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51. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission

Author

Karthikeyan, Smruthi, primary, Levy, Joshua I, additional, De Hoff, Peter, additional, Humphrey, Greg, additional, Birmingham, Amanda, additional, Jepsen, Kristen, additional, Farmer, Sawyer, additional, Tubb, Helena M., additional, Valles, Tommy, additional, Tribelhorn, Caitlin E, additional, Tsai, Rebecca, additional, Aigner, Stefan, additional, Sathe, Shashank, additional, Moshiri, Niema, additional, Henson, Benjamin, additional, Mark, Adam M., additional, Hakim, Abbas, additional, Baer, Nathan A, additional, Barber, Tom, additional, Belda-Ferre, Pedro, additional, Chacón, Marisol, additional, Cheung, Willi, additional, Cresini, Evelyn S, additional, Eisner, Emily R, additional, Lastrella, Alma L, additional, Lawrence, Elijah S, additional, Marotz, Clarisse A, additional, Ngo, Toan T, additional, Ostrander, Tyler, additional, Plascencia, Ashley, additional, Salido, Rodolfo A, additional, Seaver, Phoebe, additional, Smoot, Elizabeth W, additional, McDonald, Daniel, additional, Neuhard, Robert M, additional, Scioscia, Angela L, additional, Satterlund, Alysson M., additional, Simmons, Elizabeth H, additional, Abelman, Dismas B., additional, Brenner, David, additional, Bruner, Judith C., additional, Buckley, Anne, additional, Ellison, Michael, additional, Gattas, Jeffrey, additional, Gonias, Steven L., additional, Hale, Matt, additional, Hawkins, Faith, additional, Ikeda, Lydia, additional, Jhaveri, Hemlata, additional, Johnson, Ted, additional, Kellen, Vince, additional, Kremer, Brendan, additional, Matthews, Gary, additional, McLawhon, Ronald W., additional, Ouillet, Pierre, additional, Park, Daniel, additional, Pradenas, Allorah, additional, Reed, Sharon, additional, Riggs, Lindsay, additional, Sanders, Alison, additional, Sollenberger, Bradley, additional, Song, Angela, additional, White, Benjamin, additional, Winbush, Terri, additional, Aceves, Christine M, additional, Anderson, Catelyn, additional, Gangavarapu, Karthik, additional, Hufbauer, Emory, additional, Kurzban, Ezra, additional, Lee, Justin, additional, Matteson, Nathaniel L, additional, Parker, Edyth, additional, Perkins, Sarah A, additional, Ramesh, Karthik S, additional, Robles-Sikisaka, Refugio, additional, Schwab, Madison A, additional, Spencer, Emily, additional, Wohl, Shirlee, additional, Nicholson, Laura, additional, Mchardy, Ian H, additional, Dimmock, David P, additional, Hobbs, Charlotte A, additional, Bakhtar, Omid, additional, Harding, Aaron, additional, Mendoza, Art, additional, Bolze, Alexandre, additional, Becker, David, additional, Cirulli, Elizabeth T, additional, Isaksson, Magnus, additional, Schiabor Barrett, Kelly M, additional, Washington, Nicole L, additional, Malone, John D, additional, Schafer, Ashleigh Murphy, additional, Gurfield, Nikos, additional, Stous, Sarah, additional, Fielding-Miller, Rebecca, additional, Garfein, Richard S., additional, Gaines, Tommi, additional, Anderson, Cheryl, additional, Martin, Natasha K., additional, Schooley, Robert, additional, Austin, Brett, additional, MacCannell, Duncan R., additional, Kingsmore, Stephen F, additional, Lee, William, additional, Shah, Seema, additional, McDonald, Eric, additional, Yu, Alexander T., additional, Zeller, Mark, additional, Fisch, Kathleen M, additional, Longhurst, Christopher, additional, Maysent, Patty, additional, Pride, David, additional, Khosla, Pradeep K., additional, Laurent, Louise C., additional, Yeo, Gene W, additional, Andersen, Kristian G, additional, and Knight, Rob, additional

Published
2021
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53. Additional file 8 of SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

Author

Marotz, Clarisse, Belda-Ferre, Pedro, Ali, Farhana, Das, Promi, Huang, Shi, Cantrell, Kalen, Jiang, Lingjing, Martino, Cameron, Diner, Rachel E., Rahman, Gibraan, McDonald, Daniel, Armstrong, George, Kodera, Sho, Donato, Sonya, Ecklu-Mensah, Gertrude, Gottel, Neil, Salas Garcia, Mariana C., Chiang, Leslie Y., Salido, Rodolfo A., Shaffer, Justin P., Bryant, Mac Kenzie, Sanders, Karenina, Humphrey, Greg, Ackermann, Gail, Haiminen, Niina, Beck, Kristen L., Kim, Ho-Cheol, Carrieri, Anna Paola, Parida, Laxmi, Vázquez-Baeza, Yoshiki, Torriani, Francesca J., Knight, Rob, Gilbert, Jack, Sweeney, Daniel A., and Allard, Sarah M.

Abstract

Additional file 7: Figure S7. Bacterial (16S rRNA gene amplicon sequencing read count) and human biomass (RNAse P Ct) is higher in floor samples than other surface sample types.

Published
2021
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54. Additional file 7 of SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

Author

Marotz, Clarisse, Belda-Ferre, Pedro, Ali, Farhana, Das, Promi, Huang, Shi, Cantrell, Kalen, Jiang, Lingjing, Martino, Cameron, Diner, Rachel E., Rahman, Gibraan, McDonald, Daniel, Armstrong, George, Kodera, Sho, Donato, Sonya, Ecklu-Mensah, Gertrude, Gottel, Neil, Salas Garcia, Mariana C., Chiang, Leslie Y., Salido, Rodolfo A., Shaffer, Justin P., Bryant, Mac Kenzie, Sanders, Karenina, Humphrey, Greg, Ackermann, Gail, Haiminen, Niina, Beck, Kristen L., Kim, Ho-Cheol, Carrieri, Anna Paola, Parida, Laxmi, Vázquez-Baeza, Yoshiki, Torriani, Francesca J., Knight, Rob, Gilbert, Jack, Sweeney, Daniel A., and Allard, Sarah M.

Subjects
body regions
Abstract

Additional file 6: Figure S6. Floor sample SARS-CoV-2 status is associated with higher biomass and with significantly different bacterial community composition. Two independent metrics were used to assess biomass; 16S rRNA gene amplicon sequencing read count, which because of our equal volume sequencing library pooling approach correlates with total bacterial load [27, 74], and the Ct value from the CDC’s human RNAse P RT-qPCR target, which correlates with human biomass. (A) Abundance of 16S rRNA gene amplicon sequencing read count in SARS-CoV-2 positive floor samples showing no correlation with SARS-CoV-2 viral load. (B) Ct value of human RNAse P in SARS-CoV-2 positive floor samples showing significant correlation with SARS-CoV-2 viral load. Statistical analysis of scatter plots represents Pearson correlation, and box plots represents independent t-tests; *p < 0.05, **p < 0.01, ***p < 0.001. The legend in panel B applies to panel A as well. (C) Effect size of significant, non-redundant variables identified from Redundancy Analysis on unweighted UniFrac PCoA of floor samples.

Published
2021
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55. Additional file 2 of Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment

Author

Minich, Jeremiah J., Ali, Farhana, Marotz, Clarisse, Belda-Ferre, Pedro, Chiang, Leslie, Shaffer, Justin P., Carpenter, Carolina S., McDonald, Daniel, Gilbert, Jack, Allard, Sarah M., Allen, Eric E., Knight, Rob, Sweeney, Daniel A., and Swafford, Austin D.

Abstract

Additional file 1: Supplemental Figure 1. Impacts of storage solution or swab type on RNA quality as measured by RNA Tapestation High Sensitivity kit. Supplemental Figure 2. Impacts of sample-type (eluent vs. swab head) on RNA recovery by swab used. Supplemental Figure 3. Adsorption volumes per swab type. Supplemental Figure 4. Total variation of human Rp gene detected from floor samples in limit of detection experiment. Supplemental Figure 5. Variation of human Rp gene amplification across swab types. Supplemental Figure 6. Intra-assay variability compared across positive controls, sample _types, and swab types. Supplemental Figure 7. Comparison of 16S rRNA microbial composition of paired patient and sample type samples collected using different swabs (in triplicate) using Unweighted UniFrac PCoA plot.

Published
2021
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56. Additional file 11 of SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

Author

Marotz, Clarisse, Belda-Ferre, Pedro, Ali, Farhana, Das, Promi, Huang, Shi, Cantrell, Kalen, Jiang, Lingjing, Martino, Cameron, Diner, Rachel E., Rahman, Gibraan, McDonald, Daniel, Armstrong, George, Kodera, Sho, Donato, Sonya, Ecklu-Mensah, Gertrude, Gottel, Neil, Salas Garcia, Mariana C., Chiang, Leslie Y., Salido, Rodolfo A., Shaffer, Justin P., Bryant, Mac Kenzie, Sanders, Karenina, Humphrey, Greg, Ackermann, Gail, Haiminen, Niina, Beck, Kristen L., Kim, Ho-Cheol, Carrieri, Anna Paola, Parida, Laxmi, Vázquez-Baeza, Yoshiki, Torriani, Francesca J., Knight, Rob, Gilbert, Jack, Sweeney, Daniel A., and Allard, Sarah M.

