John Franklin Rawls
Professor of Molecular Genetics and Microbiology
We seek to understand how the intestinal microbiome contributes to vertebrate physiology and disease. To that end, we leverage complementary zebrafish and mouse models to study the integrative physiology of host-microbiome interactions. This work has identified novel and conserved mechanisms by which intestinal bacteria regulate dietary fat metabolism and systemic innate immunity. We also apply genomic approaches in these animal models to understand the transcriptional regulatory pathways utilized by the intestinal epithelium to mediate host responses to the microbiome. Using this approach, we have identified mechanisms of transcriptional and chromatin regulation that have been conserved during vertebrate evolution and also contribute to modern human diseases such as the inflammatory bowel diseases, obesity, and diabetes. To further advance our understanding of obesity pathophysiology, we developed the zebrafish as a model system for studying adipose tissues and identifying new environmental and genetic regulators of adiposity. We are also engaged in translational research in humans and animal models to define microbial and metabolic determinants of obesity and efficacy of weight loss intervention. Grounded in comparative and integrative physiology, our research program has been effective in discovering ancient mechanisms of host-microbiome interaction that are conserved across animal taxa and contribute to the etiology of modern human diseases. These insights are advancing our understanding of host-microbiome relationships in vertebrate physiology and identifying novel therapeutic targets for human diseases ranging from inflammatory bowel disease to obesity to neurological disorders.
Current Appointments & Affiliations
- Professor of Molecular Genetics and Microbiology, Molecular Genetics and Microbiology, Basic Science Departments 2020
- Professor in Medicine, Medicine, Gastroenterology, Medicine 2020
- Professor of Cell Biology, Cell Biology, Basic Science Departments 2022
- Member of the Duke Cancer Institute, Duke Cancer Institute, Institutes and Centers 2013
Contact Information
- 323A CARL Building Box 3580, 213 Research Drive, Durham, NC 27710
- 323A CARL Building, Box 3580, Durham, NC 27710
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john.rawls@duke.edu
(919) 613-7212
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Rawls Publications
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Rawls lab webpage
- Background
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Education, Training, & Certifications
- Ph.D., Washington University in St. Louis 2001
- B.S., Emory University 1996
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Previous Appointments & Affiliations
- Associate Professor in Medicine, Medicine, Gastroenterology, Medicine 2014 - 2020
- Associate Professor of Molecular Genetics and Microbiology, Molecular Genetics and Microbiology, Basic Science Departments 2014 - 2019
- Instructor, Temporary in Molecular Genetics and Microbiology, Molecular Genetics and Microbiology, Basic Science Departments 2013 - 2014
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Leadership & Clinical Positions at Duke
- 2014-present, Director, Duke Microbiome Center (DMC)
- Recognition
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In the News
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MAY 4, 2023 Duke Today -
MAY 13, 2022 -
JUN 1, 2021 School of Medicine Magnify -
FEB 26, 2021 School of Medicine -
DEC 17, 2019 -
AUG 5, 2019 -
NOV 20, 2017 -
MAY 17, 2017 -
NOV 28, 2016 -
JUN 17, 2016 -
SEP 15, 2015 -
JUL 20, 2015 -
MAR 30, 2015 Duke Translational Medicine Institute -
MAR 24, 2015 Fox News -
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FEB 16, 2015 -
JAN 8, 2015 Duke Research Blog -
NOV 20, 2014 -
OCT 23, 2013
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Awards & Honors
- Fellow. American Academy of Microbiology. 2021
- Fellow. American Association for the Advancement of Science. 2016
- Kavli Fellow. Kavli Frontiers of Science Program. 2009
- Pew Scholar in the Biomedical Sciences. Pew Charitable Trust. 2008
- Mentored Research Scientist Development Award. National Institutes of Health. 2006
- Ruth L. Kirschstein Individual National Research Service Award. National Institutes of Health. 2002
- Spencer T. and Ann W. Olin Medical Scientist Fellow. Washington University School of Medicine. 2001
- Victor Hamburger Prize in Developmental Biology. Washington University School of Medicine. 2001
- Expertise
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Subject Headings
- Research
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Selected Grants
- Bacteria sensory transduction from gut to brain to modulate behavior awarded by National Institutes of Health 2023 - 2028
- Mechanisms of Enteroendocrine Cell Adaptation to High Fat Diet in Zebrafish awarded by National Institutes of Health 2023 - 2027
- NSF Engineering Research Center for Precision Microbiome Engineering (PreMiEr) awarded by National Science Foundation 2022 - 2027
- Duke Preparing Research Scholars in Biomedical Sciences- Post-Baccalaureate Research Education Program awarded by National Institutes of Health 2022 - 2027
- Medical Scientist Training Program awarded by National Institutes of Health 2022 - 2027
- Duke Training Grant in Digestive Diseases and Nutrition awarded by National Institutes of Health 1988 - 2027
- Training Program in Developmental and Stem Cell Biology awarded by National Institutes of Health 2001 - 2027
- Genetic determinants of Bacteroides vulgatus colonization fitness and host inflammatory responses awarded by National Institutes of Health 2023 - 2027
- Cell and Molecular Biology Training Program awarded by National Institutes of Health 2021 - 2026
- Microbial and dietary control of intestinal epithelial differentiation by HNF4A awarded by National Institutes of Health 2023 - 2025
- Microbial regulation of intestinal lipid metabolism and its physiological consequences awarded by National Institutes of Health 2021 - 2025
- Genetic and Genomics Training Grant awarded by National Institutes of Health 2020 - 2025
- Quantifying Enteric Metabolism of Branched-chain Amino Acids in Relation to Other Dietary and Microbiota Nutrients awarded by National Institutes of Health 2022 - 2024
- Duke University Program in Environmental Health awarded by National Institutes of Health 2019 - 2024
- Duke CTSA (TL1) Year 5 awarded by National Institutes of Health 2018 - 2024
- Identifying genes required for digestive physiology and lipid metabolism awarded by Carnegie Institution of Washington 2013 - 2023
- Research Training in Allergy and Clinical Immunology awarded by University of North Carolina - Chapel Hill 2000 - 2023
- Preparing Genetic Counselors for Genomic Medicine Research awarded by National Institutes of Health 2017 - 2023
- Identifying Microbial, Epithelial and Immune Cell Interactions that Mediate Mucosal Homeostasis and Determine IBD Phenotypes awarded by University of North Carolina - Chapel Hill 2013 - 2023
- Nasopharyngeal Microbiome and Risk of Bacterial Pathogen Colonization in Infants awarded by National Institutes of Health 2018 - 2023
- The role of HNF4a in maintaining intestinal epithelial cell homeostasis in the presence of microbes awarded by National Institutes of Health 2020 - 2023
- The Microbiome and Metabolism in Postnatal Growth Failure awarded by National Institutes of Health 2019 - 2023
- New Tools for Advancing Model Systems in Aquatic Symbiosis awarded by University of Oregon 2020 - 2023
