Frederic D. Bushman, Ph.D.

faculty photo
William Maul Measey Professor in Microbiology
Department: Microbiology

Contact information
426 Johnson Pavilion
Department of Microbiology
3610 Hamilton Walk
Philadelphia, PA 19104-6076
Office: (215) 573-8732
Lab: (215) 573-8733
Education:
B.A. (Biology and English)
Amherst College, 1980.
Ph.D. (Cellular and Developmental Biology)
Harvard University, 1988.
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Description of Research Expertise

Research Interests
Human microbiome, human gene therapy HIV, Poxviruses, DNA modifying enzymes, Lateral DNA transfer.

Keywords
microbiome, gene therapy, HIV, integration, integrase, poxvirus, DNA modifying enzyme, virology, variola, resolvase.

Description of Research
Research in the Bushman laboratory focuses on host-microbe interactions in health and disease, with particular focus on studies of 1) the human microbiome, 2) HIV pathogenesis, and 3) DNA integration in human gene therapy.

In recent years, our work has been driven increasingly by the remarkable new deep sequencing methods, which can produce more than 100 billion bases of DNA sequence information in a single instrument run.

For microbiome studies, this allows comprehensive analysis of microbial populations without reliance on culture-based methods, which can detect only a small fraction of all organisms present.

For studies of HIV replication, this allows analysis of complex viral populations or distributions of retroviral DNA integration sites in the human genome.

For gene therapy, this allows tracking of integrated vectors in gene-corrected subjects and molecular characterization of adverse events.

Sample acquisition can sometimes be difficult in such projects, but bioinformatic analysis afterwards is almost always harder. We have been carrying out this type of study since 2002, when we showed that HIV DNA integration in human cells was favored in active transcription units, and over the years have built up partially automated software pipelines that allow efficient analysis deep sequencing data.

Lab members and collaborators cover a range of specialties, including clinical researchers, molecular biologists, computational biologists, and statisticians.

Honors, Awards, Memberships
Fellow of the American Association for the Advancement of Science, 2014
Pioneer Award, Journal of Human Gene Therapy, 2014
Fellow of the American Academy of Microbiology, 2009
Master of Arts, Honoris Causa, University of Pennsylvania, 2004
Stohlman Scholar, Leukemia and Lymphoma Society of America, 2001
Scholar, Leukemia Society of America, Inc., 1996-2001
Special Fellow, Leukemia Society of America, Inc., 1992-1995
Fellow, Leukemia Society of America, Inc., 1989-1992
Editorial Board, Virology, 2001
Editorial Board, Journal of Virology, 1995

Rotation Projects
Rotation projects center on the human microbiome in health and disease, analysis of viral replication, and studies of integration in human gene therapy.

Lab Personnel

Staff Scientist
Young Hwang

Lab Manager
Aoife Doto

Post-doctoral Researchers
Scott Sherrill-Mix, PhD
Varun Aggarwala, PhD
Guanxiang Liang, PhD

Graduate Students
Arwa Abbas
Erik Clarke
Grant Eilers
Louis Taylor

Research Specialists
Audrey Allen
John Gregg
Abigail Lauder
Jacob Leiby
Shantan Reddy

Bioinformaticians
Jesse Connell
John Everett, PhD
Kevin McCormick
Chris Nobles, PhD

Executive Assistant to the Chair
Laurie Zimmerman

Selected Publications

Clarke Erik L, Lauder Abigail P, Hofstaedter Casey E, Hwang Young, Fitzgerald Ayannah S, Imai Ize, Biernat Wojciech, Rękawiecki Bartłomiej, Majewska Hanna, Dubaniewicz Anna, Litzky Leslie A, Feldman Michael D, Bittinger Kyle, Rossman Milton D, Patterson Karen C, Bushman Frederic D, Collman Ronald G: Microbial Lineages in Sarcoidosis: A Metagenomic Analysis Tailored for Low Microbial Content Samples. American journal of respiratory and critical care medicine Aug 2017.

