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List of works by Frederic D. Bushman

A Pilot Characterization of the Human Chronobiome

scientific article published on 7 December 2017

A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing.

scientific article

A long-term study of AAV gene therapy in dogs with hemophilia A identifies clonal expansions of transduced liver cells

scientific article published on 16 November 2020

A maraviroc-resistant HIV-1 with narrow cross-resistance to other CCR5 antagonists depends on both N-terminal and extracellular loop domains of drug-bound CCR5

scientific article published on 11 August 2010

A method to sequence and quantify DNA integration for monitoring outcome in gene therapy ⬇️

scientific article

A resurrected mammalian hAT transposable element and a closely related insect element are highly active in human cell culture

scientific article published on 22 October 2012

A role for bacterial urease in gut dysbiosis and Crohn's disease.

scientific article

A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples

scientific article

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

scientific article published on 17 August 2015

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

scientific article

Analysis of lentiviral vector integration in HIV+ study subjects receiving autologous infusions of gene modified CD4+ T cells

scientific article

Antiviral effects of autologous CD4 T cells genetically modified with a conditionally replicating lentiviral vector expressing long antisense to HIV

scientific article published on 20 December 2012

Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents

scientific article

Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts

scientific article

Assessing the potential for AAV vector genotoxicity in a murine model

scientific article

Associating microbiome composition with environmental covariates using generalized UniFrac distances

scientific article

BET proteins promote efficient murine leukemia virus integration at transcription start sites

scientific article published on July 2013

BET proteins target murine leukemia virus integration to transcription start sites.

scientific article

Bacterial colonization reprograms the neonatal gut metabolome

scientific article published on 13 April 2020

Bacteriophage Mu integration in yeast and mammalian genomes

scientific article published on 25 October 2008

Bayesian community-wide culture-independent microbial source tracking

scientific article published on 17 July 2011

Bidirectional interactions between indomethacin and the murine intestinal microbiota

scientific article published on 23 December 2015

Bidirectional transfer of Anelloviridae lineages between graft and host during lung transplantation

scientific article published on 08 October 2018

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

scientific article published on 11 February 2014

Bringing it all together: big data and HIV research

scientific article

Bromodomain and extra-terminal (BET) proteins target Moloney murine leukemia virus integration to transcription start sites.

scientific article published on 19 September 2013

Bulged DNA substrates for identifying poxvirus resolvase inhibitors

scientific article

CRISPR-engineered T cells in patients with refractory cancer

scientific article published on 07 February 2020

Challenges in vector and trial design using retroviral vectors for long-term gene correction in hematopoietic stem cell gene therapy

scientific article published in June 2012

Collaboration between Clinical and Academic Laboratories for Sequencing SARS-CoV-2 Genomes

scientific article published in 2022

Commensal bacteria-derived signals regulate basophil hematopoiesis and allergic inflammation

scientific article published on 25 March 2012

Community-wide response of the gut microbiota to enteropathogenic Citrobacter rodentium infection revealed by deep sequencing

scientific article

Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates

publication published on 04 June 2021

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

scientific article published on August 2015

Comparative analysis of the recently discovered hAT transposon TcBuster in human cells

scientific article (publication date: 2012)

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

scientific article

Comparing DNA integration site clusters with scan statistics.

scientific article

Conservation of gene cassettes among diverse viruses of the human gut.

scientific article

Conventional CD4+ T cells regulate IL-22-producing intestinal innate lymphoid cells.

scientific article published on 22 January 2014

Correction of murine β-thalassemia after minimal lentiviral gene transfer and homeostatic in vivo erythroid expansion

scientific article

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

scientific article

Cxcr2 and Cxcl5 regulate the IL-17/G-CSF axis and neutrophil homeostasis in mice

scientific article

DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer

scientific article published on 14 April 2008

DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations

scientific article published on 18 June 2007

DNA binding and cleavage by the fowlpox virus resolvase

scientific article published on 12 November 2008

DNA branch nuclease activity of vaccinia A22 resolvase

scientific article published on 21 September 2007

DNA cleavage by the A22R resolvase of vaccinia virus

scientific article published on 15 June 2006

Decade-long safety and function of retroviral-modified chimeric antigen receptor T cells

scientific article

Dendritic cell expression of the signaling molecule TRAF6 is critical for gut microbiota-dependent immune tolerance

scientific article published on 20 June 2013

Detecting contamination in viromes using ViromeQC

scientific article published on 01 December 2019

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

scientific article

Directly infected resting CD4+T cells can produce HIV Gag without spreading infection in a model of HIV latency

scientific article (publication date: 2012)

