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1. Full Text Structure, function and diversity of the healthy human microbiome
by Huttenhower, Curtis and Gevers, Dirk and Knight, Rob and Abubucker, Sahar and Badger, Jonathan H and Chinwalla, Asif T and Creasy, Heather H and Earl, Ashlee M and Fitzgerald, Michael G and Fulton, Robert S and Giglio, Michelle G and Hallsworth-Pepin, Kymberlie and Lobos, Elizabeth A and Madupu, Ramana and Magrini, Vincent and Martin, John C and Mitreva, Makedonka and Muzny, Donna M and Sodergren, Erica J and Versalovic, James and Wollam, Aye M and Worley, Kim C and Wortman, Jennifer R and Young, Sarah K and Zeng, Qiandong and Aagaard, Kjersti M and Abolude, Olukemi O and Allen-Vercoe, Emma and Alm, Eric J and Alvarado, Lucia and Andersen, Gary L and Anderson, Scott and Appelbaum, Elizabeth and Arachchi, Harindra M and Armitage, Gary and Arze, Cesar A and Ayvaz, Tulin and Baker, Carl C and Begg, Lisa and Belachew, Tsegahiwot and Bhonagiri, Veena and Bihan, Monika and Blaser, Martin J and Bloom, Toby and Bonazzi, Vivien and Paul Brooks, J and Buck, Gregory A and Buhay, Christian J and Busam, Dana A and Campbell, Joseph L and Canon, Shane R and Cantarel, Brandi L and Chain, Patrick S. G and Chen, I-Min A and Chen, Lei and Chhibba, Shaila and Chu, Ken and Ciulla, Dawn M and Clemente, Jose C and Clifton, Sandra W and Conlan, Sean and Crabtree, Jonathan and Cutting, Mary A and Davidovics, Noam J and Davis, Catherine C and Desantis, Todd Z and Deal, Carolyn and Delehaunty, Kimberley D and Dewhirst, Floyd E and Deych, Elena and Ding, Yan and Dooling, David J and Dugan, Shannon P and Michael Dunne, Wm and Scott Durkin, A and Edgar, Robert C and Erlich, Rachel L and Farmer, Candace N and Farrell, Ruth M and Faust, Karoline and Feldgarden, Michael and Felix, Victor M and Fisher, Sheila and Fodor, Anthony A and Forney, Larry J and Foster, Leslie and Di Francesco, Valentina and Friedman, Jonathan and Friedrich, Dennis C and Fronick, Catrina C and Fulton, Lucinda L and Gao, Hongyu and Garcia, Nathalia and Giannoukos, Georgia and Giblin, Christina and Giovanni, Maria Y and Goldberg, Jonathan M and Goll, Johannes and Gonzalez, Antonio and Griggs, Allison and ... and Human Microbiome Project Consortiu and Human Microbiome Project Consortium and The Human Microbiome Project Consortium and Joint Genome Institute (JGI)
Nature, ISSN 0028-0836, 06/2012, Volume 486, Issue 7402, pp. 207 - 214
Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and... 
IDENTIFICATION | BACTERIA | MULTIDISCIPLINARY SCIENCES | Metagenomics | Health | Humans | Male | Biodiversity | Bacteria - genetics | Young Adult | Phenotype | Ecosystem | Adolescent | Bacteria - classification | RNA, Ribosomal, 16S - genetics | Adult | Female | Metabolic Networks and Pathways - physiology | Metagenome | Microbiota (Symbiotic organisms) | Research | Biological diversity | Microbiology | Disease | Habitats | Taxonomy | Data processing | Skin | Life sciences | Genomes
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2. Full Text Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
by Jaffe, David B and Giannoukos, Georgia and Melnikov, Alexandre and Maguire, Jared and Fisher, Sheila and Fennell, Timothy and Gnirke, Andreas and Lander, Eric S and Brockman, William and Nusbaum, Chad and Rogov, Peter and Russ, Carsten and LeProust, Emily M and Gabriel, Stacey
Nature Biotechnology, ISSN 1087-0156, 02/2009, Volume 27, Issue 2, pp. 182 - 189
Targeting genomic loci by massively parallel sequencing requires new methods to enrich templates to be sequenced. We developed a capture method that uses... 
