Publications

Journal Publications

View a complete list of published work in MyBibliography.

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. 2024 Aug;13(21):e2302331. doi: 10.1002/adhm.202302331. Epub 2024 Mar 1. PMID: 38359321; PMCID: PMC11324859.

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. 2024 Apr 16. doi: 10.1097/SLA.0000000000006299.

Zhu X, Huang Q, Jiang L, Nguyen V-T, 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 S-WD, Shen X^*, Yao J^*, Longitudinal Intravital Imaging of Mouse Placenta, Science Advance. (2024) Mar 22, 10(12). ^*co-corresponding authors

Jiang C, Chao C-C, Li J, Ge X, Shen A, Jucaud V, Cheng C, Shen X. (2024) Tissue-resident memory T cell signatures from single-cell analysis associated with better melanoma prognosis. iScience, 2004 Mar 15;27(3), doi: 10.1016/j.isci.2024.109277.

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 X-F, Clevers H, Hsu D, Shen X. (2024) Chromatin Remodeling in Patient-Derived Colorectal Cancer Models. Advanced Science. 2024 Feb 21:e2303379. doi: 10.1002/advs.202303379.

Gurrea-Rubio M, Wu Q, Amin MA, Tsou P-S, 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, 34 (2024). doi: 10.1007/s00262-023-03578-1.

Bose S, Shen X. The KRAS tour: Studying metabolic reprogramming in isogenic pancreatic cancer organoids. Cell Stem Cell. 2024 Jan 4;31(1):1-2. doi: 10.1016/j.stem.2023.12.010. PMID: 38181746.

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. 2023 Nov 29;27(1):108288. doi: 10.1016/j.isci.2023.108288.

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, Gündüz IB, Norell T, Broderick TJ, McClain MT, Satterwhite LL, Burke TW, Petzold EA, Shen X, Woods CW, Fowler VG, 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, Müller F, Greenleaf WJ, Ecker JR. Human Immune Cell Epigenomic Signatures in Response to Infectious Diseases and Chemical Exposures. bioRxiv. 2023 Jun 30:2023.06.29.546792. doi: 10.1101/2023.06.29.546792

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. 2022 Oct 31;11(1):83. doi: 10.1186/s40164-022-00329-3.

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. 2022 Aug 16;33(10):1876-90. doi: 10.1681/ASN.2022020139.

Bose S, Barroso M, Chheda MG, Clevers H, Elez E, Kaochar S, Kopetz SE, Li X-N, 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. 2022 Oct 18;S1535-6108(22)00475-5. doi: 10.1016/j.ccell.2022.09.017.

Bose S, Yao H, Huang Q, Whitaker R, Kontos CD, Previs R, Shen X. Using Genetically Encoded Fluorescent Biosensors to Interrogate Ovarian Cancer Metabolism. Journal of Ovarian Research. (2022) 15:114. DOI:https://doi.org/10.1186/s13048-022-01046-5

Dohlman AB, Klug J, Mesko M, Gao IH, Lipkin S, Shen X, Iliev ID. A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors that is predictive of survival. Cell. (2022). 2022 Sep 29;185(20):3807-3822.e12. doi: 10.1016/j.cell.2022.09.015.

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 Report. (2022). Vol. 17 1–17 September 13. DOI:https://doi.org/10.1016/j.stemcr.2022.07.016

Bose S, Huang Q, Ma Y, Wang L, Rivera GO, Ouyang Y, Whitaker R, Gibson RA, Kontos CD, Berchuck A, Previs R, Shen X. G6PD Inhibition Sensitizes Ovarian Cancer Cells to Oxidative Stress in the Metastatic Omental Microenvironment. Cell Reports. (2022). 2022 Jun 28;39(13):111012. doi: 10.1016/j.celrep.2022.111012.

Wu Y, Wong CW, Chiles EN, Mellinger A, Bae H, Jung S, Peterson T, Wang J, Negrete M, Huang Q, Wang L, Jang C, Muddiman D, Su X, Williamson I, Shen X. Glycerate from intestinal fructose metabolism induces islet cell damage and glucose intolerance. Cell Metabolism. (2022), July 5;34(22) doi:https://doi.org/10.1016/j.cmet.2022.05.007.

