Using populations of human and microbial genomes for organism detection in metagenomes (Q35618499)

25926546

9 August 2017

title

Using populations of human and microbial genomes for organism detection in metagenomes (English)

1 reference

9 August 2017

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25926546%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Jonathan Allen

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25926546%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

author name string

Sasha K Ames

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25926546%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Shea N Gardner

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25926546%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Tom R Slezak

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25926546%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Maya B Gokhale

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25926546%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

publication date

29 April 2015

1 reference

9 August 2017

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25926546%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

volume

25

1 reference

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10 June 2020

issue

7

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25926546%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

page(s)

1056-1067

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25926546%20AND%20SRC:MED&resulttype=core&format=json

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

10 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

The landscape of human STR variation

12 July 2018

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Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Actionable diagnosis of neuroleptospirosis by next-generation sequencing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Mycoplasma contamination in the 1000 Genomes Project

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Geographic population structure analysis of worldwide human populations infers their biogeographical origins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

A physicians' wish list for the clinical application of intestinal metagenomics.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Full genome virus detection in fecal samples using sensitive nucleic acid preparation, deep sequencing, and a novel iterative sequence classification algorithm

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Tackling soil diversity with the assembly of large, complex metagenomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Kraken: ultrafast metagenomic sequence classification using exact alignments

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Strain/species identification in metagenomes using genome-specific markers

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

MePIC, metagenomic pathogen identification for clinical specimens

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Identification of novel viruses using VirusHunter--an automated data analysis pipeline

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Metagenomic species profiling using universal phylogenetic marker genes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Scalable metagenomic taxonomy classification using a reference genome database

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Short read alignment with populations of genomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

An integrated map of genetic variation from 1,092 human genomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

CD-HIT: accelerated for clustering the next-generation sequencing data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Rapid phylogenetic and functional classification of short genomic fragments with signature peptides

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

A framework for human microbiome research

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Structure, function and diversity of the healthy human microbiome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Metagenomic microbial community profiling using unique clade-specific marker genes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

lobSTR: A short tandem repeat profiler for personal genomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Virus identification in unknown tropical febrile illness cases using deep sequencing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Novel plasmid and its variant harboring both a bla(NDM-1) gene and type IV secretion system in clinical isolates of Acinetobacter lwoffii

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Fast identification and removal of sequence contamination from genomic and metagenomic datasets

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

A map of human genome variation from population-scale sequencing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

DNA signatures for detecting genetic engineering in bacteria.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Repbase Update, a database of eukaryotic repetitive elements

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Basic local alignment search tool

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484388

Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions

12 July 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25926546

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.184879.114

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25926546%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25926546%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

25926546

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25926546%20AND%20SRC:MED&resulttype=core&format=json