MULTIPLEX AMPLIFICATION | DNA FRAGMENTS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | LARGE SETS | GENOMIC SELECTION | GENES | PROBES | Nucleic Acid Hybridization | Reproducibility of Results | Biotinylation | Oligonucleotide Array Sequence Analysis | Humans | Exons - genetics | Oligonucleotides - metabolism | Sensitivity and Specificity | Bayes Theorem | Polymerase Chain Reaction | Polymorphism, Single Nucleotide - genetics | Base Composition - genetics | Genomics - methods | Sequence Analysis, DNA - methods | Polymerase chain reaction | Usage | Oligonucleotides | Physiological aspects | Nucleotide sequencing | Research | Methods | Hybridization | Ribonucleic acid--RNA | Genomics | Research methodology | Deoxyribonucleic acid--DNA
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3. Full Text Functional optimization of gene clusters by combinatorial design and assembly
by Smanski, Michael J and Bhatia, Swapnil and Zhao, Dehua and Park, YongJin and Woodruff, Lauren B. A and Giannoukos, Georgia and Ciulla, Dawn and Busby, Michele and Calderon, Johnathan and Nicol, Robert and Gordon, D. Benjamin and Densmore, Douglas and Voigt, Christopher A
Nature Biotechnology, ISSN 1087-0156, 12/2014, Volume 32, Issue 12, pp. 1241 - 1249
Large microbial gene clusters encode useful functions, including energy utilization and natural product biosynthesis, but genetic manipulation of such systems... 
NITROGEN-FIXATION GENES | PROMOTERS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | KINETICS | CONSTRUCTION | SEQUENCE | SITES | EXPRESSION | KLEBSIELLA-PNEUMONIAE | PROSPECTS | AMMONIUM | Promoter Regions, Genetic | Multigene Family | Nitrogen Fixation - genetics | Klebsiella oxytoca - genetics | Klebsiella oxytoca - physiology | Transcription, Genetic | Nitrogenase - genetics | High-Throughput Nucleotide Sequencing - methods | Operon - genetics | Genetic research | Usage | Algorithms | Research | Gene expression | Optimization techniques | Biosynthesis | Combinatorics | Ribonucleic acid--RNA | Genes | Deoxyribonucleic acid--DNA
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4. Full Text Relating the metatranscriptome and metagenome of the human gut
by Eric A. Franzosa and Xochitl C. Morgan and Nicola Segata and Levi Waldron and Joshua Reyes and Ashlee M. Earl and Georgia Giannoukos and Matthew R. Boylan and Dawn Ciulla and Dirk Gevers and Jacques Izard and Wendy S. Garrett and Andrew T. Chan and Curtis Huttenhower
Proceedings of the National Academy of Sciences, ISSN 0027-8424, 06/2014, Volume 111, Issue 22, pp. E2329 - E2338
Although the composition of the human microbiome is now well-studied, the microbiota's >8 million genes and their regulation remain largely uncharacterized.... 
HUMAN MICROBIOME | BACTERIA | ENVIRONMENTS | TWINS | MULTIDISCIPLINARY SCIENCES | GENE-EXPRESSION | COMMUNITIES | SAMPLES | Humans | Specimen Handling - methods | Gastrointestinal Tract - microbiology | Transcriptome - genetics | RNA, Bacterial - analysis | Feces - microbiology | Metagenome - genetics | Mouth - microbiology | Gastrointestinal Tract - physiology | Microbiota - genetics | Saliva - microbiology | DNA, Bacterial - analysis | Gene Expression Regulation, Bacterial | Genomics - methods | PNAS Plus | Biological Sciences
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5. Full Text Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
by Mikkelsen, TS and Ku, MC and Jaffe, DB and Issac, B and Lieberman, E and Giannoukos, G and Alvarez, P and Brockman, W and Kim, TK and Koche, RP and Lee, W and Mendenhall, E and O'Donovan, A and Presser, A and Russ, C and Xie, XH and Meissner, A and Wernig, M and Jaenisch, R and Nusbaum, C and Lander, ES and Bernstein, BE
NATURE, ISSN 0028-0836, 08/2007, Volume 448, Issue 7153, pp. 553 - U2
We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By... 
HISTONE LYSINE METHYLATION | DEVELOPMENTAL REGULATORS | DNA METHYLATION | NONCODING RNAS | MULTIDISCIPLINARY SCIENCES | EMBRYONIC STEM-CELLS | MOUSE | TRANSCRIPTION | GENE-EXPRESSION | DIFFERENTIATION | POLYCOMB | Chromatin - metabolism | Genomic Imprinting | Pluripotent Stem Cells - cytology | Genome - genetics | Male | Promoter Regions, Genetic - genetics | Pluripotent Stem Cells - metabolism | Animals | Gene Expression Regulation, Developmental | Alleles | CpG Islands - genetics | Fibroblasts | Mice | Histones - metabolism | Transcription, Genetic - genetics | Methylation | Chromatin - genetics | Cell Lineage - genetics | Chromatin | Genomics | Research methodology | Rodents | Stem cells
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6. Full Text Tracking Insertion Mutants within Libraries by Deep Sequencing and a Genome-Wide Screen for Haemophilus Genes Required in the Lung
by Jeffrey D. Gawronski and Sandy M. S. Wong and Georgia Giannoukos and Doyle V. Ward and Brian J. Akerley and John J. Mekalanos
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 9/2009, Volume 106, Issue 38, pp. 16422 - 16427
Rapid genome-wide identification of genes required for infection would expedite studies of bacterial pathogens. We developed genome-scale "negative selection"... 