- Influence of prenatal exposure to air pollution and maternal stress on microglial sculpting of neural circuits awarded by National Institutes of Health 2021 - 2023
- Home Transplant to Preserve the Microbiota and Decrease GVHD awarded by American Society of Hematology 2019 - 2022
- Cellular and Environmental Regulation of Protein Absorption and Utilization in the Early Intestine awarded by National Institutes of Health 2019 - 2022
- Gastrointestinal distress in ASD: testing the role of enteroendocrine cells awarded by University of Miami 2020 - 2022
- Fredrickson Lipid conference/NCDRC Diabetes Day awarded by North Carolina Biotechnology Center 2022
- A comprehensive research resource to define mechanisms underlying microbial regulation of host metabolism in pediatric obesity and obesity-targeted therapeutics awarded by National Institutes of Health 2016 - 2022
- Immune Compromised Zebrafish for Cell Transplantation awarded by Massachusetts General Hospital 2013 - 2022
- Genetic and Epigenetic Regulation of Intestinal Inflammation awarded by National Institutes of Health 2018 - 2022
- Enteroendocrine cells sense gut bacteria and activate a gut-brain pathway awarded by National Institutes of Health 2021
- A Novel Integrative Pathway Regulating Intestinal Glucose Sensing awarded by Pew Scholars Program 2018 - 2021
- Exploring microbial regulation of transcription factors and its effects on intestinal homeostasis awarded by Howard Hughes Medical Institute 2020 - 2021
- NRT: Integrative Bioinformatics for Investigating and Engineering Microbiomes (IBIEM) awarded by National Science Foundation 2015 - 2021
- Mechanisms of Environmental-Mixture Induced Metabolic Disruption awarded by National Institutes of Health 2019 - 2020
- Genetics Training Grant awarded by National Institutes of Health 1979 - 2020
- Organization and Function of Cellular Structure awarded by National Institutes of Health 1975 - 2020
- Microbial regulation of host nutrient metabolism awarded by National Institutes of Health 2013 - 2020
- Regulation of Luminal Protein Uptake and Trafficking By Lysosome-Rich Enterocytes awarded by National Institutes of Health 2017 - 2020
- Deconstructing how the microbiota influences the mucosal innate immune system awarded by National Institutes of Health 2014 - 2019
- Core A: Animal Models Core 2. Duke University Zebrafish Facility awarded by University of North Carolina - Chapel Hill 2016 - 2019
- Microbial and inflammatory regulation of intestinal epithelial gene transcription awarded by University of North Carolina - Chapel Hill 2016 - 2019
- Triangle Zebrafish Group Annual Retreat awarded by North Carolina Biotechnology Center 2018 - 2019
- Organotin influences on assembly and obesogenic activity of the gut microbiota awarded by National Institutes of Health 2014 - 2017
- Lightsheet Imaging System awarded by National Institutes of Health 2016 - 2017
- Role of Developmental Signaling Pathways in Tuberculosis Pathogenesis awarded by National Institutes of Health 2017
- Microbial Regulation of Nuclear Receptor Activity in the Intestinal Epithelium awarded by Baylor College of Medicine 2014 - 2016
- Microbial Ecology of the Zebrafish Intestine awarded by University of Oregon 2013 - 2015
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External Relationships
- Morgridge Institute for Research
- Netherlands Metabolomics Centre
- University of South Carolina
- Publications & Artistic Works
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Selected Publications
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Academic Articles
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Heppert, Jennifer K., Colin R. Lickwar, Matthew C. Tillman, Briana R. Davis, James M. Davison, Hsiu-Yi Lu, Wei Chen, Elisabeth M. Busch-Nentwich, David L. Corcoran, and John F. Rawls. “Conserved roles for Hnf4 family transcription factors in zebrafish development and intestinal function.” Genetics 222, no. 4 (November 30, 2022). https://doi.org/10.1093/genetics/iyac133.Full Text Link to Item
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Tong, Wenxin, Sarah A. Hannou, You Wang, Inna Astapova, Ashot Sargsyan, Ruby Monn, Venkataramana Thiriveedi, et al. “The intestine is a major contributor to circulating succinate in mice.” Faseb J 36, no. 10 (October 2022): e22546. https://doi.org/10.1096/fj.202200135RR.Full Text Link to Item
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Hurst, Jillian H., Alexander W. McCumber, Jhoanna N. Aquino, Javier Rodriguez, Sarah M. Heston, Debra J. Lugo, Alexandre T. Rotta, et al. “Age-Related Changes in the Nasopharyngeal Microbiome Are Associated With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection and Symptoms Among Children, Adolescents, and Young Adults.” Clin Infect Dis 75, no. 1 (August 24, 2022): e928–37. https://doi.org/10.1093/cid/ciac184.Full Text Open Access Copy Link to Item
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Levraud, Jean-Pierre, John F. Rawls, and Anne E. Clatworthy. “Using zebrafish to understand reciprocal interactions between the nervous and immune systems and the microbial world.” J Neuroinflammation 19, no. 1 (June 28, 2022): 170. https://doi.org/10.1186/s12974-022-02506-x.Full Text Link to Item
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Suarez, Lilianna, Asheley C. Skinner, Tracy Truong, Jessica R. McCann, John F. Rawls, Patrick C. Seed, and Sarah C. Armstrong. “Advanced Obesity Treatment Selection among Adolescents in a Pediatric Weight Management Program.” Child Obes 18, no. 4 (June 2022): 237–45. https://doi.org/10.1089/chi.2021.0190.Full Text Link to Item
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Jawahar, Jayanth, Alexander W. McCumber, Colin R. Lickwar, Caroline R. Amoroso, Sol Gomez de la Torre Canny, Sandi Wong, Margaret Morash, et al. “Starvation causes changes in the intestinal transcriptome and microbiome that are reversed upon refeeding.” Bmc Genomics 23, no. 1 (March 22, 2022): 225. https://doi.org/10.1186/s12864-022-08447-2.Full Text Link to Item
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Kelly, Matthew S., Catherine Plunkett, Yahe Yu, Jhoanna N. Aquino, Sweta M. Patel, Jillian H. Hurst, Rebecca R. Young, et al. “Non-diphtheriae Corynebacterium species are associated with decreased risk of pneumococcal colonization during infancy.” Isme J 16, no. 3 (March 2022): 655–65. https://doi.org/10.1038/s41396-021-01108-4.Full Text Link to Item
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Gomez-Martinez, Ismael, R Jarrett Bliton, Keith A. Breau, Michael J. Czerwinski, Ian A. Williamson, Jia Wen, John F. Rawls, and Scott T. Magness. “A Planar Culture Model of Human Absorptive Enterocytes Reveals Metformin Increases Fatty Acid Oxidation and Export.” Cell Mol Gastroenterol Hepatol 14, no. 2 (2022): 409–34. https://doi.org/10.1016/j.jcmgh.2022.04.009.Full Text Link to Item
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Lickwar, Colin R., James M. Davison, Cecelia Kelly, Gilberto Padilla Mercado, Jia Wen, Briana R. Davis, Matthew C. Tillman, et al. “Transcriptional Integration of Distinct Microbial and Nutritional Signals by the Small Intestinal Epithelium.” Cell Mol Gastroenterol Hepatol 14, no. 2 (2022): 465–93. https://doi.org/10.1016/j.jcmgh.2022.04.013.Full Text Link to Item
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Ye, Lihua, and John F. Rawls. “Microbial influences on gut development and gut-brain communication.” Development 148, no. 21 (November 1, 2021). https://doi.org/10.1242/dev.194936.Full Text Link to Item
