MLTreeMap--accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies (Q33650402)

28 July 2017

MLTreeMap--accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies (English)

1 reference

28 July 2017

1 reference

1 reference

Christian von Mering

4

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author name string

Manuel Stark

series ordinal

1

1 reference

28 July 2017

Simon A Berger

series ordinal

2

1 reference

28 July 2017

Alexandros Stamatakis

series ordinal

3

1 reference

28 July 2017

language of work or name

English

0 references

publication date

5 August 2010

1 reference

28 July 2017

1 reference

28 July 2017

11

1 reference

28 July 2017

461

1 reference

28 July 2017

1

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2164-11-461

28 June 2019

exact match

0 references

cites work

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A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

21 June 2018

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The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes

21 June 2018

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Central role of the cell in microbial ecology

21 June 2018

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The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

21 June 2018

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Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment

21 June 2018

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The NIH Human Microbiome Project

21 June 2018

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Community proteogenomics reveals insights into the physiology of phyllosphere bacteria

21 June 2018

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Inference of microbial recombination rates from metagenomic data

21 June 2018

1 reference

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Community-wide analysis of microbial genome sequence signatures

21 June 2018

1 reference

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Cultivating the uncultured: limits, advances and future challenges.

21 June 2018

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A bioinformatician's guide to metagenomics

21 June 2018

1 reference

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A core gut microbiome in obese and lean twins

21 June 2018

1 reference

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A computational screen for type I polyketide synthases in metagenomics shotgun data

21 June 2018

1 reference

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STRING 8--a global view on proteins and their functional interactions in 630 organisms

21 June 2018

1 reference

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NCBI Reference Sequences: current status, policy and new initiatives

21 June 2018

1 reference

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A rapid bootstrap algorithm for the RAxML Web servers

21 June 2018

1 reference

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A simple, fast, and accurate method of phylogenomic inference

21 June 2018

1 reference

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Mechanistic diversity in the RuBisCO superfamily: a novel isomerization reaction catalyzed by the RuBisCO-like protein from Rhodospirillum rubrum

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Genomic sequencing of single microbial cells from environmental samples

21 June 2018

1 reference

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Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

21 June 2018

1 reference

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Signature genes as a phylogenomic tool

21 June 2018

1 reference

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The airborne metagenome in an indoor urban environment

21 June 2018

1 reference

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Phylogenetic classification of short environmental DNA fragments

21 June 2018

1 reference

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KEGG for linking genomes to life and the environment

21 June 2018

1 reference

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Get the most out of your metagenome: computational analysis of environmental sequence data

21 June 2018

1 reference

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What's in the mix: phylogenetic classification of metagenome sequence samples

21 June 2018

1 reference

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IMG/M: a data management and analysis system for metagenomes

21 June 2018

1 reference

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Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

21 June 2018

1 reference

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Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes

21 June 2018

1 reference

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CAMERA: a community resource for metagenomics

21 June 2018

1 reference

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High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment

21 June 2018

1 reference

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Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments

21 June 2018

1 reference

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MEGAN analysis of metagenomic data

21 June 2018

1 reference

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Accurate phylogenetic classification of variable-length DNA fragments

21 June 2018

1 reference

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Microfluidic digital PCR enables multigene analysis of individual environmental bacteria

21 June 2018

1 reference

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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

21 June 2018

1 reference

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Sequencing genomes from single cells by polymerase cloning

21 June 2018

1 reference

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Toward Automatic Reconstruction of a Highly Resolved Tree of Life

21 June 2018

1 reference

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Metagenomics: DNA sequencing of environmental samples.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Metagenomic marine nitrogen fixation--feast or famine?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Was photosynthetic RuBisCO recruited by acquisitive evolution from RuBisCO-like proteins involved in sulfur metabolism?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Comparative metagenomics of microbial communities

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Metagenomics: application of genomics to uncultured microorganisms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

21 June 2018

GeneWise and Genomewise

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

The natural history of nitrogen fixation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Review and re-analysis of domain-specific 16S primers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Phylogeny estimation: traditional and Bayesian approaches

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Exploring prokaryotic diversity in the genomic era

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Molecular phylogenetics: state-of-the-art methods for looking into the past

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in pacific northwest marine sediment communities

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Phylogenetic diversity of nitrogen fixation genes in the symbiotic microbial community in the gut of diverse termites.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Bias in template-to-product ratios in multitemplate PCR

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Evolutionary trees from DNA sequences: A maximum likelihood approach

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Cultivating previously uncultured soil bacteria using a soil substrate membrane system.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

High-resolution metagenomics targets specific functional types in complex microbial communities.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Fingerprinting the genetic diversity of the biotin carboxylase gene (accC) in aquatic ecosystems as a potential marker for studies of carbon dioxide assimilation in the dark

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Prediction of effective genome size in metagenomic samples

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

Functional marker genes for identification of sulfate-reducing prokaryotes

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091657

30 October 2018

Identifiers

DOI

10.1186/1471-2164-11-461

1 reference

Dimensions Publication ID

28 July 2017

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2164-11-461

release_kp6ddwfd4fb5jag4hej4bnbr2i

9 September 2019

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/kp6ddwfd4fb5jag4hej4bnbr2i

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMCID

3091657

1 reference

28 July 2017

1 reference