Xiling Shen, PHD

Peer-Reviewed Articles

1. Eckhoff AM, Fletcher AA, Kelly MS, Dohlman A, McIntyre CA, Shen X, Iyer MK, Nussbaum DP, Allen PJ. Comprehensive Assessment of the Intrinsic Pancreatic Microbiome. Ann Surg None(None):None, 2024. PMID: 38623754.
2. Xiang K, Wang E, Mantyh J, Rupprecht G, Negrete M, Sanati G, Hsu C, Randon P, Dohlman A, Kretzschmar K, Bose S, Giroux N, Ding S, Wang L, Balcazar JP, Huang Q, Sundaramoorthy P, Xi R, McCall SJ, Wang Z, Jiang C, Kang Y, Kopetz S, Crawford GE, Lipkin SM, Wang XF, Clevers H, Hsu D, Shen X. Chromatin Remodeling in Patient-Derived Colorectal Cancer Models. Adv Sci (Weinh) 11(16):e2303379, 2024. PMID: 38380561.
3. Zhu X, Huang Q, Jiang L, Nguyen VT, Vu T, Devlin G, Shaima J, Wang X, Chen Y, Ma L, Xiang K, Wang E, Rong Q, Zhou Q, Kang Y, Asokan A, Feng L, Hsu SD, Shen X, Yao J. Longitudinal intravital imaging of mouse placenta. Sci Adv 10(12):eadk1278, 2024. PMID: 38507481.
4. Jiang C, Chao CC, Li J, Ge X, Shen A, Jucaud V, Cheng C, Shen X. Tissue-resident memory T cell signatures from single-cell analysis associated with better melanoma prognosis. iScience 27(3):109277, 2024. PMID: 38455971.
5. Gurrea-Rubio M, Wu Q, Amin MA, Tsou PS, Campbell PL, Amarista CI, Ikari Y, Brodie WD, Mattichak MN, Muraoka S, Randon PM, Lind ME, Ruth JH, Mao-Draayer Y, Ding S, Shen X, Cooney LA, Lin F, Fox DA. Activation of cytotoxic lymphocytes through CD6 enhances killing of cancer cells. Cancer Immunol Immunother 73(2):34, 2024. PMID: 38280067.
6. McClain MT, Zhbannikov I, Satterwhite LL, Henao R, Giroux NS, Ding S, Burke TW, Tsalik EL, Nix C, Balcazar JP, Petzold EA, Shen X, Woods CW. Epigenetic and transcriptional responses in circulating leukocytes are associated with future decompensation during SARS-CoV-2 infection. iScience 27(1):108288, 2024. PMID: 38179063.
7. Bose S, Shen X. The KRAS tour: Studying metabolic reprogramming in isogenic pancreatic cancer organoids. Cell Stem Cell 31(1):1-2, 2024. PMID: 38181746.
8. Wang W, Hariharan M, Bartlett A, Barragan C, Castanon R, Rothenberg V, Song H, Nery J, Aldridge A, Altshul J, Kenworthy M, Ding W, Liu H, Tian W, Zhou J, Chen H, Wei B, Gunduz IB, Norell T, Broderick TJ, McClain MT, Satterwhite LL, Burke TW, Petzold EA, Shen X, Woods CW, Fowler VG Jr, Ruffin F, Panuwet P, Barr DB, Beare JL, Smith AK, Spurbeck RR, Vangeti S, Ramos I, Nudelman G, Sealfon SC, Castellino F, Walley AM, Evans T, Muller F, Greenleaf WJ, Ecker JR. Human Immune Cell Epigenomic Signatures in Response to Infectious Diseases and Chemical Exposures. bioRxiv None(None):None, 2023. PMID: 37425926.
9. Bose S, Barroso M, Chheda MG, Clevers H, Elez E, Kaochar S, Kopetz SE, Li XN, Meric-Bernstam F, Meyer CA, Mou H, Naegle KM, Pera MF, Perova Z, Politi KA, Raphael BJ, Robson P, Sears RC, Tabernero J, Tuveson DA, Welm AL, Welm BE, Willey CD, Salnikow K, Chuang JH, Shen X. A path to translation: How 3D patient tumor avatars enable next generation precision oncology. Cancer Cell 40(12):1448-1453, 2022. PMID: 36270276.
10. Jabbar S, Mathews P, Wang X, Sundaramoorthy P, Chu E, Piryani SO, Ding S, Shen X, Doan PL, Kang Y. Thioredoxin-1 regulates self-renewal and differentiation of murine hematopoietic stem cells through p53 tumor suppressor. Exp Hematol Oncol 11(1):83, 2022. PMID: 36316713.