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Yan, Chuan, Qiqi Yang, Songfa Zhang, David G. Millar, Eric J. Alpert, Daniel Do, Alexandra Veloso, et al. “Single-cell imaging of T cell immunotherapy responses in vivo.” J Exp Med 218, no. 10 (October 4, 2021). https://doi.org/10.1084/jem.20210314.Full Text Link to Item
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Wen, Jia, Gilberto Padilla Mercado, Alyssa Volland, Heidi L. Doden, Colin R. Lickwar, Taylor Crooks, Genta Kakiyama, et al. “Fxr signaling and microbial metabolism of bile salts in the zebrafish intestine.” Sci Adv 7, no. 30 (July 2021). https://doi.org/10.1126/sciadv.abg1371.Full Text Link to Item
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Hurst, Jillian H., Alexander W. McCumber, Jhoanna N. Aquino, Javier Rodriguez, Sarah M. Heston, Debra J. Lugo, Alexandre T. Rotta, et al. “Age-related changes in the upper respiratory microbiome are associated with SARS-CoV-2 susceptibility and illness severity.” Medrxiv, March 23, 2021. https://doi.org/10.1101/2021.03.20.21252680.Full Text Open Access Copy Link to Item
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McCann, Jessica R., Nathan A. Bihlmeyer, Kimberly Roche, Cameron Catherine, Jayanth Jawahar, Lydia Coulter Kwee, Noelle E. Younge, et al. “The Pediatric Obesity Microbiome and Metabolism Study (POMMS): Methods, Baseline Data, and Early Insights.” Obesity (Silver Spring) 29, no. 3 (March 2021): 569–78. https://doi.org/10.1002/oby.23081.Full Text Open Access Copy Link to Item
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Chen, Chuyi, Yuyang Gu, Julien Philippe, Peiran Zhang, Hunter Bachman, Jinxin Zhang, John Mai, et al. “Acoustofluidic rotational tweezing enables high-speed contactless morphological phenotyping of zebrafish larvae.” Nat Commun 12, no. 1 (February 18, 2021): 1118. https://doi.org/10.1038/s41467-021-21373-3.Full Text Link to Item
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Ye, Lihua, Munhyung Bae, Chelsi D. Cassilly, Sairam V. Jabba, Daniel W. Thorpe, Alyce M. Martin, Hsiu-Yi Lu, et al. “Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways.” Cell Host Microbe 29, no. 2 (February 10, 2021): 179-196.e9. https://doi.org/10.1016/j.chom.2020.11.011.Full Text Link to Item
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Heppert, Jennifer K., James M. Davison, Cecelia Kelly, Gilberto Padilla Mercado, Colin R. Lickwar, and John F. Rawls. “Transcriptional programmes underlying cellular identity and microbial responsiveness in the intestinal epithelium.” Nat Rev Gastroenterol Hepatol 18, no. 1 (January 2021): 7–23. https://doi.org/10.1038/s41575-020-00357-6.Full Text Link to Item
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Microbiome Centers Consortium COVID Committee, Thomas O. “Coordinating and Assisting Research at the SARS-CoV-2/Microbiome Nexus.” Msystems 5, no. 6 (December 1, 2020). https://doi.org/10.1128/mSystems.00999-20.Full Text Link to Item
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Cholan, Pradeep Manuneedhi, Alvin Han, Brad R. Woodie, Maxinne Watchon, Angela Rm Kurz, Angela S. Laird, Warwick J. Britton, et al. “Conserved anti-inflammatory effects and sensing of butyrate in zebrafish.” Gut Microbes 12, no. 1 (November 2020): 1–11. https://doi.org/10.1080/19490976.2020.1824563.Full Text
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Yan, Chuan, Daniel Do, Qiqi Yang, Dalton C. Brunson, John F. Rawls, and David M. Langenau. “Single-cell imaging of human cancer xenografts using adult immunodeficient zebrafish.” Nat Protoc 15, no. 9 (September 2020): 3105–28. https://doi.org/10.1038/s41596-020-0372-y.Full Text Link to Item
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Holmes, Zachary C., Justin D. Silverman, Holly K. Dressman, Zhengzheng Wei, Eric P. Dallow, Sarah C. Armstrong, Patrick C. Seed, John F. Rawls, and Lawrence A. David. “Short-Chain Fatty Acid Production by Gut Microbiota from Children with Obesity Differs According to Prebiotic Choice and Bacterial Community Composition.” Mbio 11, no. 4 (August 11, 2020). https://doi.org/10.1128/mBio.00914-20.Full Text Link to Item
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Armstrong, Sarah C., McAllister Windom, Nathan A. Bihlmeyer, Jennifer S. Li, Svati H. Shah, Mary Story, Nancy Zucker, et al. “Rationale and design of "Hearts & Parks": study protocol for a pragmatic randomized clinical trial of an integrated clinic-community intervention to treat pediatric obesity.” Bmc Pediatr 20, no. 1 (June 26, 2020): 308. https://doi.org/10.1186/s12887-020-02190-x.Full Text Link to Item
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Loh, Nellie Y., James E. N. Minchin, Katherine E. Pinnick, Manu Verma, Marijana Todorčević, Nathan Denton, Julia El-Sayed Moustafa, et al. “RSPO3 impacts body fat distribution and regulates adipose cell biology in vitro.” Nat Commun 11, no. 1 (June 3, 2020): 2797. https://doi.org/10.1038/s41467-020-16592-z.Full Text Link to Item
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Wen, Jia, and John F. Rawls. “Feeling the Burn: Intestinal Epithelial Cells Modify Their Lipid Metabolism in Response to Bacterial Fermentation Products.” Cell Host Microbe 27, no. 3 (March 11, 2020): 314–16. https://doi.org/10.1016/j.chom.2020.02.009.Full Text Link to Item
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Martiny, Jennifer B. H., Katrine L. Whiteson, Brendan J. M. Bohannan, Lawrence A. David, Nicole A. Hynson, Margaret McFall-Ngai, John F. Rawls, et al. “The emergence of microbiome centres.” Nat Microbiol 5, no. 1 (January 2020): 2–3. https://doi.org/10.1038/s41564-019-0644-x.Full Text Link to Item
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McCann, Jessica, Nathan Bihlmeyer, Kimberly Roche, Cameron Catherine, Jayanth Jawahar, Lydia Coulter Kwee, Noelle Younge, et al. “The Pediatric Obesity Microbiome and Metabolism Study (POMMS): Methods, Baseline Data, and Early Insights,” 2020. https://doi.org/10.1101/2020.06.09.20126763.Full Text
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Ye, Lihua, Olaf Mueller, Jennifer Bagwell, Michel Bagnat, Rodger A. Liddle, and John F. Rawls. “High fat diet induces microbiota-dependent silencing of enteroendocrine cells.” Elife 8 (December 3, 2019). https://doi.org/10.7554/eLife.48479.Full Text Link to Item
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Casadei, Elisa, Luca Tacchi, Colin R. Lickwar, Scott T. Espenschied, James M. Davison, Pilar Muñoz, John F. Rawls, and Irene Salinas. “Commensal Bacteria Regulate Gene Expression and Differentiation in Vertebrate Olfactory Systems Through Transcription Factor REST.” Chem Senses 44, no. 8 (October 17, 2019): 615–30. https://doi.org/10.1093/chemse/bjz050.Full Text Link to Item
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Park, Jieun, Daniel S. Levic, Kaelyn D. Sumigray, Jennifer Bagwell, Oznur Eroglu, Carina L. Block, Cagla Eroglu, et al. “Lysosome-Rich Enterocytes Mediate Protein Absorption in the Vertebrate Gut.” Dev Cell 51, no. 1 (October 7, 2019): 7-20.e6. https://doi.org/10.1016/j.devcel.2019.08.001.Full Text Link to Item
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Espenschied, Scott T., Mark R. Cronan, Molly A. Matty, Olaf Mueller, Matthew R. Redinbo, David M. Tobin, and John F. Rawls. “Epithelial delamination is protective during pharmaceutical-induced enteropathy.” Proc Natl Acad Sci U S A 116, no. 34 (August 20, 2019): 16961–70. https://doi.org/10.1073/pnas.1902596116.Full Text Link to Item