Abstract

Additional file 10: Table S1. Hospital surface materials and cleaning practices.

Published
2021
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57. Additional file 2 of SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

Author

Marotz, Clarisse, Belda-Ferre, Pedro, Ali, Farhana, Das, Promi, Huang, Shi, Cantrell, Kalen, Jiang, Lingjing, Martino, Cameron, Diner, Rachel E., Rahman, Gibraan, McDonald, Daniel, Armstrong, George, Kodera, Sho, Donato, Sonya, Ecklu-Mensah, Gertrude, Gottel, Neil, Salas Garcia, Mariana C., Chiang, Leslie Y., Salido, Rodolfo A., Shaffer, Justin P., Bryant, Mac Kenzie, Sanders, Karenina, Humphrey, Greg, Ackermann, Gail, Haiminen, Niina, Beck, Kristen L., Kim, Ho-Cheol, Carrieri, Anna Paola, Parida, Laxmi, Vázquez-Baeza, Yoshiki, Torriani, Francesca J., Knight, Rob, Gilbert, Jack, Sweeney, Daniel A., and Allard, Sarah M.

Abstract

Additional file 1: Figure S1. Patient (n = 16) demographics (A), antibiotics intake (B), comorbidities (C).

Published
2021
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58. Additional file 3 of SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

Author

Marotz, Clarisse, Belda-Ferre, Pedro, Ali, Farhana, Das, Promi, Huang, Shi, Cantrell, Kalen, Jiang, Lingjing, Martino, Cameron, Diner, Rachel E., Rahman, Gibraan, McDonald, Daniel, Armstrong, George, Kodera, Sho, Donato, Sonya, Ecklu-Mensah, Gertrude, Gottel, Neil, Salas Garcia, Mariana C., Chiang, Leslie Y., Salido, Rodolfo A., Shaffer, Justin P., Bryant, Mac Kenzie, Sanders, Karenina, Humphrey, Greg, Ackermann, Gail, Haiminen, Niina, Beck, Kristen L., Kim, Ho-Cheol, Carrieri, Anna Paola, Parida, Laxmi, Vázquez-Baeza, Yoshiki, Torriani, Francesca J., Knight, Rob, Gilbert, Jack, Sweeney, Daniel A., and Allard, Sarah M.

Subjects
virus diseases, respiratory tract diseases
Abstract

Additional file 2: Figure S2. Ili’ spatial mapping of standard hospital (non-ICU) room and intensive care unit (ICU) room. Heatmap depicts the percent of samples collected at each site that were positive for SARS-CoV-2.

Published
2021
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59. Additional file 4 of SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

Author

Marotz, Clarisse, Belda-Ferre, Pedro, Ali, Farhana, Das, Promi, Huang, Shi, Cantrell, Kalen, Jiang, Lingjing, Martino, Cameron, Diner, Rachel E., Rahman, Gibraan, McDonald, Daniel, Armstrong, George, Kodera, Sho, Donato, Sonya, Ecklu-Mensah, Gertrude, Gottel, Neil, Salas Garcia, Mariana C., Chiang, Leslie Y., Salido, Rodolfo A., Shaffer, Justin P., Bryant, Mac Kenzie, Sanders, Karenina, Humphrey, Greg, Ackermann, Gail, Haiminen, Niina, Beck, Kristen L., Kim, Ho-Cheol, Carrieri, Anna Paola, Parida, Laxmi, Vázquez-Baeza, Yoshiki, Torriani, Francesca J., Knight, Rob, Gilbert, Jack, Sweeney, Daniel A., and Allard, Sarah M.

Abstract

Additional file 3: Figure S3. Snapshot of variability in longitudinal sample collection and SARS-CoV-2 viral RNA load per swab between patients and their hospital rooms, starting at patient admission time. For samples where SARS-CoV-2 was detected (+), a darker color indicates a higher viral load. White boxes represent samples with no detectable virus (-). Patient A was admitted 12 days after symptom onset and was moved to a general surgery unit room after 6 days in the ICU. Patient B was admitted 8 days after symptom onset and moved from general surgery to the ICU, where they were intubated. Patient C was admitted to the ICU 9 days after symptom onset, and despite having symptoms consistent with COVID-19 repeatedly tested negative by clinical nasopharyngeal swab; their only clinical positive came from a tracheal aspirate sample mid-way through their stay in the ICU.

Published
2021
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60. Additional file 9 of SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

Author

Marotz, Clarisse, Belda-Ferre, Pedro, Ali, Farhana, Das, Promi, Huang, Shi, Cantrell, Kalen, Jiang, Lingjing, Martino, Cameron, Diner, Rachel E., Rahman, Gibraan, McDonald, Daniel, Armstrong, George, Kodera, Sho, Donato, Sonya, Ecklu-Mensah, Gertrude, Gottel, Neil, Salas Garcia, Mariana C., Chiang, Leslie Y., Salido, Rodolfo A., Shaffer, Justin P., Bryant, Mac Kenzie, Sanders, Karenina, Humphrey, Greg, Ackermann, Gail, Haiminen, Niina, Beck, Kristen L., Kim, Ho-Cheol, Carrieri, Anna Paola, Parida, Laxmi, Vázquez-Baeza, Yoshiki, Torriani, Francesca J., Knight, Rob, Gilbert, Jack, Sweeney, Daniel A., and Allard, Sarah M.

Abstract

Additional file 8: Figure S8. Random Forest classifier performance with 100-fold cross validation in the outside floor (n = 108; 81 not detected vs. 27 positives) and bed rail samples (n = 46; 38 not detected vs. 8 positives).

Published
2021
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61. Additional file 6 of SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

Author

Marotz, Clarisse, Belda-Ferre, Pedro, Ali, Farhana, Das, Promi, Huang, Shi, Cantrell, Kalen, Jiang, Lingjing, Martino, Cameron, Diner, Rachel E., Rahman, Gibraan, McDonald, Daniel, Armstrong, George, Kodera, Sho, Donato, Sonya, Ecklu-Mensah, Gertrude, Gottel, Neil, Salas Garcia, Mariana C., Chiang, Leslie Y., Salido, Rodolfo A., Shaffer, Justin P., Bryant, Mac Kenzie, Sanders, Karenina, Humphrey, Greg, Ackermann, Gail, Haiminen, Niina, Beck, Kristen L., Kim, Ho-Cheol, Carrieri, Anna Paola, Parida, Laxmi, Vázquez-Baeza, Yoshiki, Torriani, Francesca J., Knight, Rob, Gilbert, Jack, Sweeney, Daniel A., and Allard, Sarah M.

Abstract

Additional file 5: Figure S5. Beta diversity has a statistically significant but weak correlation with viral load. PCoA of unweighted UniFrac distances between samples, with SARS-CoV-2 positive samples colored by viral load across the whole dataset (A) and subset by each patient with at least one surface positive (B). Statistical analysis performed with Adonis (PERMANOVA) found a small (R2

Published
2021
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62. Additional file 5 of SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

Author

Marotz, Clarisse, Belda-Ferre, Pedro, Ali, Farhana, Das, Promi, Huang, Shi, Cantrell, Kalen, Jiang, Lingjing, Martino, Cameron, Diner, Rachel E., Rahman, Gibraan, McDonald, Daniel, Armstrong, George, Kodera, Sho, Donato, Sonya, Ecklu-Mensah, Gertrude, Gottel, Neil, Salas Garcia, Mariana C., Chiang, Leslie Y., Salido, Rodolfo A., Shaffer, Justin P., Bryant, Mac Kenzie, Sanders, Karenina, Humphrey, Greg, Ackermann, Gail, Haiminen, Niina, Beck, Kristen L., Kim, Ho-Cheol, Carrieri, Anna Paola, Parida, Laxmi, Vázquez-Baeza, Yoshiki, Torriani, Francesca J., Knight, Rob, Gilbert, Jack, Sweeney, Daniel A., and Allard, Sarah M.

Abstract

Additional file 4: Figure S4. Source tracker on meta-analysis data. Floor samples formed a distinct cluster in this dataset; source tracking [31] with floor samples (n = 215) as the sink and meta-analysis samples (n = 1,990) as the source reveals that these floor samples match other built environment samples. The other built environment samples included in this meta-analysis were mostly floor (27.7%), faucet handles (19.6%), and gloves (15%).

