Frederic D Bushman

Frederic D Bushman

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Frederic D Bushman

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Retroviral Insertional Mutagenesis in Humans: Evidence for Four Genetic Mechanisms Promoting Expansion of Cell Clones.

Mol Ther 2020 Feb 7;28(2):352-356. Epub 2020 Jan 7.

Department of Microbiology, University of Pennsylvania Perelman School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymthe.2019.12.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7001082PMC
February 2020

Detecting contamination in viromes using ViromeQC.

Nat Biotechnol 2019 12;37(12):1408-1412

Department CIBIO, University of Trento, Trento, Italy.

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http://dx.doi.org/10.1038/s41587-019-0334-5DOI Listing
December 2019

Virus structures constrain transmission modes.

Nat Microbiol 2019 11 29;4(11):1778-1780. Epub 2019 Jul 29.

Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.

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http://dx.doi.org/10.1038/s41564-019-0523-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6814542PMC
November 2019

Gene therapy targeting haematopoietic stem cells for inherited diseases: progress and challenges.

Nat Rev Drug Discov 2019 06;18(6):447-462

INSERM UMR 1163, Laboratory of Human Lymphohematopoiesis, Paris, France.

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http://www.nature.com/articles/s41573-019-0020-9
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http://dx.doi.org/10.1038/s41573-019-0020-9DOI Listing
June 2019

Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness.

Cell Host Microbe 2019 May;25(5):719-729.e4

Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2019.04.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6510254PMC
May 2019

De-Discovery of the Placenta Microbiome.

Am J Obstet Gynecol 2019 03;220(3):213-214

Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA. Electronic address:

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http://dx.doi.org/10.1016/j.ajog.2018.11.1093DOI Listing
March 2019

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments.

Microbiome 2019 03 22;7(1):46. Epub 2019 Mar 22.

Division of Gastroenterology, Hepatology and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1186/s40168-019-0658-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6429786PMC
March 2019

iGUIDE: an improved pipeline for analyzing CRISPR cleavage specificity.

Genome Biol 2019 01 17;20(1):14. Epub 2019 Jan 17.

Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA.

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http://dx.doi.org/10.1186/s13059-019-1625-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6337799PMC
January 2019

Molecular analysis of bacterial contamination on stethoscopes in an intensive care unit.

Infect Control Hosp Epidemiol 2018 Dec 18:1-7. Epub 2018 Dec 18.

1Pulmonary, Allergy and Critical Care Division, Department of Medicine,University of Pennsylvania Perelman School of Medicine,Philadelphia, Pennsylvania.

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https://www.cambridge.org/core/product/identifier/S0899823X1
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http://dx.doi.org/10.1017/ice.2018.319DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6581638PMC
December 2018

Sera from Individuals with Narrowly Focused Influenza Virus Antibodies Rapidly Select Viral Escape Mutations .

J Virol 2018 10 12;92(19). Epub 2018 Sep 12.

Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA

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http://dx.doi.org/10.1128/JVI.00859-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6146816PMC
October 2018

Fully 3D printed integrated reactor array for point-of-care molecular diagnostics.

Biosens Bioelectron 2018 Jun 10;109:156-163. Epub 2018 Mar 10.

Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bios.2018.03.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172948PMC
June 2018

Toxin-positive latently infect mouse colonies and protect against highly pathogenic .

Gut 2018 05 20;67(5):860-871. Epub 2017 Feb 20.

Center for Inflammation Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA.

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http://dx.doi.org/10.1136/gutjnl-2016-313510DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5941301PMC
May 2018

A Pilot Characterization of the Human Chronobiome.

Sci Rep 2017 12 7;7(1):17141. Epub 2017 Dec 7.

Department of Systems Pharmacology and Translational Therapeutics, at the University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1038/s41598-017-17362-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5719427PMC
December 2017

Viral communities of the human gut: metagenomic analysis of composition and dynamics.

Mob DNA 2017 3;8:12. Epub 2017 Oct 3.

Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076 USA.

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http://dx.doi.org/10.1186/s13100-017-0095-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5627405PMC
October 2017

Dietary Regulation of the Gut Microbiota Engineered by a Minimal Defined Bacterial Consortium.

PLoS One 2016 13;11(5):e0155620. Epub 2016 May 13.

Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155620PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866709PMC
July 2017

swga: a primer design toolkit for selective whole genome amplification.