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Yan, Chuan, Dalton C. Brunson, Qin Tang, Daniel Do, Nicolae A. Iftimia, John C. Moore, Madeline N. Hayes, et al. “Visualizing Engrafted Human Cancer and Therapy Responses in Immunodeficient Zebrafish.” Cell 177, no. 7 (June 13, 2019): 1903-1914.e14. https://doi.org/10.1016/j.cell.2019.04.004.Full Text Link to Item
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Younge, Noelle E., Christopher B. Newgard, C Michael Cotten, Ronald N. Goldberg, Michael J. Muehlbauer, James R. Bain, Robert D. Stevens, et al. “Disrupted Maturation of the Microbiota and Metabolome among Extremely Preterm Infants with Postnatal Growth Failure.” Sci Rep 9, no. 1 (June 3, 2019): 8167. https://doi.org/10.1038/s41598-019-44547-y.Full Text Link to Item
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Murdoch, Caitlin C., Scott T. Espenschied, Molly A. Matty, Olaf Mueller, David M. Tobin, and John F. Rawls. “Intestinal Serum amyloid A suppresses systemic neutrophil activation and bactericidal activity in response to microbiota colonization.” Plos Pathog 15, no. 3 (March 2019): e1007381. https://doi.org/10.1371/journal.ppat.1007381.Full Text Link to Item
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2017 NIH-wide microbiome workshop writing team, Xiaoyin Sara. “2017 NIH-wide workshop report on "The Human Microbiome: Emerging Themes at the Horizon of the 21st Century".” Microbiome 7, no. 1 (February 26, 2019): 32. https://doi.org/10.1186/s40168-019-0627-4.Full Text Link to Item
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Murdoch, Caitlin C., and John F. Rawls. “Commensal Microbiota Regulate Vertebrate Innate Immunity-Insights From the Zebrafish.” Front Immunol 10 (2019): 2100. https://doi.org/10.3389/fimmu.2019.02100.Full Text Link to Item
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Cronan, Mark R., Molly A. Matty, Allison F. Rosenberg, Landry Blanc, Charlie J. Pyle, Scott T. Espenschied, John F. Rawls, Véronique Dartois, and David M. Tobin. “An explant technique for high-resolution imaging and manipulation of mycobacterial granulomas.” Nat Methods 15, no. 12 (December 2018): 1098–1107. https://doi.org/10.1038/s41592-018-0215-8.Full Text Link to Item
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Kelly, Matthew S., Michael G. Surette, Marek Smieja, Laura Rossi, Kathy Luinstra, Andrew P. Steenhoff, David M. Goldfarb, et al. “Pneumococcal Colonization and the Nasopharyngeal Microbiota of Children in Botswana.” Pediatr Infect Dis J 37, no. 11 (November 2018): 1176–83. https://doi.org/10.1097/INF.0000000000002174.Full Text Link to Item
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Murdoch, Caitlin, Scott Espenschied, Molly Matty, Olaf Mueller, David Tobin, and John Rawls. “Intestinal Serum Amyloid A suppresses systemic neutrophil activation and bactericidal activity in response to microbiota colonization,” October 4, 2018. https://doi.org/10.1101/435503.Full Text
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Minchin, James E. N., Catherine M. Scahill, Nicole Staudt, Elisabeth M. Busch-Nentwich, and John F. Rawls. “Deep phenotyping in zebrafish reveals genetic and diet-induced adiposity changes that may inform disease risk.” J Lipid Res 59, no. 8 (August 2018): 1536–45. https://doi.org/10.1194/jlr.D084525.Full Text Link to Item
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King, Justin, Justin Foster, James M. Davison, John F. Rawls, and Ghislain Breton. “Zebrafish Transcription Factor ORFeome for Gene Discovery and Regulatory Network Elucidation.” Zebrafish 15, no. 2 (April 2018): 202–5. https://doi.org/10.1089/zeb.2017.1486.Full Text Link to Item
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Williamson, Ian A., Jason W. Arnold, Leigh Ann Samsa, Liam Gaynor, Matthew DiSalvo, Jordan L. Cocchiaro, Ian Carroll, et al. “A High-Throughput Organoid Microinjection Platform to Study Gastrointestinal Microbiota and Luminal Physiology.” Cell Mol Gastroenterol Hepatol 6, no. 3 (2018): 301–19. https://doi.org/10.1016/j.jcmgh.2018.05.004.Full Text Link to Item
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Minchin, James E. N., and John F. Rawls. “Elucidating the role of plexin D1 in body fat distribution and susceptibility to metabolic disease using a zebrafish model system.” Adipocyte 6, no. 4 (October 2, 2017): 277–83. https://doi.org/10.1080/21623945.2017.1356504.Full Text Link to Item
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Phelps, Drake, Nichole E. Brinkman, Scott P. Keely, Emily M. Anneken, Tara R. Catron, Doris Betancourt, Charles E. Wood, Scott T. Espenschied, John F. Rawls, and Tamara Tal. “Microbial colonization is required for normal neurobehavioral development in zebrafish.” Sci Rep 7, no. 1 (September 11, 2017): 11244. https://doi.org/10.1038/s41598-017-10517-5.Full Text Link to Item
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Kelly, Matthew S., Michael G. Surette, Marek Smieja, Jeffrey M. Pernica, Laura Rossi, Kathy Luinstra, Andrew P. Steenhoff, et al. “The Nasopharyngeal Microbiota of Children With Respiratory Infections in Botswana.” Pediatr Infect Dis J 36, no. 9 (September 2017): e211–18. https://doi.org/10.1097/INF.0000000000001607.Full Text Link to Item
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McCann, J., J. Rawls, P. Seed, and S. Armstrong. “The Intestinal Microbiome and Childhood Obesity.” Current Pediatrics Reports 5, no. 3 (September 1, 2017): 150–55. https://doi.org/10.1007/s40124-017-0140-9.Full Text
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Lickwar, Colin R., J Gray Camp, Matthew Weiser, Jordan L. Cocchiaro, David M. Kingsley, Terrence S. Furey, Shehzad Z. Sheikh, and John F. Rawls. “Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells.” Plos Biol 15, no. 8 (August 2017): e2002054. https://doi.org/10.1371/journal.pbio.2002054.Full Text Open Access Copy Link to Item
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Davison, James M., Colin R. Lickwar, Lingyun Song, Ghislain Breton, Gregory E. Crawford, and John F. Rawls. “Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha.” Genome Res 27, no. 7 (July 2017): 1195–1206. https://doi.org/10.1101/gr.220111.116.Full Text Link to Item
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Minchin, James E. N., and John F. Rawls. “A classification system for zebrafish adipose tissues.” Dis Model Mech 10, no. 6 (June 1, 2017): 797–809. https://doi.org/10.1242/dmm.025759.Full Text Link to Item
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Leulier, François, Lesley T. MacNeil, Won-Jae Lee, John F. Rawls, Patrice D. Cani, Martin Schwarzer, Liping Zhao, and Stephen J. Simpson. “Integrative Physiology: At the Crossroads of Nutrition, Microbiota, Animal Physiology, and Human Health.” Cell Metab 25, no. 3 (March 7, 2017): 522–34. https://doi.org/10.1016/j.cmet.2017.02.001.Full Text Link to Item
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Melancon, E., S. Gomez De La Torre Canny, S. Sichel, M. Kelly, T. J. Wiles, J. F. Rawls, J. S. Eisen, and K. Guillemin. “Best practices for germ-free derivation and gnotobiotic zebrafish husbandry.” Methods Cell Biol 138 (2017): 61–100. https://doi.org/10.1016/bs.mcb.2016.11.005.Full Text Link to Item
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Minchin, J. E. N., and J. F. Rawls. “In vivo imaging and quantification of regional adiposity in zebrafish.” Methods Cell Biol 138 (2017): 3–27. https://doi.org/10.1016/bs.mcb.2016.11.010.Full Text Link to Item
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Bae, Sena, Olaf Mueller, Sandi Wong, John F. Rawls, and Raphael H. Valdivia. “Genomic sequencing-based mutational enrichment analysis identifies motility genes in a genetically intractable gut microbe.” Proc Natl Acad Sci U S A 113, no. 49 (December 6, 2016): 14127–32. https://doi.org/10.1073/pnas.1612753113.Full Text Link to Item
