Related references
Note: Only part of the references are listed.Genome- and Community-Level Interaction Insights in Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment
Zhichao Zhou et al.
MSYSTEMS (2020)
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes
I-Min A. Chen et al.
NUCLEIC ACIDS RESEARCH (2019)
Dynamic interaction network inference from longitudinal microbiome data
Jose Lugo-Martinez et al.
MICROBIOME (2019)
Strengthening Insights in Microbial Ecological Networks from Theory to Applications
Xiaofei Lv et al.
MSYSTEMS (2019)
Microbiome networks and change-point analysis reveal key community changes associated with cystic fibrosis pulmonary exacerbations
Mehdi Layeghifard et al.
NPJ BIOFILMS AND MICROBIOMES (2019)
Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life
Cindy J. Castelle et al.
CELL (2018)
Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery
Guillaume Bernard et al.
GENOME BIOLOGY AND EVOLUTION (2018)
Bipartite Network Analysis of Gene Sharings in the Microbial World
Eduardo Corel et al.
MOLECULAR BIOLOGY AND EVOLUTION (2018)
In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis
Promi Das et al.
PLOS ONE (2018)
Modules of co-occurrence in the cyanobacterial pan-genome reveal functional associations between groups of ortholog genes
Christian Beck et al.
PLOS GENETICS (2018)
Fungi stabilize connectivity in the lung and skin microbial ecosystems
Laura Tipton et al.
MICROBIOME (2018)
From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota
Eugen Bauer et al.
MSYSTEMS (2018)
Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in a Uranium-Contaminated Site after Bioreduction Followed by Reoxidation
Bing Li et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2018)
Genetic correlation network prediction of forest soil microbial functional organization
Bin Ma et al.
ISME JOURNAL (2018)
IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences
Adithya Murali et al.
MICROBIOME (2018)
Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes
Karen G. Lloyd et al.
MSYSTEMS (2018)
Identification of Microbial Dark Matter in Antarctic Environments
Jeff S. Bowman
FRONTIERS IN MICROBIOLOGY (2018)
Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem
Lindsey M. Solden et al.
NATURE MICROBIOLOGY (2018)
From hairballs to hypotheses-biological insights from microbial networks
Lisa Rottjers et al.
FEMS MICROBIOLOGY REVIEWS (2018)
Gene Graphics: a genomic neighborhood data visualization web application
Katherine J. Harrison et al.
BIOINFORMATICS (2018)
Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents
Dimitri V. Meier et al.
ISME JOURNAL (2017)
Hypersaline sapropels act as hotspots for microbial dark matter
Adrian-Stefan Andrei et al.
SCIENTIFIC REPORTS (2017)
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Donovan H. Parks et al.
NATURE MICROBIOLOGY (2017)
Transcriptomic changes in an animal-bacterial symbiosis under modeled microgravity conditions
Giorgio Casaburi et al.
SCIENTIFIC REPORTS (2017)
Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes
Eric D. Becraft et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2016)
Toward Accurate and Quantitative Comparative Metagenomics
Stephen Nayfach et al.
CELL (2016)
The bright side of microbial dark matter: lessons learned from the uncultivated majority
Lindsey Solden et al.
CURRENT OPINION IN MICROBIOLOGY (2016)
Network-based metabolic analysis and microbial community modeling
Cesar Cardona et al.
CURRENT OPINION IN MICROBIOLOGY (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)
DADA2: High-resolution sample inference from Illumina amplicon data
Benjamin J. Callahan et al.
NATURE METHODS (2016)
Aerobic Lineage of the Oxidative Stress Response Protein Rubrerythrin Emerged in an Ancient Microaerobic, (Hyper)Thermophilic Environment
Juan P. Cardenas et al.
Frontiers in Microbiology (2016)
Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data
Kathrin P. Asshauer et al.
BIOINFORMATICS (2015)
CCLasso: correlation inference for compositional data through Lasso
Huaying Fang et al.
BIOINFORMATICS (2015)
Functional and protein-protein interaction network analysis of colorectal cancer induced by ulcerative colitis
Yong Dai et al.
MOLECULAR MEDICINE REPORTS (2015)
Microbial community transcriptional networks are conserved in three domains at ocean basin scales
Frank O. Aylward et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Determinants of community structure in the global plankton interactome
Gipsi Lima-Mendez et al.
SCIENCE (2015)
Big Data: Astronomical or Genomical?
Zachary D. Stephens et al.
PLOS BIOLOGY (2015)
Sparse and Compositionally Robust Inference of Microbial Ecological Networks
Zachary D. Kurtz et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review
Felipe H. Coutinho et al.
PEERJ (2015)
Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters
Alexandre B. de Menezes et al.
ENVIRONMENTAL MICROBIOLOGY (2015)
Taxonomic relatedness shapes bacterial assembly in activated sludge of globally distributed wastewater treatment plants
Feng Ju et al.
ENVIRONMENTAL MICROBIOLOGY (2014)
Impact of single-cell genomics and metagenomics on the emerging view of extremophile microbial dark matter
Brian P. Hedlund et al.
EXTREMOPHILES (2014)
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
Ross Overbeek et al.
NUCLEIC ACIDS RESEARCH (2014)
Demonstrating microbial co-occurrence pattern analyses within and between ecosystems
Ryan J. Williams et al.
FRONTIERS IN MICROBIOLOGY (2014)
Deciphering microbial interactions and detecting keystone species with co-occurrence networks
David Berry et al.
FRONTIERS IN MICROBIOLOGY (2014)
Insights into the phylogeny and coding potential of microbial dark matter
Christian Rinke et al.
NATURE (2013)
THE BIG CHALLENGES OF BIG DATA
Vivien Marx
NATURE (2013)
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Morgan G. I. Langille et al.
NATURE BIOTECHNOLOGY (2013)
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Christian Quast et al.
NUCLEIC ACIDS RESEARCH (2013)
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
Paul J. McMurdie et al.
PLOS ONE (2013)
Culturing captures members of the soil rare biosphere
Ashley Shade et al.
ENVIRONMENTAL MICROBIOLOGY (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)
Vertical distribution of microbial communities in a perennially stratified Arctic lake with saline, anoxic bottom waters
Andre M. Comeau et al.
SCIENTIFIC REPORTS (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)
Gαq and Phospholipase C-β : Turn On, Turn Off, and Do It Fast
Elliott M. Ross
SCIENCE SIGNALING (2011)
Visualization of omics data for systems biology
Nils Gehlenborg et al.
NATURE METHODS (2010)
QIIME allows analysis of high-throughput community sequencing data
J. Gregory Caporaso et al.
NATURE METHODS (2010)
WHAT DO INTERACTION NETWORK METRICS TELL US ABOUT SPECIALIZATION AND BIOLOGICAL TRAITS?
Nico Bluethgen et al.
ECOLOGY (2008)
Dissecting biological dark matter with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth
Yann Marcy et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Network thinking in ecology and evolution
SR Proulx et al.
TRENDS IN ECOLOGY & EVOLUTION (2005)
The uncultured microbial majority
MS Rappe et al.
ANNUAL REVIEW OF MICROBIOLOGY (2003)