Published
2021
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63. Automated, miniaturized, and scalable screening of healthcare workers, first responders, and students for SARS-CoV-2 in San Diego County

Author

Morgan, Sydney, Aigner, Stefan, Anderson, Catelyn, Belda-Ferre, Pedro, De Hoff, Peter, Marotz, Clarisse, Sathe, Shashank, Zeller, Mark, Ahmed, Noorsher, Audhya, Xaver, Baer, Nathan, Barber, Tom, Barrick, Bethany, Batachari, Lakshmi, Betty, Maryann, Blue, Steven, Brainard, Brent, Buckley, Tyler, Case, Jamie, Castro-Martinez, Anelizze, Chacón, Marisol, Cheung, Willi, Chong, LaVonnye, Coufal, Nicole, Crescini, Evelyn, DeGrand, Scott, Dimmock, David, Joelle Donofrio-Odmann, J, Eisner, Emily, Estaki, Mehrbod, Vargas, Lizbeth Franco, Freddock, Michele, Gallant, Robert, Galmozzi, Andrea, Gao, Nina, Gilmer, Sheldon, Grzelak, Edyta, Hakim, Abbas, Hart, Jonathan, Hobbs, Charlotte, Humphrey, Greg, Ilkenhans, Nadja, Jacobs, Marni, Kahn, Christopher, Kapadia, Bhavika, Kim, Matthew, Kurian, Sunil, Lastrella, Alma, Lawrence, Elijah, Lee, Kari, Liang, Qishan, Liliom, Hanna, Sardo, Valentina Lo, Logan, Robert, Machnicki, Michal, Magallanes, Celestine, Mah, Clarence, Malacki, Denise, Marina, Ryan, Marsh, Christopher, Martin, Natasha, Matteson, Nathaniel, Maunder, Daniel, McBride, Kyle, McDonald, Bryan, McDonald, Daniel, McGraw, Michelle, Meadows, Audra, Meyer, Michelle, Morey, Amber, Mueller, Jasmine, Ngo, Toan, Nguyen, Julie, Nguyen, Viet, Nicholson, Laura, Nouri, Alhakam, Nudell, Victoria, Nunez, Eugenio, O’Neill, Kyle, Tyler Ostrander, R, Pantham, Priyadarshini, Park, Samuel, Picone, David, Plascencia, Ashley, Pratumchai, Isaraphorn, Quigley, Michael, Ragsac, Michelle Franc, Richardson, Andrew, Robles-Sikisaka, Refugio, Ruiz, Christopher, Ryan, Justin, Sacco, Lisa, Saraf, Sharada, Seaver, Phoebe, Sewall, Leigh, Smoot, Elizabeth, Sweeney, Kathleen, Tekkatte, Chandana, Tsai, Rebecca, and Valentine, Holly

Subjects
Pediatric, Vaccine Related, Pediatric Research Initiative, Infectious Diseases, Emerging Infectious Diseases, Good Health and Well Being, Clinical Research, Prevention, Biodefense
Abstract

Background Successful containment strategies for SARS-CoV-2, the causative virus of the COVID-19 pandemic, have involved widespread population testing that identifies infections early and enables rapid contact tracing. In this study, we developed a rapid and inexpensive RT- qPCR testing pipeline for population-level SARS-CoV-2 detection, and used this pipeline to establish a clinical laboratory dedicated to COVID-19 testing at the University of California San Diego (UCSD) with a processing capacity of 6,000 samples per day and next-day result turnaround times. Methods and findings Using this pipeline, we screened 6,786 healthcare workers and first responders, and 21,220 students, faculty, and staff from UCSD. Additionally, we screened 6,031 preschool-grade 12 students and staff from public and private schools across San Diego County that remained fully or partially open for in-person teaching during the pandemic. Between April 17, 2020 and February 5, 2021, participants provided 161,582 nasal swabs that were tested for the presence of SARS-CoV-2. Overall, 752 positive tests were obtained, yielding a test positivity rate of 0.47%. While the presence of symptoms was significantly correlated with higher viral load, most of the COVID-19 positive participants who participated in symptom surveys were asymptomatic at the time of testing. The positivity rate among preschool-grade 12 schools that remained open for in-person teaching was similar to the positivity rate at UCSD and lower than that of San Diego County, with the children in private schools being less likely to test positive than the adults at these schools. Conclusions Most schools across the United States have been closed for in-person learning for much of the 2020-2021 school year, and their safe reopening is a national priority. However, as there are no vaccines against SARS-CoV-2 currently available to the majority of school-aged children, the traditional strategies of mandatory masking, physical distancing, and repeated viral testing of students and staff remain key components of risk mitigation in these settings. The data presented here suggest that the safety measures and repeated testing actions taken by participating healthcare and educational facilities were effective in preventing outbreaks, and that a similar combination of risk-mitigation strategies and repeated testing may be successfully adopted by other healthcare and educational systems.

Published
2021

64. Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence

Author

Salido, Rodolfo A., primary, Cantú, Victor J., additional, Clark, Alex E., additional, Leibel, Sandra L., additional, Foroughishafiei, Anahid, additional, Saha, Anushka, additional, Hakim, Abbas, additional, Nouri, Alhakam, additional, Lastrella, Alma L., additional, Castro-Martínez, Anelizze, additional, Plascencia, Ashley, additional, Kapadia, Bhavika, additional, Xia, Bing, additional, Ruiz, Christopher, additional, Marotz, Clarisse A., additional, Maunder, Daniel, additional, Lawrence, Elijah S., additional, Smoot, Elizabeth W., additional, Eisner, Emily, additional, Crescini, Evelyn S., additional, Kohn, Laura, additional, Franco Vargas, Lizbeth, additional, Chacón, Marisol, additional, Betty, Maryann, additional, Machnicki, Michal, additional, Wu, Min Yi, additional, Baer, Nathan A., additional, Belda-Ferre, Pedro, additional, De Hoff, Peter, additional, Seaver, Phoebe, additional, Ostrander, R. Tyler, additional, Tsai, Rebecca, additional, Sathe, Shashank, additional, Aigner, Stefan, additional, Morgan, Sydney C., additional, Ngo, Toan T., additional, Barber, Tom, additional, Cheung, Willi, additional, Carlin, Aaron F., additional, Yeo, Gene W., additional, Laurent, Louise C., additional, Fielding-Miller, Rebecca, additional, and Knight, Rob, additional

Published
2021
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65. Reference data-set driven metabolomics

Author

Gauglitz, Julia, primary, West, Kiana, additional, Bittremieux, Wout, additional, Williams, Candace, additional, Weldon, Kelly, additional, Panitchpakdi, Morgan, additional, Diottavio, Francesca, additional, Aceves, Christine, additional, Brown, Elizabeth, additional, Sikora, Nicole, additional, Jarmusch, Alan, additional, Martino, Cameron, additional, Tripathi, Anupriya, additional, Meehan, Michael, additional, Dorrestein, Kathleen, additional, Shaffer, Justin, additional, Coras, Roxana, additional, Vargas, Fernando, additional, Goldasich, Lindsay DeRight, additional, Schwartz, Tara, additional, Bryant, MacKenzie, additional, Humphrey, Greg, additional, Johnson, Abigail, additional, Spengler, Katharina, additional, Belda-Ferre, Pedro, additional, Diaz, Edgar, additional, McDonald, Daniel, additional, Zhu, Qiyun, additional, Emmanuel, Elijah, additional, Wang, Mingxun, additional, Marotz, Clarisse, additional, Sprecher, Kate, additional, RObles, Daniela Vargas, additional, Withrow, Dana, additional, Ackermann, Gail, additional, Herrera, Lourdes, additional, Bradford, Barry, additional, Marques, Lucas Maciel Mauriz, additional, Amaral, Juliano Geraldo, additional, Silva, Rodrigo Moreira, additional, Veras, Flávio Protaso, additional, Cunha, Thiago Mattar, additional, Oliveira, Rene Donizeti Ribeiro, additional, Louzada-Junior, Paulo, additional, Mills, Robert, additional, Piotrowski, Paulina, additional, Servetas, Stephanie, additional, DaSilva, Sandra, additional, Jones, Christina, additional, Lin, Nancy, additional, Lippa, Katrice, additional, Jackson, Scott, additional, Daouk, Rima Kaddurah, additional, Galasko, Douglas, additional, Dulai, Parambir, additional, Kalashnikova, Tatyana, additional, Wittenberg, Curt, additional, Gonzalez, David, additional, Terkeltaub, Robert, additional, Doty, Megan, additional, Kim, Jae, additional, Rhee, Kyung, additional, Beauchamp-Walters, Julia, additional, Wright, Kenneth, additional, Dominguez-Bello, Maria Gloria, additional, Manery, Mark, additional, Oliveira, Michelli, additional, Boland, Brigid, additional, Lopes, Norberto, additional, Guma, Monica, additional, Swafford, Austin, additional, Dutton, Rachel, additional, Knight, Rob, additional, and Dorrestein, Pieter, additional

Published
2021
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66. Automated, miniaturized, and scalable screening of healthcare workers, first responders, and students for SARS-CoV-2 in San Diego County

