[ Undergraduate co-authors underlined ]

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Najla El Jurdi, Shernan G. Holtan, Andrea Hoeschen, Jessica Kennedy, Benjamin Hillmann, Brian C. Betts, Margaret L. MacMillan, Daniel J. Weisdorf, Alexander Khoruts, Armin Rashidi, and Robin Shields-Cutler. Pre-transplant and longitudinal changes in faecal microbiome characteristics are associated with subsequent development of chronic graft-versus-host disease. Br J Haematol . 2023; 00: 1-7.  https://doi.org/10.1111/bjh.19016

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Lisa C. Corewyn, Mary A. Kelaita, Jenny Nollman, Isabel Hagnauer, Kinndle Blanco-Peña, Robert G. Lessnau, Jonathan B. Clayton, Robin Shields-Cutler, and Kari Brossard Stoos. Hematology and blood biochemistry in a declining population of mantled howler monkeys (Alouatta palliata palliata) at La Pacifica, Costa Rica. 2023. Journal of Medical Primatology. https://doi.org/10.1111/jmp.12669

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Brossard Stoos KA, Ren J, Shields-Cutler RR, Sams KL, Caldwell S, Ho MB, Rivara G, Whistler CA, Jones SH, Wiedmann M, DeMent J, Getchell RG and Marquis H.  Coastal water bacteriophages infect various sets of Vibrio parahaemolyticus sequence types. (2022) Front. Microbiol. 13:1041942. doi: 10.3389/fmicb.2022.1041942

Wills, M.O.*; Shields-Cutler, R.R.*‡; Brunmeier, E.; Weissenborn, M.; Murphy, T.; Knights, D.; Johnson, T.J.; Clayton, J.B‡. Host Species and Captivity Distinguish the Microbiome Compositions of a Diverse Zoo-Resident Non-Human Primate Population. (2022) Diversity. 14, 715. https://doi.org/10.3390/d14090715

* Co-first authors. ‡ Co-corresponding authors. Published open access in journal’s Special Issue on Primate Microbiome Diversity and Its Impacts on Host Health, Ecology, and Evolution.

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Gavin Turner, Madeline Smith, Andrea L. Hoeschen, Jessica A. Wilson, Jessica Kennedy, Max Abramson, Qing Cao, Najla El Jurdi, Margaret L. MacMillan, Daniel J. Weisdorf, Bruce R. Blazar, Alexander Khoruts, Robin R. Shields‐Cutler, Dan Knights, Shernan G. Holtan, Armin Rashidi. Shotgun sequencing of the faecal microbiome to predict response to steroids in patients with lower gastrointestinal acute graft-versus-host disease: An exploratory analysis. (2021) British Journal of Haematology, 192(3), e69–e73. https://doi.org/10.1111/bjh.17238

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Lam T. Khuat, Catherine T. Le, Chien-Chun Steven Pai, Robin R. Shields-Cutler, Shernan Holtan, Armin Rashidi, Sarah Parker, Daniel Knights, Jesus I. Luna, Cordelia Dunai, Ziming Wang, Ian R. Sturgill, Kevin Stoffel, Alexander A. Merleev, Emanual Maverakis, Helen Raybould, Mingyi Chen, Robert J. Canter, Arta M. Monjazeb, James L. M. Ferrara, John E. Levine, Dan L. Longo, Mehrdad Abedi, Bruce R. Blazar, and William J. Murphy. Obesity-Induced Microbiome Alterations Result in Severe Gastrointestinal Graft-Versus-Host Disease Following Allogeneic Hematopoietic Stem Cell Transplantation. (2020) Science Translational Medicine. 12(571) doi: 10.1126/scitranslmed.aay7713

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Benjamin Hillmann, Gabriel A. Al-Ghalith, Robin R. Shields-Cutler, Qiyun Zhu, Rob Knight, and Dan Knights. SHOGUN: a modular, accurate, and scalable framework for microbiome quantification. (2020) Bioinformatics. https://doi.org/10.1093/bioinformatics/btaa277

