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Streamlined 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 Share Save
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SARS-CoV-2 infectivity can be modulated through bacterial grooming of the glycocalyx Martino, 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
ChIP provides 10-fold microbial DNA enrichment from tissue while minimizing bias Bhute, Shrikant; Sanders, Jon G.; Song, Se Jin; Lavoie, Sydney; Swafford, Austin; Guccione, Caitlin; Patel, Lucas; Gonzalez, Antonio; Rooks, Michelle G.; Knight, Rob; Bartko, Andrew Share Save
Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies Brennan, 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
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The impact of breastfeeding on the preterm infant's microbiome and metabolome: a pilot study Escalante, Keriann Schulkers; Bai-Tong, Shiyu S.; Allard, Sarah M.; Ecklu-Mensah, Gertrude; Sanchez, Concepcion; Song, Se Jin; Gilbert, Jack; Bode, Lars; Dorrestein, Pieter; Knight, Rob; Gonzalez, David J.; Leibel, Sydney A.; Leibel, Sandra L. Share Save
Robustness of cancer microbiome signals over a broad range of methodological variation (vol 43, pg 1127, 2024) Sepich-Poore, Gregory D.; McDonald, Daniel; Kopylova, Evguenia; Guccione, Caitlin; Zhu, Qiyun; Austin, George; Carpenter, Carolina; Fraraccio, Serena; Wandro, Stephen; Kosciolek, Tomasz; Janssen, Stefan; Metcalf, Jessica L.; Song, Se Jin; Kanbar, Jad; Miller-Montgomery, Sandrine; Heaton, Robert; Mckay, Rana; Patel, Sandip Pravin; Swafford, Austin D.; Korem, Tal; Knight, Rob Share Save
Robustness of cancer microbiome signals over a broad range of methodological variation Sepich-Poore, Gregory D.; Mcdonald, Daniel; Kopylova, Evguenia; Guccione, Caitlin; Zhu, Qiyun; Austin, George; Carpenter, Carolina; Fraraccio, Serena; Wandro, Stephen; Kosciolek, Tomasz; Janssen, Stefan; Metcalf, Jessica L.; Song, Se Jin; Kanbar, Jad; Miller-Montgomery, Sandrine; Heaton, Robert; Mckay, Rana; Patel, Sandip Pravin; Swafford, Austin D.; Korem, Tal; Knight, Rob Share Save
Effects of variation in sample storage conditions and swab order on 16S vaginal microbiome analyses Kumar, Tanya; Bryant, MacKenzie; Cantrell, Kalen; Song, Se Jin; McDonald, Daniel; Tubb, Helena M.; Farmer, Sawyer; Lewis, Amanda; Lukacz, Emily S.; Brubaker, Linda; Knight, Rob Share Save
A multi-study analysis enables identification of potential microbial features associated with skin aging signs Myers, Tyler; Bouslimani, Amina; Huang, Shi; Hansen, Shalisa T.; Clavaud, Cecile; Azouaoui, Anissa; Ott, Alban; Gueniche, Audrey; Bouez, Charbel; Zheng, Qian; Aguilar, Luc; Knight, Rob; Moreau, Magali; Song, Se Jin Share Save
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Greengenes2 unifies microbial data in a single reference tree (Jul, 10.1038/s41587-023-01845-1, 2023) McDonald, Daniel; Jiang, Yueyu; Balaban, Metin; Cantrell, Kalen; Zhu, Qiyun; Gonzalez, Antonio; Morton, James T.; Nicolaou, Giorgia; Parks, Donovan H.; Karst, Soren M.; Albertsen, Mads; Hugenholtz, Philip; DeSantis, Todd; Song, Se Jin; Bartko, Andrew; Havulinna, Aki S.; Jousilahti, Pekka; Cheng, Susan; Inouye, Michael; Niiranen, Teemu; Jain, Mohit; Salomaa, Veikko; Lahti, Leo; Mirarab, Siavash; Knight, Rob Share Save
Greengenes2 unifies microbial data in a single reference tree McDonald, Daniel; Jiang, Yueyu; Balaban, Metin; Cantrell, Kalen; Zhu, Qiyun; Gonzalez, Antonio; Morton, James T. T.; Nicolaou, Giorgia; Parks, Donovan H. H.; Karst, Soren M.; Albertsen, Mads; Hugenholtz, Philip; DeSantis, Todd; Song, Se Jin; Bartko, Andrew; Havulinna, Aki S. S.; Jousilahti, Pekka; Cheng, Susan; Inouye, Michael; Niiranen, Teemu; Jain, Mohit; Salomaa, Veikko; Lahti, Leo; Mirarab, Siavash; Knight, Rob Share Save
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Effects of Variation in Urine Sample Storage Conditions on 16S Urogenital Microbiome Analyses Kumar, Tanya; Bryant, MacKenzie; Cantrell, Kalen; Song, Se Jin; McDonald, Daniel; Tubb, Helena M. M.; Farmer, Sawyer; Lukacz, Emily S. S.; Brubaker, Linda; Knight, Rob Share Save
Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References Hakim, Daniel; Wandro, Stephen; Zengler, Karsten; Zaramela, Livia S.; Nowinski, Brent; Swafford, Austin; Zhu, Qiyun; Song, Se Jin; Gonzalez, Antonio; McDonald, Daniel; Knight, Rob Share Save
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