Genetic transposition | Transposons | Lungs | Pathogenesis | Genes | Virulence | Libraries | Infections | Sequencing | Haemophilus influenzae | Mutagenesis | Illumina | Mariner | Transposon | PULMONARY CLEARANCE | LIPOPOLYSACCHARIDE BIOSYNTHESIS | MULTIDISCIPLINARY SCIENCES | ESCHERICHIA-COLI | BACTERIAL VIRULENCE | mutagenesis | transposon | pathogenesis | SHIGELLA-FLEXNERI | IN-VITRO | INFLUENZAE TYPE-B | mariner | STRAIN RD | HYDROGEN-PEROXIDE | ENTERIC BACTERIA | Lung - microbiology | Genome-Wide Association Study | Chromosomes, Bacterial - genetics | Mutagenesis, Insertional - methods | Genes, Bacterial - genetics | Genomic Library | Haemophilus influenzae - genetics | Chromosome Mapping | Genome, Bacterial - genetics | Animals | DNA Transposable Elements - genetics | Haemophilus Infections - microbiology | Mice | Mutation | Haemophilus influenzae - growth & development | insertional mutagenesis | Oxidative stress | Pathogens | Animal models | Lung | Antimicrobial agents | Genomes | Survival | transposon mutagenesis | Infection | Nutrients | Models | Chromosomes | Fitness | Index Medicus | Biological Sciences
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7. Full Text A framework for human microbiome research
by Methé, Barbara A and Nelson, Karen E and Pop, Mihai and Creasy, Heather H and Giglio, Michelle G and Huttenhower, Curtis and Gevers, Dirk and Petrosino, Joseph F and Abubucker, Sahar and Badger, Jonathan H and Chinwalla, Asif T and Earl, Ashlee M and Fitzgerald, Michael G and Fulton, Robert S and Hallsworth-Pepin, Kymberlie and Lobos, Elizabeth A and Madupu, Ramana and Magrini, Vincent and Martin, John C and Mitreva, Makedonka and Muzny, Donna M and Sodergren, Erica J and Versalovic, James and Wollam, Aye M and Worley, Kim C and Wortman, Jennifer R and Young, Sarah K and Zeng, Qiandong and Aagaard, Kjersti M and Abolude, Olukemi O and Allen-Vercoe, Emma and Alm, Eric J and Alvarado, Lucia and Andersen, Gary L and Anderson, Scott and Appelbaum, Elizabeth and Arachchi, Harindra M and Armitage, Gary and Arze, Cesar A and Ayvaz, Tulin and Baker, Carl C and Begg, Lisa and Belachew, Tsegahiwot and Bhonagiri, Veena and Bihan, Monika and Blaser, Martin J and Bloom, Toby and Bonazzi, Vivien R and Brooks, Paul and Buck, Gregory A and Buhay, Christian J and Busam, Dana A and Campbell, Joseph L and Canon, Shane R and Cantarel, Brandi L and Chain, Patrick S and Chen, I-Min A and Chen, Lei and Chhibba, Shaila and Chu, Ken and Ciulla, Dawn M and Clemente, Jose C and Clifton, Sandra W and Conlan, Sean and Crabtree, Jonathan and Cutting, Mary A and Davidovics, Noam J and Davis, Catherine C and Desantis, Todd Z and Deal, Carolyn and Delehaunty, Kimberley D and Dewhirst, Floyd E and Deych, Elena and Ding, Yan and Dooling, David J and Dugan, Shannon P and Michael Dunne, W and Scott Durkin, A and Edgar, Robert C and Erlich, Rachel L and Farmer, Candace N and Farrell, Ruth M and Faust, Karoline and Feldgarden, Michael and Felix, Victor M and Fisher, Sheila and Fodor, Anthony A and Forney, Larry and Foster, Leslie and Di Francesco, Valentina and Friedman, Jonathan and Friedrich, Dennis C and Fronick, Catrina C and Fulton, Lucinda L and Gao, Hongyu and Garcia, Nathalia and Giannoukos, Georgia and Giblin, Christina and Giovanni, Maria Y and Goldberg, Jonathan M and ... and Human Microbiome Project Consortiu and Human Microbiome Project Consortium and The Human Microbiome Project Consortium and Joint Genome Institute (JGI)
Nature, ISSN 0028-0836, 06/2012, Volume 486, Issue 7402, pp. 215 - 221
A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The... 
MULTIDISCIPLINARY SCIENCES | CATALOG | Young Adult | Reference Standards | Humans | Adolescent | Metagenomics - methods | RNA, Ribosomal, 16S - genetics | Adult | Female | Male | Statistics as Topic | Bacteria - genetics | Metagenome | Genetic research | Microbiological research | Genomes | Research | Microbiota (Symbiotic organisms) | Studies | Medicine | Microbiology | Publications | Taxonomy | Genomics | Data processing | Manuscripts
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