Graduate Group in Genomics and Computational Biology

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.
Permanent link
 

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.


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

Instructor of Medicine
Brendan Kelley

Post-doctoral Researchers
Anatoly Dryga
Chris Nobles
Scott Sherrill-Mix
Jacque Young

Graduate Students
Arwa Abbas
Alexandra Bryson
Christel Chehoud
Erik Clarke
Sesh Sundararaman

Research Specialists
Abigail Lauder
Alice Laughlin
Frances Male

Programmers
Aubrey Bailey
Yinghua Wu

Executive Assistant to the Chair
Laurie Zimmerman

Selected Publications

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.

Clarke Erik L, Sundararaman Sesh A, Seifert Stephanie N, Bushman Frederic D, Hahn Beatrice H, Brisson Dustin: swga: A primer design toolkit for selective whole genome amplification. Bioinformatics (Oxford, England) Feb 2017.

Etienne-Mesmin Lucie, Chassaing Benoit, Adekunle Oluwaseyi, Mattei Lisa M, Bushman Frederic D, Gewirtz Andrew T: Toxin-positive Clostridium difficile latently infect mouse colonies and protect against highly pathogenic C. difficile. Gut Feb 2017.

Zhang Shirley L, Bai Lei, Goel Namni, Bailey Aubrey, Jang Christopher J, Bushman Frederic D, Meerlo Peter, Dinges David F, Sehgal Amita: Human and rat gut microbiome composition is maintained following sleep restriction. Proceedings of the National Academy of Sciences of the United States of America 114(8): E1564-E1571, Feb 2017.

Mauk Michael, Song Jinzhao, Bau Haim H, Gross Robert, Bushman Frederic D, Collman Ronald G, Liu Changchun: Miniaturized devices for point of care molecular detection of HIV. Lab on a chip 17(3): 382-394, Jan 2017.

Hannigan Geoffrey D, Zheng Qi, Meisel Jacquelyn S, Minot Samuel S, Bushman Frederick D, Grice Elizabeth A: Evolutionary and functional implications of hypervariable loci within the skin virome. PeerJ 5: e2959, 2017.

back to top
Last updated: 04/19/2017
The Trustees of the University of Pennsylvania