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
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
Administration of nucleoside-modified mRNA encoding broadly neutralizing antibody protects humanized mice from HIV-1 challenge
Pardi, Norbert, Secreto, Anthony J., Shan, Xiaochuan, Debonera, Fotini, Glover, Joshua, Yi, Yanjie, Muramatsu, Hiromi, Ni, Houping, Mui, Barbara L., Tam, Ying K., Shaheen, Farida, Collman, Ronald G., Karikó, Katalin, Danet-Desnoyers, Gwenn A., Madden, Thomas D., Hope, Michael J., Weissman, Drew
Published in Nature communications (02.03.2017)
Published in Nature communications (02.03.2017)
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Journal Article
Human caspase-4 mediates noncanonical inflammasome activation against gram-negative bacterial pathogens
Casson, Cierra N., Yu, Janet, Reyes, Valeria M., Taschuk, Frances O., Yadav, Anjana, Copenhaver, Alan M., Nguyen, Hieu T., Collman, Ronald G., Shin, Sunny
Published in Proceedings of the National Academy of Sciences - PNAS (26.05.2015)
Published in Proceedings of the National Academy of Sciences - PNAS (26.05.2015)
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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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Journal Article
Optimizing methods and dodging pitfalls in microbiome research
Kim, Dorothy, Hofstaedter, Casey E, Zhao, Chunyu, Mattei, Lisa, Tanes, Ceylan, Clarke, Erik, Lauder, Abigail, Sherrill-Mix, Scott, Chehoud, Christel, Kelsen, Judith, Conrad, Máire, Collman, Ronald G, Baldassano, Robert, Bushman, Frederic D, Bittinger, Kyle
Published in Microbiome (05.05.2017)
Published in Microbiome (05.05.2017)
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Journal Article
Detection of SARS-CoV-2 RNA using RT-LAMP and molecular beacons
Sherrill-Mix, Scott, Hwang, Young, Roche, Aoife M, Glascock, Abigail, Weiss, Susan R, Li, Yize, Haddad, Leila, Deraska, Peter, Monahan, Caitlin, Kromer, Andrew, Graham-Wooten, Jevon, Taylor, Louis J, Abella, Benjamin S, Ganguly, Arupa, Collman, Ronald G, Van Duyne, Gregory D, Bushman, Frederic D
Published in Genome Biology (03.06.2021)
Published in Genome Biology (03.06.2021)
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Journal Article
Innate Lymphoid Cells Promote Anatomical Containment of Lymphoid-Resident Commensal Bacteria
Sonnenberg, Gregory F., Monticelli, Laurel A., Alenghat, Theresa, Fung, Thomas C., Hutnick, Natalie A., Kunisawa, Jun, Shibata, Naoko, Grunberg, Stephanie, Sinha, Rohini, Zahm, Adam M., Tardif, Mélanie R., Sathaliyawala, Taheri, Kubota, Masaru, Farber, Donna L., Collman, Ronald G., Shaked, Abraham, Fouser, Lynette A., Weiner, David B., Tessier, Philippe A., Friedman, Joshua R., Kiyono, Hiroshi, Bushman, Frederic D., Chang, Kyong-Mi, Artis, David
Published in Science (American Association for the Advancement of Science) (08.06.2012)
Published in Science (American Association for the Advancement of Science) (08.06.2012)
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Journal Article
The Role of the Lung Microbiome in Health and Disease: A National Heart, Lung, and Blood Institute Workshop Report
HUANG, Yvonne J, CHARLSON, Emily S, COLLMAN, Ronald G, COLOMBINI-HATCH, Sandra, MARTINEZ, Fernando D, SENIOR, Robert M
Published in American journal of respiratory and critical care medicine (15.06.2013)
Published in American journal of respiratory and critical care medicine (15.06.2013)
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Journal Article
Supraphysiologic control over HIV-1 replication mediated by CD8 T cells expressing a re-engineered CD4-based chimeric antigen receptor
Leibman, Rachel S, Richardson, Max W, Ellebrecht, Christoph T, Maldini, Colby R, Glover, Joshua A, Secreto, Anthony J, Kulikovskaya, Irina, Lacey, Simon F, Akkina, Sarah R, Yi, Yanjie, Shaheen, Farida, Wang, Jianbin, Dufendach, Keith A, Holmes, Michael C, Collman, Ronald G, Payne, Aimee S, Riley, James L
