Related references
Note: Only part of the references are listed.Microbial abundance, activity and population genomic profiling with mOTUs2
Alessio Milanese et al.
NATURE COMMUNICATIONS (2019)
Network-based prediction of drug combinations
Feixiong Cheng et al.
NATURE COMMUNICATIONS (2019)
The gut microbiota heterogeneity and assembly changes associated with the IBD
Yang Sun et al.
SCIENTIFIC REPORTS (2019)
MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome
Anjun Ma et al.
BIOINFORMATICS (2019)
The Integrative Human Microbiome Project
Lita M. Proctor et al.
NATURE (2019)
Difficulty in inferring microbial community structure based on co-occurrence network approaches
Hokuto Hirano et al.
BMC BIOINFORMATICS (2019)
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Evan Bolyen et al.
NATURE BIOTECHNOLOGY (2019)
Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences
Himel Mallick et al.
NATURE COMMUNICATIONS (2019)
Biomarker discovery in inflammatory bowel diseases using network-based feature selection
Mostafa Abbas et al.
PLOS ONE (2019)
DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays
Amrit Singh et al.
BIOINFORMATICS (2019)
Microbial network disturbances in relapsing refractory Crohn's disease
Bahtiyar Yilmaz et al.
NATURE MEDICINE (2019)
Microbial Fermentation of Dietary Protein: An Important Factor in Diet-Microbe-Host Interaction
Natalie E. Diether et al.
MICROORGANISMS (2019)
The MetaCyc database of metabolic pathways and enzymes
Ron Caspi et al.
NUCLEIC ACIDS RESEARCH (2018)
IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics
Lev I. Levitsky et al.
JOURNAL OF PROTEOME RESEARCH (2018)
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis
Jasmine Chong et al.
NUCLEIC ACIDS RESEARCH (2018)
Single-cell metagenomics: challenges and applications
Yuan Xu et al.
PROTEIN & CELL (2018)
The Genome-Scale Integrated Networks in Microorganisms
Tong Hao et al.
FRONTIERS IN MICROBIOLOGY (2018)
Metatranscriptome of human faecal microbial communities in a cohort of adult men
Galeb S. Abu-Ali et al.
NATURE MICROBIOLOGY (2018)
From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota
Eugen Bauer et al.
MSYSTEMS (2018)
No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects
Antoine Danchin et al.
MICROBIAL BIOTECHNOLOGY (2018)
Species-level functional profiling of metagenomes and metatranscriptomes
Eric A. Franzosa et al.
NATURE METHODS (2018)
Genomic data integration systematically biases interactome mapping
Michael A. Skinnider et al.
PLOS COMPUTATIONAL BIOLOGY (2018)
Evaluating the Information Content of Shallow Shotgun Metagenomics
Benjamin Hillmann et al.
MSYSTEMS (2018)
Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes
Anna Heintz-Buschart et al.
NATURE MICROBIOLOGY (2017)
The trajectory of microbial single-cell sequencing
Tanja Woyke et al.
NATURE METHODS (2017)
compleXView: a server for the interpretation of protein abundance and connectivity information to identify protein complexes
Victor Solis-Mezarino et al.
NUCLEIC ACIDS RESEARCH (2017)
Disentangling Interactions in the Microbiome: A Network Perspective
Mehdi Layeghifard et al.
TRENDS IN MICROBIOLOGY (2017)
Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis
Jaeyun Sung et al.
NATURE COMMUNICATIONS (2017)
The gut microbiome in atherosclerotic cardiovascular disease
Zhuye Jie et al.
NATURE COMMUNICATIONS (2017)
Dissecting the human microbiome with single-cell genomics
Andrew C. Tolonen et al.
GENOME MEDICINE (2017)
A review of active learning approaches to experimental design for uncovering biological networks
Yuriy Sverchkov et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
Drug Target Protein-Protein Interaction Networks: A Systematic Perspective
Yanghe Feng et al.
BIOMED RESEARCH INTERNATIONAL (2017)
Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation
Shany Ofaim et al.
