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1. Full Text Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis
by Scholz, Matthew B and Lo, Chien-Chi and Chain, Patrick SG and Joint Genome Institute (JGI)
Current opinion in biotechnology, ISSN 0958-1669, 2011, Volume 23, Issue 1, pp. 9 - 15
Internal Medicine | Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Biochemical Research Methods | Science & Technology | High-Throughput Nucleotide Sequencing - economics | Algorithms | Metagenomics - methods | Metagenomics - economics | Sequence Analysis, DNA - economics | High-Throughput Nucleotide Sequencing - methods | Sequence Analysis, DNA - methods | Analysis | Index Medicus | Biotechnology | Costs | Communities | Data processing | Raw | Genomes | Sequencing | Bioinformatics
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2. Full Text Accurate read-based metagenome characterization using a hierarchical suite of unique signatures
by Freitas, Tracey Allen K and Li, Po-E and Scholz, Matthew B and Chain, Patrick S. G
Nucleic acids research, ISSN 0305-1048, 05/2015, Volume 43, Issue 10, pp. e69 - e69
Life Sciences & Biomedicine | Biochemistry & Molecular Biology | Science & Technology | Feces - microbiology | Algorithms | Air Microbiology | Humans | Metagenomics - methods | Software | Francisella tularensis - genetics | Francisella tularensis - isolation & purification | Metagenome | Index Medicus | Methods Online
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3. Full Text Rapid evaluation and quality control of next generation sequencing data with FaQCs
by Lo, Chien-Chi and Chain, Patrick S.G and Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
BMC bioinformatics, ISSN 1471-2105, 11/2014, Volume 15, Issue 1, pp. 366 - 366
Next generation sequencing analysis | Data preprocessing | Trimming | Quality control | Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Biochemical Research Methods | Science & Technology | Mathematical & Computational Biology | Computational Biology - methods | Algorithms | Genes, Bacterial - genetics | Genomics | Polymorphism, Single Nucleotide - genetics | Software | Computational Biology - standards | High-Throughput Nucleotide Sequencing - methods | Research Design | Quality Control | Genetic polymorphisms | Information management | Index Medicus | Automation | Filtering | Computation | Parallel processing | Sequencing | Failure | BASIC BIOLOGICAL SCIENCES | Biological Science | MATHEMATICS AND COMPUTING
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4. Full Text Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill
by Mason, Olivia U and Hazen, Terry C and Borglin, Sharon and Chain, Patrick S G and Dubinsky, Eric A and Fortney, Julian L and Han, James and Holman, Hoi-Ying N and Hultman, Jenni and Lamendella, Regina and MacKelprang, Rachel and Malfatti, Stephanie and Tom, Lauren M and Tringe, Susannah G and Woyke, Tanja and Zhou, Jizhong and Rubin, Edward M and Jansson, Janet K and Joint Genome Institute (JGI)
The ISME Journal, ISSN 1751-7362, 09/2012, Volume 6, Issue 9, pp. 1715 - 1727
single-cell genomics | Oceanospirillales | metatranscriptomics | Gulf oil spill | metagenomics | Deepwater Horizon | Environmental Sciences & Ecology | Ecology | Life Sciences & Biomedicine | Microbiology | Science & Technology | Archaea - physiology | Petroleum Pollution | Seawater - microbiology | Hydrocarbons - metabolism | Oceanospirillaceae - genetics | Transcriptome | Biodiversity | Bacteria - genetics | Archaea - genetics | Gulf of Mexico | Oceanospirillaceae - metabolism | RNA, Ribosomal, 16S | Single-Cell Analysis | Metagenome | Index Medicus | Original
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5. Full Text The Genome Sequence of the Obligately Chemolithoautotrophic, Facultatively Anaerobic Bacterium Thiobacillus denitrificans
by Harry R. Beller and Patrick S. G. Chain and Tracy E. Letain and Anu Chakicherla and Frank W. Larimer and Paul M. Richardson and Matthew A. Coleman and Ann P. Wood and Donovan P. Kelly
Journal of Bacteriology, ISSN 0021-9193, 02/2006, Volume 188, Issue 4, pp. 1473 - 1488
Fundamental and applied biological sciences. Psychology | Biological and medical sciences | Miscellaneous | Microbiology | Bacteriology | Genome, Bacterial | Thiobacillus - drug effects | Oxidation-Reduction | Hydrogenase - genetics | Bacterial Proteins - genetics | Metals, Heavy - pharmacology | Molecular Sequence Data | Cytochromes c - genetics | Uranium - metabolism | Thiobacillus - metabolism | Sulfur Compounds - metabolism | Ion Transport - genetics | Thiobacillus - genetics | Genetic aspects | Research | Sulfur bacteria | Nucleotide sequence | Bacterial genetics | Oxidation | Metabolism | Genomics | Index Medicus | Genomics and Proteomics
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6. Full Text Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage
by Dodsworth, Jeremy A and Blainey, Paul C and Murugapiran, Senthil K and Swingley, Wesley D and Ross, Christian A and Tringe, Susannah G and Chain, Patrick S. G and Scholz, Matthew B and Lo, Chien-Chi and Raymond, Jason and Quake, Stephen R and Hedlund, Brian P and Joint Genome Institute (JGI)
Nature communications, ISSN 2041-1723, 2013, Volume 4, Issue 1, pp. 1854 - 1854
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Metagenome - genetics | Energy Metabolism | Single-Cell Analysis - methods | Bacteria - cytology | Metagenomics - methods | Molecular Sequence Data | Cell Membrane - metabolism | Phylogeny | Fermentation | Bacteria - genetics | Principal Component Analysis | Cellulose - metabolism | Index Medicus
