Selected publications

Selected publications:

  1. Cadwell K, Patel K, Maloney N, Liu TC, Storer CE, Xavier R, Head R, Stappenbeck TS, Virgin HW IV. Virus-host interaction determines contributions of Crohn’s Disease susceptibility gene Atg16L1 to intestinal pathology. Cell 2010: 141(7): 1135-45. PMID: 20602997; PMC2908380.
  2. VanDussen KL*, Liu TC*, Li D, Towfic F, Modiano N, Winter R, Haritunians T, Taylor KD, Dhall D, Targan SR, Xavier RJ, McGovern DP, and Stappenbeck TS. Genetic variants synthesize to produce Paneth Cell Phenotypes that define subtypes of Crohn’s Disease. Gastroenterology. 2014:146:200-209. *: equal contribution. PMID: 24076061; PMC3899786.
  3. Liu TC, Gao F, McGovern DP, Stappenbeck TS. Spatial and temporal stability of Paneth cell phenotypes in Crohn’s Disease: Implications for prognostic cellular biomarker development. Inflammatory Bowel Disease. 2014: 20(4): 646-651. PMID: 24552829.
  4. Liu TC, Stappenbeck TS. Genetics and pathogenesis of inflammatory bowel disease. Annual Review of Pathology: Mechanisms of Disease, Vol 11. 2016. 11:127-48. PMID: 26907531. PMCID: 4961083.
  5. Liu TC, Gurram B, Baldridge M, Head R, Lam V, Luo C, Cao Y, Simpson P, Hayward M, Holtz M, Bousounis P, Noe J, Lerner D, Cabrera J, Biank V, Stephens M, Huttenhower C, McGovern D, Xavier R, Stappenbeck T, Salzman N. Paneth cell defects in Crohn’s disease patients promotes dysbiosis. JCI Insight. 2016 1(8):e86907. PMID: 27699268. PMCID: PMC5033844.
  6. Liu TC, Naito T, Liu Z, VanDussen KL, Haritunians T, Li D, Endo K, Kawai Y, Nagasaki M, Kinouchi Y, McGovern DPB, Shimosegawa T, Kauta Y, Stappenbeck TS. LRRK2 but not ATG16L1 is associated with Paneth cell defect in Japanese Crohn’s disease patients. JCI Insight (co-corresponding author). 2017 Mar 23; 2(6): e91917. PMID: 28352666. PMCID: PMC5358495.
  7. Liu TC, Kern JT, VanDussen KL, Xiong S, Kaiko GE, Wilen CB, Rajala MW, Caruso R, Holtzman MJ, Gao F, McGovern DPM, Nunez G, Head RD, Stappenbeck TS. Interaction between smoking and ATG16L1T300A triggers Paneth cell defects in Crohn’s disease. J Clin Invest. 2018; 128(11): 5110-5122. PMID: 30137026. PMCID: PMC6205411.
  8. Kaiko GE, Chen F, Lai CW, Chiang IL, Perrigoue J, Stojmirovic A, Li K, Muegge BD, Jain U, VanDussen KL, Goggins BJ, Keely S, Weaver J, Foster PS, Lawrence DA, Liu TC, Stappenbeck TS. PAI-1 augments mucosal damage in colitis. Science Transl Med. 2019; 11(482). pii:eaat0852.
  9. Liu TC, VanBurkirk K, Ali A, Kelly MP, Holtz LR, Yilmaz OH, Sadiq K, Iqbal N, Amadi B, Syed S, Ahmed T, Moore SR, Ndao IM, Isaacs MH, Pfeifer JD, Atlas H, Tarr PI, Denno DM, Moskaluk CA. A Novel histological index for evaluation of environmental enteric dysfunction identifies geographic-specific features of enteropathy among children with suboptimal growth. PLoS Negl Trop Dis 2020 Jan 13; 14(1):e0007975.
  10. Sun L, Marsh J, Matlock MK, Chen L, Gaut JP, Brunt EM, Swamidass SJ, Liu TC. Deep learning quantification of percent steatosis in donor liver biopsy frozen sections. EBiomedicine 2020 Oct; 60:103029. With Commentary in EBioMedicine 2020 Nov; 61:103064. Golse N. AI finally provides augmented intelligence to liver surgeons.
  11. Marsh J, Liu TC, Wilson PC, Swamidass SJ, Gaut JP. Development and validation of a deep learning model to quantify glomerulosclerosis in kidney biopsy specimens. JAMA Network Open. 2020 4(1):e2030939. PMID: 33471115.
