Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans von Johnson, Abigail J., Vangay, Pajau, Al-Ghalith, Gabriel A., Hillmann, Benjamin M., Ward, Tonya L., Shields-Cutler, Robin R., Kim, Austin D., Shmagel, Anna Konstantinovna, Syed, Arzang N., Walter, Jens, Menon, Ravi, Koecher, Katie, Knights, Dan

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Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders von Saffouri, George B., Shields-Cutler, Robin R., Chen, Jun, Yang, Yi, Lekatz, Heather R., Hale, Vanessa L., Cho, Janice M., Battaglioli, Eric J., Bhattarai, Yogesh, Thompson, Kevin J., Kalari, Krishna K., Behera, Gaurav, Berry, Jonathan C., Peters, Stephanie A., Patel, Robin, Schuetz, Audrey N., Faith, Jeremiah J., Camilleri, Michael, Sonnenburg, Justin L., Farrugia, Gianrico, Swann, Jonathan R., Grover, Madhusudan, Knights, Dan, Kashyap, Purna C.

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Evaluating the Information Content of Shallow Shotgun Metagenomics von Hillmann, Benjamin, Al-Ghalith, Gabriel A, Shields-Cutler, Robin R, Zhu, Qiyun, Gohl, Daryl M, Beckman, Kenneth B, Knight, Rob, Knights, Dan

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Pre-transplant and longitudinal changes in faecal microbiome characteristics are associated with subsequent development of chronic graft-versus-host disease von El Jurdi, Najla, Holtan, Shernan G, Hoeschen, Andrea, Velguth, Jessica, Hillmann, Benjamin, Betts, Brian C, MacMillan, Margaret L, Weisdorf, Daniel J, Khoruts, Alexander, Rashidi, Armin, Shields-Cutler, Robin

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Shotgun sequencing of the faecal microbiome to predict response to steroids in patients with lower gastrointestinal acute graft‐versus‐host disease: An exploratory analysis von Turner, Gavin, Smith, Madeline, Hoeschen, Andrea L., Wilson, Jessica A., Kennedy, Jessica, Abramson, Max, Cao, Qing, El Jurdi, Najla, MacMillan, Margaret L., Weisdorf, Daniel J., Blazar, Bruce R., Khoruts, Alexander, Shields‐Cutler, Robin R., Knights, Dan, Holtan, Shernan G., Rashidi, Armin

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Bacterial community structure and function distinguish gut sites in captive red‐shanked doucs (Pygathrix nemaeus) von Clayton, Jonathan B., Shields‐Cutler, Robin R., Hoops, Susan L., Al‐Ghalith, Gabriel A., Sha, John C. M., Johnson, Timothy J., Knights, Dan

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SplinectomeR Enables Group Comparisons in Longitudinal Microbiome Studies von Shields-Cutler, Robin R, Al-Ghalith, Gabe A, Yassour, Moran, Knights, Dan

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Early E. casseliflavus gut colonization and outcomes of allogeneic hematopoietic cell transplantation von Rashidi, Armin, Ebadi, Maryam, Shields-Cutler, Robin R, Kruziki, Kathryn, Manias, Dawn A, Barnes, Aaron M T, DeFor, Todd E, Ferrieri, Patricia, Young, Jo-Anne H, Knights, Dan, Blazar, Bruce R, Weisdorf, Daniel J, Dunny, Gary M

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Hematology and blood biochemistry in a declining population of mantled howler monkeys (Alouatta palliata palliata) at La Pacifica, Costa Rica von Corewyn, Lisa C, Kelaita, Mary A, Nollman, Jenny, Hagnauer, Isabel, Blanco-Peña, Kinndle, Lessnau, Robert G, Clayton, Jonathan B, Shields-Cutler, Robin, Stoos, Kari Brossard

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Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity von Zhang, Xue-Song, Li, Jackie, Krautkramer, Kimberly A, Badri, Michelle, Battaglia, Thomas, Borbet, Timothy C, Koh, Hyunwook, Ng, Sandy, Sibley, Rachel A, Li, Yuanyuan, Pathmasiri, Wimal, Jindal, Shawn, Shields-Cutler, Robin R, Hillmann, Ben, Al-Ghalith, Gabriel A, Ruiz, Victoria E, Livanos, Alexandra, van 't Wout, Angélique B, Nagalingam, Nabeetha, Rogers, Arlin B, Sumner, Susan Jenkins, Knights, Dan, Denu, John M, Li, Huilin, Ruggles, Kelly V, Bonneau, Richard, Williamson, R Anthony, Rauch, Marcus, Blaser, Martin J

