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  1. Raab JR, Wager KE, Morowitz JM, Magness ST, Gracz AD. Intestinal stem cell differentiation is associated with dynamic changes in the chromatin landscape. bioRxiv. May 23, 2019.


  1. Gracz AD*, Samsa LA, Fordham MF, Trotier DC, Altizer BA, Lo Y, Bao K, Starmer J, Shroyer NF, Reinhardt RL, Magness ST*. Sox4 drives Atoh1-independent intestinal secretory differentiation toward tuft and enteroendocrine fates. Gastroenterology, 2018 (Nov); 155(5):1508-1523. Epub 2018 Jul 25. *co-corresponding authorship.

  2. Altizer BA, Gracz AD, Williamson IA, Zhao Q, Magness ST. Elevated IL22 inhibits epithelial stem cell expansion in an ileal organoid model. Cell and Molecular Gastroenterology and Hepatology, 2018 (Jul); 4;7(1)1-17.

  3. Roche KC, Gracz AD, Lui X, Newton V, Magness ST. SOX9 maintains reserve stem cells and preserves radio-resistance in mouse small intestine. Gastroenterology, 2015 (Nov);149(6):1553-1563. Epub 2015 Jul 11.

  4. Gracz AD, Williamson IA, Roche KC, Johnston MJ, Wang F, Wang Y, Attayek P, Balowski J, Liu X, Laurenza RJ, Gaynor L, Sims CE, Galanko J, Li L, Allbritton NL, Magness ST. A high throughput platform for stem cell-niche co-cultures and downstream gene expression analysis. Nature Cell Biology, 2015 Mar; 17(3):340-9. Epub 2015 Feb 9.

  5. Ahmad AA, Wang Y, Gracz AD, Sims CE, Magness ST, Allbritton NL. Optimization of 3-D organotypic primary colonic cultures for organ-on-chip applications. J Biol Eng. 2014 Apr 1;8:9.

  6. Wang F, Scoville D, He XC, Box A, Perry J, Smith NR, Nanye NL, Davies PS, Fuller M, Haug JS, McClain M, Gracz AD, Ding S, Stelzner M, Dunn J, Magness ST, Wong M, Martin M, Helmrath M, Li L. Isolation and characterization of intestinal stem cells based on surface marker combinations and colony-formation assay. Gastroenterology. 2013 Aug; 145(2): 383-95.e1-21. Epub 2013 May 2.

  7. Gracz AD*, Fuller MK*, Wang F, Stelzner M, Dunn JC, Martin M, Li L, Magness ST. CD24- and CD44-expression profiles facilitate differential isolation of ‘active’ and ‘reserve’ intestinal epithelial stem cell populations from human small intestine. Stem Cells. 2013 Sep; 31(9): 2024-30. *authors contributed equally to this work.

  8. Van Landeghem LM, Santoro A, Krebs A, Mah AT, Dehmer JJ, Gracz AD, Scull BP, McNaughton K, Magness ST, and Lund PK. Activation of two distinct Sox9-EGFP expressing intestinal stem cell populations during crypt regeneration after irradiation. Am J Physiol Gastrointest Liver Physiol. 2012 May 15; 302(10):G1111-32. Epub 2012 Feb 23

  9. Ramalingam S, Daughtridge GW, Johnston MJ, Gracz AD, Magness ST. Distinct levels of Sox9 expression mark colon epithelial stem cells that form colonoids in culture. Am J Physiol Gastrointest Liver Physiol. 2012 Jan; 302(1): G10-20. Epub 2011 Oct 13

  10. von Furstenberg RJ, Gulati AS, Baxi A, Doherty JM, Stappenbeck TS, Gracz AD, Magness ST, Henning SJ. Sorting mouse jejunal epithelial cells with CD24 yields a population with characteristics of intestinal epithelial stem cells. Am J Physiol Gastrointest Liver Physiol. 2011 Mar; 300(3): G409-17. Epub 2010 Dec 23.

  11. Gracz AD, Ramalingam S, Magness ST. Sox9-expression marks a subset of CD24-expressing small intestine epithelial stem cells that form organoids in vitro. Am J Physiol Gastrointest Liver Physiol. 2010 May; 298(5): G590-600. Epub 2010 Feb 25.


  1. Gracz AD, Magness ST. Defining hierarchies of stemness in the intestine: biomarkers and regulatory pathways. Am J Physiol Gastrointest Liver Physiol. 2014 Aug 1;307(3):G260-G273. Epub 2014 Jun 12.

  2. Gracz AD and Magness ST. Sry-box (SOX) transcription factors in gastrointestinal physiology and disease. Am J Physiol Gastrointest Liver Physiol. 2011 Apr; 300(4): G503-15. Epub 2011 Feb 3.


  1. Altizer BA, Gracz AD*, Magness ST*. Organoid cultures for assessing intestinal epithelial differentiation and function in response to type-2 inflammation. in press, Methods Mol Biol. *co-corresponding authorship.

  2. Gracz AD, Puthoff BJ, Magness ST, Identification, isolation, and culture of intestinal epithelial stem cells from murine intestine. Methods Mol Biol. 2012; 879:89-107.