11. Bose S, Yao H, Huang Q, Whitaker R, Kontos CD, Previs RA, Shen X. Using genetically encoded fluorescent biosensors to interrogate ovarian cancer metabolism. J Ovarian Res 15(1):114, 2022. PMID: 36266675.
12. Dangi A, Husain I, Jordan CZ, Yu S, Natesh N, Shen X, Kwun J, Luo X. Blocking CCL8-CCR8-Mediated Early Allograft Inflammation Improves Kidney Transplant Function. J Am Soc Nephrol 33(10):1876-1890, 2022. PMID: 35973731.
13. Li M, Beaumont N, Ma C, Rojas J, Vu T, Harlacher M, O'Connell G, Gessner RC, Kilian H, Kasatkina L, Chen Y, Huang Q, Shen X, Lovell JF, Verkhusha VV, Czernuszewicz T, Yao J. Three-Dimensional Deep-Tissue Functional and Molecular Imaging by Integrated Photoacoustic, Ultrasound, and Angiographic Tomography (PAUSAT). IEEE Trans Med Imaging 41(10):2704-2714, 2022. PMID: 35442884.
14. Dohlman AB, Klug J, Mesko M, Gao IH, Lipkin SM, Shen X, Iliev ID. A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors. Cell 185(20):3807-3822.e12, 2022. PMID: 36179671.
15. Wang Z, Boretto M, Millen R, Natesh N, Reckzeh ES, Hsu C, Negrete M, Yao H, Quayle W, Heaton BE, Harding AT, Bose S, Driehuis E, Beumer J, Rivera GO, van Ineveld RL, Gex D, DeVilla J, Wang D, Puschhof J, Geurts MH, Yeung A, Hamele C, Smith A, Bankaitis E, Xiang K, Ding S, Nelson D, Delubac D, Rios A, Abi-Hachem R, Jang D, Goldstein BJ, Glass C, Heaton NS, Hsu D, Clevers H, Shen X. Rapid tissue prototyping with micro-organospheres. Stem Cell Reports 17(9):1959-1975, 2022. PMID: 35985334.
16. Wu Y, Wong CW, Chiles EN, Mellinger AL, Bae H, Jung S, Peterson T, Wang J, Negrete M, Huang Q, Wang L, Jang C, Muddiman DC, Su X, Williamson I, Shen X. Glycerate from intestinal fructose metabolism induces islet cell damage and glucose intolerance. Cell Metab 34(7):1042-1053.e6, 2022. PMID: 35688154.
17. Bose S, Huang Q, Ma Y, Wang L, Rivera GO, Ouyang Y, Whitaker R, Gibson RA, Kontos CD, Berchuck A, Previs RA, Shen X. G6PD inhibition sensitizes ovarian cancer cells to oxidative stress in the metastatic omental microenvironment. Cell Rep 39(13):111012, 2022. PMID: 35767962.
18. Ding S, Hsu C, Wang Z, Natesh NR, Millen R, Negrete M, Giroux N, Rivera GO, Dohlman A, Bose S, Rotstein T, Spiller K, Yeung A, Sun Z, Jiang C, Xi R, Wilkin B, Randon PM, Williamson I, Nelson DA, Delubac D, Oh S, Rupprecht G, Isaacs J, Jia J, Chen C, Shen JP, Kopetz S, McCall S, Smith A, Gjorevski N, Walz AC, Antonia S, Marrer-Berger E, Clevers H, Hsu D, Shen X. Patient-derived micro-organospheres enable clinical precision oncology. Cell Stem Cell 29(6):905-917.e6, 2022. PMID: 35508177.
19. Zhu X, Huang Q, DiSpirito A, Vu T, Rong Q, Peng X, Sheng H, Shen X, Zhou Q, Jiang L, Hoffmann U, Yao J. Real-time whole-brain imaging of hemodynamics and oxygenation at micro-vessel resolution with ultrafast wide-field photoacoustic microscopy. Light Sci Appl 11(1):138, 2022. PMID: 35577780.
20. Giroux NS, Ding S, McClain MT, Burke TW, Petzold E, Chung HA, Rivera GO, Wang E, Xi R, Bose S, Rotstein T, Nicholson BP, Chen T, Henao R, Sempowski GD, Denny TN, De Ussel MI, Satterwhite LL, Ko ER, Ginsburg GS, Kraft BD, Tsalik EL, Shen X, Woods C. Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion. Res Sq None(None):None, 2022. PMID: 35411343.
21. Naqvi I, Giroux N, Olson L, Morrison SA, Llanga T, Akinade TO, Zhu Y, Zhong Y, Bose S, Arvai S, Abramson K, Chen L, Que L, Kraft B, Shen X, Lee J, Leong KW, Nair SK, Sullenger B. DAMPs/PAMPs induce monocytic TLR activation and tolerance in COVID-19 patients; nucleic acid binding scavengers can counteract such TLR agonists. Biomaterials 283:121393, 2022. PMID: 35349874.