Bioinformatics 2017 Jul;33(14):2071-2077

Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870857PMC
July 2017

A Model-Based Approach For Species Abundance Quantification Based On Shotgun Metagenomic Data.

Stat Biosci 2017 Jun 16;9(1):13-27. Epub 2016 May 16.

Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.

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http://link.springer.com/10.1007/s12561-016-9148-x
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http://dx.doi.org/10.1007/s12561-016-9148-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5612490PMC
June 2017

Optimizing methods and dodging pitfalls in microbiome research.

Microbiome 2017 05 5;5(1):52. Epub 2017 May 5.

Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.

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http://dx.doi.org/10.1186/s40168-017-0267-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5420141PMC
May 2017

Associations of the vaginal microbiota with HIV infection, bacterial vaginosis, and demographic factors.

AIDS 2017 04;31(7):895-904

aDepartment of Microbiology, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania bDepartment of Cellular and Molecular Biology, Feinberg School of Medicine, Northwestern University cCORE Center, Stroger Hospital of Cook County, Chicago, Illinois, USA.

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http://dx.doi.org/10.1097/QAD.0000000000001421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370567PMC
April 2017

Genome Sequence of a Toxin-Positive Strain Isolated from Murine Feces.

Genome Announc 2017 Apr 6;5(14). Epub 2017 Apr 6.

Center for Inflammation Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA.

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http://dx.doi.org/10.1128/genomeA.00088-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5383883PMC
April 2017

A role for glycolipid biosynthesis in severe fever with thrombocytopenia syndrome virus entry.

PLoS Pathog 2017 Apr 7;13(4):e1006316. Epub 2017 Apr 7.

Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1006316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397019PMC
April 2017

Human and rat gut microbiome composition is maintained following sleep restriction.

Proc Natl Acad Sci U S A 2017 02 8;114(8):E1564-E1571. Epub 2017 Feb 8.

Chronobiology Program, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104;

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http://dx.doi.org/10.1073/pnas.1620673114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5338418PMC
February 2017

Miniaturized devices for point of care molecular detection of HIV.

Lab Chip 2017 01;17(3):382-394

Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

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http://dx.doi.org/10.1039/c6lc01239fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5285266PMC
January 2017

Structural Basis for Inhibitor-Induced Aggregation of HIV Integrase.

PLoS Biol 2016 Dec 9;14(12):e1002584. Epub 2016 Dec 9.

Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1002584DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5147827PMC
December 2016

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota.

Microbiome 2016 Jun 23;4(1):29. Epub 2016 Jun 23.

Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA.

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http://dx.doi.org/10.1186/s40168-016-0172-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4917942PMC
June 2016

Peptidoglycan from the gut microbiota governs the lifespan of circulating phagocytes at homeostasis.

Blood 2016 05 17;127(20):2460-71. Epub 2016 Mar 17.

Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; and Department of Microbiology, New York University School of Medicine, New York, NY.

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http://dx.doi.org/10.1182/blood-2015-10-675173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4874226PMC
May 2016

Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation.

mBio 2016 Mar 29;7(2):e00322. Epub 2016 Mar 29.

Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA

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http://dx.doi.org/10.1128/mBio.00322-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4817255PMC
March 2016

Composition and dynamics of the respiratory tract microbiome in intubated patients.

Microbiome 2016 Feb 11;4. Epub 2016 Feb 11.

Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1186/s40168-016-0151-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4750361PMC
February 2016

Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production.

Gut 2016 Jan 26;65(1):63-72. Epub 2014 Nov 26.

Division of Gastroenterology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania, USA Departments of Biostatistics & Epidemiology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1136/gutjnl-2014-308209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4583329PMC
January 2016

Alterations of the Subgingival Microbiota in Pediatric Crohn's Disease Studied Longitudinally in Discovery and Validation Cohorts.

Inflamm Bowel Dis 2015 Dec;21(12):2797-805

*Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; †Department of Microbiology; and ‡Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.

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http://dx.doi.org/10.1097/MIB.0000000000000557DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4950860PMC
December 2015

Bidirectional interactions between indomethacin and the murine intestinal microbiota.

Elife 2015 Dec 23;4:e08973. Epub 2015 Dec 23.

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.

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http://dx.doi.org/10.7554/eLife.08973DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755745PMC
December 2015

A reverse transcription loop-mediated isothermal amplification assay optimized to detect multiple HIV subtypes.

PLoS One 2015 12;10(2):e0117852. Epub 2015 Feb 12.

Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117852PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4326360PMC
November 2015

Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats.

