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1. Full Text De-Discovery of the Placenta Microbiome
by Bushman, Frederic D
American Journal of Obstetrics and Gynecology, ISSN 0002-9378, 03/2019, Volume 220, Issue 3, pp. 213 - 214
OBSTETRICS & GYNECOLOGY
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2. Full Text Role of PSIP 1/LEDGF/p75 in lentiviral infectivity and integration targeting
by Marshall, Heather M and Ronen, Keshet and Berry, Charles and Llano, Manuel and Sutherland, Heidi and Saenz, Dyana and Bickmore, Wendy and Poeschla, Eric and Bushman, Frederic D
PLoS ONE, 12/2007, Volume 2, Issue 12
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3. Full Text Sunbeam: An extensible pipeline for analyzing metagenomic sequencing experiments
by Clarke, Erik L and Taylor, Louis J and Zhao, Chunyu and Connell, Andrew and Lee, Jung-Jin and Fett, Bryton and Bushman, Frederic D and Bittinger, Kyle
Microbiome, ISSN 2049-2618, 03/2019, Volume 7, Issue 1, pp. 46 - 46
BackgroundAnalysis of mixed microbial communities using metagenomic sequencing experiments requires multiple preprocessing and analytical steps to interpret... 
Shotgun metagenomic sequencing | Software | Sunbeam | Quality control | Pipeline | VISUALIZATION | READ ALIGNMENT | ACCURATE | MICROBIOLOGY | COMMUNITY | DATABASE | DIET | GUT MICROBIOME | UPDATE | PROGRAM | Computational Biology - methods | Algorithms | Humans | Metagenomics - methods | Data Analysis | Data Mining | High-Throughput Nucleotide Sequencing | Sequence Analysis, DNA - methods | Pipe lines | Genomes | Genomics | Enzymes | Data analysis | Automation | Documentation | Experiments | Flexibility | Computer programs | Researchers | Decontamination | Phylogenetics | Bioinformatics | Deoxyribonucleic acid--DNA | Index Medicus
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4. Full Text Lack of detection of a human placenta microbiome in samples from preterm and term deliveries
by Leiby, Jacob S and McCormick, Kevin and Sherrill-Mix, Scott and Clarke, Erik L and Kessler, Lyanna R and Taylor, Louis J and Hofstaedter, Casey E and Roche, Aoife M and Mattei, Lisa M and Bittinger, Kyle and Elovitz, Michal A and Leite, Rita and Parry, Samuel and Bushman, Frederic D
Microbiome, ISSN 2049-2618, 10/2018, Volume 6, Issue 1, pp. 196 - 196
Background: Historically, the human womb has been thought to be sterile in healthy pregnancies, but this idea has been challenged by recent studies using DNA... 
Placenta | Preterm birth | 16S rRNA gene | Microbiome | Shotgun metagenomics | MEMBRANES | MICROBIOLOGY | BACTERIAL | RIBOSOMAL-RNA | AMNIOTIC-FLUID | SILVA | COMMUNITY | SEQUENCE | DIVERSITY | INFECTION | LABOR | Premature Birth | Humans | Bacteria - genetics | Sequence Analysis, DNA | Placenta - microbiology | Pregnancy | Uterus - microbiology | Bacteria - isolation & purification | DNA, Bacterial - genetics | Microbiota - genetics | RNA, Ribosomal, 16S - genetics | Adult | Female | Term Birth | Composition | Microbiota (Symbiotic organisms) | Genetic aspects | Health aspects | Microbial colonies | Childbirth | Neonates | Gnotobiotics | rRNA 16S | Nucleotide sequence | Taxonomy | Premature birth | Microbiomes | Sterility | Data bases | Microbiota | Microorganisms | Uterus | Bacteria | Bioinformatics | Colonization | Deoxyribonucleic acid--DNA | Cesarean section | DNA sequencing | Index Medicus
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5. Full Text Gene activity in primary T cells infected with HIV 89.6 : Intron retention and induction of genomic repeats