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Boursier, Jérôme, Olaf Mueller, Matthieu Barret, Mariana Machado, Lionel Fizanne, Felix Araujo-Perez, Cynthia D. Guy, et al. “The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota.” Hepatology 63, no. 3 (March 2016): 764–75. https://doi.org/10.1002/hep.28356.Full Text Link to Item
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Burns, Adam R., W Zac Stephens, Keaton Stagaman, Sandi Wong, John F. Rawls, Karen Guillemin, and Brendan Jm Bohannan. “Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development.” Isme J 10, no. 3 (March 2016): 655–64. https://doi.org/10.1038/ismej.2015.142.Full Text Link to Item
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Stephens, W Zac, Adam R. Burns, Keaton Stagaman, Sandi Wong, John F. Rawls, Karen Guillemin, and Brendan J. M. Bohannan. “The composition of the zebrafish intestinal microbial community varies across development.” Isme J 10, no. 3 (March 2016): 644–54. https://doi.org/10.1038/ismej.2015.140.Full Text Link to Item
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Williamson, Lauren L., Erin A. McKenney, Zoie E. Holzknecht, Christine Belliveau, John F. Rawls, Susan Poulton, William Parker, and Staci D. Bilbo. “Got worms? Perinatal exposure to helminths prevents persistent immune sensitization and cognitive dysfunction induced by early-life infection.” Brain Behav Immun 51 (January 2016): 14–28. https://doi.org/10.1016/j.bbi.2015.07.006.Full Text Link to Item
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Gomez de la Torre Canny, Sol, and John F. Rawls. “Baby, It's Cold Outside: Host-Microbiota Relationships Drive Temperature Adaptations.” Cell Host Microbe 18, no. 6 (December 9, 2015): 635–36. https://doi.org/10.1016/j.chom.2015.11.009.Full Text Link to Item
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Wong, Sandi, W Zac Stephens, Adam R. Burns, Keaton Stagaman, Lawrence A. David, Brendan J. M. Bohannan, Karen Guillemin, and John F. Rawls. “Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut.” Mbio 6, no. 5 (September 29, 2015): e00687–e00615. https://doi.org/10.1128/mBio.00687-15.Full Text Link to Item
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Wang, Liuyang, Stefan H. Oehlers, Scott T. Espenschied, John F. Rawls, David M. Tobin, and Dennis C. Ko. “CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation.” Genome Biol 16, no. 1 (September 15, 2015): 190. https://doi.org/10.1186/s13059-015-0722-1.Full Text Open Access Copy Link to Item
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Minchin, James E. N., Ingrid Dahlman, Christopher J. Harvey, Niklas Mejhert, Manvendra K. Singh, Jonathan A. Epstein, Peter Arner, Jesús Torres-Vázquez, and John F. Rawls. “Plexin D1 determines body fat distribution by regulating the type V collagen microenvironment in visceral adipose tissue.” Proc Natl Acad Sci U S A 112, no. 14 (April 7, 2015): 4363–68. https://doi.org/10.1073/pnas.1416412112.Full Text Link to Item
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Marjoram, Lindsay, Ashley Alvers, M Elizabeth Deerhake, Jennifer Bagwell, Jamie Mankiewicz, Jordan L. Cocchiaro, Rebecca W. Beerman, et al. “Epigenetic control of intestinal barrier function and inflammation in zebrafish.” Proc Natl Acad Sci U S A 112, no. 9 (March 3, 2015): 2770–75. https://doi.org/10.1073/pnas.1424089112.Full Text Link to Item
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McKenney, Erin A., Lauren Williamson, Anne D. Yoder, John F. Rawls, Staci D. Bilbo, and William Parker. “Alteration of the rat cecal microbiome during colonization with the helminth Hymenolepis diminuta.” Gut Microbes 6, no. 3 (2015): 182–93. https://doi.org/10.1080/19490976.2015.1047128.Full Text Link to Item
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Camp, J Gray, Christopher L. Frank, Colin R. Lickwar, Harendra Guturu, Tomas Rube, Aaron M. Wenger, Jenny Chen, Gill Bejerano, Gregory E. Crawford, and John F. Rawls. “Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape.” Genome Res 24, no. 9 (September 2014): 1504–16. https://doi.org/10.1101/gr.165845.113.Full Text Link to Item
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Kanther, Michelle, Sarah Tomkovich, Sun Xiaolun, Melinda R. Grosser, Jaseol Koo, Edward J. Flynn, Christian Jobin, and John F. Rawls. “Commensal microbiota stimulate systemic neutrophil migration through induction of serum amyloid A.” Cell Microbiol 16, no. 7 (July 2014): 1053–67. https://doi.org/10.1111/cmi.12257.Full Text Link to Item
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Minchin, James E. N., Victoria C. Williams, Yaniv Hinits, SiewHui Low, Panna Tandon, Chen-Ming Fan, John F. Rawls, and Simon M. Hughes. “Oesophageal and sternohyal muscle fibres are novel Pax3-dependent migratory somite derivatives essential for ingestion.” Development 140, no. 20 (October 15, 2013): 4296–4296. https://doi.org/10.1242/dev.103184.Full Text
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Gratacap, Remi L., John F. Rawls, and Robert T. Wheeler. “Mucosal candidiasis elicits NF-κB activation, proinflammatory gene expression and localized neutrophilia in zebrafish.” Dis Model Mech 6, no. 5 (September 2013): 1260–70. https://doi.org/10.1242/dmm.012039.Full Text Link to Item
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Wong, Sandi, Thomas Waldrop, Steven Summerfelt, John Davidson, Frederic Barrows, P Brett Kenney, Timothy Welch, et al. “Aquacultured rainbow trout (Oncorhynchus mykiss) possess a large core intestinal microbiota that is resistant to variation in diet and rearing density.” Appl Environ Microbiol 79, no. 16 (August 2013): 4974–84. https://doi.org/10.1128/AEM.00924-13.Full Text Link to Item
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Boursier, Jerome, John F. Rawls, and Anna Mae Diehl. “Obese humans with nonalcoholic fatty liver disease display alterations in fecal microbiota and volatile organic compounds.” Clin Gastroenterol Hepatol 11, no. 7 (July 2013): 876–78. https://doi.org/10.1016/j.cgh.2013.04.016.Full Text Link to Item
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Minchin, James E. N., Victoria C. Williams, Yaniv Hinits, Siewhui Low, Panna Tandon, Chen-Ming Fan, John F. Rawls, and Simon M. Hughes. “Oesophageal and sternohyal muscle fibres are novel Pax3-dependent migratory somite derivatives essential for ingestion.” Development 140, no. 14 (July 2013): 2972–84. https://doi.org/10.1242/dev.090050.Full Text Link to Item
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Sadler, Kirsten C., John F. Rawls, and Steven A. Farber. “Getting the inside tract: new frontiers in zebrafish digestive system biology.” Zebrafish 10, no. 2 (June 2013): 129–31. https://doi.org/10.1089/zeb.2013.1500.Full Text Link to Item
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McMenamin, Sarah K., James E. N. Minchin, Tiffany N. Gordon, John F. Rawls, and David M. Parichy. “Dwarfism and increased adiposity in the gh1 mutant zebrafish vizzini.” Endocrinology 154, no. 4 (April 2013): 1476–87. https://doi.org/10.1210/en.2012-1734.Full Text Link to Item
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Onyiah, Joseph C., Shehzad Z. Sheikh, Nitsan Maharshak, Erin C. Steinbach, Steven M. Russo, Taku Kobayashi, Lantz C. Mackey, et al. “Carbon monoxide and heme oxygenase-1 prevent intestinal inflammation in mice by promoting bacterial clearance.” Gastroenterology 144, no. 4 (April 2013): 789–98. https://doi.org/10.1053/j.gastro.2012.12.025.Full Text Link to Item
