISEASES (2019)
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps
Alexander T. Dilthey et al.
NATURE COMMUNICATIONS (2019)
Impact of Host DNA and Sequencing Depth on the Taxonomic Resolution of Whole Metagenome Sequencing for Microbiome Analysis
Joana Pereira-Marques et al.
FRONTIERS IN MICROBIOLOGY (2019)
A systematic sequencing-based approach for microbial contaminant detection and functional inference
Sung-Joon Park et al.
BMC BIOLOGY (2019)
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
Edoardo Pasolli et al.
CELL (2019)
Errors in long-read assemblies can critically affect protein prediction
Mick Watson et al.
NATURE BIOTECHNOLOGY (2019)
Tracking virus outbreaks in the twenty-first century
Nathan D. Grubaugh et al.
NATURE MICROBIOLOGY (2019)
A review of methods and databases for metagenomic classification and assembly
Florian P. Breitwieser et al.
BRIEFINGS IN BIOINFORMATICS (2019)
DNA extraction for human microbiome studies: the issue of standardization
K. Leigh Greathouse et al.
GENOME BIOLOGY (2019)
World Health Organization Global Gonococcal Antimicrobial Surveillance Program (WHO GASP): review of new data and evidence to inform international collaborative actions and research efforts
Magnus Unemo et al.
SEXUAL HEALTH (2019)
APPLICATIONS OF NEXT-GENERATION SEQUENCING Towards a genomics-informed, real-time, global pathogen surveillance system
Jennifer L. Gardy et al.
NATURE REVIEWS GENETICS (2018)
Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes (vol 19, 2017)
Sheng-Yong Niu et al.
BRIEFINGS IN BIOINFORMATICS (2018)
Development and Optimization of Metagenomic Next-Generation Sequencing Methods for Cerebrospinal Fluid Diagnostics
Patricia J. Simner et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2018)
Determining Performance Metrics for Targeted Next-Generation Sequencing Panels Using Reference Materials
Megan H. Cleveland et al.
JOURNAL OF MOLECULAR DIAGNOSTICS (2018)
Multiplexed identification, quantification and genotyping of infectious agents using a semiconductor biochip
Arjang Hassibi et al.
NATURE BIOTECHNOLOGY (2018)
Best practices for analysing microbiomes
Rob Knight et al.
NATURE REVIEWS MICROBIOLOGY (2018)
A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa
Marike Geldenhuys et al.
PLOS ONE (2018)
The Global Virome Project
Dennis Carroll et al.
SCIENCE (2018)
Metagenomic Virome Analysis of Culex Mosquitoes from Kenya and China
Evans Atoni et al.
VIRUSES-BASEL (2018)
Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen
Robert D. Stewart et al.
NATURE COMMUNICATIONS (2018)
ASaiM: a Galaxy-based framework to analyze microbiota data
Berenice Batut et al.
GIGASCIENCE (2018)
DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data
Gustavo Arango-Argoty et al.
MICROBIOME (2018)
Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries
Patrick Munk et al.
NATURE MICROBIOLOGY (2018)
American Gut: an Open Platform for Citizen Science Microbiome Research
Daniel McDonald et al.
MSYSTEMS (2018)
On the Road to Strain-Resolved Comparative Metagenomics
Nicola Segata
MSYSTEMS (2018)
High-quality genome sequences of uncultured microbes by assembly of read clouds
Alex Bishara et al.
NATURE BIOTECHNOLOGY (2018)
Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform
Po-E Li et al.
NUCLEIC ACIDS RESEARCH (2017)
The Global Threat of Animal Influenza Viruses of Zoonotic Concern: Then and Now
Marc-Alain Widdowson et al.
JOURNAL OF INFECTIOUS DISEASES (2017)
Shotgun metagenomics, from sampling to analysis
Christopher Quince et al.
NATURE BIOTECHNOLOGY (2017)
Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software
Alexander Sczyrba et al.
NATURE METHODS (2017)
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
Joshua Quick et al.
NATURE PROTOCOLS (2017)
Reference standards for next-generation sequencing
Simon A. Hardwick et al.
NATURE REVIEWS GENETICS (2017)
Bacterial colonization and succession in a newly opened hospital
Simon Lax et al.
SCIENCE TRANSLATIONAL MEDICINE (2017)
Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome
Brandon Brooks et al.
NATURE COMMUNICATIONS (2017)
Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks
Don Klinkenberg et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
The metagenomic data life-cycle: standards and best practices
Petra ten Hoopen et al.
GIGASCIENCE (2017)
A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data
Despoina D. Roumpeka et al.
FRONTIERS IN GENETICS (2017)
Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics
Karel Sedlar et al.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2017)
Metagenomic-based Surveillance of Pacific Coast tick Dermacentor occidentalis Identifies Two Novel Bunyaviruses and an Emerging Human Ricksettsial Pathogen
Jerome Bouquet et al.
SCIENTIFIC REPORTS (2017)
Laboratory-acquired infections of Salmonella enterica serotype Typhi in South Africa: phenotypic and genotypic analysis of isolates
Anthony Marius Smith et al.
BMC INFECTIOUS DISEASES (2017)
Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection
Robert Schlaberg et al.
ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE (2017)
Advancements in Next-Generation Sequencing
Shawn E. Levy et al.
ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, VOL 17 (2016)
Advances in Understanding Bacterial Pathogenesis Gained from Whole-Genome Sequencing and Phylogenetics
Elizabeth Klemm et al.
CELL HOST & MICROBE (2016)
Use of Whole Genome Sequencing and Patient Interviews To Link a Case of Sporadic Listeriosis to Consumption of Prepackaged Lettuce
K. A. Jackson et al.
JOURNAL OF FOOD PROTECTION (2016)
Challenges in the analysis of viral metagenomes
Rebecca Rose et al.
VIRUS EVOLUTION (2016)
A simplified Sanger sequencing method for full genome sequencing of multiple subtypes of human influenza A viruses
Yi-Mo Deng et al.
JOURNAL OF CLINICAL VIROLOGY (2015)
World Health Organization Global Estimates and Regional Comparisons of the Burden of Foodborne Disease in 2010
Arie H. Havelaar et al.
PLOS MEDICINE (2015)
Lack of Evidence for Plague or Anthrax on the New York City Subway
Joel Ackelsberg et al.
CELL SYSTEMS (2015)
Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics (vol 1, pg 72, 2015)
Ebrahim Afshinnekoo et al.
CELL SYSTEMS (2015)
ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes
Sushim Kumar Gupta et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2014)
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
Susannah J. Salter et al.
BMC BIOLOGY (2014)
A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
Samia N. Naccache et al.
GENOME RESEARCH (2014)
Environmental Surveillance for Polioviruses in the Global Polio Eradication Initiative
Humayun Asghar et al.
JOURNAL OF INFECTIOUS DISEASES (2014)
Binning metagenomic contigs by coverage and composition
Johannes Alneberg et al.
NATURE METHODS (2014)
Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples
Michael J. Strong et al.
PLOS PATHOGENS (2014)
The Comprehensive Antibiotic Resistance Database
Andrew G. McArthur et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2013)
The Genomic Standards Consortium
Dawn Field et al.
PLOS BIOLOGY (2011)
Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology
Erik K. Binga et al.
ISME JOURNAL (2008)
Executive summary of the AVMA One Health Initiative Task Force report
Lonnie J. King et al.
JAVMA-JOURNAL OF THE AMERICAN VETERINARY MEDICAL ASSOCIATION (2008)
Nipah virus encephalitis outbreak in Malaysia
SK Lam et al.
CLINICAL INFECTIOUS DISEASES (2002)