by Sherrill-Mix, Scott and Ocwieja, Karen E and Bushman, Frederic D
Retrovirology, 09/2015, Volume 12, Issue 1
HERV | Retrotransposons | HIV | Splicing | Transcription | Expression | RNA-Seq | T cell | Chimera
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6. Full Text Engineering the Human Genome: Reflections on the Beginning
by Bushman, Frederic D
Human Gene Therapy, ISSN 1043-0342, 05/2014, Volume 25, Issue 5, pp. 395 - 400
Pioneer Perspective | MEDICINE, RESEARCH & EXPERIMENTAL | SEVERE COMBINED IMMUNODEFICIENCY | LEUKEMIA-VIRUS INTEGRATION | RETROVIRAL DNA INTEGRATION | HUMAN GUT VIROME | BACTERIOPHAGE-MU | IN-VITRO | LAMBDA-PHAGE REPRESSOR | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | LENTIVIRAL VECTOR | GENETICS & HEREDITY | GENE-THERAPY | TRANSCRIPTION START SITES | DNA-Binding Proteins - metabolism | Genetic Therapy | Genetic Engineering | HIV - physiology | History, 21st Century | Virus Integration - physiology | History, 20th Century | Humans | Genome, Human - genetics | Index Medicus
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7. Full Text Rapid evolution of the human gut virome
by Samuel Minot and Alexandra Bryson and Christel Chehoud and Gary D. Wu and James D. Lewis and Frederic D. Bushman
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 7/2013, Volume 110, Issue 30, pp. 12450 - 12455
Humans are colonized by immense populations of viruses, which metagenomic analysis shows are mostly unique to each individual. To investigate the origin and... 
Bacteriophages | Metagenomics | Microbiota | Genetic variation | Humans | Viruses | Evolution | Bacteria | Genomes | Animal cells | CRISPR | Diversity generating retroelement | Microbiome | SYSTEM | BACTERIOPHAGE | VIRAL COMMUNITY | RNA | MULTIDISCIPLINARY SCIENCES | microbiome | COLITIS | metagenomics | diversity generating retroelement | SEQUENCE | DIVERSITY | VIRUSES | Viruses - genetics | DNA, Viral - genetics | Intestines - virology | Evolution, Molecular | DNA polymerases | Physiological aspects | Microbial genetics | Evolutionary genetics | Research | Mutation | DNA polymerase | Genomics | Index Medicus | Biological Sciences
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8. Full Text Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents
by Hoffmann, Christian and Dollive, Serena and Grunberg, Stephanie and Chen, Jun and Li, Hongzhe and Wu, Gary D and Lewis, James D and Bushman, Frederic D
PLoS ONE, ISSN 1932-6203, 06/2013, Volume 8, Issue 6, pp. e66019 - e66019
Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to... 
MULTIDISCIPLINARY SCIENCES | DISEASE | FERMENTATION | DIVERSITY | INFECTION | SAMPLES | COMMUNITIES | INTESTINE | METHANOBREVIBACTER-SMITHII | 16S RIBOSOMAL-RNA | SURFACES | Fungi | Bacteria | Diet | Fatty acids | Health care | Populations | Disease | Amino acids | Viruses | Population studies | Epidemiology | Gene sequencing | Microorganisms | Microbiota | Questionnaires | Nutrients | Deoxyribonucleic acid--DNA | Carbohydrates | Archaea | Population structure | Abundance | Fermentation | Medicine | Toxins | High protein diet | DNA sequencing | Index Medicus | Deoxyribonucleic acid | DNA
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9. Full Text Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock
by Xue Liang and Frederic D. Bushman and Garret A. FitzGerald
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 8/2015, Volume 112, Issue 33, pp. 10479 - 10484
In mammals, multiple physiological, metabolic, and behavioral processes are subject to circadian rhythms, adapting to changing light in the environment. Here... 
