From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems
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Title
From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems
Authors
Keywords
Biological dark matter, Pan-genomics, data recycling, Eco-systems biology, Metagenome-wide modeling, Virus-host association
Journal
CELLULAR AND MOLECULAR LIFE SCIENCES
Volume 72, Issue 22, Pages 4287-4308
Publisher
Springer Nature
Online
2015-08-08
DOI
10.1007/s00018-015-2004-1
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Note: Only part of the references are listed.- Decoding the jargon of bottom-up metabolic systems biology
- (2015) Óttar Rolfsson et al. BIOESSAYS
- Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species
- (2015) Sharon Greenblum et al. CELL
- Biogeography of the Intestinal Mucosal and Lumenal Microbiome in the Rhesus Macaque
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- (2015) Karoline Faust et al. CURRENT OPINION IN MICROBIOLOGY
- Unusual biology across a group comprising more than 15% of domain Bacteria
- (2015) Christopher T. Brown et al. NATURE
- A new antibiotic kills pathogens without detectable resistance
- (2015) Losee L. Ling et al. NATURE
- Complex archaea that bridge the gap between prokaryotes and eukaryotes
- (2015) Anja Spang et al. NATURE
- Metabolic dependencies drive species co-occurrence in diverse microbial communities
- (2015) Aleksej Zelezniak et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Application of a Neutral Community Model To Assess Structuring of the Human Lung Microbiome
- (2015) Arvind Venkataraman et al. mBio
- High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats
- (2015) Jizhong Zhou et al. mBio
- Genomes of Planktonic Acidimicrobiales : Widening Horizons for Marine Actinobacteria by Metagenomics
- (2015) Carolina Megumi Mizuno et al. mBio
- Microbial taxonomy in the post-genomic era: Rebuilding from scratch?
- (2014) Cristiane C. Thompson et al. ARCHIVES OF MICROBIOLOGY
- The Unculturables: targeted isolation of bacterial species associated with canine periodontal health or disease from dental plaque
- (2014) Ian J Davis et al. BMC MICROBIOLOGY
- Ammonia oxidation-dependent growth of group I.1bThaumarchaeotain acidic red soil microcosms
- (2014) Yucheng Wu et al. FEMS MICROBIOLOGY ECOLOGY
- Taxonomical and functional microbial community selection in soybean rhizosphere
- (2014) Lucas W Mendes et al. ISME Journal
- Estimation method for serial dilution experiments
- (2014) Avishai Ben-David et al. JOURNAL OF MICROBIOLOGICAL METHODS
- Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
- (2014) H Bjørn Nielsen et al. NATURE BIOTECHNOLOGY
- Fast and sensitive protein alignment using DIAMOND
- (2014) Benjamin Buchfink et al. NATURE METHODS
- Binning metagenomic contigs by coverage and composition
- (2014) Johannes Alneberg et al. NATURE METHODS
- Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses
- (2014) B. L. Hurwitz et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Ten years of next-generation sequencing technology
- (2014) Erwin L. van Dijk et al. TRENDS IN GENETICS
- Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics
- (2014) William R. Harcombe et al. Cell Reports
- Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps
- (2014) Joshua N. Burton et al. G3-Genes Genomes Genetics
- Emergent Biosynthetic Capacity in Simple Microbial Communities
- (2014) Hsuan-Chao Chiu et al. PLoS Computational Biology
- Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms
- (2014) Martial Marbouty et al. eLife
- Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat
- (2014) Anna Hanke et al. Frontiers in Microbiology
- Kraken: ultrafast metagenomic sequence classification using exact alignments
- (2014) Derrick E Wood et al. GENOME BIOLOGY
- FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares
- (2014) Genivaldo Gueiros Z. Silva et al. PeerJ
- Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products
- (2014) Christopher W. Beitel et al. PeerJ
- Methods for integration of transcriptomic data in genome-scale metabolic models
- (2014) Min Kyung Kim et al. Computational and Structural Biotechnology Journal
- Explaining microbial phenotypes on a genomic scale: GWAS for microbes
- (2013) B. E. Dutilh et al. Briefings in Functional Genomics
- Combining “Omics” Strategies to Analyze the Biotechnological Potential of Complex Microbial Environments
