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1. Full Text Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample
by Luo, Chengwei and Tsementzi, Despina and Kyrpides, Nikos and Read, Timothy and Konstantinidis, Konstantinos T and Joint Genome Institute (JGI)
PLoS ONE, ISSN 1932-6203, 2012, Volume 7, Issue 2, p. e30087
Next-generation sequencing (NGS) is commonly used in metagenomic studies of complex microbial communities but whether or not different NGS platforms recover... 
GENERATION | CATALOG | ALIGNMENT | BLAST | MULTIDISCIPLINARY SCIENCES | GENOME | Genome, Bacterial | Base Composition | Sequence Analysis, DNA - methods | Metagenomics - methods | DNA, Bacterial | Genomes | Polymers | Analysis | Genes | Genomics | DNA | Platforms | Microbial activity | Communities | Genetic diversity | Environmental engineering | Gene sequencing | Complexity | Datasets | Microorganisms | Algorithms | Protocol | Assemblies | Bioinformatics | Genotypes | Deoxyribonucleic acid--DNA | DNA sequencing | Deoxyribonucleic acid
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2. Full Text Comparative Metagenomic and Metatranscriptomic Analysis of Hindgut Paunch Microbiota in Wood- and Dung-Feeding Higher Termites
by He, Shaomei and Ivanova, Natalia and Kirton, Edward and Allgaier, Martin and Bergin, Claudia and Scheffrahn, Rudolf H and Kyrpides, Nikos C and Warnecke, Falk and Tringe, Susannah G and Hugenholtz, Philip and Joint Genome Institute (JGI) and Teknisk-naturvetenskapliga vetenskapsområdet and Biologiska sektionen and Uppsala universitet and Institutionen för ekologi och genetik and Limnologi
PLoS ONE, ISSN 1932-6203, 04/2013, Volume 8, Issue 4, p. e61126
Termites effectively feed on many types of lignocellulose assisted by their gut microbial symbionts. To better understand the microbial decomposition of... 
PHYLOGENETIC DIVERSITY | FORMATE DEHYDROGENASE | CATTLE DUNG | BACTERIAL COMMUNITY STRUCTURE | PROFILES | GENE DIVERSITY | SEQUENCE DATA | MULTIDISCIPLINARY SCIENCES | GUT | GLYCOSIDE HYDROLASES | CUBITERMES SPP | Isoptera - genetics | Isoptera - microbiology | Metagenomics | Wood - parasitology | Bacteria - metabolism | Nitrogen - metabolism | Plant Cells - metabolism | RNA, Messenger - genetics | Gastrointestinal Tract - microbiology | Feeding Behavior | Gene Expression Profiling | Phylogeny | Isoptera - enzymology | RNA, Messenger - metabolism | Bacteria - genetics | Chemotaxis - genetics | Metagenome - genetics | Animals | Lignin - metabolism | Cattle | Feces - parasitology | Cell Wall - metabolism | Glycoside Hydrolases - metabolism | Enzymes | Fixation | Microbiota (Symbiotic organisms) | RNA | Analysis | Genes | Termites | Nitrogen | Carbohydrate composition | Hemicellulose | Divergence | Motility | rRNA 16S | Laboratories | Ecosystems | Taxonomy | Genomes | Dung | Ecosystem biology | Symbionts | Microorganisms | Microbiota | Lignocellulose | Energy | Chemical attack | Nitrogen fixation | Genetics | Bacteria | Nutrients | Bioinformatics | Carbohydrates | Wood | Hindgut | Rumen | Ecology | Fermentation | Chemotaxis | Feeding | Homoacetogenesis | Diet | Herbivores | Glycoside hydrolase | Naturvetenskap | Natural Sciences
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3. Full Text Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream
by Kyrpides, Nikos C and Joint Genome Institute (JGI)
Nature Biotechnology, ISSN 1087-0156, 07/2009, Volume 27, Issue 7, pp. 627 - 632
As we approach the completed sequencing of 1,000 microbial genomes, the field of microbial genomics is poised at a crossroads. The future holds great promise... 
