(Q34783183)

4 August 2017

MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information (English)

1 reference

4 August 2017

4

Steven J Hallam

1 reference

4 August 2017

Kishori M Konwar

1

1 reference

PubMed ID

23800136

4 August 2017

Niels W Hanson

series ordinal

2

1 reference

PubMed ID

23800136

4 August 2017

Antoine P Pagé

series ordinal

3

1 reference

4 August 2017

21 June 2013

1 reference

4 August 2017

1 reference

4 August 2017

14

1 reference

4 August 2017

202

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2105-14-202

4 August 2017

0 references

cites work

A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP)

1 reference

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Metabolic reconstruction for metagenomic data and its application to the human microbiome

7 July 2018

1 reference

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The pathway tools pathway prediction algorithm

7 July 2018

1 reference

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Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset

7 July 2018

1 reference

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Microbial ecology of expanding oxygen minimum zones

7 July 2018

1 reference

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Construction and completion of flux balance models from pathway databases

7 July 2018

1 reference

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Browsing metabolic and regulatory networks with BioCyc

7 July 2018

1 reference

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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

7 July 2018

1 reference

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IMG/M: the integrated metagenome data management and comparative analysis system

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

Connecting genotype to phenotype in the era of high-throughput sequencing.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

Adaptive seeds tame genomic sequence comparison

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

High-throughput generation, optimization and analysis of genome-scale metabolic models

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

An advanced web query interface for biological databases

7 July 2018

1 reference

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Prodigal: prokaryotic gene recognition and translation initiation site identification

7 July 2018

1 reference

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7 July 2018

A primer on metagenomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

Patterns of diversity in marine phytoplankton

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

Machine learning methods for metabolic pathway prediction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

FIGfams: yet another set of protein families

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

A bioinformatician's guide to metagenomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

MetaSim: a sequencing simulator for genomics and metagenomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

The microbial engines that drive Earth's biogeochemical cycles.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

KEGG Atlas mapping for global analysis of metabolic pathways

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

The RAST Server: rapid annotations using subsystems technology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

Emergent biogeography of microbial communities in a model ocean

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

CAMERA: a community resource for metagenomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

MEGAN analysis of metagenomic data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

The Pathway Tools cellular overview diagram and Omics Viewer

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

Visualization of comparative genomic analyses by BLAST score ratio

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

Enzyme-specific profiles for genome annotation: PRIAM

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

Efficient clustering of large EST data sets on parallel computers

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

The Pathway Tools software

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

RefSeq and LocusLink: NCBI gene-centered resources

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

The COG database: new developments in phylogenetic classification of proteins from complete genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

The EcoCyc and MetaCyc databases

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

KEGG: kyoto encyclopedia of genes and genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

Twilight zone of protein sequence alignments

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

Basic local alignment search tool

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

Predicting bacterial community assemblages using an artificial neural network approach

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3695837

Towards microbial systems science: integrating microbial perspective, from genomes to biomes

26 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23800136

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-14-202

1 reference

journals/bmcbi/KonwarHPH13

4 August 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

4 August 2017

1 reference

PubMed ID

23800136