1. Capdevila C, Miller J, Cheng L, Kornberg A, George JJ, Lee H, Botella T, Moon CS, Murray JW, Lam S, Calderon RI, Malagola E, Whelan G, Lin CS, Han A, Wang TC, Sims PA, & Yan KS. Time-resolved fate mapping identifies the intestinal upper crypt zone as an origin of Lgr5+ crypt base columnar cells. Cell. 2024 Jun 6;187(12):3039-3055.e14. doi: 10.1016/j.cell.2024.05.001. PMID: 38848677. (*Commentary on this work by Li & Sumigray published in same issue of Cell)
2. Malagola E, Vasciaveo A, Ochiai Y, Kim W, Zheng B, Zanella L, Wang ALE, Middelhof M, Nienhuser H, Deng L, Wu F, Waterbury QT, Belin B, LaBella J, Zamechek LB, Wong MH, Li L, Guha C, Cheng CW, Yan KS, Califano A & Wang TC. Isthmal progenitor cells contribute to homeostatic cellular turnover and support regeneration following intestinal injury. Cell. 2024 Jun 6;187(12):3056-3071.e17. doi: 10.1016/j.cell.2024.05.004. PMID: 38848678. (*Commentary on this work by Li & Sumigray published in same issue of Cell)
3. Ke X, van Soldt B, Vlahos L, Zhou Y, Qian J, George J, Capdevila C, Glass I, Yan K, Califano A & Cardoso WV. Morphogenesis and regeneration share a conserved core transition cell state program that controls lung epithelial cell fate. Dev Cell. 2024 Dec 9:S1534-5807(24)00699-3.doi: 10.1016/j.devcel.2024.11.017. PMID: 39667932
4. Hwang Y, Shimamura Y, Tanaka J, Miura A, Sawada A, Sarmah H, Shimizu D, Kondo Y, Lee H, Martini F, Ninish Z, Yan KS, Yamada K & Mori M. FGF2 promotes the expansion of parietal mesothelial progenitor pools and inhibits BMP4-mediated smooth muscle cell differentiation. Front Cell Dev Biol. 2024 Sep 23;12:1387237. doi:10.3389/fcell.2024.1387237. PMID: 39376629
5. Jiang Z, Waterbury QT, Malagola E, Fu N, Kim W, Ochiai Y, Wu F, Guha C, Shawber CJ, Yan KS, Wang TC. Microbial-dependent recruitment of immature myeloid cells promotes intestinal regeneration. Cell Mol Gastroenterol Hepatol. 2024;17(3):321-346. doi: 10.1016/j.jcmgh.2023.10.007. PMID: 37898454.
6. Kornberg A, Botella T, Moon CS, Rao S, Gelbs J, Cheng L, Miller J, Bacarella AM, Garcia-Vilas JA, Varga J, Yu X, Krupska I, Bush E, Garcia-Carrasquillo R, Lebwohl B, Krishnareddy S, Lewis S, Green PH, Bhagat G, Yan KS & Han A. Gluten induces rapid reprogramming of natural memory αβ and γδ intraepithelial T cells to induce cytotoxicity in celiac disease. Sci Immunol 2023 July 21;8(85)eadf4312. PMID: 37450575.
7. Flashner S, Martin C, Matsuura N, Shimonosono M, Tomita Y, Morimoto M, Okolo O, Yu VX, Parikh AS, KleinSzanto AJP, Yan K, Gabre JT, Lu C, Momen-Heravi F, Rustgi AK, & Nakagawa N. Modeling oral-esophageal squamous cell carcinoma in 3D organoids. J Vis Exp. 2022 Dec 23;(190).doi:10.3791/64676. PMID 36622034.
8. Hein RFC, Wu JH, Holloway EM, Frum T, Conchola AS, Tsai YH, Fine AS, Miller AJ, Szenker-Ravi E, Yan KS, Kuo CJ, Glass I, Reversade B, & Spence JR. R-SPONDIN2+ mesenchymal cells form the bud tip progenitor niche during human lung development. Dev Cell. 2022 Jun7:S1534-5807(22)00367-7. PMID: 35679862.