FRONTIERS IN MICROBIOLOGY (2017)
The Protein Interactome of Streptococcus pneumoniae and Bacterial Meta-interactomes Improve Function Predictions
S. Wuchty et al.
MSYSTEMS (2017)
Computational Approaches for Integrative Analysis of the Metabolome and Microbiome
Jasmine Chong et al.
METABOLITES (2017)
KEGG as a reference resource for gene and protein annotation
Minoru Kanehisa et al.
NUCLEIC ACIDS RESEARCH (2016)
Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China
Bin Ma et al.
ISME JOURNAL (2016)
Microbiome Networks: A Systems Framework for Identifying Candidate Microbial Assemblages for Disease Management
R. Poudel et al.
PHYTOPATHOLOGY (2016)
Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation
Matthew T. Agler et al.
PLOS BIOLOGY (2016)
MetaTrans: an open-source pipeline for metatranscriptomics
Xavier Martinez et al.
SCIENTIFIC REPORTS (2016)
Use of Metatranscriptomics in Microbiome Research
Stavros Bashiardes et al.
BIOINFORMATICS AND BIOLOGY INSIGHTS (2016)
CCLasso: correlation inference for compositional data through Lasso
Huaying Fang et al.
BIOINFORMATICS (2015)
MAGNA plus plus : Maximizing Accuracy in Global Network Alignment via both node and edge conservation
V. Vijayan et al.
BIOINFORMATICS (2015)
Investigating microbial co-occurrence patterns based on metagenomic compositional data
Yuguang Ban et al.
BIOINFORMATICS (2015)
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
Duy Tin Truong et al.
NATURE METHODS (2015)
High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats
Jizhong Zhou et al.
MBIO (2015)
Genome-wide protein-protein interactions and protein function exploration in cyanobacteria
Qi Lv et al.
SCIENTIFIC REPORTS (2015)
Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities
BoonFei Tan et al.
FRONTIERS IN MICROBIOLOGY (2015)
Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks
Hugo Roume et al.
NPJ BIOFILMS AND MICROBIOMES (2015)
Variable selection for generalized canonical correlation analysis
Arthur Tenenhaus et al.
BIOSTATISTICS (2014)
The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease
Lita M. Proctor
CELL HOST & MICROBE (2014)
Diffuse symbioses: roles of plant-plant, plant-microbe and microbe-microbe interactions in structuring the soil microbiome
Matthew G. Bakker et al.
MOLECULAR ECOLOGY (2014)
Similarity network fusion for aggregating data types on a genomic scale
Bo Wang et al.
NATURE METHODS (2014)
Deciphering microbial interactions and detecting keystone species with co-occurrence networks
David Berry et al.
FRONTIERS IN MICROBIOLOGY (2014)
Metaproteomics: Harnessing the Power of High Performance Mass Spectrometry to Identify the Suite of Proteins That Control Metabolic Activities in Microbial Communities
Robert L. Hettich et al.
ANALYTICAL CHEMISTRY (2013)
High throughput sequencing methods and analysis for microbiome research
Julia M. Di Bella et al.
JOURNAL OF MICROBIOLOGICAL METHODS (2013)
UPARSE: highly accurate OTU sequences from microbial amplicon reads
Robert C. Edgar
NATURE METHODS (2013)
Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules
Roie Levy et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency
Qin Ma et al.
GENOMICS PROTEOMICS & BIOINFORMATICS (2013)
The activity level of a microbial community function can be predicted from its metatranscriptome
Damian E. Helbling et al.
ISME JOURNAL (2012)
The oral metagenome in health and disease
Pedro Belda-Ferre et al.
ISME JOURNAL (2012)
A framework for human microbiome research
Barbara A. Methe et al.
NATURE (2012)
A metagenome-wide association study of gut microbiota in type 2 diabetes
Junjie Qin et al.
NATURE (2012)
Structure, function and diversity of the healthy human microbiome
Curtis Huttenhower et al.
NATURE (2012)
Microbial interactions: from networks to models
Karoline Faust et al.
NATURE REVIEWS MICROBIOLOGY (2012)
Metabolomics: the apogee of the omics trilogy
Gary J. Patti et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2012)
SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways
Nurcan Tuncbag et al.