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, Williamson I, Nelson DA, Delubac D, Oh S, Rupprecht G, Isaacs J, Jia J, Shen JP, Kopetz S, McCall S, Smith A, Gjorevski N, Walz AC, Antonia S, Berger EM, Clevers H, Hsu D, Shen X. Patient-derived micro-organospheres enable clinical precision oncology. Cell Stem Cell. (2022), Jun 2;29(6):905-914 doi:https://doi.org/10.1016/j.stem.2022.04.006.

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. Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion. Sci Rep. 2022 Jul 9;12(1):11714. doi: 10.1038/s41598-022-15668-8.

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. 2022 May 17;11(1):138. doi: 10.1038/s41377-022-00836-2.

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. 2022 Apr;283:121393. Epub 2022 Jan 28. doi: 10.1016/j.biomaterials.2022.121393.

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. 2022 Apr 20;PP. doi: 10.1109/TMI.2022.3168859. Online ahead of print. PMID: 35442884.

Artola-Borán 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, Müller A. Mycobacterial infection aggravates Helicobacter pylori-induced gastric preneoplastic pathology by redirection of de novo induced Treg cells. Cell Rep. 2022 Feb 8;38(6):110359. doi: 10.1016/j.celrep.2022.110359.

Mines R, Lipniacki T, Shen X. Slow Nucleosome Dynamics set the Transcriptional Speed Limit and Induce RNA Polymerase II Traffic Jams and Bursts. PLOS Computational Biology. 2022 Feb 10;18(2):e1009811.

Murthy P, Xi R, Arguijo D, Everitt J, Kocak D, Kobayashi Y, Bozec A, Vicent S, Xiang K, Ding S, Crawford GE, Hsu D, Tata PR, Reddy T, Shen X. Epigenetic basis of Kras mediated epithelial-cellular proliferation and plasticity, Developmental Cell. 2022 Feb 7;57(3):310-328.e9. doi: 10.1016/j.devcel.2022.01.006.

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. 2021 Nov;8(6):067501. doi: 10.1117/1.JMI.8.6.067501. Epub 2021 Dec 20.

Bose S, Clevers H, Shen X. Promises and Challenges of Organoid-Guided Precision Medicine. Med 2(9):1011-1026 Sep 2021.

Wang L, Wang E, Balcazar JP, Wu Z, Xiang K, Wang Y, Huang Q, Negrete M, Chen K-Y, 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. Advanced Science Aug 10;e2004673. doi: 10.1002/advs.202004673 (2021).

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. Nature Communications 12, no. 1 (2021).

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 Medicine 13, no. 1 (2021)

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 (MAIT) Cell Responses Differ by Sex in COVID-19. Med (N Y) (2021). *equal corresponding author.

Garrett AD, 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. Journal of Neural Engineering (2021). May 12. doi: 10.1088/1741-2552/ac0089

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 and Diseases 8, no. 2 (2021): 203-214.

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, Huang EH. Induced organoids derived from patients with ulcerative colitis recapitulate colitic reactivity. Nature Communications 12, no. 1 (2021).

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, no. 4 (2021): 603-622.

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. Nature Communications 12, no. 1 (2021).

Dohlman A, Mendoza DA, Ding S, Gao M, Dressman H, Iliev ID, Lipkin SM, Shen X. (2020) The Cancer Microbiome Atlas (TCMA): A Pan-Cancer Comparative Analysis to Distinguish Organ-Associated Microbiota from Equiprevalent Contaminants. Cell Host & Microbe, 2020 Dec 21;S1931-3128(20)30663-6. doi: 10.1016/j.chom.2020.12.001.

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. Nature Communications 12, no. 1 (2021).

Sarvestani SK, DeHaan RK, Miller PG, Bose S, Shen X, Shuler ML, Huang EH. A Tissue Engineering Approach to Metastatic Colon Cancer. iScience 23, no. 11 (2020).

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, no. 22 (2020). *equal corresponding author.

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, no. 20 (2020).

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. Molecular Cancer Therapeutics (2020).

Altunel E, Roghani RS, Chen K-Y, 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, no. 1 (2020).

Davis R, Lafata K, Li X, Souma N, Howell D, Shen X, Barisoni L.  (2020) A Deep Learning Approach to Analysis of Kidney Transplant Frozen Sections. In Modern Pathology, 1573. Vol. 33., 2020.

