Optimizing UniFrac with OpenACC Yields Greater Than One Thousand Times Speed Increase

por Sfiligoi, Igor, Armstrong, George, Gonzalez, Antonio, McDonald, Daniel, Knight, Rob
Publicado 2022

Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data

por Armstrong, George, Martino, Cameron, Rahman, Gibraan, Gonzalez, Antonio, Vázquez-Baeza, Yoshiki, Mishne, Gal, Knight, Rob
Publicado 2021

Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data

por Armstrong, George, Rahman, Gibraan, Martino, Cameron, McDonald, Daniel, Gonzalez, Antonio, Mishne, Gal, Knight, Rob
Publicado 2022

Context-aware dimensionality reduction deconvolutes gut microbial community dynamics

por Martino, Cameron, Shenhav, Liat, Marotz, Clarisse, Armstrong, George, McDonald, Daniel, Vázquez-Baeza, Yoshiki, Morton, James T., Jiang, Lingjing, Dominguez-Bello, Maria Gloria, Swafford, Austin D., Halperin, Eran, Knight, Rob
Publicado 2020

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

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

Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes

por Armstrong, George, Cantrell, Kalen, Huang, Shi, McDonald, Daniel, Haiminen, Niina, Carrieri, Anna Paola, Zhu, Qiyun, Gonzalez, Antonio, McGrath, Imran, Beck, Kristen L., Hakim, Daniel, Havulinna, Aki S., Méric, Guillaume, Niiranen, Teemu, Lahti, Leo, Salomaa, Veikko, Jain, Mohit, Inouye, Michael, Swafford, Austin D., Kim, Ho-Cheol, Parida, Laxmi, Vázquez-Baeza, Yoshiki, Knight, Rob
Publicado 2021

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

EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

por Cantrell, Kalen, Fedarko, Marcus W., Rahman, Gibraan, McDonald, Daniel, Yang, Yimeng, Zaw, Thant, Gonzalez, Antonio, Janssen, Stefan, Estaki, Mehrbod, Haiminen, Niina, Beck, Kristen L., Zhu, Qiyun, Sayyari, Erfan, Morton, James T., Armstrong, George, Tripathi, Anupriya, Gauglitz, Julia M., Marotz, Clarisse, Matteson, Nathaniel L., Martino, Cameron, Sanders, Jon G., Carrieri, Anna Paola, Song, Se Jin, Swafford, Austin D., Dorrestein, Pieter C., Andersen, Kristian G., Parida, Laxmi, Kim, Ho-Cheol, Vázquez-Baeza, Yoshiki, Knight, Rob
Publicado 2021

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