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McFall-Ngai, Margaret, Michael G. Hadfield, Thomas C. G. Bosch, Hannah V. Carey, Tomislav Domazet-Lošo, Angela E. Douglas, Nicole Dubilier, et al. “Animals in a bacterial world, a new imperative for the life sciences.” Proc Natl Acad Sci U S A 110, no. 9 (February 26, 2013): 3229–36. https://doi.org/10.1073/pnas.1218525110.Full Text Link to Item
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Cocchiaro, Jordan L., and John F. Rawls. “Microgavage of zebrafish larvae.” J Vis Exp, no. 72 (February 20, 2013): e4434. https://doi.org/10.3791/4434.Full Text Link to Item
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Goldsmith, Jason R., Jordan L. Cocchiaro, John F. Rawls, and Christian Jobin. “Glafenine-induced intestinal injury in zebrafish is ameliorated by μ-opioid signaling via enhancement of Atf6-dependent cellular stress responses.” Dis Model Mech 6, no. 1 (January 2013): 146–59. https://doi.org/10.1242/dmm.009852.Full Text Link to Item
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Sanapareddy, Nina, Ryan M. Legge, Biljana Jovov, Amber McCoy, Lauren Burcal, Felix Araujo-Perez, Thomas A. Randall, et al. “Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans.” Isme J 6, no. 10 (October 2012): 1858–68. https://doi.org/10.1038/ismej.2012.43.Full Text Link to Item
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Semova, Ivana, Juliana D. Carten, Jesse Stombaugh, Lantz C. Mackey, Rob Knight, Steven A. Farber, and John F. Rawls. “Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish.” Cell Host Microbe 12, no. 3 (September 13, 2012): 277–88. https://doi.org/10.1016/j.chom.2012.08.003.Full Text Link to Item
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Wong, Sandi, and John F. Rawls. “Intestinal microbiota composition in fishes is influenced by host ecology and environment.” Mol Ecol 21, no. 13 (July 2012): 3100–3102. https://doi.org/10.1111/j.1365-294x.2012.05646.x.Full Text Link to Item
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Rawls, J. F. “Special issue: gut microbial communities in health and disease.” Gut Microbes 3, no. 4 (2012): 277–78. https://doi.org/10.4161/gmic.20485.Full Text
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Camp, J Gray, Amelia L. Jazwa, Chad M. Trent, and John F. Rawls. “Intronic cis-regulatory modules mediate tissue-specific and microbial control of angptl4/fiaf transcription.” Plos Genet 8, no. 3 (2012): e1002585. https://doi.org/10.1371/journal.pgen.1002585.Full Text Link to Item
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Rawls, John F. “Special issue: gut microbial communities in health and disease.” Gut Microbes 3, no. 4 (2012): 277–78. https://doi.org/10.4161/gmic.20485.Full Text Link to Item
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Roeselers, Guus, Erika K. Mittge, W Zac Stephens, David M. Parichy, Colleen M. Cavanaugh, Karen Guillemin, and John F. Rawls. “Evidence for a core gut microbiota in the zebrafish.” Isme J 5, no. 10 (October 2011): 1595–1608. https://doi.org/10.1038/ismej.2011.38.Full Text Link to Item
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Kanther, Michelle, Xiaolun Sun, Marcus Mühlbauer, Lantz C. Mackey, Edward J. Flynn, Michel Bagnat, Christian Jobin, and John F. Rawls. “Microbial colonization induces dynamic temporal and spatial patterns of NF-κB activation in the zebrafish digestive tract.” Gastroenterology 141, no. 1 (July 2011): 197–207. https://doi.org/10.1053/j.gastro.2011.03.042.Full Text Link to Item
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Milligan-Myhre, Kathryn, Jeremy R. Charette, Ryan T. Phennicie, W Zac Stephens, John F. Rawls, Karen Guillemin, and Carol H. Kim. “Study of host-microbe interactions in zebrafish.” Methods Cell Biol 105 (2011): 87–116. https://doi.org/10.1016/B978-0-12-381320-6.00004-7.Full Text Link to Item
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Minchin, James E. N., and John F. Rawls. “In vivo analysis of white adipose tissue in zebrafish.” Methods Cell Biol 105 (2011): 63–86. https://doi.org/10.1016/B978-0-12-381320-6.00003-5.Full Text Link to Item
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Kanther, Michelle, and John F. Rawls. “Host-microbe interactions in the developing zebrafish.” Curr Opin Immunol 22, no. 1 (February 2010): 10–19. https://doi.org/10.1016/j.coi.2010.01.006.Full Text Link to Item
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Volkman, Hannah E., Tamara C. Pozos, John Zheng, J Muse Davis, John F. Rawls, and Lalita Ramakrishnan. “Tuberculous granuloma induction via interaction of a bacterial secreted protein with host epithelium.” Science 327, no. 5964 (January 22, 2010): 466–69. https://doi.org/10.1126/science.1179663.Full Text Link to Item
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Shen, Xiang Jun, John F. Rawls, Thomas Randall, Lauren Burcal, Caroline N. Mpande, Natascha Jenkins, Biljana Jovov, Zaid Abdo, Robert S. Sandler, and Temitope O. Keku. “Molecular characterization of mucosal adherent bacteria and associations with colorectal adenomas.” Gut Microbes 1, no. 3 (2010): 138–47. https://doi.org/10.4161/gmic.1.3.12360.Full Text Link to Item
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Flynn, Edward J., Chad M. Trent, and John F. Rawls. “Ontogeny and nutritional control of adipogenesis in zebrafish (Danio rerio).” J Lipid Res 50, no. 8 (August 2009): 1641–52. https://doi.org/10.1194/jlr.M800590-JLR200.Full Text Link to Item
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Camp, J Gray, Michelle Kanther, Ivana Semova, and John F. Rawls. “Patterns and scales in gastrointestinal microbial ecology.” Gastroenterology 136, no. 6 (May 2009): 1989–2002. https://doi.org/10.1053/j.gastro.2009.02.075.Full Text Link to Item
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Pham, Linh N., Michelle Kanther, Ivana Semova, and John F. Rawls. “Methods for generating and colonizing gnotobiotic zebrafish.” Nat Protoc 3, no. 12 (2008): 1862–75. https://doi.org/10.1038/nprot.2008.186.Full Text Link to Item
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Rawls, John F. “Enteric infection and inflammation alter gut microbial ecology.” Cell Host Microbe 2, no. 2 (August 16, 2007): 73–74. https://doi.org/10.1016/j.chom.2007.07.006.Full Text Link to Item
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Rawls, John F., Michael A. Mahowald, Andrew L. Goodman, Chad M. Trent, and Jeffrey I. Gordon. “In vivo imaging and genetic analysis link bacterial motility and symbiosis in the zebrafish gut.” Proc Natl Acad Sci U S A 104, no. 18 (May 1, 2007): 7622–27. https://doi.org/10.1073/pnas.0702386104.Full Text Link to Item
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Rawls, John F., Michael A. Mahowald, Ruth E. Ley, and Jeffrey I. Gordon. “Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection.” Cell 127, no. 2 (October 20, 2006): 423–33. https://doi.org/10.1016/j.cell.2006.08.043.Full Text Link to Item
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Rawls, John F., Buck S. Samuel, and Jeffrey I. Gordon. “Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota.” Proc Natl Acad Sci U S A 101, no. 13 (March 30, 2004): 4596–4601. https://doi.org/10.1073/pnas.0400706101.Full Text Link to Item
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Rawls, John F., and Stephen L. Johnson. “Temporal and molecular separation of the kit receptor tyrosine kinase's roles in zebrafish melanocyte migration and survival.” Dev Biol 262, no. 1 (October 1, 2003): 152–61. https://doi.org/10.1016/s0012-1606(03)00386-5.Full Text Link to Item