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Dimitrios N. Sidiropoulos; Gabe Al-Ghalith, Robin R. Shields-Cutler, Tonya Ward, Abigail J. Johnson, Pajau Vangay, Dan Knights, Purna C. Kashyap, Yibo Xian, Amanda E. Ramer-Tait, and Jonathan B. Clayton. Wild primate microbiomes prevent weight gain in germ-free mice. (2020) Animal Microbiome. https://doi.org/10.1186/s42523-020-00033-9 

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Erica Arriaga-Gomez, Jaclyn Kline, Elizabeth Emanuel, Nefeli Neamonitaki, Tenzin Yangdon, Hayley Zacheis, Dogukan Pasha, JJ Lim, Susan Bush, Beebie Boo, Hanna Mengistu, Ruby Kinnamon, Robin Shields-Cutler, 
Elizabeth Wattenberg, Devavani Chatterjea. Repeated vaginal exposures to the common cosmetic and household preservative methylisothiazolinone induce persistent, mast cell-dependent genital pain in ND4 mice. (2019) Int. J. Mol. Sci. 20(21), 5361; https://doi.org/10.3390/ijms20215361

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Armin Rashidi, Maryam Ebadib, Robin R. Shields-Cutler, Kathryn Geldarte, Dawn A. Maniase, Aaron Barnese, Todd E. DeForg, Patricia Ferrierif, Jo-Anne H. Youngh, Dan Knights, Bruce R. Blazar, Daniel J. Weisdorf, Gary M. Dunny. Early E. casseliflavus gut colonization and outcomes of allogeneic hematopoietic cell transplantation. (2019) PLoS ONE. https://doi.org/10.1371/journal.pone.0220850

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Abigail J. Johnson, Pajau Vangay, Gabe A. Al-Ghalith, Benjamin M. Hillmann, Tonya L. Ward, Robin R. Shields-Cutler, Austin D. Kim, Anna Konstantinovna Shmagel, Arzang N. Syed, Personalized Microbiome Class Students, Jens Walter, Ravi Menon, Katie Koecher, Dan Knights. Daily sampling reveals personalized diet-microbiome associations. (2019) Cell Host & Microbe. https://doi.org/10.1016/j.chom.2019.05.005

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George B. Saffouri*, Robin Shields-Cutler*, Jun Chen, Yi Yang, Heather R. Lekatz, Vanessa L. Hale, Janice M. Cho, Eric J. Battaglioli, Yogesh Bhattarai, Kevin J. Thompson, Krishna K. Kalari, Gaurav Behera, Jonathan C. Berry, Stephanie A. Peters, Robin Patel, Audrey N. Schuetz, Jeremiah J. Faith, Michael Camilleri, Justin L. Sonnenburg, Gianrico Farrugia, Jonathan R. Swann, Madhusudan Grover, Dan Knights, Purna C. Kashyap. Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders. (2019) Nature Communications. https://doi.org/10.1038/s41467-019-09964-7

* authors contributed equally

Highlighted in Nature Reviews: Gastroenterology and Hepatology, June 2019. doi:10.1038/s41575-019-0171-5

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Jonathan B. Clayton, Robin R. Shields-Cutler, Susan L. Hoops, Gabriel A. Al-Ghalith, John C.M. Sha, Timothy J. Johnson, and Dan Knights. Bacterial community structure and function distinguish gut sites in captive red-shanked doucs (Pygathrix nemaeus). (2019) American Journal of Primatology. https://doi.org/10.1002/ajp.22977

        - Center for Open Science Open Materials and Open Data badges

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Armin Rashidi, Thomas Kaiser, Robin Shields-Cutler, Carolyn Graiziger, Shernan Holtan, Tauseef Ur Rehman, Justin Wasko, Daniel Weisdorf, Gary Dunny, Alexander Khoruts, and Christopher Staley. Dysbiosis patterns during re-induction/salvage versus induction chemotherapy for acute leukemia. (2019) Scientific Reports 9, Article number: 6083. https://doi.org/10.1038/s41598-019-42652-6