Gender differences | Circadian rhythm | Bmal1 gene | Microbiome | BACTERIAL SYMBIONT | HUMAN GUT MICROBIOTA | MULTIDISCIPLINARY SCIENCES | COMPONENTS | microbiome | gender differences | OBESITY | EVOLUTION | DIET | METABOLISM | CYANOBACTERIA | AUTOIMMUNITY | circadian rhythm | DYNAMICS | RNA, Ribosomal, 16S - metabolism | ARNTL Transcription Factors - genetics | Mice, Inbred C57BL | Male | Circadian Rhythm | Mice, Knockout | Microbiota | Algorithms | Animals | Intestines - microbiology | Sequence Analysis, RNA | Gene Deletion | Sex Factors | Female | Mice | Feces | Principal Component Analysis | Oscillometry | Circadian rhythms | Physiological aspects | Microbiota (Symbiotic organisms) | Observations | Bacteria | Gender | Rodents | Index Medicus | Biological Sciences
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10. Full Text 462 - A Role for Bacterial Urease in Crohn's Disease and Gut Dysbiosis
by Ni, Josephine and Shen, Ting-Chin David and Chen, Eric Z and Bailey, Aubrey and Roggiani, Manuela and Sirota-Madi, Alexandra and Friedman, Elliot S and Chau, Lillian and Albenberg, Lindsey and Baldassano, Robert N and Braun, Jonathan and Xavier, Ramnik and Clish, Clary B and Yudkoff, Marc and Li, Hongzhe and Goulian, Mark and Bushman, Frederic D and Lewis, James D and Wu, Gary D
Gastroenterology, ISSN 0016-5085, 04/2017, Volume 152, Issue 5, pp. S111 - S111
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11. Full Text T cell dynamics and response of the microbiota after gene therapy to treat X-linked severe combined immunodeficiency
by Clarke, Erik L and Connell, A. Jesse and Six, Emmanuelle and Kadry, Nadia A and Abbas, Arwa A and Hwang, Young and Everett, John K and Hofstaedter, Casey E and Marsh, Rebecca and Armant, Myriam and Kelsen, Judith and Notarangelo, Luigi D and Collman, Ronald G and Hacein-Bey-Abina, Salima and Kohn, Donald B and Cavazzana, Marina and Fischer, Alain and Williams, David A and Pai, Sung-Yun and Bushman, Frederic D
Genome Medicine, ISSN 1756-994X, 09/2018, Volume 10, Issue 1, pp. 70 - 70
Background: Mutation of the IL2RG gene results in a form of severe combined immune deficiency (SCID-X1), which has been treated successfully with hematopoietic... 
INTERLEUKIN-2 | HIV | VIVO | TRANSPLANT | GENETICS & HEREDITY | SITES | SCID PATIENTS | SELECTION | ASSOCIATION | DNA INTEGRATION | VECTOR | Usage | Genetic transformation | Research | Gene mutations | Gene therapy | Index Medicus
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12. Full Text Retroviral integration and human gene therapy
by Bushman, Frederic D
Journal of Clinical Investigation, ISSN 0021-9738, 08/2007, Volume 117, Issue 8, pp. 2083 - 2086
Long-term correction of genetic diseases requires permanent integration of therapeutic genes into chromosomes of affected cells. Retroviral vectors are the... 