Author

Morgan, Sydney C, primary, Aigner, Stefan, additional, Anderson, Catelyn, additional, Belda-Ferre, Pedro, additional, De Hoff, Peter, additional, Marotz, Clarisse A, additional, Sathe, Shashank, additional, Zeller, Mark, additional, Ahmed, Noorsher, additional, Audhya, Xaver, additional, Baer, Nathan A, additional, Barber, Tom, additional, Barrick, Bethany, additional, Batachari, Lakshmi, additional, Betty, Maryann, additional, Blue, Steven M, additional, Brainard, Brent, additional, Buckley, Tyler, additional, Case, Jamie, additional, Castro-Martinez, Anelizze, additional, Chacón, Marisol, additional, Cheung, Willi, additional, Chong, LaVonnye, additional, Coufal, Nicole G, additional, Crescini, Evelyn S, additional, DeGrand, Scott, additional, Dimmock, David P, additional, Joelle Donofrio-Odmann, J, additional, Eisner, Emily R, additional, Estaki, Mehrbod, additional, Vargas, Lizbeth Franco, additional, Freddock, Michele, additional, Gallant, Robert M, additional, Galmozzi, Andrea, additional, Gao, Nina J, additional, Gilmer, Sheldon, additional, Grzelak, Edyta M, additional, Hakim, Abbas, additional, Hart, Jonathan, additional, Hobbs, Charlotte, additional, Humphrey, Greg, additional, Ilkenhans, Nadja, additional, Jacobs, Marni, additional, Kahn, Christopher A, additional, Kapadia, Bhavika K, additional, Kim, Matthew, additional, Kurian, Sunil, additional, Lastrella, Alma L, additional, Lawrence, Elijah S, additional, Lee, Kari, additional, Liang, Qishan, additional, Liliom, Hanna, additional, Sardo, Valentina Lo, additional, Logan, Robert, additional, Machnicki, Michal, additional, Magallanes, Celestine G, additional, Mah, Clarence K, additional, Malacki, Denise, additional, Marina, Ryan J, additional, Marsh, Christopher, additional, Martin, Natasha K, additional, Matteson, Nathaniel L, additional, Maunder, Daniel J, additional, McBride, Kyle, additional, McDonald, Bryan, additional, McDonald, Daniel, additional, McGraw, Michelle, additional, Meadows, Audra R, additional, Meyer, Michelle, additional, Morey, Amber L, additional, Mueller, Jasmine R, additional, Ngo, Toan T, additional, Nguyen, Julie, additional, Nguyen, Viet, additional, Nicholson, Laura J, additional, Nouri, Alhakam, additional, Nudell, Victoria, additional, Nunez, Eugenio, additional, O’Neill, Kyle, additional, Tyler Ostrander, R, additional, Pantham, Priyadarshini, additional, Park, Samuel S, additional, Picone, David, additional, Plascencia, Ashley, additional, Pratumchai, Isaraphorn, additional, Quigley, Michael, additional, Ragsac, Michelle Franc, additional, Richardson, Andrew C, additional, Robles-Sikisaka, Refugio, additional, Ruiz, Christopher A, additional, Ryan, Justin, additional, Sacco, Lisa, additional, Saraf, Sharada, additional, Seaver, Phoebe, additional, Sewall, Leigh, additional, Smoot, Elizabeth W, additional, Sweeney, Kathleen M, additional, Tekkatte, Chandana, additional, Tsai, Rebecca, additional, Valentine, Holly, additional, Walsh, Shawn, additional, Williams, August, additional, Wu, Min Yi, additional, Xia, Bing, additional, Yee, Brian, additional, Zhang, Jason Z, additional, Andersen, Kristian G, additional, Farnaes, Lauge, additional, Knight, Rob, additional, Yeo, Gene W, additional, and Laurent, Louise C, additional

Published
2021
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67. Feasibility of SARS-CoV-2 virus detection from consumer-grade cotton swabs

Author

Minich, Jeremiah J, Ali, Farhana, Marotz, Clarisse, Belda-Ferre, Pedro, Shaffer, Justin P., Carpenter, Carolina S., McDonald, Daniel, Gilbert, Jack A, Allard, Sarah M., Knight, Rob, Sweeney, Daniel A, and Swafford, Austin D.

Subjects
Article
Abstract

To control the growing COVID-19 pandemic, increased testing and containment is essential, yet clinical-grade sampling supplies are expensive and rapidly being depleted. We demonstrate the feasibility of using alternative consumer-grade swabs stored in 95% ethanol rather than viral transport media to detect SARS-CoV-2 from ten hospitalized persons and hospital rooms.

Published
2020

68. Naturalization of the microbiota developmental trajectory of Cesarean-born neonates after vaginal seeding

Author

0000-0003-0750-5709, 0000-0002-1076-8326, 0000-0001-9334-1258, 0000-0001-8706-2850, 0000-0002-1148-1976, #NODATA#, 0000-0003-0876-9060, 0000-0001-6226-0957, 0000-0002-6273-4160, 0000-0003-0684-7539, 0000-0001-7343-3120, 0000-0001-8212-0521, 0000-0002-6204-4864, 0000-0002-7744-3550, 0000-0002-0975-9019, 0000-0002-8879-6159, Song, Se Jin, Wang, Jincheng, Martino, Cameron, Jiang, Lingjing, Thompson, Wesley K., Shenhav, Liat, McDonald, Daniel, Marotz, Clarisse, Harris, Paul R., Hernandez, Caroll D., Henderson, Nora, Ackley, Elizabeth, Nardella, Deanna, Gillihan, Charles, Montacuti, Valentina, Schweizer, William, Jay, Melanie, Combellick, Joan, Sun, Haipeng, García-Mantrana, Izaskun, Gil Raga, Fernando, Collado, María Carmen, Rivera Viñas, Juana I., Campos Rivera, Maribel, Ruiz Calderón, Jean F., Knight, Rob, Domínguez Bello, María Gloria, 0000-0003-0750-5709, 0000-0002-1076-8326, 0000-0001-9334-1258, 0000-0001-8706-2850, 0000-0002-1148-1976, #NODATA#, 0000-0003-0876-9060, 0000-0001-6226-0957, 0000-0002-6273-4160, 0000-0003-0684-7539, 0000-0001-7343-3120, 0000-0001-8212-0521, 0000-0002-6204-4864, 0000-0002-7744-3550, 0000-0002-0975-9019, 0000-0002-8879-6159, Song, Se Jin, Wang, Jincheng, Martino, Cameron, Jiang, Lingjing, Thompson, Wesley K., Shenhav, Liat, McDonald, Daniel, Marotz, Clarisse, Harris, Paul R., Hernandez, Caroll D., Henderson, Nora, Ackley, Elizabeth, Nardella, Deanna, Gillihan, Charles, Montacuti, Valentina, Schweizer, William, Jay, Melanie, Combellick, Joan, Sun, Haipeng, García-Mantrana, Izaskun, Gil Raga, Fernando, Collado, María Carmen, Rivera Viñas, Juana I., Campos Rivera, Maribel, Ruiz Calderón, Jean F., Knight, Rob, and Domínguez Bello, María Gloria

Abstract

Early microbiota perturbations are associated with disorders that involve immunological underpinnings. Cesarean section (CS)-born babies show altered microbiota development in relation to babies born vaginally. Here we present the first statistically powered longitudinal study to determine the effect of restoring exposure to maternal vaginal fluids after CS birth.

Published
2021

69. Severe acute respiratory coronavirus virus 2 (SARS-CoV-2) screening among symptom-free healthcare workers

Author

Demmer, Ryan T., primary, Ulrich, Angela K., additional, Wiggen, Talia D., additional, Strickland, Ali, additional, Naumchik, Brianna M., additional, Kulasingam, Shalini, additional, Stovitz, Steven D., additional, Marotz, Clarisse, additional, Belda-Ferre, Pedro, additional, Humphrey, Greg, additional, De Hoff, Peter, additional, Laurent, Louise, additional, Kline, Susan, additional, and Knight, Rob, additional

Published
2021
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71. Emergence of an early SARS-CoV-2 epidemic in the United States

Author

Zeller, Mark, primary, Gangavarapu, Karthik, additional, Anderson, Catelyn, additional, Smither, Allison R., additional, Vanchiere, John A., additional, Rose, Rebecca, additional, Snyder, Daniel J., additional, Dudas, Gytis, additional, Watts, Alexander, additional, Matteson, Nathaniel L., additional, Robles-Sikisaka, Refugio, additional, Marshall, Maximilian, additional, Feehan, Amy K., additional, Sabino-Santos, Gilberto, additional, Bell-Kareem, Antoinette R., additional, Hughes, Laura D., additional, Alkuzweny, Manar, additional, Snarski, Patricia, additional, Garcia-Diaz, Julia, additional, Scott, Rona S., additional, Melnik, Lilia I., additional, Klitting, Raphaëlle, additional, McGraw, Michelle, additional, Belda-Ferre, Pedro, additional, DeHoff, Peter, additional, Sathe, Shashank, additional, Marotz, Clarisse, additional, Grubaugh, Nathan, additional, Nolan, David J., additional, Drouin, Arnaud C., additional, Genemaras, Kaylynn J., additional, Chao, Karissa, additional, Topol, Sarah, additional, Spencer, Emily, additional, Nicholson, Laura, additional, Aigner, Stefan, additional, Yeo, Gene W., additional, Farnaes, Lauge, additional, Hobbs, Charlotte A., additional, Laurent, Louise C., additional, Knight, Rob, additional, Hodcroft, Emma B., additional, Khan, Kamran, additional, Fusco, Dahlene N., additional, Cooper, Vaughn S., additional, Lemey, Phillipe, additional, Gardner, Lauren, additional, Lamers, Susanna L., additional, Kamil, Jeremy P., additional, Garry, Robert F., additional, Suchard, Marc A., additional, and Andersen, Kristian G., additional

Published
2021
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72. Automated, Miniaturized, and Scalable Screening of Healthcare Workers, First Responders, and Students for SARS-Cov-2 in San Diego County