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Rawls, John F., Matthew R. Frieda, Anthony R. McAdow, Jason P. Gross, Chad M. Clayton, Candy K. Heyen, and Stephen L. Johnson. “Coupled mutagenesis screens and genetic mapping in zebrafish.” Genetics 163, no. 3 (March 2003): 997–1009. https://doi.org/10.1093/genetics/163.3.997.Full Text Link to Item
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Rawls, J. F., E. M. Mellgren, and S. L. Johnson. “How the zebrafish gets its stripes.” Dev Biol 240, no. 2 (December 15, 2001): 301–14. https://doi.org/10.1006/dbio.2001.0418.Full Text Link to Item
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Rawls, J. F., and S. L. Johnson. “Requirements for the kit receptor tyrosine kinase during regeneration of zebrafish fin melanocytes.” Development 128, no. 11 (June 2001): 1943–49. https://doi.org/10.1242/dev.128.11.1943.Full Text Link to Item
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Parichy, D. M., E. M. Mellgren, J. F. Rawls, S. S. Lopes, R. N. Kelsh, and S. L. Johnson. “Mutational analysis of endothelin receptor b1 (rose) during neural crest and pigment pattern development in the zebrafish Danio rerio.” Dev Biol 227, no. 2 (November 15, 2000): 294–306. https://doi.org/10.1006/dbio.2000.9899.Full Text Link to Item
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Rawls, J. F., and S. L. Johnson. “Zebrafish kit mutation reveals primary and secondary regulation of melanocyte development during fin stripe regeneration.” Development 127, no. 17 (September 2000): 3715–24. https://doi.org/10.1242/dev.127.17.3715.Full Text Link to Item
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Parichy, D. M., J. F. Rawls, S. J. Pratt, T. T. Whitfield, and S. L. Johnson. “Zebrafish sparse corresponds to an orthologue of c-kit and is required for the morphogenesis of a subpopulation of melanocytes, but is not essential for hematopoiesis or primordial germ cell development.” Development 126, no. 15 (August 1999): 3425–36. https://doi.org/10.1242/dev.126.15.3425.Full Text Link to Item
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Bear, J. E., J. F. Rawls, and C. L. Saxe. “SCAR, a WASP-related protein, isolated as a suppressor of receptor defects in late Dictyostelium development.” J Cell Biol 142, no. 5 (September 7, 1998): 1325–35. https://doi.org/10.1083/jcb.142.5.1325.Full Text Link to Item
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Book Sections
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Atlas, Ronald M., Kjersti M. Aagaard, Elaine Hsiao, Yvonne Huang, Curtis Huttenhower, Rosa Krajmalnik-Brown, Susan Lynch, et al. “Risk Assessment: Incorporating Chemical-Microbiome Interactions.” In ENVIRONMENTAL CHEMICALS, THE HUMAN MICROBIOME, AND HEALTH RISK: A RESEARCH STRATEGY, 71–83, 2018.Link to Item
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Atlas, Ronald M., Kjersti M. Aagaard, Elaine Hsiao, Yvonne Huang, Curtis Huttenhower, Rosa Krajmalnik-Brown, Susan Lynch, et al. “Current Methods for Studying the Human Microbiome.” In ENVIRONMENTAL CHEMICALS, THE HUMAN MICROBIOME, AND HEALTH RISK: A RESEARCH STRATEGY, 49–70, 2018.Link to Item
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Atlas, Ronald M., Kjersti M. Aagaard, Elaine Hsiao, Yvonne Huang, Curtis Huttenhower, Rosa Krajmalnik-Brown, Susan Lynch, et al. “Microbiome Variation.” In ENVIRONMENTAL CHEMICALS, THE HUMAN MICROBIOME, AND HEALTH RISK: A RESEARCH STRATEGY, 16–33, 2018.Link to Item
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Atlas, Ronald M., Kjersti M. Aagaard, Elaine Hsiao, Yvonne Huang, Curtis Huttenhower, Rosa Krajmalnik-Brown, Susan Lynch, et al. “Environmental Chemicals, the Human Microbiome, and Health Risk: A Research Strategy Summary.” In ENVIRONMENTAL CHEMICALS, THE HUMAN MICROBIOME, AND HEALTH RISK: A RESEARCH STRATEGY, 1–8, 2018.Link to Item
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Atlas, Ronald M., Kjersti M. Aagaard, Elaine Hsiao, Yvonne Huang, Curtis Huttenhower, Rosa Krajmalnik-Brown, Susan Lynch, et al. “Characterizing Interactions Between the Human Microbiome and Environmental Chemicals.” In ENVIRONMENTAL CHEMICALS, THE HUMAN MICROBIOME, AND HEALTH RISK: A RESEARCH STRATEGY, 34–48, 2018.Link to Item
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Atlas, Ronald M., Kjersti M. Aagaard, Elaine Hsiao, Yvonne Huang, Curtis Huttenhower, Rosa Krajmalnik-Brown, Susan Lynch, et al. “Research Strategy.” In ENVIRONMENTAL CHEMICALS, THE HUMAN MICROBIOME, AND HEALTH RISK: A RESEARCH STRATEGY, 84–105, 2018.Link to Item
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Atlas, Ronald M., Kjersti M. Aagaard, Elaine Hsiao, Yvonne Huang, Curtis Huttenhower, Rosa Krajmalnik-Brown, Susan Lynch, et al. “Environmental Chemicals, the Human Microbiome, and Health Risk: A Research Strategy Introduction.” In ENVIRONMENTAL CHEMICALS, THE HUMAN MICROBIOME, AND HEALTH RISK: A RESEARCH STRATEGY, 9–15, 2018.Link to Item
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Conference Papers
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Williamson, Ian A., Chi Wut Wong, Yanru Wu, Xiaoyang Su, John F. Rawls, and Xiling Shen. “Dietary Fat Increases Intestinal Fructose Conversion to Glycerate that Accumlates in Circulation, Driving Glucose Intolerance.” In Gastroenterology, 161:E25–26, 2021.Link to Item
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Suarez, Lilianna, Asheley Skinner, Tracy Truong, Jessica McCann, Lawrence David, John Rawls, Patrick Seed, and Sarah Armstrong. “The Selection of Obesity Treatment Among Adolescents in a Pediatric Weight Management Program.” In Obesity, 28:33–33, 2020.Link to Item
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Yan, Chuan, Qiqi Yang, Daniel Do, Dalton Brunson, John Iafrate, John Rawls, and David M. Langenau. “Dynamic single-cell imaging of human cancer growth and therapy responses following engraftment into immunodeficient zebrafish.” In Cancer Research, 80:29–29, 2020.Link to Item
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Canny, Sol Gomez de la Torre, Olaf Mueller, and John Franklin Rawls. “Tributyltin exposure alters post-embryonic growth and intestinal microbiota assembly in zebrafish.” In Faseb Journal, Vol. 31. FEDERATION AMER SOC EXP BIOL, 2017.Link to Item
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Ye, Lihua, Rodger A. Liddle, and John F. Rawls. “Dietary Regulation of Enteroendocrine Cell Function is Microbiota Dependent.” In Gastroenterology, 152:S824–S824. Elsevier BV, 2017. https://doi.org/10.1016/s0016-5085(17)32846-9.Full Text
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Loh, N. Y., K. E. Pinnick, J. E. N. Minchin, M. J. Neville, J. F. Rawls, F. Karpe, and C. Christodoulides. “RSPO3 functions via LGR4 to regulate human body fat distribution by eliciting diverse biological responses in abdominal and gluteal progenitors.” In Diabetologia, 59:S297–S297. SPRINGER, 2016.Link to Item
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Boursier, Jerome, Olaf Mueller, Matthieu Barret, Mariana V. Machado, Lionel Fizanne, Cynthia D. Guy, John F. Rawls, et al. “Increasing severity of NAFLD is associated with gut dysbiosis and modification of the metabolic function of the gut microbiota.” In Hepatology, 62:1274A-1274A. WILEY-BLACKWELL, 2015.Link to Item
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Tomkovich, Sarah E., Michelle Kanther, Xiaolun Sun, Melinda R. Grosser, Ja Seol Koo, Edward J. Flynn, Christian Jobin, and John F. Rawls. “Commensal Microbiota Stimulate Systemic Neutrophil Migration Through Induction of Serum Amyloid A.” In Gastroenterology, 146:S291–S291, 2014.Link to Item