Bauer M, Nascakova Z, Mihai A-I, Cheng PF, Levesque MP, Lampart S, Hurwitz R, Pfannkuch L, Dobrovolna J, Jacobs M, Bartfeld S, Dohlman A, Shen X, Gall AA, Salama NR, Töpfer A, Weber A, Meyer TF, Janscak P, Müller A. The ALPK1/TIFA/NF-κB axis links a bacterial carcinogen to R-loop-induced replication stress. Nature Communications 11, no. 1 (2020).

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 P, Zhang S, Daniel AR, Kirsch DG, Kang Y, Capel B, Asokan A, Silver DL, Jaenisch R, Shen X. (2020) Intravital Imaging of Mouse Embryos. Science. 368, no. 6487 (2020): 181-186.doi:10.1126/science.aba0210

Shen X. (2020) An imprecise path to precision medicine. Nature Medicine 26, no. 1 (2020):14. doi; 10.1038/s41591-019-0718-6

Rakhilin N, Garrett A, Eom C-Y, Chavez K, Small DM, Daniel A, Kaelberer MM, Mejooli MA, Huang Q, Ding S, Kirsch DG, Bohórquez DV, Nishimura N, Barth BB, Shen X. (2019). An intravital window to image the colon in real time. Nature Communications. 10, no.1.

Dohlman AB, Shen X. (2019) Mapping the microbial interactome: Statistical and experimental approaches for microbiome network inference. Experimental Biology and Medicine 244, no. 6 (2019): 445-458.

Roper J, Shen X. (2019) Novel Three-Dimensional Cultures of Patient-Derived Cancer and Tumor Immune Cells. Gastroenterology 157, no. 1 (2019): 260-261.

Xi R, Murthy P, Tung K-L, Guy CD, Wan J, Li F, Wang Z, Li X, Varanko A, Rakhilin N, Xin Y, Liu B, Qian S-B, Su L, Han Y, Shen X (2019) SENP3-mediated host defense response contains HBV replication and restores protein synthesis. PLoS One 14, no. 1 (2019).

Wang L, Wang E, Wang Y, Mines R, Xiang K, Sun Z, Zhou G, Chen K-Y, Rakhilin N, Chao S, Ye G, Wu Z, Yan H, Shen H, Everitt J, Bu P, Shen X. (2018) miR-34a is a microRNA safeguard for Citrobacter-induced inflammatory colon oncogenesis, eLife, 2018;7:e39479 doi: 10.7554/eLife.39479.

Xu Y, Huang L, Kirschman JL, Vanover DA, Tiwari PM, Santangelo PJ, Shen X, Russell DG. (2019) Exploitation of Synthetic mRNA to Drive Immune Effector Cell Recruitment and Functional Reprogramming In Vivo. The Journal of Immunology, ji1800924; doi: 10.4049/jimmunol.1800924.

Kaelberer M, Buchanan K, Klein M, Barth B, Wen G, Montoya M, Shen X, Bohórquez V. (2018). A Gut-Brain Neural Circuit for Nutrient Sensory Transduction. Science, 361 (6408), doi: 10.1126/science.aat5236.

Choi J, Rakhilin N, Gadamsetty P, Joe DJ, Tabrizian T, Lipkin SM, Huffman DM, Shen X, Nishimura N (2018), Intestinal crypts recover rapidly from focal damage with coordinated motion of stem cells that is impaired by aging. Scientific Reports, 8, no. 1.

Bu P, Chen KY, Xiang K, Johnson C, Crown S, Rakhilin N, Ai Y, Wang L, Xi R, Astapova I, Han Y, Li J, Barth BB, Lu M, Gao Z, Zhang L, Herman M, Hsu D, Zhang G-F, Shen X. (2018) Aldolase b mediated fructose metabolism drives metabolic reprogramming of colon cancer liver metastasis. Cell Metabolism, 27 (6), 1249–1262, June 5, 2018. doi: 10.1016/j.cmet.2018.04.003.

Murthy PKL, Srinivasan T, Bochter MS, Varanko A, Xi R, Tung KL, Fatih S, Xu K, Maletic-Savatic M, Cole SE, Shen X. (2018) Spatially Specific Fringe Modulation of Notch Ligands Supports Intestinal Homeostasis. eLife, 2018;7:e35710 doi: 10.7554/eLife.35710.