9. Abrams J, Camilleri M, Merchant J, Rustgi AK & Yan K. Presentation of the Julius M. Friedenwald Medal to Timothy C. Wang, MD, AGAF. Gastroenterology. 2022 Jun;162(7):2086-2091.doi:10.1053/j.gastro.2022.03.021. Epub 2022 April 17. PMID: 35443933.
10. Masuda K, Kornberg A, Miller J, Lin S, Suek N, Botella T, Secener KA, Baccarella AM, Cheng L, Ingham M,
Rosario V, Al-Mazrou AM, Lee-Kong SA, Kiran RP, Stoeckius M, Smibert P, De Portillo A, Oberstein PE, Sims PA, Yan KS & Han A. Multiplexed single-cell analysis reveals prognostic and non-prognostic T cell types in human colorectal cancer. JCI Insight. 2022 Feb 22. e154646. PMID: 35192548.
11. Flashner S, Yan KS & Nakagawa H. 3D Organoids: An untapped platform for studying host-microbe interactions in esophageal cancers. Microorganisms. 2021 Oct 20;9(11):2182. PMID: 34835308.
12. Maan ZN, Rinkevich Y, Barrera J, Chen K, Henn D, Foster D, Bonham CA, Padmanabhan J, Sivaraj D, Duscher D, Hu M, Yan KS, Januszyk M, Longaker MT, Weissman IL & Gurtner GC. Epidermal-derived Hedgehog signaling drives mesenchymal proliferation during digit tip regeneration. J Clin Med. 2021 Sept 20;10(18):4261. PMID: 34575372.
13. Capdevila C, Trifas M, Miller J, Anderson T, Sims PA & Yan KS. Cellular origins and lineage relationships of the intestinal epithelium. Am J Physiol Gastrointest Liver Physiol. 2021 Aug 25. doi: 10.1152/ajpgi.00188.2021. PMID: 34431400.
14. Miller J & Yan KS. COVID-19 gastrointestinal symptoms and attenuation of the immune response to SARSCoV-2. Gastroenterology. 2021 March 19:S0016-5085(21)00538-2. doi: 10.1053/9j.gastro.2021.03.029. PMID: 33753106.
15. Norkin M, Capdevila C, Calderon RI, Su T, Trifas M, Ordonez-Moran P, Yan KS. Single-cell studies of intestinal stem cell heterogeneity during homeostasis and regeneration. Methods Mol Biol. 2020;2171:155-167. doi: 10.1007/978-1-0716-0747-3_9. PMID: 32705640.
16. Capdevila C, Calderon RI, Bush EC, Sheldon-Collins K, Sims PA, Yan KS. Single-cell transcriptional profiling of the intestinal epithelium. Methods Mol Biol. 2020;2171:129-153. doi: 10.1007/978-1-0716-0747-3_8. PMID: 32705639.
17. Bohin N, McGowan KP, Carlson EA, Yan KS, Samuelson LC. Insulin-like Growth Factor-1 and mTORC1 signaling promote the intestinal regenerative response after irradiation injury. Cell Mol Gastroenterol Hepatol. 2020 Jun 2;S2352-345X(20)30089-8. doi: 10.1016/j.jcmgh.2020.05.013. Online ahead of print. PMID: 32502530
18. Middelhoff M, Nienhuser H, Valenti G, Maurer HC, Hayakawa Y, Takahashi R, Kim W, Jiang Z, Malagola E, Cuti K, Tailor Y, Zamechek LB, Renz BW, Quante M, Yan KS, Wang TC. Prox1-positive cells monitor and sustain the murine intestinal epithelial cholinergic niche. Nat Commun. 2020 Jan 8;11(1):111. doi: 10.1038/s41467-01913850-7. PMID: 31913277
19. Yan KS. Advice for the Next Generation: Kelley Yan, Cell Stem Cell, 2019 Jun6;24(6):852-854. https://doi.org/10.1016/j.stem.2019.05.004
20. Hayakawa Y, Tsuboi M, Asfaha S, Kinoshita H, Niikura R, Konishi M, Hata M, Oya Y, Kim W, Middelhoff M, Hikiba Y, Higashijima N, Ihara S, Ushiku T, Fukayama M, Tailor Y, Hirata Y, Guha C, Yan KS, Koike K & Wang TC. BHLHA15-positive secretory precursor cells can give rise to tumors in intestine and colon in mice. Gastroenterology. 2018 Nov15. pii: S0016-5085(18)35272-7. PMID:30448068.
