Not logged inStreamlined extraction of nucleic acids and metabolites from low- and high-biomass samples using isopropanol and matrix tubes
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 .png)
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SaveSARS-CoV-2 infectivity can be modulated through bacterial grooming of the glycocalyxMartino, Cameron; Kellman, Benjamin P.; Sandoval, Daniel R.; Clausen, Thomas Mandel; Cooper, Robert; Benjdia, Alhosna; Soualmia, Feryel; Clark, Alex E.; Garretson, Aaron F.; Marotz, Clarisse A.; Song, Se Jin; Wandro, Stephen; Zaramela, Livia S.; Salido, Rodolfo A.; Zhu, Qiyun; Armingol, Erick; Vazquez-Baeza, Yoshiki; Mcdonald, Daniel; Sorrentino, James T.; Taylor, Bryn; Belda-Ferre, Pedro; Das, Promi; Ali, Farhana; Liang, Chenguang; Zhang, Yujie; Schifanella, Luca; Covizzi, Alice; Lai, Alessia; Riva, Agostino; Basting, Christopher; Broedlow, Courtney Ann; Havulinna, Aki S.; Jousilahti, Pekka; Estaki, Mehrbod; Kosciolek, Tomasz; Kuplicki, Rayus; Victor, Teresa A.; Paulus, Martin P.; Savage, Kristen E.; Benbow, Jennifer L.; Spielfogel, Emma S.; Anderson, Cheryl A. M.; Martinez, Maria Elena; Lacey, James V.; Huang, Shi; Haiminen, Niina; Parida, Laxmi; Kim, Ho-Cheol; Gilbert, Jack A.; Sweeney, Daniel A.; Allard, Sarah M.; Swafford, Austin D.; Cheng, Susan; Inouye, Michael; Niiranen, Teemu; Jain, Mohit; Salomaa, Veikko; Zengler, Karsten; Klatt, Nichole R.; Hasty, Jeff; Berteau, Olivier; Carlin, Aaron F.; Esko, Jeffrey D.; Lewis, Nathan E.; Knight, Rob Share Save Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution (vol 8, e00006-23, 2023)Brennan, Caitriona; Salido, Rodolfo A.; Belda-Ferre, Pedro; Bryant, Mackenzie; Cowart, Charles; Tiu, Maria D.; Gonzalez, Antonio; Mcdonald, Daniel; Tribelhorn, Caitlin; Zarrinpar, Amir; Knight, Rob Share Save Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy (vol 7, 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 Share Save Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studiesBrennan, Caitriona; Belda-Ferre, Pedro; Zuffa, Simone; Charron-Lamoureux, Vincent; Mohanty, Ipsita; Ackermann, Gail; Allaband, Celeste; Ambre, Madison; Boyer, Tara; Bryant, MacKenzie; Cantrell, Kalen; Gonzalez, Antonio; McDonald, Daniel; Salido, Rodolfo A.; Song, Se Jin; Wright, Gillian; Dorrestein, Pieter C.; Knight, Rob Share Save Pangenome comparison of Bacteroides fragilis genomospecies unveils genetic diversity and ecological insightsOles, Renee E.; Terrazas, Marvic Carrillo; Loomis, Luke R.; Hsu, Chia-Yun; Tribelhorn, Caitlin; Belda-Ferre, Pedro; Ea, Allison C.; Bryant, Mackenzie; Young, Jocelyn A.; Carrow, Hannah C.; Sandborn, William J.; Dulai, Parambir S.; Sivagnanam, Mamata; Pride, David; Knight, Rob; Chu, Hiutung Share Save Enhancing untargeted metabolomics using metadata-based source annotationGauglitz, 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. Share Save Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distributionBrennan, Caitriona; Salido, Rodolfo A.; Belda-Ferre, Pedro; Bryant, MacKenzie; Cowart, Charles; Tiu, Maria D.; Gonzalez, Antonio; McDonald, Daniel; Tribelhorn, Caitlin; Zarrinpar, Amir; Knight, Rob Share Save Bacterial and Chemical Evidence of Coastal Water Pollution from the Tijuana River in Sea Spray AerosolPendergraft, Matthew A.; Belda-Ferre, Pedro; Petras, Daniel; Morris, Clare K.; Mitts, Brock A.; Aron, Allegra T.; Bryant, MacKenzie; Schwartz, Tara; Ackermann, Gail; Humphrey, Greg; Kaandorp, Ethan; Dorrestein, Pieter C.; Knight, Rob; Prather, Kimberly A. Share Save Sentinel Cards Provide Practical SARS-CoV-2 Monitoring in School SettingsCantu, Victor J.; Sanders, Karenina; Belda-Ferre, Pedro; Salido, Rodolfo A.; Tsai, Rebecca; Austin, Brett; Jordan, William; Asudani, Menka; Walster, Amanda; Magallanes, Celestine