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A contamination focused approach for optimizing the single-cell RNA-seq experiment.
Arceneaux D, Chen Z, Simmons AJ, Heiser CN, Southard-Smith AN, Brenan MJ, Yang Y, Chen B, Xu Y, Choi E, Campbell JD, Liu Q, Lau KS. Arceneaux D, et al. Among authors: xu y. iScience. 2023 Jun 29;26(7):107242. doi: 10.1016/j.isci.2023.107242. eCollection 2023 Jul 21. iScience. 2023. PMID: 37496679 Free PMC article.
Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps.
Chen B, Scurrah CR, McKinley ET, Simmons AJ, Ramirez-Solano MA, Zhu X, Markham NO, Heiser CN, Vega PN, Rolong A, Kim H, Sheng Q, Drewes JL, Zhou Y, Southard-Smith AN, Xu Y, Ro J, Jones AL, Revetta F, Berry LD, Niitsu H, Islam M, Pelka K, Hofree M, Chen JH, Sarkizova S, Ng K, Giannakis M, Boland GM, Aguirre AJ, Anderson AC, Rozenblatt-Rosen O, Regev A, Hacohen N, Kawasaki K, Sato T, Goettel JA, Grady WM, Zheng W, Washington MK, Cai Q, Sears CL, Goldenring JR, Franklin JL, Su T, Huh WJ, Vandekar S, Roland JT, Liu Q, Coffey RJ, Shrubsole MJ, Lau KS. Chen B, et al. Among authors: xu y. Cell. 2021 Dec 22;184(26):6262-6280.e26. doi: 10.1016/j.cell.2021.11.031. Epub 2021 Dec 14. Cell. 2021. PMID: 34910928 Free PMC article.
MTGR1 is required to maintain small intestinal stem cell populations.
Williams C, Brown R, Zhao Y, Wang J, Chen Z, Blunt K, Pilat J, Parang B, Choksi Y, Lau K, Hiebert S, Short S, Jacobse J, Xu Y, Yang Y, Goettel J. Williams C, et al. Among authors: xu y. Res Sq [Preprint]. 2023 Sep 21:rs.3.rs-3315071. doi: 10.21203/rs.3.rs-3315071/v1. Res Sq. 2023. Update in: Cell Death Differ. 2024 Sep;31(9):1170-1183. doi: 10.1038/s41418-024-01346-x PMID: 37790452 Free PMC article. Updated. Preprint.
A Specialized Epithelial Cell Type Regulating Mucosal Immunity and Driving Human Crohn's Disease.
Li J, Simmons AJ, Chiron S, Ramirez-Solano MA, Tasneem N, Kaur H, Xu Y, Revetta F, Vega PN, Bao S, Cui C, Tyree RN, Raber LW, Conner AN, Beaulieu DB, Dalal RL, Horst SN, Pabla BS, Huo Y, Landman BA, Roland JT, Scoville EA, Schwartz DA, Washington MK, Shyr Y, Wilson KT, Coburn LA, Lau KS, Liu Q. Li J, et al. Among authors: xu y. bioRxiv [Preprint]. 2023 Oct 2:2023.09.30.560293. doi: 10.1101/2023.09.30.560293. bioRxiv. 2023. Update in: Nat Commun. 2024 Aug 22;15(1):7204. doi: 10.1038/s41467-024-51580-7 PMID: 37873404 Free PMC article. Updated. Preprint.
MTGR1 is required to maintain small intestinal stem cell populations.
Short SP, Brown RE, Chen Z, Pilat JM, McElligott BA, Meenderink LM, Bickart AC, Blunt KM, Jacobse J, Wang J, Simmons AJ, Xu Y, Yang Y, Parang B, Choksi YA, Goettel JA, Lau KS, Hiebert SW, Williams CS. Short SP, et al. Among authors: xu y. Cell Death Differ. 2024 Sep;31(9):1170-1183. doi: 10.1038/s41418-024-01346-x. Epub 2024 Jul 25. Cell Death Differ. 2024. PMID: 39048708 Free PMC article.
Identification and multimodal characterization of a specialized epithelial cell type associated with Crohn's disease.
Li J, Simmons AJ, Hawkins CV, Chiron S, Ramirez-Solano MA, Tasneem N, Kaur H, Xu Y, Revetta F, Vega PN, Bao S, Cui C, Tyree RN, Raber LW, Conner AN, Pilat JM, Jacobse J, McNamara KM, Allaman MM, Raffa GA, Gobert AP, Asim M, Goettel JA, Choksi YA, Beaulieu DB, Dalal RL, Horst SN, Pabla BS, Huo Y, Landman BA, Roland JT, Scoville EA, Schwartz DA, Washington MK, Shyr Y, Wilson KT, Coburn LA, Lau KS, Liu Q. Li J, et al. Among authors: xu y. Nat Commun. 2024 Aug 22;15(1):7204. doi: 10.1038/s41467-024-51580-7. Nat Commun. 2024. PMID: 39169060 Free PMC article.
Temporal recording of mammalian development and precancer.
Islam M, Yang Y, Simmons AJ, Shah VM, Musale KP, Xu Y, Tasneem N, Chen Z, Trinh LT, Molina P, Ramirez-Solano MA, Sadien ID, Dou J, Rolong A, Chen K, Magnuson MA, Rathmell JC, Macara IG, Winton DJ, Liu Q, Zafar H, Kalhor R, Church GM, Shrubsole MJ, Coffey RJ, Lau KS. Islam M, et al. Among authors: xu y. Nature. 2024 Oct;634(8036):1187-1195. doi: 10.1038/s41586-024-07954-4. Epub 2024 Oct 30. Nature. 2024. PMID: 39478207 Free PMC article.
Endocrine islet β-cell subtypes with differential function are derived from biochemically distinct embryonic endocrine islet progenitors that are regulated by maternal nutrients.
Gu G, Brown M, Agan V, Nevills S, Hu R, Simmons A, Xu Y, Yang Y, Yagan M, Najam S, Dadi P, Sampson L, Magnuson M, Jacobson D, Lau K, Hodges E. Gu G, et al. Among authors: xu y. Res Sq [Preprint]. 2024 Mar 7:rs.3.rs-3946483. doi: 10.21203/rs.3.rs-3946483/v1. Res Sq. 2024. PMID: 38496675 Free PMC article. Preprint.
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