MEDICINE, RESEARCH & EXPERIMENTAL | CELLS | SEVERE COMBINED IMMUNODEFICIENCY | VECTOR INTEGRATION | SCID-X1 | LENTIVIRAL VECTOR | IN-VIVO | TRANSCRIPTION | GENOME-WIDE ANALYSIS | TRANSDUCTION | SELECTION | Antigens, CD34 | Genetic Therapy | Virus Integration - genetics | Cell Proliferation | T-Lymphocytes | Humans | Lymphopoiesis - genetics | X-Linked Combined Immunodeficiency Diseases - genetics | Cell Survival - genetics | X-Linked Combined Immunodeficiency Diseases - therapy | Hematopoietic Stem Cells - metabolism | Gammaretrovirus | Time Factors | Mutagenesis, Insertional | Genetic Vectors | Genome, Human | Quantitative Trait Loci | Care and treatment | Research | Gene therapy | Retrovirus infections | Index Medicus | Abridged Index Medicus
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13. Full Text Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes
by Gary D. Wu and Jun Chen and Christian Hoffmann and Kyle Bittinger and Ying-Yu Chen and Sue A. Keilbaugh and Meenakshi Bewtra and Dan Knights and William A. Walters and Rob Knight and Rohini Sinha and Erin Gilroy and Kernika Gupta and Robert Baldassano and Lisa Nessel and Hongzhe Li and Frederic D. Bushman and James D. Lewis
Science, ISSN 0036-8075, 10/2011, Volume 334, Issue 6052, pp. 105 - 108
Diet strongly affects human health, partly by modulating gut microbiome composition. We used diet inventories and 16S rDNA sequencing to characterize fecal... 
Taxa | Metagenomics | Microbiota | Diet | REPORTS | Ribosomal DNA | Nutrients | Prevotella | Fatty acids | Genera | Bacteroides | MULTIDISCIPLINARY SCIENCES | GENOME | Dietary Carbohydrates - administration & dosage | Cross-Sectional Studies | Humans | Middle Aged | Dietary Fiber - administration & dosage | Child, Preschool | Gastrointestinal Tract - microbiology | Ruminococcus - isolation & purification | Young Adult | Feces - microbiology | Bacteria - isolation & purification | Time Factors | Ruminococcus - classification | Adolescent | Dietary Fats - administration & dosage | Bacteria - classification | Adult | Bacteroides - classification | Prevotella - isolation & purification | Child | Metagenome | Bacteroides - isolation & purification | Prevotella - classification | Physiological aspects | Genetic aspects | Research | Nucleotide sequencing | Health aspects | DNA sequencing | Bacteria | Microorganisms | Feces | Health | Index Medicus
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14. Full Text Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis
by Koeth, Robert A and Wang, Zeneng and Levison, Bruce S and Buffa, Jennifer A and Org, Elin and Sheehy, Brendan T and Britt, Earl B and Fu, Xiaoming and Wu, Yuping and Li, Lin and Smith, Jonathan D and Didonato, Joseph A and Chen, Jun and Li, Hongzhe and Wu, Gary D and Lewis, James D and Warrier, Manya and Brown, J Mark and Krauss, Ronald M and Tang, W.H. Wilson and Bushman, Frederic D and Lusis, Aldons J and Hazen, Stanley L
Nature Medicine, ISSN 1078-8956, 05/2013, Volume 19, Issue 5, pp. 576 - 585
Intestinal microbiota metabolism of choline and phosphatidylcholine produces trimethylamine (MA), which is further metabolized to a proatherogenic species,... 
MEDICINE, RESEARCH & EXPERIMENTAL | BILE-ACID | PROTEIN | BIOCHEMISTRY & MOLECULAR BIOLOGY | CELL BIOLOGY | DIET | REVERSE CHOLESTEROL TRANSPORT | GUT MICROBIOME | CARDIOVASCULAR-DISEASE | MICE | CORONARY-HEART-DISEASE | RECEPTORS | EXPRESSION | Atherosclerosis - physiopathology | Humans | Methylamines - blood | Carnitine - chemistry | Carnitine - metabolism | Cholesterol - metabolism | Choline - chemistry | Desmosterol - metabolism | Meat | Mice, Knockout | Atherosclerosis - etiology | Macrophages - metabolism | Animals | Intestines - microbiology | Time Factors | Mass Spectrometry | Female | Atherosclerosis - microbiology | Mice | Metagenome | Methylamines - metabolism | RNA - metabolism | Physiological aspects | Levocarnitine | Genetic aspects | Research | Microbiota (Symbiotic organisms) | Microbial metabolism | Biomedical research | Diet | Risk factors | Atherosclerosis | Index Medicus
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