22. Artola-Boran M, Fallegger A, Priola M, Jeske R, Waterboer T, Dohlman AB, Shen X, Wild S, He J, Levesque MP, Yousefi S, Simon HU, Cheng PF, Muller A. Mycobacterial infection aggravates Helicobacter pylori-induced gastric preneoplastic pathology by redirection of de novo induced Treg cells. Cell Rep 38(6):110359, 2022. PMID: 35139377.
23. Kadur Lakshminarasimha Murthy P, Xi R, Arguijo D, Everitt JI, Kocak DD, Kobayashi Y, Bozec A, Vicent S, Ding S, Crawford GE, Hsu D, Tata PR, Reddy T, Shen X. Epigenetic basis of oncogenic-Kras-mediated epithelial-cellular proliferation and plasticity. Dev Cell 57(3):310-328.e9, 2022. PMID: 35134344.
24. Mines RC, Lipniacki T, Shen X. Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts. PLoS Comput Biol 18(2):e1009811, 2022. PMID: 35143483.
25. Li X, Davis RC, Xu Y, Wang Z, Souma N, Sotolongo G, Bell J, Ellis M, Howell D, Shen X, Lafata KJ, Barisoni L. Deep learning segmentation of glomeruli on kidney donor frozen sections. J Med Imaging (Bellingham) 8(6):067501, 2021. PMID: 34950750.
26. Wang L, Wang E, Prado Balcazar J, Wu Z, Xiang K, Wang Y, Huang Q, Negrete M, Chen KY, Li W, Fu Y, Dohlman A, Mines R, Zhang L, Kobayashi Y, Chen T, Shi G, Shen JP, Kopetz S, Tata PR, Moreno V, Gersbach C, Crawford G, Hsu D, Huang E, Bu P, Shen X. Chromatin Remodeling of Colorectal Cancer Liver Metastasis is Mediated by an HGF-PU.1-DPP4 Axis. Adv Sci (Weinh) 8(19):e2004673, 2021. PMID: 34378358.
27. Yu C, Littleton S, Giroux NS, Mathew R, Ding S, Kalnitsky J, Yang Y, Petzold E, Chung HA, Rivera GO, Rotstein T, Xi R, Ko ER, Tsalik EL, Sempowski GD, Denny TN, Burke TW, McClain MT, Woods CW, Shen X, Saban DR. Mucosal-associated invariant T cell responses differ by sex in COVID-19. Med 2(6):755-772.e5, 2021. PMID: 33870241.
28. Garrett A, Rakhilin N, Wang N, McKey J, Cofer G, Anderson RB, Capel B, Johnson GA, Shen X. Mapping the peripheral nervous system in the whole mouse via compressed sensing tractography. J Neural Eng 18(4), 2021. PMID: 33979784.
29. Dai Z, Yang X, Wu F, Wang L, Xiang K, Li P, Lv Q, Tang J, Dohlman A, Dai L, Shen X, You L. Living fabrication of functional semi-interpenetrating polymeric materials. Nat Commun 12(1):3422, 2021. PMID: 34103521.
30. Wang L, Balmat TJ, Antonia AL, Constantine FJ, Henao R, Burke TW, Ingham A, McClain MT, Tsalik EL, Ko ER, Ginsburg GS, DeLong MR, Shen X, Woods CW, Hauser ER, Ko DC. An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility. Genome Med 13(1):83, 2021. PMID: 34001247.
31. Tung KL, Chen KY, Negrete M, Chen T, Safi A, Aljamal AA, Song L, Crawford GE, Ding S, Hsu DS, Shen X. Integrated chromatin and transcriptomic profiling of patient-derived colon cancer organoids identifies personalized drug targets to overcome oxaliplatin resistance. Genes Dis 8(2):203-214, 2021. PMID: 33997167.
32. McClain MT, Constantine FJ, Henao R, Liu Y, Tsalik EL, Burke TW, Steinbrink JM, Petzold E, Nicholson BP, Rolfe R, Kraft BD, Kelly MS, Saban DR, Yu C, Shen X, Ko EM, Sempowski GD, Denny TN, Ginsburg GS, Woods CW. Dysregulated transcriptional responses to SARS-CoV-2 in the periphery. Nat Commun 12(1):1079, 2021. PMID: 33597532.
33. Dohlman AB, Arguijo Mendoza D, Ding S, Gao M, Dressman H, Iliev ID, Lipkin SM, Shen X. The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants. Cell Host Microbe 29(2):281-298.e5, 2021. PMID: 33382980.