  12. Ma C, Storer CE, Chandran U, LaFramboise WA, Petrosko P, Frank M, Hartman DJ, Pantanowitz L, Haritunians T, Head RD, Liu TC. Crohn’s disease-associated ATG16L1 T300A genotype is associated with improved survival in gastric cancer. EBioMedicine. 2021 Apr 24;67:103347.
  13. Liu TC, Kern JT, Jain U, Sonnek NM, Xiong S, Simpson KF, VanDussen KL, Winkler ES, Haritunians T, Malique A, Lu Q, Sasaki Y, Storer C, Diamond MS, Head RD, McGovern DPB, Stappenbeck TS. Western diet induces Paneth cell defects through microbiome alterations and farnesoid X receptor and type I interferon activation. Cell Host Microbe. 2021 May 12:S1931-3128(21)00180-3.
  14. Balasubramanian I, Bandyopadhyay S, Flores J, Lin X, Liu H, Sun S, Golovchenko NB. Liu Y, Patel R, Bianchi-Smak J, Joseph I, Suntornsaratoon P, Vargas J, Green PHR, Bhagt G, Ferraris R, Lagana SM, Ying W, Zhang Y, Wang Z, Li WV, Singh S, Zhou Z, Kollias G, Yu S, Wei Z, Bonder EM, Zhang L, Edelblum KL, Liu TC*, Gao N*. Stress activated Paneth cell subset propagates inflammation. The EMBO Journal. 2023 Sep 18:e113975 Online ahead of print (*co-corresponding author).
  15. Mweetwa MN, Haritunians T, Dube S, Chandwe K, Amadi B, Zyambo K, Liu TC, McGovern D, Kelly P. Genetic variation in environmental enteropathy and stunting in Zambian children: A pilot genome wide association study using the H3Africa chip. PLoS One. 2023;18(9):e0291311. PMID: 37756315.
  16. Malique A, Sun S, Chandwe K, Amadi B, Haritunians T, Jain U, Muegge BD, Frein J, Sasaki Y, Foster A, Storer CE, Mengesha E, Kern J, McGovern DPB, Head RD, Kelly P, Liu TC. NAD+ precursors and bile acid sequestration treat preclinical refractory environmental enteric dysfunction. Sci Transl Med. 2024 Jan 3;16(728):eabq4145. PMID: 38170788. Reported in Newsweek, MSN.
  17. Ma C, Haritunians T, Gremida AK, Syal G, Shah J, Yang S, Ramos Del Aguila de Rivers C, Storer CE, Chen L, Mengesha E, Mujukian A, Hanna M, Fleshner P, Binion DG, VanDussen KL, Stappenbeck TS, Head RD, Ciorba MA, McGovern DPB, Liu TC. Ileal Paneth Cell Phenotype is a Cellular Biomarker for Pouch Complications in Ulcerative Colitis. J Crohns Colitis 2024 July. Online ahead of print. PMID: 38953127.
  18. Hung CT, Ma C, Panda SK, Trsan T, Hodel M, Frein J, Foster A, Sun S, Wu HT, Kern J, Mishra R, Jain U, Ho YC, Colonna M, Stappenbeck TS, Liu TC. Western diet reduces small intestinal intraepithelial lymphocytes via FXR-Interferon pathway. Mucosal Immunol 2024 July. Online ahead of print. PMID: 38992433.
  19. Sun S, Hodel M, Wang X, De Vicente J, Haritunians T, Debebe A, Ma C, Malique A, Nguyen HN, Agam M, Rishra R, Frein J, Foster A, Ballentine S, Kern J, Yang S, Mengesha E, Balasubramanian I, Arguello A, Estrada AA, Gao N, Peter I, McGovern DPB, Henry AG, Stappenbeck TS, Liu TC. Macrophage LRRK2 hyperactivity impairs autophagy and induces Paneth cell dysfunction. Science Immunology 2024 Nov. 9, eadi7907.
  20. Kang L, Sarullo K, Marsh JN, Khonde P, Ma C, Haritunians T, Mujukian A, Mengesha E, McGovern DPB, Stappenbeck TS, Swamidass SJ, Liu TC. Development of a deep learning algorithm for Paneth cell density quantification for inflammatory bowel disease. EBioMedicine 2024 Dec.