Graduate Group in Genomics and Computational Biology

Frederic D. Bushman, Ph.D.

faculty photo
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
B.A. (Biology and English)
Amherst College, 1980.
Ph.D. (Cellular and Developmental Biology)
Harvard University, 1988.
Permanent link

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

Aubrey Bailey
Kyle Bittinger
Nirav Malani

Administrative Coordinator
Laurie Zimmerman

Selected Publications

Young J C, Chehoud C, Bittinger K, Bailey A, Diamond J M, Cantu E, Haas A R, Abbas A, Frye L, Christie J D, Bushman F D, Collman R G: Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients. American Journal of Transplantation 15(1): 200-209, Jan 2015.

Ocwieja Karen E, Sherrill-Mix Scott, Liu Changchun, Song Jinzhao, Bau Haim, Bushman Frederic D: A Reverse Transcription Loop-Mediated Isothermal Amplification Assay Optimized to Detect Multiple HIV Subtypes. PloS one 10(2): e0117852, 2015.

Wu Gary D, Compher Charlene, Chen Eric Z, Smith Sarah A, Shah Rachana D, Bittinger Kyle, Chehoud Christel, Albenberg Lindsey G, Nessel Lisa, Gilroy Erin, Star Julie, Weljie Aalim M, Flint Harry J, Metz David C, Bennett Michael J, Li Hongzhe, Bushman Frederic D, Lewis James D: Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut Nov 2014.

Albenberg Lindsey, Esipova Tatiana V, Judge Colleen P, Bittinger Kyle, Chen Jun, Laughlin Alice, Grunberg Stephanie, Baldassano Robert N, Lewis James D, Li Hongzhe, Thom Stephen R, Bushman Frederic D, Vinogradov Sergei A, Wu Gary D: Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Gastroenterology 147(5): 1055-63.e8, Nov 2014.

Liang Xue, Bushman Frederic D, FitzGerald Garret A: Time in motion: the molecular clock meets the microbiome. Cell 159(3): 469-70, Oct 2014.

Hacein-Bey-Abina Salima, Pai Sung-Yun, Gaspar H Bobby, Armant Myriam, Berry Charles C, Blanche Stephane, Bleesing Jack, Blondeau Johanna, de Boer Helen, Buckland Karen F, Caccavelli Laure, Cros Guilhem, De Oliveira Satiro, Fernández Karen S, Guo Dongjing, Harris Chad E, Hopkins Gregory, Lehmann Leslie E, Lim Annick, London Wendy B, van der Loo Johannes C M, Malani Nirav, Male Frances, Malik Punam, Marinovic M Angélica, McNicol Anne-Marie, Moshous Despina, Neven Benedicte, Oleastro Matías, Picard Capucine, Ritz Jerome, Rivat Christine, Schambach Axel, Shaw Kit L, Sherman Eric A, Silberstein Leslie E, Six Emmanuelle, Touzot Fabien, Tsytsykova Alla, Xu-Bayford Jinhua, Baum Christopher, Bushman Frederic D, Fischer Alain, Kohn Donald B, Filipovich Alexandra H, Notarangelo Luigi D, Cavazzana Marina, Williams David A, Thrasher Adrian J: A modified γ-retrovirus vector for X-linked severe combined immunodeficiency. The New England journal of medicine 371(15): 1407-17, Oct 2014.

Bittinger Kyle, Charlson Emily S, Loy Elizabeth, Shirley David J, Haas Andrew R, Laughlin Alice, Yi Yanjie, Wu Gary D, Lewis James D, Frank Ian, Cantu Edward, Diamond Joshua M, Christie Jason D, Collman Ronald G, Bushman Frederic D: Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing. Genome biology 15(10): 487, Oct 2014.

Korn LL, Thomas HL, Hubbeling HG, Spencer SP, Sinha R, Simkins HM, Salzman NH, Bushman FD, Laufer TM: Conventional CD4+ T cells regulate IL-22-producing intestinal innate lymphoid cells. Mucosal Immunol. (Epub ahead of print)(5): 1045-57, Sep 2014.

Osborne Lisa C, Monticelli Laurel A, Nice Timothy J, Sutherland Tara E, Siracusa Mark C, Hepworth Matthew R, Tomov Vesselin T, Kobuley Dmytro, Tran Sara V, Bittinger Kyle, Bailey Aubrey G, Laughlin Alice L, Boucher Jean-Luc, Wherry E John, Bushman Frederic D, Allen Judith E, Virgin Herbert W, Artis David: Coinfection. Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation. Science (New York, N.Y.) 345(6196): 578-82, Aug 2014.

Margolis David, Bushman Frederic: HIV/AIDS. Persistence by proliferation? Science (New York, N.Y.) 345(6193): 143-4, Jul 2014.

back to top
Last updated: 02/26/2015
The Trustees of the University of Pennsylvania