34. Sarvestani SK, Signs S, Hu B, Yeu Y, Feng H, Ni Y, Hill DR, Fisher RC, Ferrandon S, DeHaan RK, Stiene J, Cruise M, Hwang TH, Shen X, Spence JR, Huang EH. Induced organoids derived from patients with ulcerative colitis recapitulate colitic reactivity. Nat Commun 12(1):262, 2021. PMID: 33431859.
35. Giroux NS, Ding S, McClain MT, Burke TW, Petzold E, Chung HA, Palomino GR, Wang E, Xi R, Bose S, Rotstein T, Nicholson BP, Chen T, Henao R, Sempowski GD, Denny TN, Ko ER, Ginsburg GS, Kraft BD, Tsalik EL, Woods CW, Shen X. Chromatin remodeling in peripheral blood cells reflects COVID-19 symptom severity. bioRxiv None(None):None, 2020. PMID: 33300002.
36. Somarelli JA, Roghani RS, Moghaddam AS, Thomas BC, Rupprecht G, Ware KE, Altunel E, Mantyh JB, Kim SY, McCall SJ, Shen X, Mantyh CR, Hsu DS. A Precision Medicine Drug Discovery Pipeline Identifies Combined CDK2 and 9 Inhibition as a Novel Therapeutic Strategy in Colorectal Cancer. Mol Cancer Ther 19(12):2516-2527, 2020. PMID: 33158998.
37. Chen T, Oh S, Gregory S, Shen X, Diehl AM. Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration. JCI Insight 5(22):None, 2020. PMID: 33208554.
38. Dangi A, Natesh NR, Husain I, Ji Z, Barisoni L, Kwun J, Shen X, Thorp EB, Luo X. Single cell transcriptomics of mouse kidney transplants reveals a myeloid cell pathway for transplant rejection. JCI Insight 5(20):None, 2020. PMID: 32970632.
39. Bauer M, Nascakova Z, Mihai AI, Cheng PF, Levesque MP, Lampart S, Hurwitz R, Pfannkuch L, Dobrovolna J, Jacobs M, Bartfeld S, Dohlman A, Shen X, Gall AA, Salama NR, Topfer A, Weber A, Meyer TF, Janscak P, Muller A. The ALPK1/TIFA/NF-kappaB axis links a bacterial carcinogen to R-loop-induced replication stress. Nat Commun 11(1):5117, 2020. PMID: 33037203.
40. Altunel E, Roghani RS, Chen KY, Kim SY, McCall S, Ware KE, Shen X, Somarelli JA, Hsu DS. Development of a precision medicine pipeline to identify personalized treatments for colorectal cancer. BMC Cancer 20(1):592, 2020. PMID: 32580713.
41. Huang Q, Cohen MA, Alsina FC, Devlin G, Garrett A, McKey J, Havlik P, Rakhilin N, Wang E, Xiang K, Mathews P, Wang L, Bock C, Ruthig V, Wang Y, Negrete M, Wong CW, Murthy PKL, Zhang S, Daniel AR, Kirsch DG, Kang Y, Capel B, Asokan A, Silver DL, Jaenisch R, Shen X. Intravital imaging of mouse embryos. Science 368(6487):181-186, 2020. PMID: 32273467.
42. Shen X. An imprecise path to precision medicine. Nat Med 26(1):14, 2020. PMID: 31932784.
43. Rakhilin N, Garrett A, Eom CY, Chavez KR, Small DM, Daniel AR, Kaelberer MM, Mejooli MA, Huang Q, Ding S, Kirsch DG, Bohorquez DV, Nishimura N, Barth BB, Shen X. An intravital window to image the colon in real time. Nat Commun 10(1):5647, 2019. PMID: 31827103.
44. Roper J, Shen X. Novel Three-Dimensional Cultures of Patient-Derived Cancer and Tumor Immune Cells. Gastroenterology 157(1):260-261, 2019. PMID: 31136743.
45. Xu Y, Huang L, Kirschman JL, Vanover DA, Tiwari PM, Santangelo PJ, Shen X, Russell DG. Exploitation of Synthetic mRNA To Drive Immune Effector Cell Recruitment and Functional Reprogramming In Vivo. J Immunol 202(2):608-617, 2019. PMID: 30541883.
46. Xi R, Kadur Lakshminarasimha Murthy P, Tung KL, Guy CD, Wan J, Li F, Wang Z, Li X, Varanko A, Rakhilin N, Xin Y, Liu B, Qian SB, Su L, Han Y, Shen X. SENP3-mediated host defense response contains HBV replication and restores protein synthesis. PLoS One 14(1):e0209179, 2019. PMID: 30640896.