Lewis JD, Chen EZ, Baldassano RN, Otley AR, Griffiths AM, Lee D, Bittinger K, Bailey A, Friedman ES, Hoffmann C, Albenberg L, Sinha R, Compher C, Gilroy E, Nessel L, Grant A, Chehoud C, Li H, Wu GD, Bushman FD.: Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease. Cell Host Microbe 22(2): 247, August 2017.

Morris Emma C, Fox Thomas, Chakraverty Ronjon, Tendeiro Rita, Snell Katie, Rivat Christine, Grace Sarah, Gilmour Kimberly, Workman Sarita, Buckland Karen, Butler Katie, Chee Ronnie, Salama Alan D, Ibrahim Hazem, Hara Havinder, Duret Cecile, Mavilio Fulvio, Male Frances, Bushman Frederick D, Galy Anne, Burns Siobhan O, Gaspar H Bobby, Thrasher Adrian J: Gene therapy for Wiskott-Aldrich syndrome in a severely affected adult. Blood Jul 2017.

Pannaraj Pia S, Li Fan, Cerini Chiara, Bender Jeffrey M, Yang Shangxin, Rollie Adrienne, Adisetiyo Helty, Zabih Sara, Lincez Pamela J, Bittinger Kyle, Bailey Aubrey, Bushman Frederic D, Sleasman John W, Aldrovandi Grace M: Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome. JAMA pediatrics 171(7): 647-654, Jul 2017.

Kim Dorothy, Hofstaedter Casey E, Zhao Chunyu, Mattei Lisa, Tanes Ceylan, Clarke Erik, Lauder Abigail, Sherrill-Mix Scott, Chehoud Christel, Kelsen Judith, Conrad Máire, Collman Ronald G, Baldassano Robert, Bushman Frederic D, Bittinger Kyle: Optimizing methods and dodging pitfalls in microbiome research. Microbiome 5(1): 52, May 2017.

Chehoud Christel, Stieh Daniel J, Bailey Aubrey G, Laughlin Alice L, Allen Shannon A, McCotter Kerrie L, Sherrill-Mix Scott A, Hope Thomas J, Bushman Frederic D: Associations of the vaginal microbiota with HIV infection, bacterial vaginosis, and demographic factors. AIDS (London, England) 31(7): 895-904, Apr 2017.

Etienne-Mesmin Lucie, Chassaing Benoit, Adekunle Oluwaseyi, Mattei Lisa M, Edwards Adrianne N, McBride Shonna M, Bushman Frederic D, Gewirtz Andrew T: Genome Sequence of a Toxin-Positive Clostridium difficile Strain Isolated from Murine Feces. Genome announcements 5(14), Apr 2017.

Drake Mary Jane, Brennan Benjamin, Briley Kenneth, Bart Stephen M, Sherman Eric, Szemiel Agnieszka M, Minutillo Madeleine, Bushman Frederic D, Bates Paul: A role for glycolipid biosynthesis in severe fever with thrombocytopenia syndrome virus entry. PLoS pathogens 13(4): e1006316, Apr 2017.

Sherman Eric, Nobles Christopher, Berry Charles C, Six Emmanuelle, Wu Yinghua, Dryga Anatoly, Malani Nirav, Male Frances, Reddy Shantan, Bailey Aubrey, Bittinger Kyle, Everett John K, Caccavelli Laure, Drake Mary J, Bates Paul, Hacein-Bey-Abina Salima, Cavazzana Marina, Bushman Frederic D: INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes. Molecular therapy. Methods & clinical development 4: 39-49, Mar 2017.

Berry Charles C, Nobles Christopher, Six Emmanuelle, Wu Yinghua, Malani Nirav, Sherman Eric, Dryga Anatoly, Everett John K, Male Frances, Bailey Aubrey, Bittinger Kyle, Drake Mary J, Caccavelli Laure, Bates Paul, Hacein-Bey-Abina Salima, Cavazzana Marina, Bushman Frederic D: INSPIIRED: Quantification and Visualization Tools for Analyzing Integration Site Distributions. Molecular therapy. Methods & clinical development 4: 17-26, Mar 2017.

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Last updated: 09/11/2017
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