21. Pont AR & Yan KS. Intestinal crypts assume the fetal position in response to injury. Cell Stem Cell. 2018 Aug2;23(2):158-159. PMID:30075126.
22. Yan KS, Gevaert O, Zheng GXY, Anchang B, Probert CS, Larkin KA, Davies PS, Cheng ZF, Kaddis JS, Han A, Roelf K, Calderon RI, Cynn E, Hu X, Mandleywala K, Wilhelmy J, Grimes SM, Corney DC, Boutet SC, Terry
JM, Belgrader P, Ziraldo SB, Mikkelsen TS, Wang F, von Furstenberg RJ, Smith NR, Chandrakesan P, May R,
Chrissy MAS, Jain R, Cartwright CA, Niland JC, Hong YK, Carrington J, Breault DT, Epstein J, Houchen CW, Lynch JP, Martin MG, Plevritis SK, Curtis C, Ji HP, Li L, Henning SJ, Wong MH & Kuo CJ. Intestinal
enteroendocrine lineage cells possess homeostatic and injury-inducible stem cell activity. Cell Stem Cell. 2017 Jul6;21(1):78-90. PMID 28686870. (*Commentary in Cell Stem Cell 2017 July 6)
23. Middelhoff M, Westphalen CB, Hayakawa Y, Yan KS, Gershon MD, Wang TC, Quante M. Dclk1-expressing tuft cells: Critical modulators of the intestinal niche? Am J Physiol Gastrointest Liver Physiol. 2017 Jul 6:ajpgi.00073.2017. PMID 28684459.
24. Yan KS, Janda CY, Chang J, Zheng GXY, Larkin KA, Luca VC, Chia LA, Mah AT, Han A, Terry JM, Ootani A, Roelf K, Lee M, Yuan J, Li X, Bolen CR, Wilhelmy J, Davies PS, Ueno H, von Furstenberg RJ, Belgrader P,
Ziraldo SB, Ordonez H, Henning SJ, Wong MH, Snyder MP, Weissman IL, Hsueh AJ, Mikkelsen TS, Garcia
KC, & Kuo CJ. Non-equivalence of Wnt and R-spondin ligands during Lgr5+ intestinal stem-cell self-renewal.
Nature. 2017 May 11;545(7653):238-242. PMID: 28467820. (*Faculty of 1000 recommended;
*Commentary in Developmental Cell 2017 June5)
25. Janda CY*, Dang LT*, You C, Chang J, de Lau W, Zhong ZA, Yan KS, Marecic O, Siepe D, Li X, Moody JD, Williams BO, Clevers H, Piehler J, Baker D, Kuo CJ, & Garcia KC. Surrogate Wnt ligands that phenocopy canonical Wnt and β-catenin signalling. Nature. 2017 May 11;545(7653):234-237. PMID: 28467818.
26. Mah, AT, Yan KS, & Kuo CJ. Wnt pathway regulation of intestinal stem cells. J. Physiol. 594(17):4837-47 (2016). PMID 27581568
27. Yan KS & Kuo CJ. Ascl2 reinforces intestinal stem cell identity. Cell Stem Cell 16(2):105-6 (2015). PMID: 25658363
28. Chan CK, Seo EY, Chen JY, Lo D, McArdle A, Sinha R, Tevlin R, Seita J, Vincent-Tompkins J, Wearda T, Lu WJ, Senarath-Yapa K, Chung MT, Marecic O, Tran M, Yan KS, Upton R, Walmsley GG, Lee AS, Sahoo D,
Kuo CJ, Weissman IL, & Longaker MT. Identification and specification of the mouse skeletal stem cell. Cell 160(1-2):285-98 (2015). PMID 25594184 (*Faculty of 1000 recommended)
29. DiMarco RL, Su J, Yan KS, Dewi R, Kuo CJ & Heilshorn SC. Engineering of Three-Dimensional Microenvironments to Promote Contractile Behavior in Primary Intestinal Organoids. Integrative Biology 6(2):127-42 (2014). PMID:24343706
30. Lim X, Tan SH, Koh WL, Chau RM, Yan KS, Kuo CJ, van Amerongen R, Klein AM & Nusse R. Interfollicular epidermal stem cells self-renew via autocrine Wnt signaling. Science 342 (6163):1226-30 (2014). PMID: 24311688 (*Faculty of 1000 recommended)