Disordered microbial communities in the upper respiratory tract of cigarette smokers

scientific article

Distribution of lentiviral vector integration sites in mice following therapeutic gene transfer to treat β-thalassemia

scientific article

Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing.

scientific article

Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial

scientific article

Efficacy of gene therapy for X-linked severe combined immunodeficiency

scientific article

Engineering HIV-resistant human CD4+ T cells with CXCR4-specific zinc-finger nucleases

scientific article

Enterotypes in the landscape of gut microbial community composition.

scientific article published on 18 December 2017

Estimating abundances of retroviral insertion sites from DNA fragment length data.

scientific article

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

scientific article published on August 2015

Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment

scientific article

Gammaretroviral integration into nucleosomal target DNA in vivo

scientific article published on 11 May 2011

Gene transfer in humans using a conditionally replicating lentiviral vector

scientific article

Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria.

scientific article

Genomic safe harbors permit high β-globin transgene expression in thalassemia induced pluripotent stem cells

scientific article

Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication

scientific article (publication date: 3 October 2008)

Global landscape of HIV-human protein complexes

scientific article

HIV DNA integration

scientific article

HIV integration site distributions in resting and activated CD4+ T cells infected in culture

scientific article

HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications

scientific article published in June 2007

HIV integration targeting: a pathway involving Transportin-3 and the nuclear pore protein RanBP2

scientific article

HIV latency and integration site placement in five cell-based models.

scientific article published on 16 August 2013

HIV sequence variation associated with env antisense adoptive T-cell therapy in the hNSG mouse model

scientific article

HIV-1 capsid-cyclophilin interactions determine nuclear import pathway, integration targeting and replication efficiency

scientific article

HRP-2 determines HIV-1 integration site selection in LEDGF/p75 depleted cells

scientific article

HTLV-1 clonality during chronic infection and BLV clonality during primary infection

HTLV-1 integration into transcriptionally active genomic regions is associated with proviral expression and with HAM/TSP

scientific article

Hepatitis C virus transmission bottlenecks analyzed by deep sequencing.

scientific article

High-definition mapping of retroviral integration sites defines the fate of allogeneic T cells after donor lymphocyte infusion

scientific article

High-fat diet determines the composition of the murine gut microbiome independently of obesity

scientific article published on 23 August 2009

Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis

scientific article

Host cell factors in HIV replication: meta-analysis of genome-wide studies

scientific article

Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013

scientific article

Hypervariable loci in the human gut virome

scientific article published on 21 February 2012

In vivo genome editing restores haemostasis in a mouse model of haemophilia

scientific article (publication date: 26 June 2011)

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease

scientific article published on October 2015

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease

scientific article published on 01 August 2017

Innate lymphoid cells promote anatomical containment of lymphoid-resident commensal bacteria.

scientific article

Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria

scientific article published on 22 May 2013

Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1

scientific article

Insights from the Structure of a Smallpox Virus Topoisomerase-DNA Transition State Mimic

scientific article

Integration target site selection by a resurrected human endogenous retrovirus

scientific article published on March 2009

Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis

scientific article

Is normal hematopoiesis maintained solely by long-term multipotent stem cells?

scientific article

LEDGF hybrids efficiently retarget lentiviral integration into heterochromatin

scientific article

LEDGF/p75 is critical but not essential for multiple-round HIV 1 replication.

scientific article

LEDGF/p75-independent HIV-1 replication demonstrates a role for HRP-2 and remains sensitive to inhibition by LEDGINs

scientific article

Lack of detection of a human placenta microbiome in samples from preterm and term deliveries

scientific article published on 30 October 2018

Lentiviral gene therapy for X-linked chronic granulomatous disease

scientific article published on 27 January 2020

Linking long-term dietary patterns with gut microbial enterotypes

scientific article

Long-term safety and efficacy of lentiviral hematopoietic stem/progenitor cell gene therapy for Wiskott-Aldrich syndrome

scientific article published on 24 January 2022

Low-frequency nevirapine resistance at multiple sites may predict treatment failure in infants on nevirapine-based treatment

scientific article

Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant.

scientific article

Massively parallel pyrosequencing in HIV research

scientific article published on July 2008

Membrane-based, sedimentation-assisted plasma separator for point-of-care applications

scientific article published on 25 October 2013

Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis

scientific article

Metal cofactors in the structure and activity of the fowlpox resolvase.