47. Wang L, Wang E, Wang Y, Mines R, Xiang K, Sun Z, Zhou G, Chen KY, Rakhilin N, Chao S, Ye G, Wu Z, Yan H, Shen H, Everitt J, Bu P, Shen X. miR-34a is a microRNA safeguard for Citrobacter-induced inflammatory colon oncogenesis. Elife 7(None):None, 2018. PMID: 30543324.
48. Kaelberer MM, Buchanan KL, Klein ME, Barth BB, Montoya MM, Shen X, Bohorquez DV. A gut-brain neural circuit for nutrient sensory transduction. Science 361(6408):None, 2018. PMID: 30237325.
49. Choi J, Rakhilin N, Gadamsetty P, Joe DJ, Tabrizian T, Lipkin SM, Huffman DM, Shen X, Nishimura N. Intestinal crypts recover rapidly from focal damage with coordinated motion of stem cells that is impaired by aging. Sci Rep 8(1):10989, 2018. PMID: 30030455.
50. Gao Z, Chen KY, Mueller O, Zhang H, Rakhilin N, Chen J, Shen X. Microbiota of Inflammatory Bowel Disease Models. Annu Int Conf IEEE Eng Med Biol Soc 2018(None):2374-2377, 2018. PMID: 30440884.
51. Chen KY, Srinivasan T, Lin C, Tung KL, Gao Z, Hsu DS, Lipkin SM, Shen X. Single-Cell Transcriptomics Reveals Heterogeneity and Drug Response of Human Colorectal Cancer Organoids. Annu Int Conf IEEE Eng Med Biol Soc 2018(None):2378-2381, 2018. PMID: 30440885.
52. Bu P, Chen KY, Xiang K, Johnson C, Crown SB, Rakhilin N, Ai Y, Wang L, Xi R, Astapova I, Han Y, Li J, Barth BB, Lu M, Gao Z, Mines R, Zhang L, Herman M, Hsu D, Zhang GF, Shen X. Aldolase B-Mediated Fructose Metabolism Drives Metabolic Reprogramming of Colon Cancer Liver Metastasis. Cell Metab 27(6):1249-1262.e4, 2018. PMID: 29706565.
53. Chen KY, Shen X, Diehl AM. Prometheus revisited. J Clin Invest 128(6):2192-2193, 2018. PMID: 29708511.
54. Kadur Lakshminarasimha Murthy P, Srinivasan T, Bochter MS, Xi R, Varanko AK, Tung KL, Semerci F, Xu K, Maletic-Savatic M, Cole SE, Shen X. Radical and lunatic fringes modulate notch ligands to support mammalian intestinal homeostasis. Elife 7(None):None, 2018. PMID: 29629872.
55. Zavrel EA, Shen X. TOWARD A MICROFLUIDIC IMPLEMENTATION OF A DIGITAL POTENTIOMETER. Proc Des Med Devices Conf 2018(None):None, 2018. PMID: 30854172.
56. Zavrel EA, Shuler ML, Shen X. A SIMPLE ASPECT RATIO DEPENDENT METHOD OF PATTERNING MICROWELLS FOR SELECTIVE CELL ATTACHMENT. Proc Des Med Devices Conf 2018(None):None, 2018. PMID: 30854173.
57. Xu Y, Wang L, Zimmerman MD, Chen KY, Huang L, Fu DJ, Kaya F, Rakhilin N, Nazarova EV, Bu P, Dartois V, Russell DG, Shen X. Matrix metalloproteinase inhibitors enhance the efficacy of frontline drugs against Mycobacterium tuberculosis. PLoS Pathog 14(4):e1006974, 2018. PMID: 29698476.
58. Barth BB, Henriquez CS, Grill WM, Shen X. Electrical stimulation of gut motility guided by an in silico model. J Neural Eng 14(6):066010, 2017. PMID: 28816177.
59. Klose CSN, Mahlakoiv T, Moeller JB, Rankin LC, Flamar AL, Kabata H, Monticelli LA, Moriyama S, Putzel GG, Rakhilin N, Shen X, Kostenis E, Konig GM, Senda T, Carpenter D, Farber DL, Artis D. The neuropeptide neuromedin U stimulates innate lymphoid cells and type 2 inflammation. Nature 549(7671):282-286, 2017. PMID: 28869965.
60. Kulkarni S, Micci MA, Leser J, Shin C, Tang SC, Fu YY, Liu L, Li Q, Saha M, Li C, Enikolopov G, Becker L, Rakhilin N, Anderson M, Shen X, Dong X, Butte MJ, Song H, Southard-Smith EM, Kapur RP, Bogunovic M, Pasricha PJ. Adult enteric nervous system in health is maintained by a dynamic balance between neuronal apoptosis and neurogenesis. Proc Natl Acad Sci U S A 114(18):E3709-E3718, 2017. PMID: 28420791.
