未登录 Streamlined extraction of nucleic acids and metabolites from low- and high-biomass samples using isopropanol and matrix tubes 使用异丙醇和基质管从低生物量和高生物量样品中简化的核酸和代谢物提取 Brennan, Caitriona; Shaffer, Justin P.; Belda-Ferre, Pedro; Mohanty, Ipsita; Weng, Yuhan; Cantrell, Kalen; Ackermann, Gail; Allaband, Celeste; Bryant, Mackenzie; Farmer, Sawyer; Gonzalez, Antonio; Mcdonald, Daniel; Martino, Cameron; Meehan, Michael J.; Rahman, Gibraan; Salido, Rodolfo A.; Schwartz, Tara; Song, Se Jin; Tribelhorn, Caitlin; Tubb, Helena M.; Dorrestein, Pieter C.; Knight, Rob 分享 收藏
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Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy (vol 7, pg e00167, 2023) 基于匹配的参考基因组，同时绕过分类学，对宏基因组群落生态学进行系统发育感知分析 (第7卷，pg e00167，2023) Zhu, Qiyun; Huang, Shi; Gonzalez, Antonio; Mcgrath, Imran; Mcdonald, Daniel; Haiminen, Niina; Armstrong, George; Vazquez-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.; Meric, Guillaume; Niiranen, Teemu; Lahti, Leo; Salomaa, Veikko; Kim, Ho-Cheol; Jain, Mohit; Inouye, Michael; Gilbert, Jack A.; Knight, Rob 分享 收藏
Peripheral neuronal activation shapes the microbiome and alters gut physiology Griffiths, Jessica A.; Yoo, Bryan B.; Thuy-Boun, Peter; Cantu, Victor J.; Weldon, Kelly C.; Challis, Collin; Sweredoski, Michael J.; Chan, Ken Y.; Thron, Taren M.; Sharon, Gil; Moradian, Annie; Humphrey, Gregory; Zhu, Qiyun; Shaffer, Justin P.; Wolan, Dennis W.; Dorrestein, Pieter C.; Knight, Rob; Gradinaru, Viviana; Mazmanian, Sarkis K. 分享 收藏
Enhancing untargeted metabolomics using metadata-based source annotation Gauglitz, Julia M.; West, Kiana A.; Bittremieux, Wout; Williams, Candace L.; Weldon, Kelly C.; Panitchpakdi, Morgan; Di Ottavio, Francesca; Aceves, Christine M.; Brown, Elizabeth; Sikora, Nicole C.; Jarmusch, Alan K.; Martino, Cameron; Tripathi, Anupriya; Meehan, Michael J.; Dorrestein, Kathleen; Shaffer, Justin P.; Coras, Roxana; Vargas, Fernando; Goldasich, Lindsay DeRight; Schwartz, Tara; Bryant, MacKenzie; Humphrey, Gregory; Johnson, Abigail J.; Spengler, Katharina; Belda-Ferre, Pedro; Diaz, Edgar; McDonald, Daniel; Zhu, Qiyun; Elijah, Emmanuel O.; Wang, Mingxun; Marotz, Clarisse; Sprecher, Kate E.; Vargas-Robles, Daniela; Withrow, Dana; Ackermann, Gail; Herrera, Lourdes; Bradford, Barry J.; Marques, Lucas Maciel Mauriz; Amaral, Juliano Geraldo; Silva, Rodrigo Moreira; Veras, Flavio Protasio; Cunha, Thiago Mattar; Oliveira, Rene Donizeti Ribeiro; Louzada-Junior, Paulo; Mills, Robert H.; Piotrowski, Paulina K.; Servetas, Stephanie L.; Da Silva, Sandra M.; Jones, Christina M.; Lin, Nancy J.; Lippa, Katrice A.; Jackson, Scott A.; Daouk, Rima Kaddurah; Galasko, Douglas; Dulai, Parambir S.; Kalashnikova, Tatyana I.; Wittenberg, Curt; Terkeltaub, Robert; Doty, Megan M.; Kim, Jae H.; Rhee, Kyung E.; Beauchamp-Walters, Julia; Wright, Jr Kenneth P.; Dominguez-Bello, Maria Gloria; Manary, Mark; Oliveira, Michelli F.; Boland, Brigid S.; Lopes, Norberto Peporine; Guma, Monica; Swafford, Austin D.; Dutton, Rachel J.; Knight, Rob; Dorrestein, Pieter C. 分享 收藏
Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies 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. 分享 收藏
Postnatal exposure to ambient air pollutants is associated with the composition of the infant gut microbiota at 6-months of age 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. 分享 收藏
Enhancing untargeted metabolomics using metadata-based source annotation Gauglitz, Julia M.; West, Kiana A.; Bittremieux, Wout; Williams, Candace L.; Weldon, Kelly C.; Panitchpakdi, Morgan; Di Ottavio, Francesca; Aceves, Christine M.; Brown, Elizabeth; Sikora, Nicole C.; Jarmusch, Alan K.; Martino, Cameron; Tripathi, Anupriya; Meehan, Michael J.; Dorrestein, Kathleen; Shaffer, Justin P.; Coras, Roxana; Vargas, Fernando; Goldasich, Lindsay DeRight; Schwartz, Tara; Bryant, MacKenzie; Humphrey, Gregory; Johnson, Abigail J.; Spengler, Katharina; Belda-Ferre, Pedro; Diaz, Edgar; McDonald, Daniel; Zhu, Qiyun; Elijah, Emmanuel