Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities (Q35189993)

7 August 2017

Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities (English)

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7 August 2017

1 reference

Weili Xiong

3

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author name string

Paul E Abraham

series ordinal

1

1 reference

PubMed ID

24939130

7 August 2017

Richard J Giannone

series ordinal

2

1 reference

PubMed ID

24939130

7 August 2017

Robert L Hettich

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4

1 reference

7 August 2017

17 June 2014

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Current Protocols in Bioinformatics

7 August 2017

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7 August 2017

46

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7 August 2017

13.26.1-14

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Defining the boundaries and characterizing the landscape of functional genome expression in vascular tissues of Populus using shotgun proteomics.

7 August 2017

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https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Microbial communities in acid mine drainage.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Enigmatic, ultrasmall, uncultivated Archaea.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

De novo analysis of peptide tandem mass spectra by spectral graph partitioning.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Characterization of the active bacterial community involved in natural attenuation processes in arsenic-rich creek sediments

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

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

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

TANDEM: matching proteins with tandem mass spectra

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

TagRecon: high-throughput mutation identification through sequence tagging

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation.

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Search and clustering orders of magnitude faster than BLAST

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

PepNovo: de novo peptide sequencing via probabilistic network modeling

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Open mass spectrometry search algorithm

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Proteomic characterization of cellular and molecular processes that enable the Nanoarchaeum equitans--Ignicoccus hospitalis relationship.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

The KEGG resource for deciphering the genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

iPath: interactive exploration of biochemical pathways and networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Label-free quantitative proteomics for the extremely thermophilic bacterium Caldicellulosiruptor obsidiansis reveal distinct abundance patterns upon growth on cellobiose, crystalline cellulose, and switchgrass

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Individual genome assembly from complex community short-read metagenomic datasets

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

ScanRanker: Quality assessment of tandem mass spectra via sequence tagging

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Accurate phylogenetic classification of variable-length DNA fragments

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Assembly algorithms for next-generation sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

MSNovo: a dynamic programming algorithm for de novo peptide sequencing via tandem mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Interpretation of shotgun proteomic data: the protein inference problem

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Rapid and accurate peptide identification from tandem mass spectra

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Meta-IDBA: a de Novo assembler for metagenomic data

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Probability-based protein identification by searching sequence databases using mass spectrometry data

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

The Pfam protein families database

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

A metagenome-wide association study of gut microbiota in type 2 diabetes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

The Uncultured Microbial Majority

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

FragGeneScan: predicting genes in short and error-prone reads

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

An iterative workflow for mining the human intestinal metaproteome

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

DNA sequencing with chain-terminating inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

The COG database: an updated version includes eukaryotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Community structure and metabolism through reconstruction of microbial genomes from the environment

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Environmental genome shotgun sequencing of the Sargasso Sea

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Sipros/ProRata: a versatile informatics system for quantitative community proteomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Prokaryotes: the unseen majority

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Guidelines for the next 10 years of proteomics

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

iPath2.0: interactive pathway explorer

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

DBParser: web-based software for shotgun proteomic data analyses

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Combining gene prediction methods to improve metagenomic gene annotation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Proteomic parsimony through bipartite graph analysis improves accuracy and transparency

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Protein analysis by shotgun/bottom-up proteomics

21 January 2018

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https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Shotgun metaproteomics of the human distal gut microbiota

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

Statistical Analysis of Membrane Proteome Expression Changes inSaccharomycescerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F0471250953.BI1326S46

10.1002/0471250953.BI1326S46

21 January 2018

Identifiers

DOI

1 reference

7 August 2017

1 reference

PubMed ID

24939130