Publications



VirusSeeker, a computational pipeline for virus discovery and virome composition analysis.
Virology 2017 Mar 18;503:21-30. Epub 2017 Jan 18.
Departments of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA. Electronic address:

Lactobacillus-Deficient Cervicovaginal Bacterial Communities Are Associated with Increased HIV Acquisition in Young South African Women.
Immunity 2017 Jan 10;46(1):29-37. Epub 2017 Jan 10.
Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Cambridge, MA 02139, USA; Harvard Medical School, Boston, MA 02115, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02115, USA. Electronic address:

Sequential Infection with Common Pathogens Promotes Human-like Immune Gene Expression and Altered Vaccine Response.
Cell Host Microbe 2016 May 20;19(5):713-9. Epub 2016 Apr 20.
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address:


Endolysosomal trafficking of viral G protein-coupled receptor functions in innate immunity and control of viral oncogenesis.
Proc Natl Acad Sci U S A 2016 Mar 29;113(11):2994-9. Epub 2016 Feb 29.
Department of Internal Medicine, Center for Autophagy Research, University of Texas Southwestern Medical Center, Dallas, TX 75390; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390; Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390







Gut DNA viromes of Malawian twins discordant for severe acute malnutrition.
Proc Natl Acad Sci U S A 2015 Sep 8;112(38):11941-6. Epub 2015 Sep 8.
Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63108; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110;



The Cytosolic Sensor cGAS Detects Mycobacterium tuberculosis DNA to Induce Type I Interferons and Activate Autophagy.
Cell Host Microbe 2015 Jun 2;17(6):811-819. Epub 2015 Jun 2.
Department of Microbiology and Immunology, Program in Microbial Pathogenesis and Host Defense, University of California, San Francisco, San Francisco, CA 94158, USA.

Cervicovaginal bacteria are a major modulator of host inflammatory responses in the female genital tract.
Immunity 2015 May;42(5):965-76
Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Cambridge, MA 02139, USA; Division of Infectious Disease, Massachusetts General Hospital, Boston, MA 02115, USA. Electronic address:

Construction and evaluation of novel rhesus monkey adenovirus vaccine vectors.
J Virol 2015 Feb 19;89(3):1512-22. Epub 2014 Nov 19.
Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA Ragon Institute of MGH, MIT, and Harvard, Boston, Massachusetts, USA

Type I interferons link viral infection to enhanced epithelial turnover and repair.
Cell Host Microbe 2015 Jan 4;17(1):85-97. Epub 2014 Dec 4.
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address:



Autophagy is essential for effector CD8(+) T cell survival and memory formation.
Nat Immunol 2014 Dec 2;15(12):1152-61. Epub 2014 Nov 2.
Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA.

Coinfection. Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation.
Science 2014 Aug 17;345(6196):578-82. Epub 2014 Jul 17.
Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

The parasitophorous vacuole membrane of Toxoplasma gondii is targeted for disruption by ubiquitin-like conjugation systems of autophagy.
Immunity 2014 Jun 12;40(6):924-35. Epub 2014 Jun 12.
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address:

Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense.
Proc Natl Acad Sci U S A 2014 May 12;111(21):7741-6. Epub 2014 May 12.
Broad Institute, Cambridge, MA 02142;Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114;Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114;Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114;



Vaccine activation of the nutrient sensor GCN2 in dendritic cells enhances antigen presentation.
Science 2014 Jan 5;343(6168):313-317. Epub 2013 Dec 5.
Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, 954 Gatewood Road, Atlanta, GA 30329, USA.

Atg16l1 is required for autophagy in intestinal epithelial cells and protection of mice from Salmonella infection.
Gastroenterology 2013 Dec 21;145(6):1347-57. Epub 2013 Aug 21.
Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.



Identification of novel viruses using VirusHunter--an automated data analysis pipeline.
PLoS One 2013 22;8(10):e78470. Epub 2013 Oct 22.
Departments of Pathology & Immunology, Washington University School of Medicine, and the Midwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, St. Louis, Missouri, United States of America.


Persistent enteric murine norovirus infection is associated with functionally suboptimal virus-specific CD8 T cell responses.
J Virol 2013 Jun 17;87(12):7015-31. Epub 2013 Apr 17.
Department of Medicine, Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA.






Exercise-induced BCL2-regulated autophagy is required for muscle glucose homeostasis.
Nature 2012 Jan 18;481(7382):511-5. Epub 2012 Jan 18.
Center for Autophagy Research, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA.

Identification and sequencing of a novel rodent gammaherpesvirus that establishes acute and latent infection in laboratory mice.
J Virol 2011 Mar 5;85(6):2642-56. Epub 2011 Jan 5.
Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Ave., Box 8118, St. Louis, MO 63110, USA.


Delivery of cytosolic components by autophagic adaptor protein p62 endows autophagosomes with unique antimicrobial properties.
Immunity 2010 Mar 4;32(3):329-41. Epub 2010 Mar 4.
Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA.

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