61. Chen KY, Srinivasan T, Tung KL, Belmonte JM, Wang L, Murthy PKL, Choi J, Rakhilin N, King S, Varanko AK, Witherspoon M, Nishimura N, Glazier JA, Lipkin SM, Bu P, Shen X. A Notch positive feedback in the intestinal stem cell niche is essential for stem cell self-renewal. Mol Syst Biol 13(4):927, 2017. PMID: 28455349.
62. Wang Y, Huang D, Chen KY, Cui M, Wang W, Huang X, Awadellah A, Li Q, Friedman A, Xin WW, Di Martino L, Cominelli F, Miron A, Chan R, Fox JG, Xu Y, Shen X, Kalady MF, Markowitz S, Maillard I, Lowe JB, Xin W, Zhou L. Fucosylation Deficiency in Mice Leads to Colitis and Adenocarcinoma. Gastroenterology 152(1):193-205.e10, 2017. PMID: 27639802.
63. Chen HJ, Wei Z, Sun J, Bhattacharya A, Savage DJ, Serda R, Mackeyev Y, Curley SA, Bu P, Wang L, Chen S, Cohen-Gould L, Huang E, Shen X, Lipkin SM, Copeland NG, Jenkins NA, Shuler ML. A recellularized human colon model identifies cancer driver genes. Nat Biotechnol 34(8):845-51, 2016. PMID: 27398792.
64. Wang L, Bu P, Shen X. Asymmetric division: An antitumor player?. Mol Cell Oncol 3(4):e1164279, 2016. PMID: 27652318.
65. Rakhilin N, Barth B, Choi J, Munoz NL, Kulkarni S, Jones JS, Small DM, Cheng YT, Cao Y, LaVinka C, Kan E, Dong X, Spencer M, Pasricha P, Nishimura N, Shen X. Simultaneous optical and electrical in vivo analysis of the enteric nervous system. Nat Commun 7(None):11800, 2016. PMID: 27270085.
66. Srinivasan T, Walters J, Bu P, Than EB, Tung KL, Chen KY, Panarelli N, Milsom J, Augenlicht L, Lipkin SM, Shen X. NOTCH Signaling Regulates Asymmetric Cell Fate of Fast- and Slow-Cycling Colon Cancer-Initiating Cells. Cancer Res 76(11):3411-21, 2016. PMID: 27197180.
67. Rothschild DE, Srinivasan T, Aponte-Santiago LA, Shen X, Allen IC. The Ex Vivo Culture and Pattern Recognition Receptor Stimulation of Mouse Intestinal Organoids. J Vis Exp None(111):None, 2016. PMID: 27285214.
68. Srinivasan T, Than EB, Bu P, Tung KL, Chen KY, Augenlicht L, Lipkin SM, Shen X. Notch signalling regulates asymmetric division and inter-conversion between lgr5 and bmi1 expressing intestinal stem cells. Sci Rep 6(None):26069, 2016. PMID: 27181744.
69. Wang L, Bu P, Ai Y, Srinivasan T, Chen HJ, Xiang K, Lipkin SM, Shen X. A long non-coding RNA targets microRNA miR-34a to regulate colon cancer stem cell asymmetric division. Elife 5(None):None, 2016. PMID: 27077950.
70. Cao Y, Rakhilin N, Gordon PH, Shen X, Kan EC. A real-time spike classification method based on dynamic time warping for extracellular enteric neural recording with large waveform variability. J Neurosci Methods 261(None):97-109, 2016. PMID: 26719239.
71. Bu P, Wang L, Chen KY, Srinivasan T, Murthy PK, Tung KL, Varanko AK, Chen HJ, Ai Y, King S, Lipkin SM, Shen X. A miR-34a-Numb Feedforward Loop Triggered by Inflammation Regulates Asymmetric Stem Cell Division in Intestine and Colon Cancer. Cell Stem Cell 18(2):189-202, 2016. PMID: 26849305.
72. Joe DJ, Hwang J, Johnson C, Cha HY, Lee JW, Shen X, Spencer MG, Tiwari S, Kim M. Surface Functionalized Graphene Biosensor on Sapphire for Cancer Cell Detection. J Nanosci Nanotechnol 16(1):144-51, 2016. PMID: 27398439.
73. Li J, Ai Y, Wang L, Bu P, Sharkey CC, Wu Q, Wun B, Roy S, Shen X, King MR. Targeted drug delivery to circulating tumor cells via platelet membrane-functionalized particles. Biomaterials 76(None):52-65, 2016. PMID: 26519648.