- (2013) Alinne Castro et al. CURRENT PROTEIN & PEPTIDE SCIENCE
- The ecology of differences: assessing community assembly with trait and evolutionary distances
- (2013) Marc Cadotte et al. ECOLOGY LETTERS
- Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform
- (2013) J. S. McLean et al. GENOME RESEARCH
- Changes in assembly processes in soil bacterial communities following a wildfire disturbance
- (2013) Scott Ferrenberg et al. ISME Journal
- Multifactorial diversity sustains microbial community stability
- (2013) Oylum Erkus et al. ISME Journal
- The microbial gene diversity along an elevation gradient of the Tibetan grassland
- (2013) Yunfeng Yang et al. ISME Journal
- High throughput sequencing methods and analysis for microbiome research
- (2013) Julia M. Di Bella et al. JOURNAL OF MICROBIOLOGICAL METHODS
- Insights into the phylogeny and coding potential of microbial dark matter
- (2013) Christian Rinke et al. NATURE
- Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome
- (2013) Sheetal R. Modi et al. NATURE
- Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
- (2013) Mads Albertsen et al. NATURE BIOTECHNOLOGY
- IMG 4 version of the integrated microbial genomes comparative analysis system
- (2013) Victor M. Markowitz et al. NUCLEIC ACIDS RESEARCH
- Identification of a Novel Human Papillomavirus by Metagenomic Analysis of Samples from Patients with Febrile Respiratory Illness
- (2013) John L. Mokili et al. PLoS One
- Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean
- (2013) B. K. Swan et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments
- (2013) J. M. Monk et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Genomes from Metagenomics
- (2013) I. Sharon et al. SCIENCE
- Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla
- (2013) R. S. Kantor et al. mBio
- Can You Sequence Ecology? Metagenomics of Adaptive Diversification
- (2013) Christopher J. Marx PLOS BIOLOGY
- Estimation of viral richness from shotgun metagenomes using a frequency count approach
- (2013) Heather K Allen et al. Microbiome
- Reference-independent comparative metagenomics using cross-assembly: crAss
- (2012) Bas E. Dutilh et al. BIOINFORMATICS
- Classification of metagenomic sequences: methods and challenges
- (2012) S. S. Mande et al. BRIEFINGS IN BIOINFORMATICS
- A Whole-Cell Computational Model Predicts Phenotype from Genotype
- (2012) Jonathan R. Karr et al. CELL
- Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities
- (2012) Robert L. Hettich et al. CURRENT OPINION IN MICROBIOLOGY
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- (2012) A. Stern et al. GENOME RESEARCH
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- (2012) Cesar O Flores et al. ISME Journal
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- (2012) E. J. Stewart JOURNAL OF BACTERIOLOGY
- Mathematical optimization applications in metabolic networks
- (2012) Ali R. Zomorrodi et al. METABOLIC ENGINEERING
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- (2012) Peter E Larsen et al. NATURE METHODS
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- (2012) Roger S. Lasken NATURE REVIEWS MICROBIOLOGY
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- (2012) Natalya Yutin et al. PLoS One
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- (2012) Amaro E. Trindade-Silva et al. PLoS One
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- (2012) Piotr Zakrzewski et al. PLoS One
- Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
- (2012) N. Fierer et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla
- (2012) K. C. Wrighton et al. SCIENCE
- Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota
- (2012) V. Iverson et al. SCIENCE
- Phage–bacteria infection networks
- (2012) Joshua S. Weitz et al. TRENDS IN MICROBIOLOGY
- Metagenomics and future perspectives in virus discovery
- (2012) John L Mokili et al. Current Opinion in Virology
- OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities
- (2012) Ali R. Zomorrodi et al. PLoS Computational Biology
- Marine Viruses: Truth or Dare
- (2011) Mya Breitbart Annual Review of Marine Science
- Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates
- (2011) Li C Xia et al. BMC Systems Biology
- Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis
- (2011) Matthew B. Scholz et al. CURRENT OPINION IN BIOTECHNOLOGY
- The human gut virome: Inter-individual variation and dynamic response to diet
- (2011) S. Minot et al. GENOME RESEARCH