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US Immigration Westernizes the Human Gut Microbiome von Vangay, Pajau, Johnson, Abigail J., Ward, Tonya L., Al-Ghalith, Gabriel A., Shields-Cutler, Robin R., Hillmann, Benjamin M., Lucas, Sarah K., Beura, Lalit K., Thompson, Emily A., Till, Lisa M., Batres, Rodolfo, Paw, Bwei, Pergament, Shannon L., Saenyakul, Pimpanitta, Xiong, Mary, Kim, Austin D., Kim, Grant, Masopust, David, Martens, Eric C., Angkurawaranon, Chaisiri, McGready, Rose, Kashyap, Purna C., Culhane-Pera, Kathleen A., Knights, Dan

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Coastal water bacteriophages infect various sets of Vibrio parahaemolyticus sequence types von Brossard Stoos, Kari A, Ren, Jennifer, Shields-Cutler, Robin R, Sams, Kelly L, Caldwell, Shannon, Ho, Marvin B, Rivara, Gregg, Whistler, Cheryl A, Jones, Stephen H, Wiedmann, Martin, DeMent, Jamie, Getchell, Rodman G, Marquis, Hélène

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SHOGUN: a modular, accurate and scalable framework for microbiome quantification von Hillmann, Benjamin, Al-Ghalith, Gabriel A, Shields-Cutler, Robin R, Zhu, Qiyun, Knight, Rob, Knights, Dan

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Host Species and Captivity Distinguish the Microbiome Compositions of a Diverse Zoo-Resident Non-Human Primate Population von Wills, Maya O, Shields-Cutler, Robin R, Brunmeier, Emily, Weissenborn, Madison, Murphy, Tami, Knights, Dan, Johnson, Timothy J, Clayton, Jonathan B

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Dysbiosis patterns during re-induction/salvage versus induction chemotherapy for acute leukemia von Rashidi, Armin, Kaiser, Thomas, Shields-Cutler, Robin, Graiziger, Carolyn, Holtan, Shernan G., Rehman, Tauseef Ur, Wasko, Justin, Weisdorf, Daniel J., Dunny, Gary, Khoruts, Alexander, Staley, Christopher

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Wild primate microbiomes prevent weight gain in germ-free mice von Sidiropoulos, Dimitrios N, Al-Ghalith, Gabriel A, Shields-Cutler, Robin R, Ward, Tonya L, Johnson, Abigail J, Vangay, Pajau, Knights, Dan, Kashyap, Purna C, Xian, Yibo, Ramer-Tait, Amanda E, Clayton, Jonathan B

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Human Metabolome-derived Cofactors Are Required for the Antibacterial Activity of Siderocalin in Urine von Shields-Cutler, Robin R., Crowley, Jan R., Miller, Connelly D., Stapleton, Ann E., Cui, Weidong, Henderson, Jeffrey P.

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Human Urinary Composition Controls Antibacterial Activity of Siderocalin von Shields-Cutler, Robin R., Crowley, Jan R., Hung, Chia S., Stapleton, Ann E., Aldrich, Courtney C., Marschall, Jonas, Henderson, Jeffrey P.

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SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control von Al-Ghalith, Gabriel A, Hillmann, Benjamin, Ang, Kaiwei, Shields-Cutler, Robin, Knights, Dan

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Repeated Vaginal Exposures to the Common Cosmetic and Household Preservative Methylisothiazolinone Induce Persistent, Mast Cell-Dependent Genital Pain in ND4 Mice von Arriaga-Gomez, Erica, Kline, Jaclyn, Emanuel, Elizabeth, Neamonitaki, Nefeli, Yangdon, Tenzin, Zacheis, Hayley, Pasha, Dogukan, Lim, Jinyoung, Bush, Susan, Boo, Beebie, Mengistu, Hanna, Kinnamon, Ruby, Shields-Cutler, Robin, Wattenberg, Elizabeth, Chatterjea, Devavani

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