scientific article

Methods for integration site distribution analyses in animal cell genomes

scientific article

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

scientific article

Modulating target site selection during human immunodeficiency virus DNA integration in vitro with an engineered tethering factor

scientific article published on September 2006

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

scientific article published on 18 December 2018

Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease

scientific article published on 11 August 2020

Nondividing cells: a safer bet for integrating vectors?

scientific article

Plasmodium falciparum-like parasites infecting wild apes in southern Cameroon do not represent a recurrent source of human malaria

scientific article

Publisher Correction: Enterotypes in the landscape of gut microbial community composition

scientific article published on 13 February 2018

PyNAST: a flexible tool for aligning sequences to a template alignment

scientific article (publication date: 15 January 2010)

QIIME allows analysis of high-throughput community sequencing data

scientific article

Quantitation of HIV DNA integration: effects of differential integration site distributions on Alu-PCR assays

scientific article published on 21 January 2013

Quantitative phosphoproteomics reveals extensive cellular reprogramming during HIV-1 entry

scientific article

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

scientific article published in 2023

Rapid evolution of the human gut virome

scientific article published on 08 July 2013

Recombinant adeno-associated virus integration sites in murine liver after ornithine transcarbamylase gene correction

scientific article published on May 2013

Recommendations for measuring HIV reservoir size in cure-directed clinical trials

scientific article published on 07 September 2020

Redondovirus Diversity and Evolution on Global, Individual, and Molecular Scales

scientific article published on 18 August 2021

Regulation of catalysis by the smallpox virus topoisomerase

scientific article published on 10 October 2006

Retroviral integration and human gene therapy

scientific article published on August 2007

Role of PSIP1/LEDGF/p75 in lentiviral infectivity and integration targeting

scientific article

Role of the PWWP domain of lens epithelium-derived growth factor (LEDGF)/p75 cofactor in lentiviral integration targeting

scientific article published on 10 October 2011

SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021

scientific article published on 08 February 2022

Safe harbours for the integration of new DNA in the human genome

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

scientific article

Selection of target sites for mobile DNA integration in the human genome

scientific article (publication date: 24 November 2006)

Short pyrosequencing reads suffice for accurate microbial community analysis

scientific article published on 18 September 2007

Single-cell transcriptional landscapes reveal HIV-1-driven aberrant host gene transcription as a potential therapeutic target

scientific article published on 01 May 2020

Single-particle image reconstruction of a tetramer of HIV integrase bound to DNA.

scientific article published on 11 November 2006

Solution conformations of prototype foamy virus integrase and its stable synaptic complex with U5 viral DNA.

scientific article

Structural Basis for Inhibitor-Induced Aggregation of HIV Integrase

scientific article

Structural Basis for Specificity in the Poxvirus Topoisomerase

Structural properties of HIV integrase. Lens epithelium-derived growth factor oligomers

scientific article

Structure-constrained sparse canonical correlation analysis with an application to microbiome data analysis

scientific article

Succession in the gut microbiome following antibiotic and antibody therapies for Clostridium difficile

scientific article

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments

Switching between raltegravir resistance pathways analyzed by deep sequencing

scientific article

T cell dynamics and response of the microbiota after gene therapy to treat X-linked severe combined immunodeficiency

article

The BET family of proteins targets moloney murine leukemia virus integration near transcription start sites

scientific article

The Perioperative Lung Transplant Virome: Torque Teno Viruses Are Elevated in Donor Lungs and Show Divergent Dynamics in Primary Graft Dysfunction

scientific article

The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones

scientific article

The human gut virome: inter-individual variation and dynamic response to diet

scientific article

The interferon response inhibits HIV particle production by induction of TRIM22

scientific article published in February 2008

The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis

scientific article

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

scientific article

The stepwise assembly of the neonatal virome is modulated by breastfeeding

scientific article published on 15 April 2020

Topographical continuity of bacterial populations in the healthy human respiratory tract

scientific article published on 16 June 2011

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

scientific article published on 20 February 2017

Transient Expression of an LEDGF/p75 Chimera Retargets Lentivector Integration and Functionally Rescues in a Model for X-CGD.

scientific article published on 5 March 2013

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

scientific article published on 23 April 2014

Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes

scientific article published on 25 April 2007

Viral DNA tethering domains complement replication-defective mutations in the p12 protein of MuLV Gag

scientific article published on 9 May 2013

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

scientific article published on 3 October 2017

Virus structures constrain transmission modes

scientific article published on 29 July 2019

Widespread colonization of the lung by Tropheryma whipplei in HIV infection

scientific article published on May 2013

iGUIDE: an improved pipeline for analyzing CRISPR cleavage specificity

piggyBac transposase tools for genome engineering

scientific article published on 30 May 2013

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