74. Sun S, Shi G, Sha H, Ji Y, Han X, Shu X, Ma H, Inoue T, Gao B, Kim H, Bu P, Guber RD, Shen X, Lee AH, Iwawaki T, Paton AW, Paton JC, Fang D, Tsai B, Yates JR 3rd, Wu H, Kersten S, Long Q, Duhamel GE, Simpson KW, Qi L. IRE1alpha is an endogenous substrate of endoplasmic-reticulum-associated degradation. Nat Cell Biol 17(12):1546-55, 2015. PMID: 26551274.
75. Chen HJ, Sun J, Huang Z, Hou H Jr, Arcilla M, Rakhilin N, Joe DJ, Choi J, Gadamsetty P, Milsom J, Nandakumar G, Longman R, Zhou XK, Edwards R, Chen J, Chen KY, Bu P, Wang L, Xu Y, Munroe R, Abratte C, Miller AD, Gumus ZH, Shuler M, Nishimura N, Edelmann W, Shen X, Lipkin SM. Comprehensive models of human primary and metastatic colorectal tumors in immunodeficient and immunocompetent mice by chemokine targeting. Nat Biotechnol 33(6):656-60, 2015. PMID: 26006007.
76. Bu P, Wang L, Chen KY, Rakhilin N, Sun J, Closa A, Tung KL, King S, Kristine Varanko A, Xu Y, Huan Chen J, Zessin AS, Shealy J, Cummings B, Hsu D, Lipkin SM, Moreno V, Gumus ZH, Shen X. miR-1269 promotes metastasis and forms a positive feedback loop with TGF-beta. Nat Commun 6(None):6879, 2015. PMID: 25872451.
77. Chen KY, Joe DJ, Shealy JB, Land BR, Shen X. A bio-inspired spatial patterning circuit. Annu Int Conf IEEE Eng Med Biol Soc 2014(None):86-9, 2014. PMID: 25569903.
78. Chen KY, Liu X, Bu P, Lin CS, Rakhilin N, Locasale JW, Shen X. A metabolic signature of colon cancer initiating cells. Annu Int Conf IEEE Eng Med Biol Soc 2014(None):4759-62, 2014. PMID: 25571056.
79. Shin YJ, Chen KY, Sayed AH, Hencey B, Shen X. Post-translational regulation enables robust p53 regulation. BMC Syst Biol 7(None):83, 2013. PMID: 23992617.
80. Bu P, Chen KY, Chen JH, Wang L, Walters J, Shin YJ, Goerger JP, Sun J, Witherspoon M, Rakhilin N, Li J, Yang H, Milsom J, Lee S, Zipfel W, Jin MM, Gumus ZH, Lipkin SM, Shen X. A microRNA miR-34a-regulated bimodal switch targets Notch in colon cancer stem cells. Cell Stem Cell 12(5):602-15, 2013. PMID: 23642368.
81. Li J, Bu P, Chen KY, Shen X. Spatial perturbation with synthetic protein scaffold reveals robustness of asymmetric cell division. J Biomed Sci Eng 6(2):134-143, 2013. PMID: 25750689.
82. Chen HJ, Edwards R, Tucci S, Bu P, Milsom J, Lee S, Edelmann W, Gumus ZH, Shen X, Lipkin S. Chemokine 25-induced signaling suppresses colon cancer invasion and metastasis. J Clin Invest 122(9):3184-96, 2012. PMID: 22863617.
83. Shin YJ, Sayed AH, Shen X. Adaptive models for gene networks. PLoS One 7(2):e31657, 2012. PMID: 22359614.
84. Shin YJ, Sayed AH, Shen X. Using an adaptive gene network model for self-organizing multicellular behavior. Annu Int Conf IEEE Eng Med Biol Soc 2012(None):5449-53, 2012. PMID: 23367162.
85. Shin YJ, Hencey B, Lipkin SM, Shen X. Frequency domain analysis reveals external periodic fluctuations can generate sustained p53 oscillation. PLoS One 6(7):e22852, 2011. PMID: 21829536.
86. Tan MH, Kozdon JB, Shen X, Shapiro L, McAdams HH. An essential transcription factor, SciP, enhances robustness of Caulobacter cell cycle regulation. Proc Natl Acad Sci U S A 107(44):18985-90, 2010. PMID: 20956288.
87. Sikandar S, Dizon D, Shen X, Li Z, Besterman J, Lipkin SM. The class I HDAC inhibitor MGCD0103 induces cell cycle arrest and apoptosis in colon cancer initiating cells by upregulating Dickkopf-1 and non-canonical Wnt signaling. Oncotarget 1(7):596-605, 2010. PMID: 21317455.
88. Shen X, Collier J, Dill D, Shapiro L, Horowitz M, McAdams HH. Architecture and inherent robustness of a bacterial cell-cycle control system. Proc Natl Acad Sci U S A 105(32):11340-5, 2008. PMID: 18685108.
