All Stories

  1. Designing fiber–gut microbiome interactions with active learning

    Article • Nature Chemical Biology, July 2026, Springer Science + Business Media

    Dr John F Rawls

  2. Identification of intestinal enteroendocrine cell subtypes and their associated hormones in zebrafish

    Article • PLoS Biology, December 2025, PLOS

    Dr John F Rawls

  3. Epithelial transcription factor Elf3 mediates host immune responses to microbiota and protects against aerocystitis in zebrafish

    Article • mBio, December 2025, ASM Journals

    Dr John F Rawls

  4. Environmental Microbial Cues Alter Embryonic Development and Stress Responses in Vertebrates: Insights From the Zebrafish ( Danio rerio ) Model

    Article • Molecular Ecology, November 2025, Wiley

    Dr John F Rawls

  5. Identifying Antibiotic Effects of Investigational Drugs on Commensal Bacteria with Machine Learning

    Article • June 2025, American Chemical Society (ACS)

    Jessica McCann, Dr John F Rawls

  6. Role of the upper airway microbiota in respiratory virus and bacterial pathobiont dynamics in the first year of life

    Article • Nature Communications, June 2025, Springer Science + Business Media

    Dr John F Rawls

  7. Protein absorption in the zebrafish gut is regulated by interactions between lysosome rich enterocytes and the microbiome

    Article • eLife, March 2025, eLife

    Dr John F Rawls

  8. Protein absorption in the zebrafish gut is regulated by interactions between lysosome rich enterocytes and the microbiome

    Article • eLife, March 2025, eLife

    Dr John F Rawls

  9. Protein absorption in the zebrafish gut is regulated by interactions between lysosome rich enterocytes and the microbiome

    Article • February 2025, eLife

    Dr John F Rawls

  10. Early subclinical stages of the inflammatory bowel diseases: insights from human and animal studies

    Article • AJP Gastrointestinal and Liver Physiology, January 2025, American Physiological Society

    Dr John F Rawls

  11. Zebrafish are resilient to the loss of major diacylglycerol acyltransferase enzymes

    Article • Journal of Biological Chemistry, December 2024, Elsevier

    Dr John F Rawls

  12. Protein absorption in the zebrafish gut is regulated by interactions between lysosome rich enterocytes and the microbiome

    Article • October 2024, eLife

    Dr John F Rawls

  13. The role of the microbiota in respiratory virus-bacterial pathobiont relationships in the upper respiratory tract

    Article • October 2024, openRxiv

    Dr John F Rawls

  14. Protein absorption in the zebrafish gut is regulated by interactions between lysosome rich enterocytes and the microbiome

    Article • June 2024, openRxiv

    Dr John F Rawls

  15. The External Microbiome Communicates with the Developing Zebrafish ( Danio rerio ) Embryo Through the Chorion and Influences Developmental Trajectory

    Article • May 2024, openRxiv

    Dr John F Rawls

  16. Publisher Correction: Pla2g12b drives expansion of triglyceride-rich lipoproteins

    Article • Nature Communications, March 2024, Springer Science + Business Media

    Dr John F Rawls

  17. Pla2g12b drives expansion of triglyceride-rich lipoproteins

    Article • Nature Communications, March 2024, Springer Science + Business Media

    Dr John F Rawls

  18. Conserved roles for Hnf4 family transcription factors in zebrafish development and intestinal function

    Article • Genetics, October 2022, Oxford University Press (OUP)

    Dr John F Rawls

  19. Pla2g12b is Essential for Expansion of Nascent Lipoprotein Particles

    Article • August 2022, Cold Spring Harbor Laboratory Press

    Dr John F Rawls

  20. Using zebrafish to understand reciprocal interactions between the nervous and immune systems and the microbial world

    Article • Journal of Neuroinflammation, June 2022, Springer Science + Business Media

    Dr John F Rawls

  21. Transcriptomics informs design of a planar human enterocyte culture system that reveals metformin enhances fatty acid export

    Article • January 2022, Cold Spring Harbor Laboratory Press

    Dr John F Rawls

  22. “The Intestine is a Major Contributor to Circulating TCA Cycle Intermediates in Mice”

    Article • January 2022, Cold Spring Harbor Laboratory Press

    Dr John F Rawls, Jessica McCann

  23. Microbial influences on gut development and gut-brain communication

    Article • Development, November 2021, The Company of Biologists

    Dr John F Rawls

  24. Tributyltin exposure leads to increased adiposity and reduced abundance of leptogenic bacteria in the zebrafish intestine