BIOTECHNOLOGY & APPLIED MICROBIOLOGY | ANNOTATION | OCEAN | BIOLOGY | PROKARYOTES | TOOL | Databases, Genetic | Genomics - economics | Genome, Bacterial | Genomics - trends | Database Management Systems | Genomics - standards | Microbial genetics | Technology application | Usage | Genomics | Forecasts and trends | Nucleotide sequencing | Methods | Biotechnology | Microbiology | Technological change
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4. Full Text Insights into the phylogeny and coding potential of microbial dark matter
by Rinke, Christian and Schwientek, Patrick and Sczyrba, Alexander and Ivanova, Natalia N and Anderson, Iain J and Cheng, Jan-Fang and Darling, Aaron and Malfatti, Stephanie and Swan, Brandon K and Gies, Esther A and Dodsworth, Jeremy A and Hedlund, Brian P and Tsiamis, George and Sievert, Stefan M and Liu, Wen-Tso and Eisen, Jonathan A and Hallam, Steven J and Kyrpides, Nikos C and Stepanauskas, Ramunas and Rubin, Edward M and Hugenholtz, Philip and Woyke, Tanja and Joint Genome Institute (JGI)
Nature, ISSN 0028-0836, 2013, Volume 499, Issue 7459, pp. 431 - 437
Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the... 
HYDROTHERMAL VENT | BACTERIA | ARCHAEA | METAGENOMICS | MULTIDISCIPLINARY SCIENCES | LATERAL GENE-TRANSFER | SP-NOV | DIVERSITY | EUKARYOTES | DIVISION | GENOME | Metagenomics | Bacteria - metabolism | Molecular Sequence Data | Archaea - isolation & purification | Phylogeny | Archaea - classification | Bacteria - genetics | Sequence Analysis, DNA | Genome, Bacterial - genetics | Archaea - metabolism | Bacteria - isolation & purification | Metagenome - genetics | Ecosystem | Genome, Archaeal - genetics | Bacteria - classification | Archaea - genetics | Single-Cell Analysis | Biosphere | Usage | Research | Nucleotide sequencing | DNA sequencing | Trees | Evolution | Microbiology | Genomics | Genes
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5. Full Text CRISPR Recognition Tool (CRT): A tool for automatic detection of clustered regularly interspaced palindromic repeats
by Bland, Charles and Ramsey, Teresa L and Sabree, Fareedah and Lowe, Micheal and Brown, Kyndall and Kyrpides, Nikos C and Hugenholtz, Philip
BMC Bioinformatics, ISSN 1471-2105, 06/2007, Volume 8, Issue 1, pp. 209 - 209
Background: Clustered Regularly Interspaced Palindromic Repeats ( CRISPRs) are a novel type of direct repeat found in a wide range of bacteria and archaea.... 
EVOLUTIONARY | DNA REPEATS | ALGORITHM | BIOCHEMICAL RESEARCH METHODS | BACTERIAL GENOMES | IDENTIFICATION | ALIGNMENT SCORE | ELEMENTS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | SEQUENCE | MATHEMATICAL & COMPUTATIONAL BIOLOGY | REPETITIVE DNA | PROKARYOTES | Interspersed Repetitive Sequences - genetics | Algorithms | Base Pairing | Artificial Intelligence | Chromosome Mapping - methods | Software | Sequence Analysis, DNA - methods | Pattern Recognition, Automated - methods | Trinucleotide repeats | Genetic aspects | Genomes | Research | Bacterial genetics | Archaeabacteria
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6. Full Text The M5nr: A novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools
by Wilke, Andreas and Harrison, Travis and Wilkening, Jared and Field, Dawn and Glass, Elizabeth M and Kyrpides, Nikos and Mavrommatis, Konstantinos and Meyer, Folker
BMC Bioinformatics, ISSN 1471-2105, 06/2012, Volume 13, Issue 1, pp. 141 - 141
Background: Computing of sequence similarity results is becoming a limiting factor in metagenome analysis. Sequence similarity search results encoded in an... 