89. Shen X, Kahn JM, Horowitz MA. Compensation for multimode fiber dispersion by adaptive optics. Opt Lett 30(22):2985-7, 2005. PMID: 16315696.

Other Articles

1. Khorsandi D, Yang JW, Foster S, Khosravi S, Hosseinzadeh Kouchehbaghi N, Zarei F, Lee YB, Runa F, Gangrade A, Voskanian L, Adnan D, Zhu Y, Wang Z, Jucaud V, Dokmeci MR, Shen X, Bishehsari F, Kelber JA, Khademhosseini A, de Barros NR Patient-Derived Organoids as Therapy Screening Platforms in Cancer Patients. Adv Healthc Mater 13(21):e2302331, 2024. PMID: 38359321.
2. Habowski AN, Budagavi DP, Scherer SD, Aurora AB, Caligiuri G, Flynn WF, Langer EM, Brody JR, Sears RC, Foggetti G, Arnal Estape A, Nguyen DX, Politi KA, Shen X, Hsu DS, Peehl DM, Kurhanewicz J, Sriram R, Suarez M, Xiao S, Du Y, Li XN, Navone NM, Labanca E, Willey CD Patient-Derived Models of Cancer in the NCI PDMC Consortium: Selection, Pitfalls, and Practical Recommendations. Cancers (Basel) 16(3), 2024. PMID: 38339316.
3. Giroux NS, Ding S, McClain MT, Burke TW, Petzold E, Chung HA, Rivera GO, Wang E, Xi R, Bose S, Rotstein T, Nicholson BP, Chen T, Henao R, Sempowski GD, Denny TN, De Ussel MI, Satterwhite LL, Ko ER, Ginsburg GS, Kraft BD, Tsalik EL, Shen X, Woods CW Author Correction: Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion. Sci Rep 13(1):6462, 2023. PMID: 37081034.
4. Bose S, Clevers H, Shen X Promises and Challenges of Organoid-Guided Precision Medicine. Med 2(9):1011-1026, 2021. PMID: 34617071.
5. Huang Q, Garrett A, Bose S, Blocker S, Rios AC, Clevers H, Shen X The frontier of live tissue imaging across space and time. Cell Stem Cell 28(4):603-622, 2021. PMID: 33798422.
6. Sarvestani SK, DeHaan RK, Miller PG, Bose S, Shen X, Shuler ML, Huang EH A Tissue Engineering Approach to Metastatic Colon Cancer. iScience 23(11):101719, 2020. PMID: 33205026.
7. Davis R, Lafata K, X Li, N Souma, D Howell, Shen X, Barisoni L A Deep Learning Approach to Analysis of Kidney Transplant Frozen Sections. Modern Pathology 33(None):1573, 2020. PMID: None.
8. Dohlman AB, Shen X Mapping the microbial interactome: Statistical and experimental approaches for microbiome network inference. Exp Biol Med (Maywood) 244(6):445-458, 2019. PMID: 30880449.
9. Mines R, Chen KY, Shen X Agent-Based Modelling to Delineate Spatiotemporal Control Mechanisms of the Stem Cell Niche. Methods Mol Biol 1975(None):3-35, 2019. PMID: 31062303.
10. Barth BB, Huang HI, Hammer GE, Shen X Opportunities and Challenges for Single-Unit Recordings from Enteric Neurons in Awake Animals. Micromachines (Basel) 9(9):None, 2018. PMID: 30424361.
11. Barth BB, Shen X Computational motility models of neurogastroenterology and neuromodulation. Brain Res 1693(Pt B):174-179, 2018. PMID: 29903620.
12. Johnson C, Warmoes MO, Shen X, Locasale JW Epigenetics and cancer metabolism. Cancer Lett 356(2 Pt A):309-14, 2015. PMID: 24125862.
13. Murthy PKL, Srinivasan T, Bochter MS, Varanko A, Xi R, Tung KL, Fatih S, Xu K, Maletic-Savatic M, Cole SE, Shen X Spatially Specific Fringe Modulation of Notch Ligands Supports Intestinal Homeostasis. eLife None(None):None. PMID: None.

Editorials

1. Bu P, Chen KY, Lipkin SM, Shen X. Asymmetric division: a marker for cancer stem cells in early stage tumors?. Oncotarget 4(7):950-1, 2013. PMID: 23807730.

Book Chapters

1. Petritsch C, Shen X. Chapter 11: Asymmetric Division of Cancer Stem Cells. In: Cancer Stem Cells: Targeting the Roots of Cancer, Seeds of Metastasis, and Sources of Therapy Resistance. 1. Academic Press, None, 2016.