Retrovirology 2015 Sep 17;12:79. Epub 2015 Sep 17.

Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 425 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1186/s12977-015-0205-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574318PMC
September 2015

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA.

Bioinformatics 2015 Aug 29;31(15):2461-8. Epub 2015 Mar 29.

Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btv183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4514928PMC
August 2015

Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohn's Disease.

Inflamm Bowel Dis 2015 Aug;21(8):1786-93

*Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; †Department of Pediatric, Division of Gastroenterology and Nutrition Seattle Children's Hospital, Seattle, Washington; and University of Washington; ‡Department of Pediatrics, IWK Health Centre, Halifax, NS, Canada; §Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada; ||School of Nursing, University of Pennsylvania, Philadelphia, Pennsylvania; ¶Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; **Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; and ††Department of Medicine, Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.

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http://pdfs.journals.lww.com/ibdjournal/2015/08000/Comparati
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http://dx.doi.org/10.1097/MIB.0000000000000426DOI Listing
August 2015

Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease.

Inflamm Bowel Dis 2015 Aug;21(8):1948-56

*Division of Gastroenterology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania; †Department of Microbiology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania; and ‡Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.

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http://dx.doi.org/10.1097/MIB.0000000000000454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4509842PMC
August 2015

Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock.

Proc Natl Acad Sci U S A 2015 Aug 3;112(33):10479-84. Epub 2015 Aug 3.

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, PA 19104;

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http://dx.doi.org/10.1073/pnas.1501305112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547234PMC
August 2015

Structural and sequencing analysis of local target DNA recognition by MLV integrase.

Nucleic Acids Res 2015 Jun 12;43(11):5647-63. Epub 2015 May 12.

Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA

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http://dx.doi.org/10.1093/nar/gkv410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477651PMC
June 2015

Coherence analysis discriminates between retroviral integration patterns in CD34(+) cells transduced under differing clinical trial conditions.

Mol Ther Methods Clin Dev 2015 29;2:15015. Epub 2015 Apr 29.

Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead , Westmead, Australia ; The University of Sydney, Discipline of Paediatrics and Child Health , Westmead, Australia.

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http://dx.doi.org/10.1038/mtm.2015.15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4445430PMC
June 2015

Inflammation-associated microbiota in pediatric eosinophilic esophagitis.

Microbiome 2015 1;3:23. Epub 2015 Jun 1.

Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA 19104 USA ; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA.

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http://dx.doi.org/10.1186/s40168-015-0085-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4450515PMC
June 2015

Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9.

mBio 2015 Jun 16;6(3):e00648. Epub 2015 Jun 16.

Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA

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http://dx.doi.org/10.1128/mBio.00648-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4471564PMC
June 2015

Nuclemeter: a reaction-diffusion based method for quantifying nucleic acids undergoing enzymatic amplification.

Sci Rep 2014 Dec 5;4:7335. Epub 2014 Dec 5.

Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

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http://dx.doi.org/10.1038/srep07335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256561PMC
December 2014

Host Factors in Retroviral Integration and the Selection of Integration Target Sites.

Microbiol Spectr 2014 Dec;2(6)

Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.

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http://www.asmscience.org/content/book/10.1128/9781555819217
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http://dx.doi.org/10.1128/microbiolspec.MDNA3-0026-2014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4525071PMC
December 2014

Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota.

Gastroenterology 2014 Nov 18;147(5):1055-63.e8. Epub 2014 Jul 18.

Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania. Electronic address:

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http://dx.doi.org/10.1053/j.gastro.2014.07.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4252572PMC
November 2014

A modified γ-retrovirus vector for X-linked severe combined immunodeficiency.