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Pajau Vangay, Abigail J. Johnson, Tonya L. Ward, Gabe A. Al-Ghalith, Robin R. Shields-Cutler, Benjamin M. Hillmann, Sarah K. Lucas, Lalit K. Beura, Emily A. Thompson, Lisa M. Till, Rodolfo Batres, Bwei Paw, Shannon L. Pergament, Pimpanitta Saenyakul, Mary Xiong, Austin Kim, Grant Kim, David Masopust, Eric C. Martens, Chaisiri Angkurawaranon, Rose McGready, Purna C. Kashyap, Kathleen A. Culhane-Pera, Dan Knights. U.S. immigration westernizes the human gut microbiome. (2018) Cell. 175 (4) 962-972. DOI:https://doi.org/10.1016/j.cell.2018.10.029

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Benjamin Hillmann, Gabriel Al-Ghalith, Robin R. Shields-Cutler, Qiyun Zhu, Daryl Gohl, Kenneth Beckman, Rob Knight, & Dan Knights. Evaluating the information content of shallow shotgun metagenomics sequencing. (2018) mSystems. 3 (6) e00069-18; DOI: 10.1128/mSystems.00069-18

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Xue-Song Zhang, […] Robin R. Shields-Cutler, Benjamin Hillmann, Gabriel A. Al-Ghalith, […] Dan Knights, John M. Denu, Huilin Li, Kelly V. Ruggles, Richard Bonneau, Anthony R. Williamson, Marcus Rauch, & Martin J. Blaser. Antibiotic-induced acceleration of Type 1 diabetes alters intestinal innate pathway maturation. (2018) eLife 7:e37816 DOI: 10.7554/eLife.37816

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Al-Ghalith GA, Hillmann B, Ang K, Shields-Cutler R, & Knights D. SHI7 is a self-learning pipeline for multipurpose short-read DNA quality control. (2018) mSystems 3:e00202-17.

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Robin R. Shields-Cutler, G. Al-Ghalith, M. Yassour, & D. Knights. SplinectomeR enables group comparisons in longitudinal microbiome studies. (2018) Frontiers in Microbiology, 9, 785.

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Armin Rashidi*, Maryam Ebadi*, Robin R. Shields-Cutler*, Todd E. DeFor, Gabriel A. Al-Ghalith, Jo-Anne Young, Daniel Knights, & Daniel J. Weisdorf. Pre-transplant gut colonization with intrinsically vancomycin-resistant enterococci and outcomes of allogeneic hematopoietic cell transplantation. (2018) Biology of Blood and Marrow Transplantation. DOI: 10.1016/j.bbmt.2018.01.025

* Authors contributed equally

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Robin R. Shields-Cutler, Jan R. Crowley, Connelly D. Miller, Weidong Cui, Jeffrey P. Henderson. Human Metabolome-Derived Cofactors are Required for the Antibacterial Activity of Siderocalin in Urine. (2016) Journal of Biological Chemistry. doi: 10.1074/jbc.M116.759183

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Robin R. Shields-Cutler, Jan R. Crowley, Chia S. Hung, Ann E. Stapleton, Courtney C. Aldrich, Jonas Marschall, and Jeffrey P. Henderson. Human urinary composition controls antibacterial activity of siderocalin. (2015) Journal of Biological Chemistry, 290 (26), 15949-15960.

• Faculty of 1000 Prime Recommended, for “special significance to the field of Chemical Biology”

• Selected as JBC “Paper of the Week”

• Cover feature for June 26, 2015 issue

• Press coverage by Time, Oprah Magazine, NBC Today Show, Daily Mail UK, Wash U Record, BioMed Podcast, Infection Control Today, Science Daily, and MedicalResearch.com

• Feature article on This Week in Microbiology podcast Episode 107: "The Battle in your Bladder"

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Emily E. Ricotta, Nan Wang, Robin Cutler, Jeffrey G. Lawrence, and Tricia L. Humphreys. Rapid Divergence of Two Classes of Haemophilus ducreyi. (2011) Journal of Bacteriology 193 (12), 2941-2947.