- De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities
- (2011) Priya Narasingarao et al. ISME Journal
- Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage
- (2011) Chris L Dupont et al. ISME Journal
- Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale
- (2011) Tancredi Caruso et al. ISME Journal
- Statistical structure of host-phage interactions
- (2011) C. O. Flores et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Bacterial community assembly based on functional genes rather than species
- (2011) C. Burke et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen
- (2011) M. Hess et al. SCIENCE
- The Unified Neutral Theory of Biodiversity and Biogeography at Age Ten
- (2011) James Rosindell et al. TRENDS IN ECOLOGY & EVOLUTION
- The Human Gut Microbiome: Ecology and Recent Evolutionary Changes
- (2010) Jens Walter et al. Annual Review of Microbiology
- Use of Ichip for High-Throughput In Situ Cultivation of "Uncultivable" Microbial Species
- (2010) D. Nichols et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model
- (2010) K. Yizhak et al. BIOINFORMATICS
- Search and clustering orders of magnitude faster than BLAST
- (2010) Robert C. Edgar BIOINFORMATICS
- Predicting conserved protein motifs with Sub-HMMs
- (2010) Kevin Horan et al. BMC BIOINFORMATICS
- Siderophores from Neighboring Organisms Promote the Growth of Uncultured Bacteria
- (2010) Anthony D'Onofrio et al. CHEMISTRY & BIOLOGY
- Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time
- (2010) D. T. Pride et al. GENOME RESEARCH
- Viral and microbial community dynamics in four aquatic environments
- (2010) Beltran Rodriguez-Brito et al. ISME Journal
- Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism
- (2010) R.M.T. Fleming et al. JOURNAL OF THEORETICAL BIOLOGY
- Species abundance distributions and richness estimations in fungal metagenomics - lessons learned from community ecology
- (2010) MARTIN UNTERSEHER et al. MOLECULAR ECOLOGY
- Genomic and functional adaptation in surface ocean planktonic prokaryotes
- (2010) Shibu Yooseph et al. NATURE
- High-throughput generation, optimization and analysis of genome-scale metabolic models
- (2010) Christopher S Henry et al. NATURE BIOTECHNOLOGY
- A protocol for generating a high-quality genome-scale metabolic reconstruction
- (2010) Ines Thiele et al. Nature Protocols
- Environments that Induce Synthetic Microbial Ecosystems
- (2010) Niels Klitgord et al. PLoS Computational Biology
- Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly
- (2009) Bas E. Dutilh et al. BIOINFORMATICS
- Metabolic modelling of syntrophic-like growth of a 1,3-propanediol producer, Clostridium butyricum, and a methanogenic archeon, Methanosarcina mazei, under anaerobic conditions
- (2009) Marcin Bizukojc et al. BIOPROCESS AND BIOSYSTEMS ENGINEERING
- The merging of community ecology and phylogenetic biology
- (2009) Jeannine Cavender-Bares et al. ECOLOGY LETTERS
- Relative roles of niche and neutral processes in structuring a soil microbial community
- (2009) Alex J Dumbrell et al. ISME Journal
- Initial community evenness favours functionality under selective stress
- (2009) Lieven Wittebolle et al. NATURE
- Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
- (2009) Arthur Brady et al. NATURE METHODS
- Explaining microbial population genomics through phage predation
- (2009) Francisco Rodriguez-Valera et al. NATURE REVIEWS MICROBIOLOGY
- Assembling the Marine Metagenome, One Cell at a Time
- (2009) Tanja Woyke et al. PLoS One
- Host cell-free growth of the Q fever bacterium Coxiella burnetii
- (2009) A. Omsland et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Community-wide analysis of microbial genome sequence signatures
- (2009) Gregory J Dick et al. GENOME BIOLOGY
- Short Peptide Induces an "Uncultivable" Microorganism To Grow In Vitro
- (2008) D. Nichols et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
- (2008) F Meyer et al. BMC BIOINFORMATICS
- Binning sequences using very sparse labels within a metagenome
- (2008) Chon-Kit Chan et al. BMC BIOINFORMATICS
- Functional metagenomic profiling of nine biomes
- (2008) Elizabeth A. Dinsdale et al. NATURE
- SAR11 marine bacteria require exogenous reduced sulphur for growth
- (2008) H. James Tripp et al. NATURE
- Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota
- (2008) Céline Brochier-Armanet et al. NATURE REVIEWS MICROBIOLOGY
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