    Article • July 2021, Cold Spring Harbor Laboratory Press

    Dr John F Rawls

  25. Acoustofluidic rotational tweezing enables high-speed contactless morphological phenotyping of zebrafish larvae

    Article • Nature Communications, February 2021, Springer Science + Business Media

    Dr John F Rawls

  26. Transcriptional programmes underlying cellular identity and microbial responsiveness in the intestinal epithelium

    Article • Nature Reviews Gastroenterology & Hepatology, October 2020, Springer Science + Business Media

    Dr John F Rawls

  27. The emergence of microbiome centres

    Article • Nature Microbiology, December 2019, Springer Science + Business Media

    Dr John F Rawls, Prof. Jonathan A. Eisen

  28. High fat diet induces microbiota-dependent silencing of enteroendocrine cells

    Article • eLife, December 2019, eLife

    Dr John F Rawls

  29. Epithelial delamination is protective during pharmaceutical-induced enteropathy

    Article • Proceedings of the National Academy of Sciences, August 2019, Proceedings of the National Academy of Sciences

    Dr John F Rawls

  30. High fat diet induces microbiota-dependent silencing of enteroendocrine cells

    Article • June 2019, Cold Spring Harbor Laboratory Press

    Dr John F Rawls

  31. Intestinal Serum amyloid A suppresses systemic neutrophil activation and bactericidal activity in response to microbiota colonization

    Article • PLoS Pathogens, March 2019, PLOS

    Dr John F Rawls

  32. Intestinal Serum Amyloid A suppresses systemic neutrophil activation and bactericidal activity in response to microbiota colonization

    Article • October 2018, Cold Spring Harbor Laboratory Press

    Dr John F Rawls

  33. Deep phenotyping in zebrafish reveals genetic and diet-induced adiposity changes that may inform disease risk

    Article • Journal of Lipid Research, August 2018, Elsevier

    Dr John F Rawls

  34. Elucidating the role of plexin D1 in body fat distribution and susceptibility to metabolic disease using a zebrafish model system

    Article • Adipocyte, August 2017, Taylor & Francis

    Dr John F Rawls

  35. A classification system for zebrafish adipose tissues

    Article • Disease Models & Mechanisms, January 2017, The Company of Biologists

    Dr John F Rawls

  36. Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

    Article • The ISME Journal, August 2015, Nature

    Dr John F Rawls

  37. Plexin D1 determines body fat distribution by regulating the type V collagen microenvironment in visceral adipose tissue

    Article • Proceedings of the National Academy of Sciences, March 2015, Proceedings of the National Academy of Sciences

    Dr John F Rawls

  38. Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape

    Article • Genome Research, June 2014, Cold Spring Harbor Laboratory Press

    Dr John F Rawls

  39. Sa1764 Commensal Microbiota Stimulate Systemic Neutrophil Migration Through Induction of Serum Amyloid A

    Article • Gastroenterology, May 2014, Elsevier

    Dr John F Rawls

  40. Commensal microbiota stimulate systemic neutrophil migration through induction of Serum amyloid A

    Article • Cellular Microbiology, January 2014, Wiley

    Dr John F Rawls

  41. Oesophageal and sternohyal muscle fibres are novel Pax3-dependent migratory somite derivatives essential for ingestion

    Article • Development, October 2013, The Company of Biologists

    Dr John F Rawls

  42. Obese Humans With Nonalcoholic Fatty Liver Disease Display Alterations in Fecal Microbiota and Volatile Organic Compounds

    Article • Clinical Gastroenterology and Hepatology, July 2013, Elsevier

    Dr John F Rawls

  43. Aquacultured Rainbow Trout (Oncorhynchus mykiss) Possess a Large Core Intestinal Microbiota That Is Resistant to Variation in Diet and Rearing Density

    Article • Applied and Environmental Microbiology, June 2013, ASM Journals

    Dr John F Rawls

  44. Oesophageal and sternohyal muscle fibres are novel Pax3-dependent migratory somite derivatives essential for ingestion

    Article • Development, June 2013, The Company of Biologists

    Dr John F Rawls

  45. Getting the Inside Tract: New Frontiers in Zebrafish Digestive System Biology

    Article • Zebrafish, June 2013, Mary Ann Liebert Inc

    Dr John F Rawls

  46. Mucosal candidiasis elicits NF- B activation, proinflammatory gene expression and localized neutrophilia in zebrafish