Author

Morgan, Sydney C., primary, Aigner, Stefan, additional, Anderson, Catelyn, additional, Belda-Ferre, Pedro, additional, De Hoff, Peter, additional, Marotz, Clarisse, additional, Sathe, Shashank, additional, Zeller, Mark, additional, Ahmed, Noorsher, additional, Audhya, Xaver, additional, Baer, Nathan A., additional, Barber, Tom, additional, Barrick, Bethany, additional, Batachari, Lakshmi, additional, Betty, Maryann, additional, Blue, Steven M., additional, Brainard, Brent, additional, Buckley, Tyler, additional, Case, Jamie, additional, Castro-Martinez, Anelizze, additional, Chacón, Marisol, additional, Cheung, Willi, additional, Chong, LaVonnye, additional, Coufal, Nicole G., additional, Crescini, Evelyn S., additional, DeGrand, Scott, additional, Dimmock, David P., additional, Donofrio-Odmann, J. Joelle, additional, Eisner, Emily R., additional, Estaki, Mehrbod, additional, Franco Vargas, Lizbeth, additional, Freddock, Michelle, additional, Gallant, Robert M., additional, Galmozzi, Andrea, additional, Gao, Nina J., additional, Gilmer, Sheldon, additional, Grzelak, Edyta M., additional, Hakim, Abbas, additional, Hart, Jonathan, additional, Hobbs, Charlotte, additional, Humphrey, Gregory, additional, Ilkenhans, Nadja, additional, Jacobs, Marni, additional, Kahn, Christopher A., additional, Kapadia, Bhavika K., additional, Kim, Matthew, additional, Kurian, Sunil, additional, Lastrella, Alma L., additional, Lawrence, Elijah S., additional, Lee, Kari, additional, Liang, Qishan, additional, Liliom, Hanna, additional, Lo Sardo, Valentina, additional, Logan, Robert, additional, Machnicki, Michal, additional, Magallanes, Celestine G., additional, Mah, Clarence K., additional, Malacki, Denise, additional, Marina, Ryan J., additional, Marsh, Christopher, additional, Martin, Natasha K., additional, Matteson, Nathaniel L., additional, Maunder, Daniel J., additional, McBride, Kyle, additional, McDonald, Bryan, additional, McGraw, Michelle, additional, Meadows, Audra R., additional, Meyer, Michelle, additional, Morey, Amber L., additional, Mueller, Jasmine R., additional, Ngo, Toan T., additional, Nguyen, Viet, additional, Nicholson, Laura J., additional, Nouri, Alhakam, additional, Nudell, Victoria, additional, Nunez, Eugenio, additional, O&apos;Neill, Kyle, additional, Ostrander, R. Tyler, additional, Pantham, Priyadarshini, additional, Park, Samuel S., additional, Picone, David, additional, Plascencia, Ashley, additional, Pratumchai, Isaraphorn, additional, Quigley, Michael, additional, Ragsac, Michelle Franc, additional, Richardson, Andrew C., additional, Robles-Sikisaka, Refugio, additional, Ruiz, Christopher A., additional, Ryan, Justin, additional, Sacco, Lisa, additional, Saraf, Sharada, additional, Seaver, Phoebe, additional, Sewall, Leigh, additional, Smoot, Elizabeth W., additional, Sweeney, Kathleen M., additional, Tekkatte, Chandana, additional, Tsai, Rebecca, additional, Valentine, Holly, additional, Walsh, Shawn, additional, Williams, August, additional, Wu, Min Yi, additional, Xia, Bing, additional, Yee, Brian, additional, Zhang, Jason Z., additional, Andersen, Kristian G., additional, Farnaes, Lauge, additional, Knight, Rob, additional, Yeo, Gene W., additional, and Laurent, Louise C., additional

Published
2021
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73. Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment

Author

Minich, Jeremiah, primary, Ali, Farhana, additional, Marotz, Clarisse, additional, Belda-Ferre, Pedro, additional, Chiang, Leslie, additional, Shaffer, Justin P., additional, Carpenter, Carolina S., additional, McDonald, Daniel, additional, Gilbert, Jack, additional, Allard, Sarah M., additional, Allen, Eric E, additional, Knight, Rob, additional, Sweeney, Daniel A., additional, and Swafford, Austin D., additional

Published
2020
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74. Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment

Author

Marotz, Clarisse, primary, Belda-Ferre, Pedro, additional, Ali, Farhana, additional, Das, Promi, additional, Huang, Shi, additional, Cantrell, Kalen, additional, Jiang, Lingjing, additional, Martino, Cameron, additional, Diner, Rachel E., additional, Rahman, Gibraan, additional, McDonald, Daniel, additional, Armstrong, George, additional, Kodera, Sho, additional, Donato, Sonya, additional, Ecklu-Mensah, Gertrude, additional, Gottel, Neil, additional, Salas Garcia, Mariana C., additional, Chiang, Leslie Y., additional, Salido, Rodolfo A., additional, Shaffer, Justin P., additional, Bryant, MacKenzie, additional, Sanders, Karenina, additional, Humphrey, Greg, additional, Ackermann, Gail, additional, Haiminen, Niina, additional, Beck, Kristen L., additional, Kim, Ho-Cheol, additional, Carrieri, Anna Paola, additional, Parida, Laxmi, additional, Vázquez-Baeza, Yoshiki, additional, Torriani, Francesca J., additional, Knight, Rob, additional, Gilbert, Jack A., additional, Sweeney, Daniel A., additional, and Allard, Sarah M., additional

Published
2020
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75. A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities

Author

Shaffer, Justin P., primary, Marotz, Clarisse, additional, Belda-Ferre, Pedro, additional, Martino, Cameron, additional, Wandro, Stephen, additional, Estaki, Mehrbod, additional, Salido, Rodolfo A., additional, Carpenter, Carolina S., additional, Zaramela, Livia S., additional, Minich, Jeremiah J., additional, Bryant, MacKenzie, additional, Sanders, Karenina, additional, Fraraccio, Serena, additional, Ackermann, Gail, additional, Humphrey, Gregory, additional, Swafford, Austin D., additional, Miller-Montgomery, Sandrine, additional, and Knight, Rob, additional

Published
2020
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76. EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic datasets

Author

Cantrell, Kalen, primary, Fedarko, Marcus W., additional, Rahman, Gibraan, additional, McDonald, Daniel, additional, Yang, Yimeng, additional, Zaw, Thant, additional, Gonzalez, Antonio, additional, Janssen, Stefan, additional, Estaki, Mehrbod, additional, Haiminen, Niina, additional, Beck, Kristen L., additional, Zhu, Qiyun, additional, Sayyari, Erfan, additional, Morton, Jamie, additional, Tripathi, Anupriya, additional, Gauglitz, Julia M., additional, Marotz, Clarisse, additional, Matteson, Nathaniel L., additional, Martino, Cameron, additional, Sanders, Jon G., additional, Carrieri, Anna Paola, additional, Song, Se Jin, additional, Swafford, Austin D., additional, Dorrestein, Pieter C., additional, Andersen, Kristian G., additional, Parida, Laxmi, additional, Kim, Ho-Cheol, additional, Vázquez-Baeza, Yoshiki, additional, and Knight, Rob, additional

Published
2020
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77. Context-aware dimensionality reduction deconvolutes gut microbial community dynamics

Author

Martino, Cameron, primary, Shenhav, Liat, additional, Marotz, Clarisse A., additional, Armstrong, George, additional, McDonald, Daniel, additional, Vázquez-Baeza, Yoshiki, additional, Morton, James T., additional, Jiang, Lingjing, additional, Dominguez-Bello, Maria Gloria, additional, Swafford, Austin D., additional, Halperin, Eran, additional, and Knight, Rob, additional

Published
2020
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78. Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity

Author

Martino, Cameron, primary, Kellman, Benjamin P., additional, Sandoval, Daniel R., additional, Clausen, Thomas Mandel, additional, Marotz, Clarisse A., additional, Song, Se Jin, additional, Wandro, Stephen, additional, Zaramela, Livia S., additional, Salido Benítez, Rodolfo Antonio, additional, Zhu, Qiyun, additional, Armingol, Erick, additional, Vázquez-Baeza, Yoshiki, additional, McDonald, Daniel, additional, Sorrentino, James T., additional, Taylor, Bryn, additional, Belda-Ferre, Pedro, additional, Liang, Chenguang, additional, Zhang, Yujie, additional, Schifanella, Luca, additional, Klatt, Nichole R., additional, Havulinna, Aki S., additional, Jousilahti, Pekka, additional, Huang, Shi, additional, Haiminen, Niina, additional, Parida, Laxmi, additional, Kim, Ho-Cheol, additional, Swafford, Austin D., additional, Zengler, Karsten, additional, Cheng, Susan, additional, Inouye, Michael, additional, Niiranen, Teemu, additional, Jain, Mohit, additional, Salomaa, Veikko, additional, Esko, Jeffrey D., additional, Lewis, Nathan E., additional, and Knight, Rob, additional

Published
2020
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79. SARS-CoV-2 Screening Among Symptom-Free Healthcare Workers

Author

Demmer, Ryan T., primary, Ulrich, Angela K., additional, Wiggen, Talia D., additional, Strickland, Ali, additional, Naumchik, Brianna M., additional, Kulasingam, Shalini, additional, Stovitz, Steven D., additional, Marotz, Clarisse, additional, Belda-Ferre, Pedro, additional, Humphrey, Greg, additional, De Hoff, Peter, additional, Laurent, Louise, additional, Kline, Susan, additional, and Knight, Rob, additional

Published
2020
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80. Reference data based insights expand understanding of human metabolomes