GENOMES | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | KEGG | IDENTIFIERS | BLAST | RESOURCE | Proteins - genetics | Metagenomics | Databases, Protein | Computational Biology | Software | Proteins - chemistry | Databases, Nucleic Acid | Amino acid sequence | Databases | Genetic algorithms | Data processing | Bioinformatics | Limiting factors | Computer applications
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7. Full Text Uncovering Earth's virome
by Paez-Espino, David and Eloe-Fadrosh, Emiley A and Pavlopoulos, Georgios A and Thomas, Alex D and Huntemann, Marcel and Mikhailova, Natalia and Rubin, Edward and Ivanova, Natalia N and Kyrpides, Nikos C
Nature, ISSN 0028-0836, 08/2016, Volume 536, Issue 7617, pp. 425 - 430
Viruses are the most abundant biological entities on Earth, but challenges in detecting, isolating, and classifying unknown viruses have prevented exhaustive... 
BACTERIOPHAGE | PROTEIN | SEQUENCES | GENE | DATABASE | MULTIDISCIPLINARY SCIENCES | ENVIRONMENT | ALGORITHM | MARINE VIRUSES | RESISTANCE | PHAGE | Metagenomics | Viruses - isolation & purification | Datasets as Topic | Viruses - genetics | Genome, Viral - genetics | Humans | Phylogeography | DNA, Viral - analysis | Host Specificity | Phylogeny | Biodiversity | Host-Pathogen Interactions | Viruses - classification | Metagenome - genetics | Animals | Ecosystem | Genes, Viral | Bacteriophages - genetics | RNA, Transfer - genetics | Aquatic Organisms - virology | Clustered Regularly Interspaced Short Palindromic Repeats - genetics | Earth (Planet) | Sequence Analysis | DNA, Viral - genetics | Viruses | Genetic aspects | Identification and classification | Distribution | Proteins | Biogeography | Genomes | Ecosystems
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8. Full Text A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
by Lykidis, Athanasios and Lang, Elke and Zemla, Adam and Kerfeld, Cheryl and Singer, Mitchell and Dalin, Eileen and Chen, Feng and Pukall, Rüdiger and Pati, Amrita and Goodwin, Lynne and Chain, Patrick and Kyrpides, Nikos C and Hooper, Sean D and Bruce, David and Copeland, Alex and Cheng, Jan-Fang and Wu, Martin and Lucas, Susan and D'haeseleer, Patrik and Gronow, Sabine and Rubin, Edward M and Han, Cliff and Kunin, Victor and Lapidus, Alla and Hugenholtz, Philip and Anderson, Iain J and Spring, Stefan and Klenk, Hans-Peter and Tindall, Brian J and Ivanova, Natalia N and Wu, Dongying and Mavromatis, Konstantinos and Eisen, Jonathan A and Nolan, Matt and Joint Genome Institute (JGI)
Nature, ISSN 0028-0836, 12/2009, Volume 462, Issue 7276, pp. 1056 - 1060
Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms. There are now nearly 1,000... 
PROJECTS | MICROBIAL DIVERSITY | MULTIDISCIPLINARY SCIENCES | PROTEIN FAMILIES | DATABASE GOLD | SEQUENCE | Protein Structure, Tertiary | Amino Acid Sequence | Bacterial Proteins - chemistry | Databases, Genetic | Models, Molecular | Molecular Sequence Data | Phylogeny | Biodiversity | Archaea - classification | Bacteria - genetics | Genes, rRNA - genetics | Genome, Bacterial - genetics | Sequence Alignment | Genome, Archaeal - genetics | Actins - chemistry | Bacteria - classification | Archaea - genetics | Nucleotide sequence | Analysis | Biological diversity | Proteins | Phylogenetics | Bacteria | Microbiology | Genes | Genomics | Microorganisms | Databases | Equivalence | Archaea | Genomes | Sequencing
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9. Full Text Improving Microbial Genome Annotations in an Integrated Database Context
by Chen, I.-Min A and Markowitz, Victor M and Chu, Ken and Anderson, Iain and Mavromatis, Konstantinos and Kyrpides, Nikos C and Ivanova, Natalia N and Joint Genome Institute (JGI)
PLoS ONE, ISSN 1932-6203, 02/2013, Volume 8, Issue 2, p. e54859
Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of... 
