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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 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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3. Full Text Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
by Giannoukos, Georgia and Ciulla, Dawn M and Huang, Katherine and Haas, Brian J and Izard, Jacques and Levin, Joshua Z and Livny, Jonathan and Earl, Ashlee M and Gevers, Dirk and Ward, Doyle V and Nusbaum, Chad and Birren, Bruce W and Gnirke, Andreas
Genome Biology, ISSN 1474-760X, 03/2012, Volume 13, Issue 3, pp. R23 - r23
We have developed a process for transcriptome analysis of bacterial communities that accommodates both intact and fragmented starting RNA and combines... 
CATALOG | TEMPERATURE | SEQUENCES | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GUT MICROBIOME | LIGHT | GENES | GENETICS & HEREDITY | RIBOSOMAL-RNA | PROCHLOROCOCCUS | DUPLEX-SPECIFIC NUCLEASE | DNA, Complementary - analysis | Humans | RNA, Messenger - analysis | Feces - microbiology | RNA, Messenger - biosynthesis | Prochlorococcus - genetics | Chemical Fractionation | Escherichia coli - genetics | DNA, Complementary - biosynthesis | RNA, Bacterial - genetics | Rhodobacter sphaeroides - genetics | High-Throughput Nucleotide Sequencing | Microbial Consortia - genetics | Gene Expression Regulation, Bacterial
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4. Full Text Evaluation of 16s rDNA-based community profiling for human microbiome research
by Ward, Doyle V and Gevers, Dirk and Giannoukos, Georgia and Earl, Ashlee M and Methé, Barbara A and Sodergren, Erica and Feldgarden, Michael and Ciulla, Dawn M and Tabbaa, Diana and Arze, Cesar and Appelbaum, Elizabeth and Aird, Leigh and Anderson, Scott and Ayvaz, Tulin and Belter, Edward and Bihan, Monika and Bloom, Toby and Crabtree, Jonathan and Courtney, Laura and Carmichael, Lynn and Dooling, David and Erlich, Rachel L and Farmer, Candace and Fulton, Lucinda and Fulton, Robert and Gao, Hongyu and Gill, John A and Haas, Brian J and Hemphill, Lisa and Hall, Otis and Hamilton, Susanna G and Hepburn, Theresa A and Lennon, Niall J and Joshi, Vandita and Kells, Cristyn and Kovar, Christie L and Kalra, Divya and Li, Kelvin and Lewis, Lora and Leonard, Shawn and Muzny, Donna M and Mardis, Elaine and Mihindukulasuriya, Kathie and Magrini, Vincent and O'Laughlin, Michelle and Pohl, Craig and Qin, Xiang and Ross, Keenan and Ross, Matthew C and Rogers, Yu-Hui A and Singh, Navjeet and Shang, Yue and Wilczek-Boney, Katarzyna and Wortman, Jennifer R and Worley, Kim C and Youmans, Bonnie P and Yooseph, Shibu and Zhou, Yanjiao and Schloss, Patrick D and Wilson, Richard and Gibbs, Richard A and Nelson, Karen E and Weinstock, George and DeSantis, Todd Z and Petrosino, Joseph F and Highlander, Sarah K and Birren, Bruce W and Jumpstart Consortium Human Microbi and Jumpstart Consortium Human Microbiome Project Data Generation Working Group
PLoS ONE, ISSN 1932-6203, 06/2012, Volume 7, Issue 6, p. e39315
The Human Microbiome Project will establish a reference data set for analysis of the microbiome of healthy adults by surveying multiple body sites from 300... 