    Article • Disease Models & Mechanisms, May 2013, The Company of Biologists

    Dr John F Rawls

  47. Dwarfism and Increased Adiposity in thegh1Mutant Zebrafishvizzini

    Article • Endocrinology, April 2013, Endocrine Society

    Dr John F Rawls

  48. Microgavage of Zebrafish Larvae

    Article • Journal of Visualized Experiments, February 2013, MyJove Corporation

    Dr John F Rawls

  49. Microbiota Regulate Intestinal Absorption and Metabolism of Fatty Acids in the Zebrafish

    Article • Cell Host & Microbe, September 2012, Elsevier

    Dr John F Rawls

  50. Glafenine-induced intestinal injury in zebrafish is ameliorated by  -opioid signaling via enhancement of Atf6-dependent cellular stress responses

    Article • Disease Models & Mechanisms, August 2012, The Company of Biologists

    Dr John F Rawls

  51. Intestinal microbiota composition in fishes is influenced by host ecology and environment

    Article • Molecular Ecology, June 2012, Wiley

    Dr John F Rawls

  52. 989 Glafenine Induced ER Stress and Intestinal Damage is Reversed by the Mu-Opioid Agonist DALDA Through Enhanced Autophagic Responses in Zebrafish

    Article • Gastroenterology, May 2012, Elsevier

    Dr John F Rawls

  53. Intronic Cis-Regulatory Modules Mediate Tissue-Specific and Microbial Control of angptl4/fiaf Transcription

    Article • PLoS Genetics, March 2012, PLOS

    Dr John F Rawls

  54. Heme oxygenase-1 expression and function is protective against innate immune responses to the enteric microbiota

    Article • Inflammatory Bowel Diseases, December 2011, Wolters Kluwer Health

    Dr John F Rawls

  55. Microbial Colonization Induces Dynamic Temporal and Spatial Patterns of NF-κB Activation in the Zebrafish Digestive Tract

    Article • Gastroenterology, July 2011, Elsevier

    Dr John F Rawls

  56. Evidence for a core gut microbiota in the zebrafish

    Article • The ISME Journal, April 2011, Nature

    Dr John F Rawls

  57. In vivo Analysis of White Adipose Tissue in Zebrafish

    Article • January 2011, Elsevier

    Dr John F Rawls

  58. Study of Host–Microbe Interactions in Zebrafish

    Article • January 2011, Elsevier

    Dr John F Rawls

  59. 562 Microbiota-Induced Serum Amyloid A is an Important Mediator of Innate Immune Response in Zebrafish

    Article • Gastroenterology, May 2010, Elsevier

    Dr John F Rawls

  60. Host–microbe interactions in the developing zebrafish

    Article • Current Opinion in Immunology, February 2010, Elsevier

    Dr John F Rawls

  61. Patterns and Scales in Gastrointestinal Microbial Ecology

    Article • Gastroenterology, May 2009, Elsevier

    Dr John F Rawls

  62. Ontogeny and nutritional control of adipogenesis in zebrafish (Danio rerio)

    Article • Journal of Lipid Research, April 2009, American Society for Biochemistry & Molecular Biology (ASBMB)

    Dr John F Rawls

  63. Methods for generating and colonizing gnotobiotic zebrafish

    Article • Nature Protocols, November 2008, Nature

    Dr John F Rawls

  64. 91 Generation and Characterization of a Novel Nf-κB Reporter System to Study Bacteria-Host Interactions in the Zebrafish Intestine

    Article • Gastroenterology, April 2008, Elsevier

    Dr John F Rawls

  65. In vivo imaging and genetic analysis link bacterial motility and symbiosis in the zebrafish gut

    Article • Proceedings of the National Academy of Sciences, May 2007, Proceedings of the National Academy of Sciences

    Dr John F Rawls

  66. Reciprocal Gut Microbiota Transplants from Zebrafish and Mice to Germ-free Recipients Reveal Host Habitat Selection

    Article • Cell, October 2006, Elsevier

    Ruth Ley, Dr John F Rawls

  67. Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota

    Article • Proceedings of the National Academy of Sciences, March 2004, Proceedings of the National Academy of Sciences

    Dr John F Rawls

  68. Temporal and molecular separation of the kit receptor tyrosine kinase's roles in zebrafish melanocyte migration and survival

    Article • Developmental Biology, October 2003, Elsevier

    Dr John F Rawls

  69. How the Zebrafish Gets Its Stripes

    Article • Developmental Biology, December 2001, Elsevier

    Dr John F Rawls

  70. Mutational Analysis of Endothelin Receptor b1 (rose) during Neural Crest and Pigment Pattern Development in the Zebrafish Danio rerio

    Article • Developmental Biology, November 2000, Elsevier

    Dr John F Rawls