Author

Gauglitz, Julia M., primary, Bittremieux, Wout, additional, Williams, Candace L., additional, Weldon, Kelly C., additional, Panitchpakdi, Morgan, additional, Di Ottavio, Francesca, additional, Aceves, Christine M., additional, Brown, Elizabeth, additional, Sikora, Nicole C., additional, Jarmusch, Alan K., additional, Martino, Cameron, additional, Tripathi, Anupriya, additional, Sayyari, Erfan, additional, Shaffer, Justin P., additional, Coras, Roxana, additional, Vargas, Fernando, additional, Goldasich, Lindsay DeRight, additional, Schwartz, Tara, additional, Bryant, MacKenzie, additional, Humphrey, Gregory, additional, Johnson, Abigail J., additional, Spengler, Katharina, additional, Belda-Ferre, Pedro, additional, Diaz, Edgar, additional, McDonald, Daniel, additional, Zhu, Qiyun, additional, Nguyen, Dominic S., additional, Elijah, Emmanuel O., additional, Wang, Mingxun, additional, Marotz, Clarisse, additional, Sprecher, Kate E., additional, Robles, Daniela Vargas, additional, Withrow, Dana, additional, Ackermann, Gail, additional, Herrera, Lourdes, additional, Bradford, Barry J., additional, Mauriz Marques, Lucas Maciel, additional, Amaral, Juliano Geraldo, additional, Silva, Rodrigo Moreira, additional, Veras, Flávio Protaso, additional, Cunha, Thiago Mattar, additional, Ribeiro Oliveira, Rene Donizeti, additional, Louzada-Junior, Paulo, additional, Mills, Robert H., additional, Galasko, Douglas, additional, Dulai, Parambir S., additional, Wittenberg, Curt, additional, Gonzalez, David J., additional, Terkeltaub, Robert, additional, Doty, Megan M., additional, Kim, Jae H., additional, Rhee, Kyung E., additional, Beauchamp-Walters, Julia, additional, Wright, Kenneth P., additional, Dominguez-Bello, Maria Gloria, additional, Manary, Mark, additional, Oliveira, Michelli F., additional, Boland, Brigid S., additional, Lopes, Norberto Peporine, additional, Guma, Monica, additional, Swafford, Austin D., additional, Dutton, Rachel J., additional, Knight, Rob, additional, and Dorrestein, Pieter C., additional

Published
2020
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81. Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment

Author

Minich, Jeremiah J., primary, Ali, Farhana, additional, Marotz, Clarisse, additional, Belda-Ferre, Pedro, additional, Chiang, Leslie, additional, Shaffer, Justin P., additional, Carpenter, Carolina S., additional, McDonald, Daniel, additional, Gilbert, Jack, additional, Allard, Sarah M., additional, Allen, Eric E, additional, Knight, Rob, additional, Sweeney, Daniel A., additional, and Swafford, Austin D., additional

Published
2020
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82. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, Bolyen, Evan, Rideout, Jai Ram, Dillon, Matthew R., Bokulich, Nicholas A., Abnet, Christian C., Al-Ghalith, Gabriel A., Alexander, Harriet, Alm, Eric J, Arumugam, Manimozhiyan, Asnicar, Francesco, Bai, Yang, Bisanz, Jordan E., Bittinger, Kyle, Brejnrod, Asker, Brislawn, Colin J., Brown, C. Titus, Callahan, Benjamin J., Caraballo-Rodríguez, Andrés Mauricio, Chase, John, Cope, Emily K., Da Silva, Ricardo, Diener, Christian, Dorrestein, Pieter C., Douglas, Gavin M., Durall, Daniel M., Duvallet, Claire, Edwardson, Christian F., Ernst, Madeleine, Estaki, Mehrbod, Fouquier, Jennifer, Gauglitz, Julia M., Gibbons, Sean M., Gibson, Deanna L., Gonzalez, Antonio, Gorlick, Kestrel, Guo, Jiarong, Hillmann, Benjamin, Holmes, Susan, Holste, Hannes, Huttenhower, Curtis, Huttley, Gavin A., Janssen, Stefan, Jarmusch, Alan K., Jiang, Lingjing, Kaehler, Benjamin D., Kang, Kyo Bin, Keefe, Christopher R., Keim, Paul, Kelley, Scott T., Knights, Dan, Koester, Irina, Kosciolek, Tomasz, Kreps, Jorden, Langille, Morgan G. I., Lee, Joslynn, Ley, Ruth, Liu, Yong-Xin, Loftfield, Erikka, Lozupone, Catherine, Maher, Massoud, Marotz, Clarisse, Martin, Bryan D., McDonald, Daniel, McIver, Lauren J., Melnik, Alexey V., Metcalf, Jessica L., Morgan, Sydney C., Morton, Jamie T., Naimey, Ahmad Turan, Navas-Molina, Jose A., Nothias, Louis Felix, Orchanian, Stephanie B., Pearson, Talima, Peoples, Samuel L., Petras, Daniel, Preuss, Mary Lai, Pruesse, Elmar, Rasmussen, Lasse Buur, Rivers, Adam, Robeson, Michael S., Rosenthal, Patrick, Segata, Nicola, Shaffer, Michael, Shiffer, Arron, Sinha, Rashmi, Song, Se Jin, Spear, John R., Swafford, Austin D., Thompson, Luke R., Torres, Pedro J., Trinh, Pauline, Tripathi, Anupriya, Turnbaugh, Peter J., Ul-Hasan, Sabah, van der Hooft, Justin J. J., Vargas, Fernando, Vázquez-Baeza, Yoshiki, Vogtmann, Emily, von Hippel, Max, Walters, William, Wan, Yunhu, Wang, Mingxun, Warren, Jonathan, Weber, Kyle C., Williamson, Charles H. D., Willis, Amy D., Xu, Zhenjiang Zech, Zaneveld, Jesse R., Zhang, Yilong, Zhu, Qiyun, Knight, Rob, Caporaso, J. Gregory, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, Bolyen, Evan, Rideout, Jai Ram, Dillon, Matthew R., Bokulich, Nicholas A., Abnet, Christian C., Al-Ghalith, Gabriel A., Alexander, Harriet, Alm, Eric J, Arumugam, Manimozhiyan, Asnicar, Francesco, Bai, Yang, Bisanz, Jordan E., Bittinger, Kyle, Brejnrod, Asker, Brislawn, Colin J., Brown, C. Titus, Callahan, Benjamin J., Caraballo-Rodríguez, Andrés Mauricio, Chase, John, Cope, Emily K., Da Silva, Ricardo, Diener, Christian, Dorrestein, Pieter C., Douglas, Gavin M., Durall, Daniel M., Duvallet, Claire, Edwardson, Christian F., Ernst, Madeleine, Estaki, Mehrbod, Fouquier, Jennifer, Gauglitz, Julia M., Gibbons, Sean M., Gibson, Deanna L., Gonzalez, Antonio, Gorlick, Kestrel, Guo, Jiarong, Hillmann, Benjamin, Holmes, Susan, Holste, Hannes, Huttenhower, Curtis, Huttley, Gavin A., Janssen, Stefan, Jarmusch, Alan K., Jiang, Lingjing, Kaehler, Benjamin D., Kang, Kyo Bin, Keefe, Christopher R., Keim, Paul, Kelley, Scott T., Knights, Dan, Koester, Irina, Kosciolek, Tomasz, Kreps, Jorden, Langille, Morgan G. I., Lee, Joslynn, Ley, Ruth, Liu, Yong-Xin, Loftfield, Erikka, Lozupone, Catherine, Maher, Massoud, Marotz, Clarisse, Martin, Bryan D., McDonald, Daniel, McIver, Lauren J., Melnik, Alexey V., Metcalf, Jessica L., Morgan, Sydney C., Morton, Jamie T., Naimey, Ahmad Turan, Navas-Molina, Jose A., Nothias, Louis Felix, Orchanian, Stephanie B., Pearson, Talima, Peoples, Samuel L., Petras, Daniel, Preuss, Mary Lai, Pruesse, Elmar, Rasmussen, Lasse Buur, Rivers, Adam, Robeson, Michael S., Rosenthal, Patrick, Segata, Nicola, Shaffer, Michael, Shiffer, Arron, Sinha, Rashmi, Song, Se Jin, Spear, John R., Swafford, Austin D., Thompson, Luke R., Torres, Pedro J., Trinh, Pauline, Tripathi, Anupriya, Turnbaugh, Peter J., Ul-Hasan, Sabah, van der Hooft, Justin J. J., Vargas, Fernando, Vázquez-Baeza, Yoshiki, Vogtmann, Emily, von Hippel, Max, Walters, William, Wan, Yunhu, Wang, Mingxun, Warren, Jonathan, Weber, Kyle C., Williamson, Charles H. D., Willis, Amy D., Xu, Zhenjiang Zech, Zaneveld, Jesse R., Zhang, Yilong, Zhu, Qiyun, Knight, Rob, and Caporaso, J. Gregory

Published
2020

83. Treating Obesity and Metabolic Syndrome with Fecal Microbiota Transplantation

Author

Marotz, Clarisse A. and Zarrinpar, Amir

Subjects
Metabolic Syndrome, obesity, Feces, Animals, Humans, Mini-Review, Fecal Microbiota Transplantation, Fecal microbiota transplant
Abstract

The worldwide prevalence of metabolic syndrome, which includes obesity and its associated diseases, is rising rapidly. The human gut microbiome is recognized as an independent environmental modulator of host metabolic health and disease. Research in animal models has demonstrated that the gut microbiome has the functional capacity to induce or relieve metabolic syndrome. One way to modify the human gut microbiome is by transplanting fecal matter, which contains an abundance of live microorganisms, from a healthy individual to a diseased one in the hopes of alleviating illness. Here we review recent evidence suggesting efficacy of fecal microbiota transplant (FMT) in animal models and humans for the treatment of obesity and its associated metabolic disorders.