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7. Full Text Whole-Genome-Based Phylogeny and Divergence of the Genus Brucella
by Jeffrey T. Foster and Stephen M. Beckstrom-Sternberg and Talima Pearson and James S. Beckstrom-Sternberg and Patrick S. G. Chain and Francisco F. Roberto and Jonathan Hnath and Tom Brettin and Paul Keim
Journal of Bacteriology, ISSN 0021-9193, 04/2009, Volume 191, Issue 8, pp. 2864 - 2870
Life Sciences & Biomedicine | Microbiology | Science & Technology | Fundamental and applied biological sciences. Psychology | Biological and medical sciences | Miscellaneous | Bacteriology | Genome, Bacterial | Animals | DNA, Bacterial - genetics | Humans | Brucella - classification | Ochrobactrum anthropi - genetics | Polymorphism, Single Nucleotide | Phylogeny | Brucella - genetics | Cluster Analysis | Evolution, Molecular | Research | Genotype & phenotype | Bacteria | Genetic diversity | Comparative analysis | Genomics | Polymorphism | Index Medicus | Computational Biology
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8. Full Text Complete Genome Sequence of Nitrosospira multiformis, an Ammonia-Oxidizing Bacterium from the Soil Environment
by Jeanette M. Norton and Martin G. Klotz and Lisa Y. Stein and Daniel J. Arp and Peter J. Bottomley and Patrick S. G. Chain and Loren J. Hauser and Miriam L. Land and Frank W. Larimer and Maria W. Shin and Shawn R. Starkenburg and Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Applied and Environmental Microbiology, ISSN 0099-2240, 06/2008, Volume 74, Issue 11, pp. 3559 - 3572
Life Sciences & Biomedicine | Microbiology | Biotechnology & Applied Microbiology | Science & Technology | Fundamental and applied biological sciences. Psychology | Biological and medical sciences | Genome, Bacterial | Multigene Family | Nitrosomonadaceae - isolation & purification | Ammonia - metabolism | Soil Microbiology | Open Reading Frames | Bacterial Proteins - genetics | Molecular Sequence Data | DNA, Bacterial - chemistry | Gene Dosage | Chromosomes, Bacterial | Sequence Analysis, DNA | Sequence Homology, Amino Acid | Nitrosomonadaceae - genetics | DNA, Bacterial - genetics | Plasmids | Repetitive Sequences, Nucleic Acid | Energy Metabolism - genetics | Metabolism - genetics | Bacteria, Nitrifying | Glycogen | Genomics | Analysis | Nitrification | Environmental aspects | Genetic aspects | Chemical properties | Soils | Ammonia | Soil microorganisms | Bacteria | Chromosomes | Bacteriology | Index Medicus | STORAGE | PLASMIDS | SOILS | UREASE | BASIC BIOLOGICAL SCIENCES | HYDROGENASES | MEMBRANES | CHROMOSOMES | ENVIRONMENTAL SCIENCES | GLYCOGEN | LACTONES | GENES | PORINS | SYNTHESIS | PROTEINS | FUNCTIONALS | Evolutionary and Genomic Microbiology
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9. Full Text Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life
by Shakya, Migun and Ahmed, Sanaa A and Davenport, Karen W and Flynn, Mark C and Lo, Chien-Chi and Chain, Patrick S. G and Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Scientific reports, ISSN 2045-2322, 02/2020, Volume 10, Issue 1, pp. 1723 - 1723
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Burkholderia - genetics | Datasets as Topic | Computational Biology | Chromosome Mapping | Escherichia - genetics | Phylogeny | Ebolavirus - genetics | Saccharomyces - genetics | Biological Evolution | Algorithms | Software | High-Throughput Nucleotide Sequencing - methods | Metagenome | Software Validation | Evolution, Molecular | Phylogenetics | Organisms | Genomes | Index Medicus | Biological science | MATHEMATICS AND COMPUTING | Genome informatics | BASIC BIOLOGICAL SCIENCES | Data processing
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10. Full Text Genome of the Epsilonproteobacterial Chemolithoautotroph Sulfurimonas denitrificans
by Stefan M. Sievert and Kathleen M. Scott and Martin G. Klotz and Patrick S. G. Chain and Loren J. Hauser and James Hemp and Michael Hügler and Miriam Land and Alla Lapidus and Frank W. Larimer and Susan Lucas and Stephanie A. Malfatti and Folker Meyer and Ian T. Paulsen and Qinghu Ren and Jörg Simon and the USF Genomics Class and USF Genom Class and USF Genomics Class and Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Applied and Environmental Microbiology, ISSN 0099-2240, 02/2008, Volume 74, Issue 4, pp. 1145 - 1156
Life Sciences & Biomedicine | Microbiology | Biotechnology & Applied Microbiology | Science & Technology | Fundamental and applied biological sciences. Psychology | Biological and medical sciences | Carbon - metabolism | Genome, Bacterial | Nitrogen - metabolism | Epsilonproteobacteria - genetics | Computational Biology | Oxidative Stress - genetics | Molecular Sequence Data | Chromosome Mapping | Signal Transduction - genetics | Phylogeny | Carboxy-Lyases - genetics | Chemotaxis - genetics | Sequence Analysis, DNA | Models, Biological | Base Sequence | Electron Transport - physiology | Chemoautotrophic Growth | Sulfur bacteria | Analysis | Environmental aspects | Oxidation-reduction reaction | Genetic aspects | Research | Bacterial genetics | Genomics | Genes | Bacteria | Oxidation | Metabolism | Sulfur | Index Medicus | CITRIC ACID | SULFUR-OXIDIZING BACTERIA | HEAVY METALS | BASIC BIOLOGICAL SCIENCES | GENES | SULFUR COMPOUNDS | SULFUR CYCLE | Evolutionary and Genomic Microbiology
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