31. Magness ST, Puthoff BJ, Crissey MA, Dunn JC, Henning SJ, Houchen CW, Kaddis JS, Kuo CJ, Li L, Lynch JP,
Martin MG, May RJ, Niland JC, Olack B, Qian D, Stelzner M, Swain J, Wang F, Wang J, Wang X, Yan K, Yu J & Wong MH. A multi-center study to standardize reporting and analyses of fluorescence-activated cell sorted murine intestinal epithelial cells. Am J Physiol Gastrointest Liver Physiol 305 (8): G542-51 (2013). PMID: 23928185
32. Barry ER, Morikawa T, Butler BL, Shrestha K, de la Rosa R, Yan KS, Fuchs CS, Magness ST, Smits R, Ogino S, Kuo CJ & Camargo FD. Restriction of intestinal stem cell expansion and the regenerative response by YAP. Nature 493 (7430):106-10 (2013). PMID:23178811 (*Faculty of 1000 recommended)
33. Yan KS, Chia LA, Li X, Ootani A, Su J, Lee JY, Su N, Luo Y, Heilshorn SC, Amieva MR, Sangiorgi E, Capecchi MR & Kuo CJ. The intestinal stem cell markers Bmi1 and Lgr5 identify two functionally distinct populations. Proc Natl Acad Sci 109(2):466-471 (2012). PMID 22190486 (*Faculty of 1000 recommended)
34. Kaltenbach T, Leung C, Wu K, Yan K, Friedland S & Soetikno R. Use of the Colonoscope Training Model with the Colonoscope 3D Imaging Probe Improved Trainee Colonoscopy Performance: A Pilot Study. Dig Dis Sci 56(5), 1496-1502 (2011). PMID: 21409379
35. Zeng L, Zhang Q, Yan K & Zhou MM. Structural Insights into piRNA recognition by the human PIWI-like 1 PAZ domain. Proteins 79(6), 2004-2009 (2011). PMID: 21465557
36. Yan KS & Pasricha PJ. Acting in Good Taste: Nutrient Sensors in the Gut. Gut 58(7):897-898 (2009). PMID: 19520884
37. Yan KS, Yan S, Farooq A, Han A, Zeng L & Zhou MM. Structure and Conserved RNA Binding of the PAZ
Domain. Nature 426, 468-474 (2003). PMID: 14615802 (*Faculty of 1000 recommended)
38. Farooq A, Zeng L, Yan KS, Ravichandran KS & Zhou MM. Coupling of Folding and Binding in the PTB Domain of the Signaling Protein Shc. Structure 11, 905-913 (2003). PMID: 12906822
39. Yan KS & Zhou MM. Examining Both Sides of a Janus PTB Domain. Structure 11, 482-484 (2003). PMID: 12737812
40. Yan KS & Zhou MM. TAGging the Target for Damage Control. Nature Structural Biology 9, 638-640 (2002). PMID: 12198481
41. Yan KS, Kuti M & Zhou MM. PTB or Not PTB—That is the Question. FEBS Letters 513, 67-70 (2002). PMID: 11911882
42. Yan KS, Kuti M, Yan S, Mujtaba S, Farooq A, Goldfarb MP & Zhou MM. FRS2 PTB Domain Conformation Regulates Interactions with Divergent Neurotrophic Receptors. Journal of Biological Chemistry 277, 1708817094 (2002). PMID: 11877385
43. Dhalluin C, Yan KS, Plotnikova O, Zeng L, Goldfarb MP & Zhou MM. 1H, 13C and 15N Resonance Assignments of the SNT PTB Domain in Complex with FGFR1 Peptide. Journal of Biomolecular NMR 18, 371-372 (2000). PMID: 11200536
44. Dhalluin C, Yan KS, Plotnikova O, Lee KW, Zeng L, Kuti M, Mujtaba S, Goldfarb MP & Zhou MM. Structural Basis of SNT PTB Domain Interactions with Distinct Neurotrophic Receptors. Molecular Cell, 6, 921-929 (2000). PMID: 11090629