Published
2016

85. Author Correction:Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 (Nature Biotechnology, (2019), 37, 8, (852-857), 10.1038/s41587-019-0209-9)

Author

Bolyen, Evan, Rideout, Jai Ram, Dillon, Matthew R., Bokulich, Nicholas A., Abnet, Christian C., Al-Ghalith, Gabriel A., Alexander, Harriet, Alm, Eric J., Arumugam, Manimozhiyan, Asnicar, Francesco, Bai, Yang, Bisanz, Jordan E., Bittinger, Kyle, Brejnrod, Asker, Brislawn, Colin J., Brown, C. Titus, Callahan, Benjamin J., Caraballo-Rodríguez, Andrés Mauricio, Chase, John, Cope, Emily K., Da Silva, Ricardo, Diener, Christian, Dorrestein, Pieter C., Douglas, Gavin M., Durall, Daniel M., Duvallet, Claire, Edwardson, Christian F., Ernst, Madeleine, Estaki, Mehrbod, Fouquier, Jennifer, Gauglitz, Julia M., Gibbons, Sean M., Gibson, Deanna L., Gonzalez, Antonio, Gorlick, Kestrel, Guo, Jiarong, Hillmann, Benjamin, Holmes, Susan, Holste, Hannes, Huttenhower, Curtis, Huttley, Gavin A., Janssen, Stefan, Jarmusch, Alan K., Jiang, Lingjing, Kaehler, Benjamin D., Kang, Kyo Bin, Keefe, Christopher R., Keim, Paul, Kelley, Scott T., Knights, Dan, Koester, Irina, Kosciolek, Tomasz, Kreps, Jorden, Langille, Morgan G.I., Lee, Joslynn, Ley, Ruth, Liu, Yong Xin, Loftfield, Erikka, Lozupone, Catherine, Maher, Massoud, Marotz, Clarisse, Martin, Bryan D., McDonald, Daniel, McIver, Lauren J., Melnik, Alexey V., Metcalf, Jessica L., Morgan, Sydney C., Morton, Jamie T., Naimey, Ahmad Turan, Navas-Molina, Jose A., Nothias, Louis Felix, Orchanian, Stephanie B., Pearson, Talima, Peoples, Samuel L., Petras, Daniel, Preuss, Mary Lai, Pruesse, Elmar, Rasmussen, Lasse Buur, Rivers, Adam, Robeson, Michael S., Rosenthal, Patrick, Segata, Nicola, Shaffer, Michael, Shiffer, Arron, Sinha, Rashmi, Song, Se Jin, Spear, John R., Swafford, Austin D., Thompson, Luke R., Torres, Pedro J., Trinh, Pauline, Tripathi, Anupriya, Turnbaugh, Peter J., Ul-Hasan, Sabah, van der Hooft, Justin J.J., Vargas, Fernando, Vázquez-Baeza, Yoshiki, Vogtmann, Emily, von Hippel, Max, Walters, William, Wan, Yunhu, Wang, Mingxun, Warren, Jonathan, Weber, Kyle C., Williamson, Charles H.D., Willis, Amy D., Xu, Zhenjiang Zech, Zaneveld, Jesse R., Zhang, Yilong, Zhu, Qiyun, Knight, Rob, Caporaso, J. Gregory, Bolyen, Evan, Rideout, Jai Ram, Dillon, Matthew R., Bokulich, Nicholas A., Abnet, Christian C., Al-Ghalith, Gabriel A., Alexander, Harriet, Alm, Eric J., Arumugam, Manimozhiyan, Asnicar, Francesco, Bai, Yang, Bisanz, Jordan E., Bittinger, Kyle, Brejnrod, Asker, Brislawn, Colin J., Brown, C. Titus, Callahan, Benjamin J., Caraballo-Rodríguez, Andrés Mauricio, Chase, John, Cope, Emily K., Da Silva, Ricardo, Diener, Christian, Dorrestein, Pieter C., Douglas, Gavin M., Durall, Daniel M., Duvallet, Claire, Edwardson, Christian F., Ernst, Madeleine, Estaki, Mehrbod, Fouquier, Jennifer, Gauglitz, Julia M., Gibbons, Sean M., Gibson, Deanna L., Gonzalez, Antonio, Gorlick, Kestrel, Guo, Jiarong, Hillmann, Benjamin, Holmes, Susan, Holste, Hannes, Huttenhower, Curtis, Huttley, Gavin A., Janssen, Stefan, Jarmusch, Alan K., Jiang, Lingjing, Kaehler, Benjamin D., Kang, Kyo Bin, Keefe, Christopher R., Keim, Paul, Kelley, Scott T., Knights, Dan, Koester, Irina, Kosciolek, Tomasz, Kreps, Jorden, Langille, Morgan G.I., Lee, Joslynn, Ley, Ruth, Liu, Yong Xin, Loftfield, Erikka, Lozupone, Catherine, Maher, Massoud, Marotz, Clarisse, Martin, Bryan D., McDonald, Daniel, McIver, Lauren J., Melnik, Alexey V., Metcalf, Jessica L., Morgan, Sydney C., Morton, Jamie T., Naimey, Ahmad Turan, Navas-Molina, Jose A., Nothias, Louis Felix, Orchanian, Stephanie B., Pearson, Talima, Peoples, Samuel L., Petras, Daniel, Preuss, Mary Lai, Pruesse, Elmar, Rasmussen, Lasse Buur, Rivers, Adam, Robeson, Michael S., Rosenthal, Patrick, Segata, Nicola, Shaffer, Michael, Shiffer, Arron, Sinha, Rashmi, Song, Se Jin, Spear, John R., Swafford, Austin D., Thompson, Luke R., Torres, Pedro J., Trinh, Pauline, Tripathi, Anupriya, Turnbaugh, Peter J., Ul-Hasan, Sabah, van der Hooft, Justin J.J., Vargas, Fernando, Vázquez-Baeza, Yoshiki, Vogtmann, Emily, von Hippel, Max, Walters, William, Wan, Yunhu, Wang, Mingxun, Warren, Jonathan, Weber, Kyle C., Williamson, Charles H.D., Willis, Amy D., Xu, Zhenjiang Zech, Zaneveld, Jesse R., Zhang, Yilong, Zhu, Qiyun, Knight, Rob, and Caporaso, J. Gregory

Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2019

87. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

Author

Bolyen, Evan, primary, Rideout, Jai Ram, additional, Dillon, Matthew R, additional, Bokulich, Nicholas A, additional, Abnet, Christian, additional, Al-Ghalith, Gabriel A, additional, Alexander, Harriet, additional, Alm, Eric J, additional, Arumugam, Manimozhiyan, additional, Asnicar, Francesco, additional, Bai, Yang, additional, Bisanz, Jordan E, additional, Bittinger, Kyle, additional, Brejnrod, Asker, additional, Brislawn, Colin J, additional, Brown, C Titus, additional, Callahan, Benjamin J, additional, Caraballo-Rodríguez, Andrés Mauricio, additional, Chase, John, additional, Cope, Emily, additional, Da Silva, Ricardo, additional, Dorrestein, Pieter C, additional, Douglas, Gavin M, additional, Durall, Daniel M, additional, Duvallet, Claire, additional, Edwardson, Christian F, additional, Ernst, Madeleine, additional, Estaki, Mehrbod, additional, Fouquier, Jennifer, additional, Gauglitz, Julia M, additional, Gibson, Deanna L, additional, Gonzalez, Antonio, additional, Gorlick, Kestrel, additional, Guo, Jiarong, additional, Hillmann, Benjamin, additional, Holmes, Susan, additional, Holste, Hannes, additional, Huttenhower, Curtis, additional, Huttley, Gavin, additional, Janssen, Stefan, additional, Jarmusch, Alan K, additional, Jiang, Lingjing, additional, Kaehler, Benjamin, additional, Kang, Kyo Bin, additional, Keefe, Christopher R, additional, Keim, Paul, additional, Kelley, Scott T, additional, Knights, Dan, additional, Koester, Irina, additional, Kosciolek, Tomasz, additional, Kreps, Jorden, additional, Langille, Morgan GI, additional, Lee, Joslynn, additional, Ley, Ruth, additional, Liu, Yong-Xin, additional, Loftfield, Erikka, additional, Lozupone, Catherine, additional, Maher, Massoud, additional, Marotz, Clarisse, additional, Martin, Bryan D, additional, McDonald, Daniel, additional, McIver, Lauren J, additional, Melnik, Alexey V, additional, Metcalf, Jessica L, additional, Morgan, Sydney C, additional, Morton, Jamie, additional, Naimey, Ahmad Turan, additional, Navas-Molina, Jose A, additional, Nothias, Louis Felix, additional, Orchanian, Stephanie B, additional, Pearson, Talima, additional, Peoples, Samuel L, additional, Petras, Daniel, additional, Preuss, Mary Lai, additional, Pruesse, Elmar, additional, Rasmussen, Lasse Buur, additional, Rivers, Adam, additional, Robeson, II, Michael S, additional, Rosenthal, Patrick, additional, Segata, Nicola, additional, Shaffer, Michael, additional, Shiffer, Arron, additional, Sinha, Rashmi, additional, Song, Se Jin, additional, Spear, John R, additional, Swafford, Austin D, additional, Thompson, Luke R, additional, Torres, Pedro J, additional, Trinh, Pauline, additional, Tripathi, Anupriya, additional, Turnbaugh, Peter J, additional, Ul-Hasan, Sabah, additional, van der Hooft, Justin JJ, additional, Vargas, Fernando, additional, Vázquez-Baeza, Yoshiki, additional, Vogtmann, Emily, additional, von Hippel, Max, additional, Walters, William, additional, Wan, Yunhu, additional, Wang, Mingxun, additional, Warren, Jonathan, additional, Weber, Kyle C, additional, Williamson, Chase HD, additional, Willis, Amy D, additional, Xu, Zhenjiang Zech, additional, Zaneveld, Jesse R, additional, Zhang, Yilong, additional, Zhu, Qiyun, additional, Knight, Rob, additional, and Caporaso, J Gregory, additional

Published
2018
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88. Are microbiome studies ready for hypothesis-driven research?