NUCLEIC ACIDS RESEARCH (2012)
Associations between Pathogens in the Upper Respiratory Tract of Young Children: Interplay between Viruses and Bacteria
Menno R. van den Bergh et al.
PLOS ONE (2012)
Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
Sharon Greenblum et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Microbial Co-occurrence Relationships in the Human Microbiome
Karoline Faust et al.
PLOS COMPUTATIONAL BIOLOGY (2012)
Inferring Correlation Networks from Genomic Survey Data
Jonathan Friedman et al.
PLOS COMPUTATIONAL BIOLOGY (2012)
Enterotypes of the human gut microbiome
Manimozhiyan Arumugam et al.
NATURE (2011)
Pathos: A web facility that uses metabolic maps to display experimental changes in metabolites identified by mass spectrometry
David P. Leader et al.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY (2011)
Introduction to Network Analysis in Systems Biology
Avi Ma'ayan
SCIENCE SIGNALING (2011)
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
Bo Liu et al.
GENOME BIOLOGY (2011)
Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression
Zhiao Shi et al.
BMC SYSTEMS BIOLOGY (2010)
A human gut microbial gene catalogue established by metagenomic sequencing
Junjie Qin et al.
NATURE (2010)
Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome
Yanbin Yin et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
A guided tour of the Trans-Proteomic Pipeline
Eric W. Deutsch et al.
PROTEOMICS (2010)
How to identify essential genes from molecular networks?
Gabriel del Rio et al.
BMC SYSTEMS BIOLOGY (2009)
Microbial community proteomics: elucidating the catalysts and metabolic mechanisms that drive the Earth's biogeochemical cycles
Paul Wilmes et al.
CURRENT OPINION IN MICROBIOLOGY (2009)
A core gut microbiome in obese and lean twins
Peter J. Turnbaugh et al.
NATURE (2009)
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
F. Meyer et al.
BMC BIOINFORMATICS (2008)
Microbial contributions to climate change through carbon cycle feedbacks
Richard D. Bardgett et al.
ISME JOURNAL (2008)
Large-scale reconstruction and phylogenetic analysis of metabolic environments
Elhanan Borenstein et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Network-based prediction of protein function
Roded Sharan et al.
MOLECULAR SYSTEMS BIOLOGY (2007)
An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality
Jeongah Yoon et al.
BIOINFORMATICS (2006)
Metaproteomics: studying functional gene expression in microbial ecosystems
P Wilmes et al.
TRENDS IN MICROBIOLOGY (2006)
Virtual identification of essential proteins within the protein interaction network of yeast
E Estrada
PROTEOMICS (2006)
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions
Heladia Salgado et al.
NUCLEIC ACIDS RESEARCH (2006)
Defining operational taxonomic units using DNA barcode data
M Blaxter et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2005)
Functional cartography of complex metabolic networks
R Guimerà et al.
NATURE (2005)
Functional and topological characterization of protein interaction networks
SH Yook et al.
PROTEOMICS (2004)
Network biology:: Understanding the cell's functional organization
AL Barabási et al.
NATURE REVIEWS GENETICS (2004)
Finding and evaluating community structure in networks
MEJ Newman et al.
PHYSICAL REVIEW E (2004)
Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph
HW Ma et al.
BIOINFORMATICS (2004)
Metagenomics: Genomic analysis of microbial communities
CS Riesenfeld et al.
ANNUAL REVIEW OF GENETICS (2004)
A protein interaction map of Drosophila melanogaster
L Giot et al.
SCIENCE (2003)
Developmental gene regulatory network architecture across 500 million years of echinoderm evolution
VF Hinman et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Hierarchical organization in complex networks -: art. no. 026112
E Ravasz et al.
PHYSICAL REVIEW E (2003)
Hierarchical organization of modularity in metabolic networks
E Ravasz et al.
SCIENCE (2002)
Engineering a reduced Escherichia coli genome
V Kolisnychenko et al.
GENOME RESEARCH (2002)
Share Paper
