Department of Microbiology

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Faculty Profile

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Frederic D. Bushman, Ph.D.

Professor of Microbiology
Department: Microbiology

Contact information
426 Johnson Pavilion
Department of Microbiology
3610 Hamilton Walk
Philadelphia, PA 19104-6076
Office: (215) 573-8732
Fax: (215) 573-4856
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.

Key words: 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.


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 Scientists
Young Hwang

Post-doctoral Researchers
Jacque Young

Graduate Students
Alexandra Bryson
Christel Chehoud
Erik Clarke
Scott Sherrill-Mix
Sesh Sundararaman

Research Specialists
Christian Hoffmann
Alice Laughlin
Frances Male
Eric Sherman

Programmers
Aubrey Bailey
Kyle Bittinger
Nirav Malani

Administrative Coordinator
Laurie Zimmerman

Selected Publications

Beck James M, Schloss Patrick D, Venkataraman Arvind, Twigg Iii Homer, Jablonski Kathleen A, Bushman Frederic D, Campbell Thomas B, Charlson Emily S, Collman Ronald G, Crothers Kristina, Curtis Jeffrey L, Drews Kimberly L, Flores Sonia C, Fontenot Andrew P, Foulkes Mary A, Frank Ian, Ghedin Elodie, Huang Laurence, Lynch Susan V, Morris Alison, Palmer Brent E, Schmidt Thomas M, Sodergren Erica, Weinstock George M, Young Vincent B: Multi-center Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals. American Journal of Respiratory and Critical Care Medicine Aug 2015.

Kelly Brendan J, Gross Robert, Bittinger Kyle, Sherrill-Mix Scott, Lewis James D, Collman Ronald G, Bushman Frederic D, Li Hongzhe: Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA. Bioinformatics (Oxford, England) 31(15): 2461-8, Aug 2015.

Lee Dale, Baldassano Robert N, Otley Anthony R, Albenberg Lindsey, Griffiths Anne M, Compher Charlene, Chen Eric Z, Li Hongzhe, Gilroy Erin, Nessel Lisa, Grant Amy, Chehoud Christel, Bushman Frederic D, Wu Gary D, Lewis James D: Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohn's Disease. Inflammatory Bowel Diseases 21(8): 1786-93, Aug 2015.

Bushman Marshall, Zimmerman Laurie, Bushman Frederic: HIV Replication in LEGO Mosaic. AIDS Research and Human Retroviruses 31(8): 772-3, Aug 2015.

Chehoud Christel, Albenberg Lindsey G, Judge Colleen, Hoffmann Christian, Grunberg Stephanie, Bittinger Kyle, Baldassano Robert N, Lewis James D, Bushman Frederic D, Wu Gary D: Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease. Inflammatory Bowel Diseases 21(8): 1948-56, Aug 2015.

Liang Xue, Bushman Frederic D, FitzGerald Garret A: Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock. Proceedings of the National Academy of Sciences of the United States of America Aug 2015.

Shen Ting-Chin David, Albenberg Lindsey, Bittinger Kyle, Chehoud Christel, Chen Ying-Yu, Judge Colleen A, Chau Lillian, Ni Josephine, Sheng Michael, Lin Andrew, Wilkins Benjamin J, Buza Elizabeth L, Lewis James D, Daikhin Yevgeny, Nissim Ilana, Yudkoff Marc, Bushman Frederic D, Wu Gary D: Engineering the gut microbiota to treat hyperammonemia. Journal of Clinical Investigation 125(7): 2841-50, Jul 2015.

Aiyer Sriram, Rossi Paolo, Malani Nirav, Schneider William M, Chandar Ashwin, Bushman Frederic D, Montelione Gaetano T, Roth Monica J: Structural and sequencing analysis of local target DNA recognition by MLV integrase. Nucleic Acids Research 43(11): 5647-63, Jun 2015.

Corrigan-Curay Jacqueline, O'Reilly Marina, Kohn Donald B, Cannon Paula M, Bao Gang, Bushman Frederic D, Carroll Dana, Cathomen Toni, Joung J Keith, Roth David, Sadelain Michel, Scharenberg Andrew M, von Kalle Christof, Zhang Feng, Jambou Robert, Rosenthal Eugene, Hassani Morad, Singh Aparna, Porteus Matthew H: Genome editing technologies: defining a path to clinic. Molecular Therapy 23(5): 796-806, May 2015.

Hacein-Bey Abina Salima, Gaspar H Bobby, Blondeau Johanna, Caccavelli Laure, Charrier Sabine, Buckland Karen, Picard Capucine, Six Emmanuelle, Himoudi Nourredine, Gilmour Kimberly, McNicol Anne-Marie, Hara Havinder, Xu-Bayford Jinhua, Rivat Christine, Touzot Fabien, Mavilio Fulvio, Lim Annick, Treluyer Jean-Marc, Héritier Sébastien, Lefrère Francois, Magalon Jeremy, Pengue-Koyi Isabelle, Honnet Géraldine, Blanche Stéphane, Sherman Eric A, Male Frances, Berry Charles, Malani Nirav, Bushman Frederic D, Fischer Alain, Thrasher Adrian J, Galy Anne, Cavazzana Marina: Outcomes following gene therapy in patients with severe Wiskott-Aldrich syndrome. JAMA 313(15): 1550-63, Apr 2015.

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Last updated: 08/24/2015
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