O.; Wang, Mingxun; Marotz, Clarisse; Sprecher, Kate E.; Vargas-Robles, Daniela; Withrow, Dana; Ackermann, Gail; Herrera, Lourdes; Bradford, Barry J.; Marques, Lucas Maciel Mauriz; Amaral, Juliano Geraldo; Silva, Rodrigo Moreira; Veras, Flavio Protasio; Cunha, Thiago Mattar; Oliveira, Rene Donizeti Ribeiro; Louzada-Junior, Paulo; Mills, Robert H.; Piotrowski, Paulina K.; Servetas, Stephanie L.; Da Silva, Sandra M.; Jones, Christina M.; Lin, Nancy J.; Lippa, Katrice A.; Jackson, Scott A.; Daouk, Rima Kaddurah; Galasko, Douglas; Dulai, Parambir S.; Kalashnikova, Tatyana I.; Wittenberg, Curt; Terkeltaub, Robert; Doty, Megan M.; Kim, Jae H.; Rhee, Kyung E.; Beauchamp-Walters, Julia; Wright, Kenneth P., Jr.; Dominguez-Bello, Maria Gloria; Manary, Mark; Oliveira, Michelli F.; Boland, Brigid S.; Lopes, Norberto Peporine; Guma, Monica; Swafford, Austin D.; Dutton, Rachel J.; Knight, Rob; Dorrestein, Pieter C. 分享 收藏
Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype 成分意识的系统发育 β 多样性措施可以更好地解决与表型相关的微生物组 Martino, Cameron; McDonald, Daniel; Cantrell, Kalen; Dilmore, Amanda Hazel; Vazquez-Baeza, Yoshiki; Shenhav, Liat; Shaffer, Justin P.; Rahman, Gibraan; Armstrong, George; Allaband, Celeste; Song, Se Jin; Knight, Rob 分享 收藏
Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy Zhu, Qiyun; Huang, Shi; Gonzalez, Antonio; McGrath, Imran; McDonald, Daniel; Haiminen, Niina; Armstrong, George; Vazquez-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.; Meric, Guillaume; Niiranen, Teemu; Lahti, Leo; Salomaa, Veikko; Kim, Ho-Cheol; Jain, Mohit; Inouye, Michael; Gilbert, Jack A.; Knight, Rob 分享 收藏
Transcriptional Profiles of a Foliar Fungal Endophyte (Pestalotiopsis, Ascomycota) and Its Bacterial Symbiont (Luteibacter, Gammaproteobacteria) Reveal Sulfur Exchange and Growth Regulation during Early Phases of Symbiotic Interaction Shaffer, Justin P.; Carter, Morgan E.; Spraker, Joseph E.; Clark, Meara; Smith, Brian A.; Hockett, Kevin L.; Baltrus, David A.; Arnold, A. Elizabeth 分享 收藏
Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases 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 分享 收藏
Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern California 早期生活的肠道微生物群与来自南加州的西班牙裔婴儿的快速生长有关 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 分享 收藏
Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities (vol 6, e01194-20, 2021) 微生物组元数据标准: 国家微生物组数据协作研讨会和后续活动的报告 (第6卷，e01194-20，2021) 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; Pa, 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. 分享 收藏
SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment 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; Vazquez-Baeza, Yoshiki; Torriani, Francesca J.; Knight, Rob; Gilbert, Jack; Sweeney, Daniel A.; Allard, Sarah M. 分享 收藏
Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical longrange sequencing information (vol 30, pg 898, 2020) Chen, Zhoutao; Pham, Long; Wu, Tsai-Chin; Mo, Guoya; Xia, Yu; Chang, Peter L.; Porter, Devin; Phan, Tan; Che, Huu; Tran, Hao; Bansal, Vikas; Shaffer, Justin; Belda-Ferre, Pedro; Humphrey, Greg; Knight, Rob; Pevzner, Pavel; Pham, Son; Wang, Yong; Lei, Ming 分享 收藏
Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities 微生物组元数据标准: 国家微生物组数据协作研讨会和后续活动的报告 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. 分享 收藏
Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment 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. 分享 收藏
Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information Chen, Zhoutao; Pham, Long; Wu, Tsai-Chin; Mo, Guoya; Xia, Yu; Chang, Peter L.; Porter, Devin; Phan, Tan; Che, Huu; Tran, Hao; Bansal, Vikas; Shaffer, Justin; Belda-Ferre, Pedro; Humphrey, Greg; Knight, Rob; Pevzner, Pavel; Pham, Son; Wang, Yong; Lei, Ming 分享 收藏
Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome 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 分享 收藏
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