Soil-borne fungi influence seed germination and mortality, with implications for coexistence of desert winter annual plants

por Li, Yue M., Shaffer, Justin P., Hall, Brenna, Ko, Hongseok
Publicado 2019

An Endohyphal Bacterium (Chitinophaga, Bacteroidetes) Alters Carbon Source Use by Fusarium keratoplasticum (F. solani Species Complex, Nectriaceae)

por Shaffer, Justin P., U'Ren, Jana M., Gallery, Rachel E., Baltrus, David A., Arnold, A. Elizabeth
Publicado 2017

Transcriptional Profiles of a Foliar Fungal Endophyte (Pestalotiopsis, Ascomycota) and Its Bacterial Symbiont (Luteibacter, Gammaproteobacteria) Reveal Sulfur Exchange and Growth R...

por Shaffer, Justin P., Carter, Morgan E., Spraker, Joseph E., Clark, Meara, Smith, Brian A., Hockett, Kevin L., Baltrus, David A., Arnold, A. Elizabeth
Publicado 2022

Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype

por Martino, Cameron, McDonald, Daniel, Cantrell, Kalen, Dilmore, Amanda Hazel, Vázquez-Baeza, Yoshiki, Shenhav, Liat, Shaffer, Justin P., Rahman, Gibraan, Armstrong, George, Allaband, Celeste, Song, Se Jin, Knight, Rob
Publicado 2022

Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern California

por Alderete, Tanya L., Jones, Roshonda B., Shaffer, Justin P., Holzhausen, Elizabeth A., Patterson, William B., Kazemian, Elham, Chatzi, Lida, Knight, Rob, Plows, Jasmine F., Berger, Paige K., Goran, Michael I.
Publicado 2021

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

por Minich, Jeremiah, 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., Swafford, Austin D.
Publicado 2020

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

por 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., Swafford, Austin D.
Publicado 2021

Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome

por Taylor, Bryn C., Lejzerowicz, Franck, Poirel, Marion, Shaffer, Justin P., Jiang, Lingjing, Aksenov, Alexander, Litwin, Nicole, Humphrey, Gregory, Martino, Cameron, Miller-Montgomery, Sandrine, Dorrestein, Pieter C., Veiga, Patrick, Song, Se Jin, McDonald, Daniel, Derrien, Muriel, Knight, Rob
Publicado 2020

Postnatal exposure to ambient air pollutants is associated with the composition of the infant gut microbiota at 6-months of age

por Bailey, Maximilian J., Holzhausen, Elizabeth A., Morgan, Zachariah E. M., Naik, Noopur, Shaffer, Justin P., Liang, Donghai, Chang, Howard H., Sarnat, Jeremy, Sun, Shan, Berger, Paige K., Schmidt, Kelsey A., Lurmann, Frederick, Goran, Michael I., Alderete, Tanya L.
Publicado 2022

Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies

por Usyk, Mykhaylo, Peters, Brandilyn A., Karthikeyan, Smruthi, McDonald, Daniel, Sollecito, Christopher C., Vazquez-Baeza, Yoshiki, Shaffer, Justin P., Gellman, Marc D., Talavera, Gregory A., Daviglus, Martha L., Thyagarajan, Bharat, Knight, Rob, Qi, Qibin, Kaplan, Robert, Burk, Robert D.
Publicado 2023

A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities

por Shaffer, Justin P., Marotz, Clarisse, Belda-Ferre, Pedro, Martino, Cameron, Wandro, Stephen, Estaki, Mehrbod, Salido, Rodolfo A., Carpenter, Carolina S., Zaramela, Livia S., Minich, Jeremiah J., Bryant, MacKenzie, Sanders, Karenina, Fraraccio, Serena, Ackermann, Gail, Humphrey, Gregory, Swafford, Austin D., Miller-Montgomery, Sandrine, Knight, Rob
Publicado 2020

A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities

por Shaffer, Justin P, Marotz, Clarisse, Belda-Ferre, Pedro, Martino, Cameron, Wandro, Stephen, Estaki, Mehrbod, Salido, Rodolfo A, Carpenter, Carolina S, Zaramela, Livia S, Minich, Jeremiah J, Bryant, MacKenzie, Sanders, Karenina, Fraraccio, Serena, Ackermann, Gail, Humphrey, Gregory, Swafford, Austin D, Miller-Montgomery, Sandrine, Knight, Rob
Publicado 2021

Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases

por Armstrong, George, Martino, Cameron, Morris, Justin, Khaleghi, Behnam, Kang, Jaeyoung, DeReus, Jeff, Zhu, Qiyun, Roush, Daniel, McDonald, Daniel, Gonazlez, Antonio, Shaffer, Justin P., Carpenter, Carolina, Estaki, Mehrbod, Wandro, Stephen, Eilert, Sean, Akel, Ameen, Eno, Justin, Curewitz, Ken, Swafford, Austin D., Moshiri, Niema, Rosing, Tajana, Knight, Rob
Publicado 2022

Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy

por Zhu, Qiyun, Huang, Shi, Gonzalez, Antonio, McGrath, Imran, McDonald, Daniel, Haiminen, Niina, Armstrong, George, Vázquez-Baeza, Yoshiki, Yu, Julian, Kuczynski, Justin, Sepich-Poore, Gregory D., Swafford, Austin D., Das, Promi, Shaffer, Justin P., Lejzerowicz, Franck, Belda-Ferre, Pedro, Havulinna, Aki S., Méric, Guillaume, Niiranen, Teemu, Lahti, Leo, Salomaa, Veikko, Kim, Ho-Cheol, Jain, Mohit, Inouye, Michael, Gilbert, Jack A., Knight, Rob
Publicado 2022

Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions

por Narunsky-Haziza, Lian, Sepich-Poore, Gregory D., Livyatan, Ilana, Asraf, Omer, Martino, Cameron, Nejman, Deborah, Gavert, Nancy, Stajich, Jason E., Amit, Guy, González, Antonio, Wandro, Stephen, Perry, Gili, Ariel, Ruthie, Meltser, Arnon, Shaffer, Justin P., Zhu, Qiyun, Balint-Lahat, Nora, Barshack, Iris, Dadiani, Maya, Gal-Yam, Einav N., Patel, Sandip Pravin, Bashan, Amir, Swafford, Austin D., Pilpel, Yitzhak, Knight, Rob, Straussman, Ravid
Publicado 2022

SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

por 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., Allard, Sarah M.
Publicado 2021

Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment

por 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, Garcia, Mariana C. Salas, Chiang, Leslie Y., Salido, Rodolfo A., Shaffer, Justin P., Bryant, MacKenzie, 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 A., Sweeney, Daniel A., Allard, Sarah M.
Publicado 2020

Correction for Vangay et al., “Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities”

por Vangay, Pajau, Burgin, Josephine, Johnston, Anjanette, Beck, Kristen L., Berrios, Daniel C., Blumberg, Kai, Canon, Shane, Chain, Patrick, Chandonia, John-Marc, Christianson, Danielle, Costes, Sylvain V., Damerow, Joan, Duncan, William D., Dundore-Arias, Jose Pablo, Fagnan, Kjiersten, Galazka, Jonathan M., Gibbons, Sean M., Hays, David, Hervey, Judson, Hu, Bin, Hurwitz, Bonnie L., Jaiswal, Pankaj, Joachimiak, Marcin P., Kinkel, Linda, Ladau, Joshua, Martin, Stanton L., McCue, Lee Ann, Miller, Kayd, Mouncey, Nigel, Mungall, Chris, Pafilis, Evangelos, Reddy, T. B. K., Richardson, Lorna, Roux, Simon, Schriml, Lynn M., Shaffer, Justin P., Sundaramurthi, Jagadish Chandrabose, Thompson, Luke R., Timme, Ruth E., Zheng, Jie, Wood-Charlson, Elisha M., Eloe-Fadrosh, Emiley A.
Publicado 2021

Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities

por Vangay, Pajau, Burgin, Josephine, Johnston, Anjanette, Beck, Kristen L., Berrios, Daniel C., Blumberg, Kai, Canon, Shane, Chain, Patrick, Chandonia, John-Marc, Christianson, Danielle, Costes, Sylvain V., Damerow, Joan, Duncan, William D., Dundore-Arias, Jose Pablo, Fagnan, Kjiersten, Galazka, Jonathan M., Gibbons, Sean M., Hays, David, Hervey, Judson, Hu, Bin, Hurwitz, Bonnie L., Jaiswal, Pankaj, Joachimiak, Marcin P., Kinkel, Linda, Ladau, Joshua, Martin, Stanton L., McCue, Lee Ann, Miller, Kayd, Mouncey, Nigel, Mungall, Chris, Pafilis, Evangelos, Reddy, T. B. K., Richardson, Lorna, Roux, Simon, Schriml, Lynn M., Shaffer, Justin P., Sundaramurthi, Jagadish Chandrabose, Thompson, Luke R., Timme, Ruth E., Zheng, Jie, Wood-Charlson, Elisha M., Eloe-Fadrosh, Emiley A.
Publicado 2021

Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity

por Shaffer, Justin P., Nothias, Louis-Félix, Thompson, Luke R., Sanders, Jon G., Salido, Rodolfo A., Couvillion, Sneha P., Brejnrod, Asker D., Lejzerowicz, Franck, Haiminen, Niina, Huang, Shi, Lutz, Holly L., Zhu, Qiyun, Martino, Cameron, Morton, James T., Karthikeyan, Smruthi, Nothias-Esposito, Mélissa, Dührkop, Kai, Böcker, Sebastian, Kim, Hyun Woo, Aksenov, Alexander A., Bittremieux, Wout, Minich, Jeremiah J., Marotz, Clarisse, Bryant, MacKenzie M., Sanders, Karenina, Schwartz, Tara, Humphrey, Greg, Vásquez-Baeza, Yoshiki, Tripathi, Anupriya, Parida, Laxmi, Carrieri, Anna Paola, Beck, Kristen L., Das, Promi, González, Antonio, McDonald, Daniel, Ladau, Joshua, Karst, Søren M., Albertsen, Mads, Ackermann, Gail, DeReus, Jeff, Thomas, Torsten, Petras, Daniel, Shade, Ashley, Stegen, James, Song, Se Jin, Metz, Thomas O., Swafford, Austin D., Dorrestein, Pieter C., Jansson, Janet K., Gilbert, Jack A., Knight, Rob
Publicado 2022