G.; Valentine, Holly; Manjoonian, Araz; Wijaya, Carrissa; Omaleki, Vinton; Aigner, Stefan; Baer, Nathan A.; Betty, Maryann; Castro-Martinez, Anelizze; Cheung, Willi; De Hoff, Peter; Eisner, Emily; Hakim, Abbas; Lastrella, Alma L.; Lawrence, Elijah S.; Ngo, Toan T.; Ostrander, Tyler; Plascencia, Ashley; Sathe, Shashank; Smoot, Elizabeth W.; Carlin, Aaron F.; Yeo, Gene W.; Laurent, Louise C.; Manlutac, Anna Liza; Fielding-Miller, Rebecca; Knight, Rob Share Save Implementation of Practical Surface SARS-CoV-2 Surveillance in School SettingsCantu, Victor J.; Belda-Ferre, Pedro; Salido, Rodolfo A.; Tsai, Rebecca; Austin, Brett; Jordan, William; Asudani, Menka; Walster, Amanda; Magallanes, Celestine G.; Valentine, Holly; Manjoonian, Araz; Wijaya, Carrissa; Omaleki, Vinton; Sanders, Karenina; Aigner, Stefan; Baer, Nathan A.; Betty, Maryann; Castro-Martinez, Anelizze; Cheung, Willi; Crescini, Evelyn S.; De Hoff, Peter; Eisner, Emily; Hakim, Abbas; Kapadia, Bhavika; Lastrella, Alma L.; Lawrence, Elijah S.; Ngo, Toan T.; Ostrander, Tyler; Sathe, Shashank; Seaver, Phoebe; Smoot, Elizabeth W.; Carlin, Aaron F.; Yeo, Gene W.; Laurent, Louise C.; Manlutac, Anna Liza; Fielding-Miller, Rebecca; Knight, Rob Share Save Enhancing untargeted metabolomics using metadata-based source annotationGauglitz, 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. Share Save SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp.Cantu, Victor J.; Salido, Rodolfo A.; Huang, Shi; Rahman, Gibraan; Tsai, Rebecca; Valentine, Holly; Magallanes, Celestine G.; Aigner, Stefan; Baer, Nathan A.; Barber, Tom; Belda-Ferre, Pedro; Betty, Maryann; Bryant, MacKenzie; Maya, Martin Casas; Castro-Martinez, Anelizze; Chacon, Marisol; Cheung, Willi; Crescini, Evelyn S.; De Hoff, Peter; Eisner, Emily; Farmer, Sawyer; Hakim, Abbas; Kohn, Laura; Lastrella, Alma L.; Lawrence, Elijah S.; Morgan, Sydney C.; Ngo, Toan T.; Nouri, Alhakam; Ostrander, R. Tyler; Plascencia, Ashley; Ruiz, Christopher A.; Sathe, Shashank; Seaver, Phoebe; Shwartz, Tara; Smoot, Elizabeth W.; Ostrander, Tyler; Valles, Thomas; Yeo, Gene W.; Laurent, Louise C.; Fielding-Miller, Rebecca; Knight, Rob Share Save Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing TaxonomyZhu, 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 Share Save Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers (vol 15, pg 3399, 2021)Zhu, Qiyun; Hou, Qiangchuan; Huang, Shi; Ou, Qianying; Huo, Dongxue; Vazquez-Baeza, Yoshiki; Cen, Chaoping; Cantu, Victor; Estaki, Mehrbod; Chang, Haibo; Belda-Ferre, Pedro; Kim, Ho-Cheol; Chen, Kaining; Knight, Rob; Zhang, Jiachao Share Save Chemical Proportionality within Molecular NetworksPetras, Daniel; Caraballo-Rodriguez, Andres Mauricio; Jarmusch, Alan K.; Molina-Santiago, Carlos; Gauglitz, Julia M.; Gentry, Emily C.; Belda-Ferre, Pedro; Romero, Diego; Tsunoda, Shirley M.; Dorrestein, Pieter C.; Wang, Mingxun Share Save Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiomeHuang, Shi; Jiang, Shuaiming; Huo, Dongxue; Allaband, Celeste; Estaki, Mehrbod; Cantu, Victor; Belda-Ferre, Pedro; Vazquez-Baeza, Yoshiki; Zhu, Qiyun; Ma, Chenchen; Li, Congfa; Zarrinpar, Amir; Liu, Yang-Yu; Knight, Rob; Zhang, Jiachao Share Save SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environmentMarotz, 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. Share Save Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkersZhu, Qiyun; Hou, Qiangchuan; Huang, Shi; Ou, Qianying; Huo, Dongxue; Vazquez-Baeza, Yoshiki; Cen, Chaoping; Cantu, Victor; Estaki, Mehrbod; Chang, Haibo; Belda-Ferre, Pedro; Kim, Ho-Cheol; Chen, Kaining; Knight, Rob; Zhang, Jiachao Share Save 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 Share Save 
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