Published in PLoS pathogens (01.10.2017)
Published in PLoS pathogens (01.10.2017)
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Journal Article
Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome
Merenstein, Carter, Liang, Guanxiang, Whiteside, Samantha A, Cobián-Güemes, Ana G, Merlino, Madeline S, Taylor, Louis J, Glascock, Abigail, Bittinger, Kyle, Tanes, Ceylan, Graham-Wooten, Jevon, Khatib, Layla A, Fitzgerald, Ayannah S, Reddy, Shantan, Baxter, Amy E, Giles, Josephine R, Oldridge, Derek A, Meyer, Nuala J, Wherry, E John, McGinniss, John E, Bushman, Frederic D, Collman, Ronald G
Published in mBio (31.08.2021)
Published in mBio (31.08.2021)
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Journal Article
Composition and dynamics of the respiratory tract microbiome in intubated patients
Kelly, Brendan J, Imai, Ize, Bittinger, Kyle, Laughlin, Alice, Fuchs, Barry D, Bushman, Frederic D, Collman, Ronald G
Published in Microbiome (11.02.2016)
Published in Microbiome (11.02.2016)
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Journal Article
Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts
Charlson, Emily S, Bittinger, Kyle, Chen, Jun, Diamond, Joshua M, Li, Hongzhe, Collman, Ronald G, Bushman, Frederic D
Published in PloS one (06.09.2012)
Published in PloS one (06.09.2012)
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Journal Article
Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals
Beck, James M, Schloss, Patrick D, Venkataraman, Arvind, Twigg, 3rd, 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
Published in American journal of respiratory and critical care medicine (01.12.2015)
Published in American journal of respiratory and critical care medicine (01.12.2015)
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Journal Article
Multiple Introductions of SARS-CoV-2 Alpha and Delta Variants into White-Tailed Deer in Pennsylvania
Marques, Andrew D, Sherrill-Mix, Scott, Everett, John K, Adhikari, Hriju, Reddy, Shantan, Ellis, Julie C, Zeliff, Haley, Greening, Sabrina S, Cannuscio, Carolyn C, Strelau, Katherine M, Collman, Ronald G, Kelly, Brendan J, Rodino, Kyle G, Bushman, Frederic D, Gagne, Roderick B, Anis, Eman
Published in mBio (26.10.2022)
Published in mBio (26.10.2022)
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Journal Article
Microbial Lineages in Sarcoidosis. A Metagenomic Analysis Tailored for Low-Microbial Content Samples
Clarke, Erik L, Lauder, Abigail P, Hofstaedter, Casey E, Hwang, Young, Fitzgerald, Ayannah S, Imai, Ize, Biernat, Wojciech, Rękawiecki, Bartłomiej, Majewska, Hanna, Dubaniewicz, Anna, Litzky, Leslie A, Feldman, Michael D, Bittinger, Kyle, Rossman, Milton D, Patterson, Karen C, Bushman, Frederic D, Collman, Ronald G
Published in American journal of respiratory and critical care medicine (15.01.2018)
Published in American journal of respiratory and critical care medicine (15.01.2018)
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Journal Article
Tracking gut microbiome and bloodstream infection in critically ill adults
Gu, Christopher H, Khatib, Layla A, Fitzgerald, Ayannah S, Graham-Wooten, Jevon, Ittner, Caroline A, Sherrill-Mix, Scott, Chuang, YuChung, Glaser, Laurel J, Meyer, Nuala J, Bushman, Frederic D, Collman, Ronald G
Published in PloS one (10.10.2023)
Published in PloS one (10.10.2023)
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Journal Article
CD4 depletion in SIV-infected macaques results in macrophage and microglia infection with rapid turnover of infected cells
Micci, Luca, Alvarez, Xavier, Iriele, Robin I, Ortiz, Alexandra M, Ryan, Emily S, McGary, Colleen S, Deleage, Claire, McAtee, Brigitte B, He, Tianyu, Apetrei, Cristian, Easley, Kirk, Pahwa, Savita, Collman, Ronald G, Derdeyn, Cynthia A, Davenport, Miles P, Estes, Jacob D, Silvestri, Guido, Lackner, Andrew A, Paiardini, Mirko
Published in PLoS pathogens (01.10.2014)
Published in PLoS pathogens (01.10.2014)
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