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Cocchiaro, Jordan L., Adam Navis, Michel Bagnat, and John F. Rawls. “Zebrafish as a model to analyze macromolecule absorption in intestinal enterocytes.” In Faseb Journal, Vol. 27. FEDERATION AMER SOC EXP BIOL, 2013.Link to Item
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Goldsmith, Jason R., Jordan L. Cocchiaro, John F. Rawls, and Christian Jobin. “Glafenine Induced ER Stress and Intestinal Damage is Reversed by the Mu-Opioid Agonist DALDA Through Enhanced Autophagic Responses in Zebrafish.” In Gastroenterology, 142:S174–S174, 2012.Link to Item
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Onyiah, Joseph C., Shehzad Z. Sheikh, Nitsan Maharshak, Steven Russo, Erin C. Steinbach, Taku Kobayashi, Lantz C. Mackey, et al. “Heme Oxygenase-1 Maintains Intestinal Homeostasis Through Augmented Enteric Bacterial Clearance.” In Gastroenterology, 142:S107–S107, 2012.Link to Item
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Sheikh, Shehzad Z., Nitsan Maharshak, Joseph Onyiah, John Rawls, and Scott Plevy. “Heme oxygenase-1 expression and function is protective against innate immune responses to the enteric microbiota.” In Inflammatory Bowel Diseases, 17:S66–S66. Oxford University Press (OUP), 2011. https://doi.org/10.1097/00054725-201112002-00212.Full Text
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Goldsmith, Jason R., John E. Rawls, and Christian Jobin. “The Neuropeptide DALDA Protects Against NSAID-Induced Acute Intestinal Injury in Zebrafish Larvae.” In Gastroenterology, 140:S474–S474, 2011.Link to Item
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Koo, Ja Seol, Michelle Kanther, John F. Rawls, and Christian Jobin. “Microbiota-Induced Serum Amyloid A is an Important Mediator of Innate Immune Response in Zebrafish.” In Gastroenterology, 138:S78–79, 2010.Link to Item
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Semova, Ivana, and John Franklin Rawls. “Microbiota and dietary nutrients regulate digestive enzyme activity in the zebrafish intestine.” In Faseb Journal, Vol. 24, 2010.Link to Item
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Volkman, Hannah E., Tamara Pozos, John Zheng, John F. Rawls, and Lalita Ramakrishnan. “The Mycobacterium marinum RD1 locus promotes virulence and macrophage aggregation into tuberculous granulomas by enhancing induction of host matrix metalloproteinase 9 in proximal epithelial cells.” In Journal of Immunology, Vol. 182, 2009.Link to Item
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Estrada-Smith, Daria, Gloria Munoz, Shilang Wang, Peter Sorensen, Radu Dobrin, John Rawls, and Daniel Pomp. “A systems biology approach for the validation of eQTL in obesity.” In Faseb Journal, Vol. 22, 2008.Link to Item
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Muehlbauer, Marcus, Michelle Kanther, Christian Jobin, and John F. Rawls. “Generation and characterization of a novel Nf-kappa B reporter system to study bacteria-host interactions in the zebrafish intestine.” In Gastroenterology, 134:A15–A15, 2008.Link to Item
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Shen, Xiang Jun, Lauren Burcal, Caroline N. Mpande, Natascha Jenkins, Thomas Randall, John E. Rawls, Robert Sandler, and Temitope Keku. “Characterization of mucosa-associated bacteria species in colorectal biopsies from normal mucosa of patients with and without adenomas.” In Gastroenterology, 134:A132–A132, 2008.Link to Item
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Rawls, John F. “Microbial community assembly and host-microbial interactions in the intestine.” In Pediatric Pulmonology, 146–48, 2007.Link to Item
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POZOS, T., H. VOLKMAN, J. RAWLS, J. GORDON, and L. RAMAKRISHNAN. “Innate immunity to tuberculosis in zebrafish: roles of MMPs.” In Matrix Biology, 25:S12–13. Elsevier BV, 2006. https://doi.org/10.1016/j.matbio.2006.08.036.Full Text
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Rawls, J. F., and S. L. Johnson. “Genetic dissection of c-kit function during embryonic melanocyte development in the zebrafish.” In Developmental Biology, 235:191–92, 2001.Link to Item
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Johnson, S. L., J. F. Rawls, and D. M. Parichy. “Dissecting kit dependent morphogenesis with conditional mutations in zebrafish.” In Developmental Biology, 210:226–226, 1999.Link to Item
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Bear, J. E., J. Rawls, and C. L. Saxe. “REMI suppression of a Dictyostelium cAMP receptor null mutant uncovers a protein, SCAR1, with significant homology to actin regulatory proteins.” In Molecular Biology of the Cell, 8:2573–2573, 1997.Link to Item
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Preprints
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Gomez-Martinez, Ismael, Jarrett Bliton, Keith Breau, Michael Czerwinski, Ian Williamson, Jia Wen, John Rawls, and Scott Magness. “Transcriptomics informs design of a planar human enterocyte culture system that reveals metformin enhances fatty acid export.” BioRxiv, 2022. https://doi.org/10.1101/2022.01.24.477515.Full Text
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Thierer, James, Ombretta Foresti, Pradeep Kumar Yadav, Meredith Wilson, Tabea Moll, Meng-Chieh Shen, Elisabeth Busch-Nentwich, et al. “Pla2g12b is Essential for Expansion of Nascent Lipoprotein Particles.” BioRxiv, 2022. https://doi.org/10.1101/2022.08.02.502564.Full Text
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Tong, Wenxin, Sarah Hannou, You Wang, Inna Astapova, Ashot Sargsyan, Ruby Monn, Venkataramana Thiriveedi, et al. ““The Intestine is a Major Contributor to Circulating TCA Cycle Intermediates in Mice”.” BioRxiv, 2022. https://doi.org/10.1101/2022.01.20.477123.Full Text
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Lickwar, Colin R., James M. Davison, Cecelia Kelly, Gilberto Padilla Mercado, Jia Wen, Briana R. Davis, Matthew C. Tillman, et al. “Transcriptional integration of distinct microbial and nutritional signals by the small intestinal epithelium.” Cold Spring Harbor Laboratory, November 3, 2021. https://doi.org/10.1101/2021.11.01.465976.Full Text
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Torre Canny, Sol Gómez de la, Olaf Mueller, Camil Craciunescu, Bruce Blumberg, and John Rawls. “Tributyltin exposure leads to increased adiposity and reduced abundance of leptogenic bacteria in the zebrafish intestine.” BioRxiv, 2021. https://doi.org/10.1101/2021.07.09.451869.Full Text
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Ye, Lihua, Olaf Mueller, Jennifer Bagwell, Michel Bagnat, Rodger Liddle, and John Rawls. “High fat diet induces microbiota-dependent silencing of enteroendocrine cells.” BioRxiv, 2019. https://doi.org/10.1101/658435.Full Text
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- Teaching & Mentoring
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Recent Courses
- UPGEN 778E: University Program in Genetics and Genomics Biological Solutions Module V 2023
- MGM 593: Research Independent Study 2022
- NEUROSCI 391: Neuroscience Independent Scholarship 1: Advanced Topics 2022
- UPGEN 778E: University Program in Genetics and Genomics Biological Solutions Module V 2022
- MGM 593: Research Independent Study 2021
- UPGEN 778E: University Program in Genetics and Genomics Biological Solutions Module V 2021
- Scholarly, Clinical, & Service Activities
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Outreach & Engaged Scholarship
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