METABOLIC PATHWAYS | MULTIDISCIPLINARY SCIENCES | Databases, Genetic | Phenotype | Molecular Sequence Annotation - methods | Microbiology | Genomes | Databases | Genomics | Analysis | Automation | Laboratories | Genes | Consistency | Metadata | Metabolism | Data bases | Proteins | Microorganisms | Annotations | Acids | Semantics | Completeness | Physiology | Respiration | Comparative analysis | Bioinformatics
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10. Full Text Protein structure determination using metagenome sequence data
by Ovchinnikov, Sergey and Park, Hahnbeom and Varghese, Neha and Huang, Po-Ssu and Pavlopoulos, Georgios A and Kim, David E and Kamisetty, Hetunandan and Kyrpides, Nikos C and Baker, David
Science, ISSN 0036-8075, 01/2017, Volume 355, Issue 6322, pp. 294 - 298
Despite decades of work by structural biologists, there are still similar to 5200 protein families with unknown structure outside the range of comparative... 
FOLD | CRYSTAL-STRUCTURE | FAMILIES | MULTIDISCIPLINARY SCIENCES | DOMAINS | STRUCTURE PREDICTION | REVEALS | Amino Acid Sequence | Computational Biology - methods | Models, Molecular | Crystallography, X-Ray | Protein Folding | Proteins - genetics | Sequence Analysis, Protein | Algorithms | Databases, Protein | Protein Conformation | Software | Proteins - chemistry | Metagenome | Evolution, Molecular | Amino acid sequence | Protein structure prediction | Methods | Sequences | Genomes | Data | Sequence | Biologists | Membrane proteins | Proteins | Model matching | Predictions | Evolution | Models | Modelling | Mathematical models | Protein structure | Alignment | Contact
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11. Full Text Functional genomics of novel secondary metabolites from diverse cyanobacteria using untargeted metabolomics
by Baran, Richard and Ivanova, Natalia N and Jose, Nick and Garcia-Pichel, Ferran and Kyrpides, Nikos C and Gugger, Muriel and Northen, Trent R and Joint Genome Institute (JGI)
Marine Drugs, ISSN 1660-3397, 10/2013, Volume 11, Issue 10, pp. 3617 - 3631
Mass spectrometry-based metabolomics has become a powerful tool for the detection of metabolites in complex biological systems and for the identification of... 
Metabolomics | Oligosaccharides | MS/MS | Mass spectrometry | Betaines | Cyanobacteria | betaines | CHEMISTRY, MEDICINAL | oligosaccharides | ESCHERICHIA-COLI | SYNECHOCOCCUS-SP. PCC-7002 | DISCOVERY | MOLECULES | SYNTHASE | GAMMA-GLUTAMYL-TRANSPEPTIDASE | DATABASE | metabolomics | GLUCOSYLGLYCEROL | cyanobacteria | SEQUENCE | mass spectrometry | SCALE | Cyanobacteria - genetics | Betaine - metabolism | Cyanobacteria - metabolism | Oligosaccharides - metabolism | Chromatography, Liquid - methods | Genomics - methods | Metabolomics - methods | Tandem Mass Spectrometry - methods | Metabolome - genetics | Life Sciences | Microbiology and Parasitology
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12. Full Text The Genomes OnLine Database (GOLD) v.5: A metadata management system based on a four level (meta)genome project classification
by Reddy, T.B.K and Thomas, Alex D and Stamatis, Dimitri and Bertsch, Jon and Isbandi, Michelle and Jansson, Jakob and Mallajosyula, Jyothi and Pagani, Ioanna and Lobos, Elizabeth A and Kyrpides, Nikos C and Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Nucleic Acids Research, ISSN 0305-1048, 01/2015, Volume 43, Issue 1, pp. D1099 - D1106
The Genomes OnLine Database (GOLD; ext-link-type="uri" xlink:href="http://www.genomesonline.org" xlink:type="simple">http://www.genomesonline.org) is a... 
METAGENOMIC PROJECTS | VERSION | PHYLOGENY | MONITOR | BIOCHEMISTRY & MOLECULAR BIOLOGY | WORLD-WIDE | Metagenomics | Internet | Databases, Nucleic Acid | Genomics | GOLD | GENERAL AND MISCELLANEOUS | BASIC BIOLOGICAL SCIENCES | Metadata | Curation | Genome | Metagenome | Database Issue
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