N Engl J Med 2014 Oct;371(15):1407-17

From the Departments of Biotherapy (S.H.-B.-A., J. Blondeau, L.C., F.T., M.C.) and Immunology and Pediatric Hematology (S.B., G.C., D.M., B.N., C.P., F.T., A.F.) and the Centre d'Étude des Déficits Immunitaires (C.P.), Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), the Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, AP-HP, INSERM (S.H.-B.-A., J. Blondeau, L.C., F.T., M.C.), Unité de Technologies Chimiques et Biologiques pour la Santé, Centre National de la Recherche Scientifique, 8258-INSERM Unité 1022, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes (S.H.-B.-A.), Immunology Laboratory, Groupe Hospitalier Universitaire Paris-Sud, AP-HP, Le Kremlin-Bicêtre (S.H.-B.-A.), Imagine Institute, Paris Descartes-Sorbonne Paris Cité University (S.B., J. Blondeau, L.C., D.M., B.N., C.P., E.S., A.F., M.C.), INSERM Unités Mixtes de Recherche 1163, Laboratory of Human Lymphohematopoiesis (J. Blondeau, L.C., E.S., F.T., A.F., M.C.), Groupe Immunoscope, Immunology Department, Institut Pasteur (A.L.), and Collège de France (A.F.) - all in Paris; Division of Hematology-Oncology (S.-Y.P., H.B., D.G., C.E.H., G.H., L.E.L., W.B.L., D.A.W.) and Division of Immunology (L.D.N.), Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute (S.-Y.P., D.G., L.E.L., W.B.L., D.A.W.), Harvard Medical School (S.-Y.P., M.A., L.E.L., W.B.L., J.R., L.E.S., A.T., L.D.N., D.A.W.), Center for Human Cell Therapy, Program in Cellular and Molecular Medicine, Boston Children's Hospital (M.A., J.R., L.E.S., A.T.), Division of Hematologic Malignancies, Dana-Farber Cancer Institute (J.R.), and the Manton Center for Orphan Disease Research (L.D.N.) - all in Boston; Great Ormond Street Hospital for Children NHS Foundation Trust (H.B.G., J.X.-B., A.J.T.) and Section of Molecular and Cellular Immunology, University College London Institute of Child Health (H.B.G., K.F.B., A.

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http://dx.doi.org/10.1056/NEJMoa1404588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4274995PMC
October 2014

Time in motion: the molecular clock meets the microbiome.

Cell 2014 Oct;159(3):469-70

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.10.020DOI Listing
October 2014

Coinfection. Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation.

Science 2014 Aug 17;345(6196):578-82. Epub 2014 Jul 17.

Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1126/science.1256942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4548887PMC
August 2014

Tumor suppressor cylindromatosis (CYLD) controls HIV transcription in an NF-κB-dependent manner.

J Virol 2014 Jul 23;88(13):7528-40. Epub 2014 Apr 23.

Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA

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http://dx.doi.org/10.1128/JVI.00239-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4054419PMC
July 2014

Comparing DNA integration site clusters with scan statistics.

Bioinformatics 2014 Jun 30;30(11):1493-500. Epub 2014 Jan 30.

Division of Biostatistics and BioInformatics, Department of Family and Preventive Medicine, University of California at San Diego, La Jolla, CA 92093-0901 and Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 425 Johnson Pavilion, Philadelphia, PA 19104-6076, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029028PMC
June 2014

Altering murine leukemia virus integration through disruption of the integrase and BET protein family interaction.

Nucleic Acids Res 2014 May 12;42(9):5917-28. Epub 2014 Mar 12.

Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, 675 Hoes Lane, Piscataway, NJ 08854, USA Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA

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http://dx.doi.org/10.1093/nar/gku175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4027182PMC
May 2014

Engineering the human genome: reflections on the beginning.

Hum Gene Ther 2014 May;25(5):395-400

Department of Microbiology, University of Pennsylvania School of Medicine , Philadelphia, PA 19104-6076.

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http://dx.doi.org/10.1089/hum.2014.2524DOI Listing
May 2014

A new class of multimerization selective inhibitors of HIV-1 integrase.

PLoS Pathog 2014 May 29;10(5):e1004171. Epub 2014 May 29.

Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1004171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4038613PMC
May 2014

Diet, gut enterotypes and health: is there a link?

Nestle Nutr Inst Workshop Ser 2013 29;77:65-73. Epub 2013 Aug 29.

Division of Gastroenterology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1159/000351385DOI Listing
April 2014

Bimodal high-affinity association of Brd4 with murine leukemia virus integrase and mononucleosomes.

Nucleic Acids Res 2014 Apr 11;42(8):4868-81. Epub 2014 Feb 11.

Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA and Department of Pharmacology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854, USA.

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http://dx.doi.org/10.1093/nar/gku135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4005663PMC
April 2014

The major cellular sterol regulatory pathway is required for Andes virus infection.

PLoS Pathog 2014 Feb 6;10(2):e1003911. Epub 2014 Feb 6.

Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1003911DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3916400PMC
February 2014

Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis.

Nature 2013 Dec 3;504(7478):153-7. Epub 2013 Nov 3.

1] Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [3] Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

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http://dx.doi.org/10.1038/nature12687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3949438PMC
December 2013