Author

Tripathi, Anupriya, primary, Marotz, Clarisse, additional, Gonzalez, Antonio, additional, Vázquez-Baeza, Yoshiki, additional, Song, Se Jin, additional, Bouslimani, Amina, additional, McDonald, Daniel, additional, Zhu, Qiyun, additional, Sanders, Jon G, additional, Smarr, Larry, additional, Dorrestein, Pieter C, additional, and Knight, Rob, additional

Published
2018
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89. American Gut: an Open Platform for Citizen Science Microbiome Research.

Author

UCL - SSS/LDRI - Louvain Drug Research Institute, McDonald, Daniel, Hyde, Embriette, Debelius, Justine W, Morton, James T, Gonzalez, Antonio, Ackermann, Gail, Aksenov, Alexander A, Behsaz, Bahar, Brennan, Caitriona, Chen, Yingfeng, DeRight Goldasich, Lindsay, Dorrestein, Pieter C, Dunn, Robert R, Fahimipour, Ashkaan K, Gaffney, James, Gilbert, Jack A, Gogul, Grant, Green, Jessica L, Hugenholtz, Philip, Humphrey, Greg, Huttenhower, Curtis, Jackson, Matthew A, Janssen, Stefan, Jeste, Dilip V, Jiang, Lingjing, Kelley, Scott T, Knights, Dan, Kosciolek, Tomasz, Ladau, Joshua, Leach, Jeff, Marotz, Clarisse, Meleshko, Dmitry, Melnik, Alexey V, Metcalf, Jessica L, Mohimani, Hosein, Montassier, Emmanuel, Navas-Molina, Jose, Nguyen, Tanya T, Peddada, Shyamal, Pevzner, Pavel, Pollard, Katherine S, Rahnavard, Gholamali, Robbins-Pianka, Adam, Sangwan, Naseer, Shorenstein, Joshua, Smarr, Larry, Song, Se Jin, Spector, Timothy, Swafford, Austin D, Thackray, Varykina G, Thompson, Luke R, Tripathi, Anupriya, Vázquez-Baeza, Yoshiki, Vrbanac, Alison, Wischmeyer, Paul, Wolfe, Elaine, Zhu, Qiyun, American Gut Consortium, Knight, Rob, Cani, Patrice D., UCL - SSS/LDRI - Louvain Drug Research Institute, McDonald, Daniel, Hyde, Embriette, Debelius, Justine W, Morton, James T, Gonzalez, Antonio, Ackermann, Gail, Aksenov, Alexander A, Behsaz, Bahar, Brennan, Caitriona, Chen, Yingfeng, DeRight Goldasich, Lindsay, Dorrestein, Pieter C, Dunn, Robert R, Fahimipour, Ashkaan K, Gaffney, James, Gilbert, Jack A, Gogul, Grant, Green, Jessica L, Hugenholtz, Philip, Humphrey, Greg, Huttenhower, Curtis, Jackson, Matthew A, Janssen, Stefan, Jeste, Dilip V, Jiang, Lingjing, Kelley, Scott T, Knights, Dan, Kosciolek, Tomasz, Ladau, Joshua, Leach, Jeff, Marotz, Clarisse, Meleshko, Dmitry, Melnik, Alexey V, Metcalf, Jessica L, Mohimani, Hosein, Montassier, Emmanuel, Navas-Molina, Jose, Nguyen, Tanya T, Peddada, Shyamal, Pevzner, Pavel, Pollard, Katherine S, Rahnavard, Gholamali, Robbins-Pianka, Adam, Sangwan, Naseer, Shorenstein, Joshua, Smarr, Larry, Song, Se Jin, Spector, Timothy, Swafford, Austin D, Thackray, Varykina G, Thompson, Luke R, Tripathi, Anupriya, Vázquez-Baeza, Yoshiki, Vrbanac, Alison, Wischmeyer, Paul, Wolfe, Elaine, Zhu, Qiyun, American Gut Consortium, Knight, Rob, and Cani, Patrice D.

Abstract

Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the United States, United Kingdom, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes compared to environmental samples; demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations; uncover new molecules and kinds of molecular communities in the human stool metabolome; and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power). We also demonstrate the utility of the living data resource and cross-cohort comparison to confirm existing associations between the microbiome and psychiatric illness and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education. IMPORTANCE We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet, which we confirm with untargeted metabolomics on hundreds of

Published
2018

90. Impacts of the Human Gut Microbiome on Therapeutics

Author

Vázquez-Baeza, Yoshiki, primary, Callewaert, Chris, additional, Debelius, Justine, additional, Hyde, Embriette, additional, Marotz, Clarisse, additional, Morton, James T., additional, Swafford, Austin, additional, Vrbanac, Alison, additional, Dorrestein, Pieter C., additional, and Knight, Rob, additional

Published
2018
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91. The Microbiome and Human Biology

Author

Knight, Rob, primary, Callewaert, Chris, additional, Marotz, Clarisse, additional, Hyde, Embriette R., additional, Debelius, Justine W., additional, McDonald, Daniel, additional, and Sogin, Mitchell L., additional

Published
2017
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95. SPOP mutation leads to genomic instability in prostate cancer

Author

Boysen, Gunther, primary, Barbieri, Christopher E, additional, Prandi, Davide, additional, Blattner, Mirjam, additional, Chae, Sung-Suk, additional, Dahija, Arun, additional, Nataraj, Srilakshmi, additional, Huang, Dennis, additional, Marotz, Clarisse, additional, Xu, Limei, additional, Huang, Julie, additional, Lecca, Paola, additional, Chhangawala, Sagar, additional, Liu, Deli, additional, Zhou, Pengbo, additional, Sboner, Andrea, additional, de Bono, Johann S, additional, Demichelis, Francesca, additional, Houvras, Yariv, additional, and Rubin, Mark A, additional

Published
2015
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96. Author response: SPOP mutation leads to genomic instability in prostate cancer

Author

Boysen, Gunther, primary, Barbieri, Christopher E, additional, Prandi, Davide, additional, Blattner, Mirjam, additional, Chae, Sung-Suk, additional, Dahija, Arun, additional, Nataraj, Srilakshmi, additional, Huang, Dennis, additional, Marotz, Clarisse, additional, Xu, Limei, additional, Huang, Julie, additional, Lecca, Paola, additional, Chhangawala, Sagar, additional, Liu, Deli, additional, Zhou, Pengbo, additional, Sboner, Andrea, additional, de Bono, Johann S, additional, Demichelis, Francesca, additional, Houvras, Yariv, additional, and Rubin, Mark A, additional

Published
2015
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97. Abstract 3844: Targeting EZH2 in neuroendocrine prostate cancer

Author

Puca, Loredana, primary, Gao, Dong, additional, Kossai, Myriam, additional, Marotz, Clarisse, additional, Mosquera, Juan Miguel, additional, MacDonald, Theresa Y., additional, Park, Kyung, additional, Rao, Rema, additional, Sboner, Andrea, additional, Chen, Yu, additional, Rubin, Mark A., additional, and Beltran, Himisha, additional

Published
2015
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98. Abstract LB-018: Defining a molecular subclass of treatment-resistant prostate cancer

Author

Beltran, Himisha, primary, Prandi, Davide, additional, Mosquera, Juan Miguel, additional, Giannopoulou, Eugenia, additional, Puca, Loredana, additional, Marotz, Clarisse, additional, Nanus, David M., additional, Tagawa, Scott T., additional, Elemento, Olivier, additional, Van Allen, Eliezer, additional, Sboner, Andrea, additional, Garraway, Levi, additional, Rubin, Mark A., additional, and Demichelis, Francesca, additional

Published
2015
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99. Abstract 1108: SPOP mutation leads to genomic instability in prostate cancer

Author

Boysen, Gunther, primary, Barbieri, Christopher E., additional, Prandi, Davide, additional, Chae, Sung-Suk, additional, Nataraj, Srilakshmi, additional, Blattner, Mirjam, additional, Marotz, Clarisse, additional, Xu, Limei, additional, Lecca, Paola, additional, Chhangawala, Sagar, additional, Zou, Pengbo, additional, Sboner, Andrea, additional, Demichelis, Francesca, additional, Houvras, Yariv, additional, and Rubin, Mark A., additional

Published
2015
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100. Abstract NG01: SPOP mutation is associated with genomic instability in prostate cancer

Author

Barbieri, Christopher E., primary, Boysen, Gunther, additional, Prandi, Davide, additional, Chae, Sung-Suk, additional, Dahiya, Arun, additional, Nataraj, Srilakshmi, additional, Blattner, Mirjam, additional, Marotz, Clarisse, additional, Xu, Limei, additional, Huang, Julie, additional, Lecca, Paola, additional, Chhangawala, Sagar, additional, Zhou, Pengbo, additional, Sboner, Andrea, additional, Demichelis, Francesca, additional, Houvras, Yariv, additional, and Rubin, Mark A., additional

Published
2015
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