DIVERSITY | SEQUENCES | MULTIDISCIPLINARY SCIENCES | ABUNDANCE | Bacteria - classification | RNA, Ribosomal, 16S - genetics | Bacteria - genetics | Metagenome | Humans | Bayes Theorem | Community structure | rRNA 16S | Profiling | Working groups | Cloning | Genes | Community participation | Genomes | Surveying | Consortia | Ecologists | Classification | Biosphere | Adults | Protocol | Bioinformatics
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5. Full Text Development of a gene-editing approach to restore vision loss in Leber congenital amaurosis type 10
by Maeder, Morgan L and Stefanidakis, Michael and Wilson, Christopher J and Baral, Reshica and Barrera, Luis Alberto and Bounoutas, George S and Bumcrot, David and Chao, Hoson and Ciulla, Dawn M and DaSilva, Jennifer A and Dass, Abhishek and Dhanapal, Vidya and Fennell, Tim J and Friedland, Ari E and Giannoukos, Georgia and Gloskowski, Sebastian W and Glucksmann, Alexandra and Gotta, Gregory M and Jayaram, Hariharan and Haskett, Scott J and Hopkins, Bei and Horng, Joy E and Joshi, Shivangi and Marco, Eugenio and Mepani, Rina and Reyon, Deepak and Ta, Terence and Tabbaa, Diana G and Samuelsson, Steven J and Shen, Shen and Skor, Maxwell N and Stetkiewicz, Pam and Wang, Tongyao and Yudkoff, Clifford and Myer, Vic E and Albright, Charles F and Jiang, Haiyan
Nature Medicine, ISSN 1078-8956, 02/2019, Volume 25, Issue 2, pp. 229 - 233
Leber congenital amaurosis type 10 is a severe retinal dystrophy caused by mutations in the CEP290 gene(1,2). We developed EDIT-101, a candidate genome-editing... 
MEDICINE, RESEARCH & EXPERIMENTAL | THERAPY | CONE PHOTORECEPTORS | ROD | BIOCHEMISTRY & MOLECULAR BIOLOGY | MUTATIONS | CAS9 | IDENTIFICATION | CEP290 | BLINDNESS | CELL BIOLOGY | Retinal degeneration | Care and treatment | Genetic aspects | Research | Gene mutations | Staphylococcus aureus | Explants | CRISPR | Blindness | Retina | Genomes | Dystrophy | Nuclease | Mutation | Gene expression | Genetic modification
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6. Full Text UDiTaS™, A genome editing detection method for indels and genome rearrangements
by Giannoukos, Georgia and Ciulla, Dawn M and Marco, Eugenio and Abdulkerim, Hayat S and Barrera, Luis A and Bothmer, Anne and Dhanapal, Vidya and Gloskowski, Sebastian W and Jayaram, Hariharan and Maeder, Morgan L and Skor, Maxwell N and Wang, Tongyao and Myer, Vic E and Wilson, Christopher J
BMC Genomics, ISSN 1471-2164, 03/2018, Volume 19, Issue 1, pp. 212 - 10
Background: Understanding the diversity of repair outcomes after introducing a genomic cut is essential for realizing the therapeutic potential of genomic... 
CRISPR/CAS9 | NGS | Translocation detection | Next generation sequencing | Gene editing | UDiTaS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | DOUBLE-STRANDED BREAKS | MUTATIONS | CLEAVAGE
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7. Full Text Analysis of Exonic Elastin Variants in Severe, Early-Onset Chronic Obstructive Pulmonary Disease
by Cho, Michael H and Ciulla, Dawn M and Klanderman, Barbara J and Hersh, Craig P and Litonjua, Augusto A and Sparrow, David and Raby, Benjamin A and Silverman, Edwin K
American Journal of Respiratory Cell and Molecular Biology, ISSN 1044-1549, 06/2009, Volume 40, Issue 6, pp. 751 - 755
The destruction of elastic fibers has been implicated in the pathogenesis of chronic obstructive pulmonary disease (COPD). Emphysema has been described in... 
Chronic obstructive pulmonary disease | Emphysema | Elastin | Genetic polymorphism | ALLELES | BIOCHEMISTRY & MOLECULAR BIOLOGY | SUSCEPTIBILITY | MELTING ANALYSIS | SMOKING | elastin | emphysema | CELL BIOLOGY | CUTIS LAXA | RESPIRATORY SYSTEM | ARTERIAL STIFFNESS | EMPHYSEMA TREATMENT TRIAL | MUTATION | COMMON | genetic polymorphism | ASSOCIATION | chronic obstructive pulmonary disease | Elastin - metabolism | Exons | Humans | Middle Aged | Emphysema - metabolism | Male | Case-Control Studies | Polymorphism, Genetic | Genetic Variation | Elastin - genetics | Pedigree | Adult | Female | Aged | Polymorphism, Single Nucleotide | Pulmonary Disease, Chronic Obstructive - metabolism | Emphysema - genetics | Pulmonary Disease, Chronic Obstructive - genetics
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8. 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 | Amino acids | Genomes | Biosynthesis | Genes | Deoxyribonucleic acid--DNA | PNAS Plus | Biological Sciences
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