Rapid evolution of the human gut virome
Minot, Samuel, Bryson, Alexandra, Chehoud, Christel, Wu, Gary D., Lewis, James D., Bushman, Frederic D.
Published in Proceedings of the National Academy of Sciences - PNAS (23.07.2013)
Published in Proceedings of the National Academy of Sciences - PNAS (23.07.2013)
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Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease
Lewis, James D., Chen, Eric Z., Baldassano, Robert N., Otley, Anthony R., Griffiths, Anne M., Lee, Dale, Bittinger, Kyle, Bailey, Aubrey, Friedman, Elliot S., Hoffmann, Christian, Albenberg, Lindsey, Sinha, Rohini, Compher, Charlene, Gilroy, Erin, Nessel, Lisa, Grant, Amy, Chehoud, Christel, Li, Hongzhe, Wu, Gary D., Bushman, Frederic D.
Published in Cell host & microbe (14.10.2015)
Published in Cell host & microbe (14.10.2015)
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Journal Article
Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome
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
Published in JAMA pediatrics (01.07.2017)
Published in JAMA pediatrics (01.07.2017)
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Journal Article
Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA
Kelly, Brendan J, Gross, Robert, Bittinger, Kyle, Sherrill-Mix, Scott, Lewis, James D, Collman, Ronald G, Bushman, Frederic D, Li, Hongzhe
Published in Bioinformatics (01.08.2015)
Published in Bioinformatics (01.08.2015)
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Journal Article
Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents
Hoffmann, Christian, Dollive, Serena, Grunberg, Stephanie, Chen, Jun, Li, Hongzhe, Wu, Gary D, Lewis, James D, Bushman, Frederic D
Published in PloS one (17.06.2013)
Published in PloS one (17.06.2013)
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Journal Article
Role of dietary fiber in the recovery of the human gut microbiome and its metabolome
Tanes, Ceylan, Bittinger, Kyle, Gao, Yuan, Friedman, Elliot S., Nessel, Lisa, Roy Paladhi, Unmesha, Chau, Lillian, Panfen, Erika, Fischbach, Michael A., Braun, Jonathan, Xavier, Ramnik J., Clish, Clary B., Li, Hongzhe, Bushman, Frederic D., Lewis, James D., Wu, Gary D.
Published in Cell host & microbe (10.03.2021)
Published in Cell host & microbe (10.03.2021)
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Journal Article
Topographical Continuity of Bacterial Populations in the Healthy Human Respiratory Tract
CHARLSON, Emily S, BITTINGER, Kyle, HAAS, Andrew R, FITZGERALD, Ayannah S, FRANK, Ian, YADAV, Anjana, BUSHMAN, Frederic D, COLLMAN, Ronald G
Published in American journal of respiratory and critical care medicine (15.10.2011)
Published in American journal of respiratory and critical care medicine (15.10.2011)
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Journal Article
PyNAST: a flexible tool for aligning sequences to a template alignment
Caporaso, J. Gregory, Bittinger, Kyle, Bushman, Frederic D., DeSantis, Todd Z., Andersen, Gary L., Knight, Rob
Published in Bioinformatics (15.01.2010)
Published in Bioinformatics (15.01.2010)
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Journal Article
A quantitative approach for measuring the reservoir of latent HIV-1 proviruses
Bruner, Katherine M., Wang, Zheng, Simonetti, Francesco R., Bender, Alexandra M., Kwon, Kyungyoon J., Sengupta, Srona, Fray, Emily J., Beg, Subul A., Antar, Annukka A. R., Jenike, Katharine M., Bertagnolli, Lynn N., Capoferri, Adam A., Kufera, Joshua T., Timmons, Andrew, Nobles, Christopher, Gregg, John, Wada, Nikolas, Ho, Ya-Chi, Zhang, Hao, Margolick, Joseph B., Blankson, Joel N., Deeks, Steven G., Bushman, Frederic D., Siliciano, Janet D., Laird, Gregory M., Siliciano, Robert F.
Published in Nature (London) (01.02.2019)
Published in Nature (London) (01.02.2019)
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Journal Article
Correlation Between Intraluminal Oxygen Gradient and Radial Partitioning of Intestinal Microbiota
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
Published in Gastroenterology (New York, N.Y. 1943) (01.11.2014)
Published in Gastroenterology (New York, N.Y. 1943) (01.11.2014)
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Journal Article
The human gut virome: inter-individual variation and dynamic response to diet
Minot, Samuel, Sinha, Rohini, Chen, Jun, Li, Hongzhe, Keilbaugh, Sue A, Wu, Gary D, Lewis, James D, Bushman, Frederic D
Published in Genome research (01.10.2011)
Published in Genome research (01.10.2011)
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Journal Article
Evaluating the state of the science for adeno-associated virus integration: An integrated perspective
Sabatino, Denise E., Bushman, Frederic D., Chandler, Randy J., Crystal, Ronald G., Davidson, Beverly L., Dolmetsch, Ricardo, Eggan, Kevin C., Gao, Guangping, Gil-Farina, Irene, Kay, Mark A., McCarty, Douglas M., Montini, Eugenio, Ndu, Adora, Yuan, Jing
Published in Molecular therapy (03.08.2022)
Published in Molecular therapy (03.08.2022)
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Journal Article
Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment
Dollive, Serena, Chen, Ying-Yu, Grunberg, Stephanie, Bittinger, Kyle, Hoffmann, Christian, Vandivier, Lee, Cuff, Christopher, Lewis, James D, Wu, Gary D, Bushman, Frederic D
Published in PloS one (19.08.2013)
Published in PloS one (19.08.2013)
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Journal Article
The stepwise assembly of the neonatal virome is modulated by breastfeeding
Liang, Guanxiang, Zhao, Chunyu, Zhang, Huanjia, Mattei, Lisa, Sherrill-Mix, Scott, Bittinger, Kyle, Kessler, Lyanna R., Wu, Gary D., Baldassano, Robert N., DeRusso, Patricia, Ford, Eileen, Elovitz, Michal A., Kelly, Matthew S., Patel, Mohamed Z., Mazhani, Tiny, Gerber, Jeffrey S., Kelly, Andrea, Zemel, Babette S., Bushman, Frederic D.
Published in Nature (London) (01.05.2020)
Published in Nature (London) (01.05.2020)
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Journal Article
Disordered microbial communities in the upper respiratory tract of cigarette smokers
Charlson, Emily S, Chen, Jun, Custers-Allen, Rebecca, Bittinger, Kyle, Li, Hongzhe, Sinha, Rohini, Hwang, Jennifer, Bushman, Frederic D, Collman, Ronald G
Published in PloS one (20.12.2010)
Published in PloS one (20.12.2010)
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