Xu Y, Wang L, Zimmerman MD, Chen K-Y, Huang L, Fu D-J, Kaya F, Rakhilin N, Nazarova EV, Bu P, Dartois V, Russell DG, Shen X. (2018) Matrix Metalloproteinase inhibitors enhance the efficacy of frontline drugs against Mycobacterium tuberculosis. PLoS Pathogen, 14(4): e1006974.

Barth BB, Huang H-I, Hammer GE, Shen X. (2018) Opportunities and Challenges for Single-Unit Recordings from Enteric Neurons in Awake Animals. Micromachines 9, 428.

Barth B, Shen X. (2018) Computational motility models of neurogastroenterology and neuromodulation, Brain Research, 1693(Pt B):174-179. doi: 10.1016/j.brainres.2018.02.038.

Klose CSN, Mahlakoiv T, Moeller JB, Rankin LC, Flamar A-L, Kabata H, Monticelli LA, Moriyama S, Putzel GG, Rakhilin N, Shen X, Kostenis E, Konig GM, Senda T, Carpenter D, Farber DL, Artis D. (2017) The neuropeptide neuromedin U stimulates innate lymphoid cells and type 2 inflammation. Nature, 549(7671):282-286 06 Sep 2017.

Barth BB, Henriquez CS, Grill WM, Shen X. (2017) Optimal electrical stimulation of gut motility guided by an in silico model. Journal of Neural Engineering. 17 Aug 2017.

Kulkarnia S, Miccib M, Lesera J, Shinc C, Tangd S-C, Fua Y-Y, Liua L, Lia Q, Sahaa M, Lia C, Enikolopove G, Beckerg L, Rakhilinh N, Anderson M, Shen X, Dong X, Bogunovic M, Pasrichaa P. (2017) Adult enteric nervous system in health is maintained by a dynamic balance between neuronal apoptosis and neurogenesis. Proc. Natl. Acad. Sci. USA. April 18, 2017, doi: 10.1073/pnas.1619406114

Chen KY, Srinivasan T, Tung KL, Belmonte JM, Choi J, Rakhilin N, King S, Varanko AK, Wang L, Witherspoon M, Nishimura N, Glazier J, Lipkin SM, Bu P, Shen X. (2017) A Notch positive feedback in the intestinal stem cell niche is essential for stem cell self-renewal. Molecular Systems Biology, 13(4): p. 927.

Wang L, Bu P, Shen X. Asymmetric division: An antitumor player? Molecular & Cellular Oncology 3, no. 4 (2016).

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 J, Xu Y, Shen X, Markowitz S, Maillard I, Lowe JB, Xin W, Zhou L. (2016) Fucosylation Deficiency in Mice Leads to Colitis and Adenocarcinoma. Gastroenterology, pii: S0016-5085(16)35029-6. doi: 10.1053/j.gastro.2016.09.004.

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 S, Copeland NG, Jenkins NA, Shuler ML. (2016) A recellularized human colon model identifies cancer driver genes. Nature Biotechnology. 34, 845-851 doi: 10.1038/nbt.3586.

Rakhilin N, Barth B, Choi J, Muñoz NL, Kulkarni S, Jones J, Small D, Cheng Y-U, Cao Y, LaVinka C, Kan E, Dong X, Spencer M, Pasricha P, Nishimura N, Shen X. (2016) Simultaneous Optical and Electrical In Vivo Analysis of the Enteric Nervous System. Nature Communication, 7:11800. doi: 10.1038/ncomms11800.

Wang L, Bu P, Ai Y, Srinivasan T, Chen HJ, Xiang K, Lipkin SM, Shen X. (2016) A Long Non-Coding RNA Targets MicroRNA miR-34a to Regulate Colon Cancer Stem Cell Asymmetric Division. eLife 2016;10.7554/eLife.14620

Srinivasan T, Bich ET, Bu P, Tung K-L, Chen K-Y, Augenlicht L, Lipkin SM, Shen X. (2016) Notch signalling regulates asymmetric division and inter-conversion between lgr5 and bmi1 expressing intestinal stem cells. Scientific Reports, 6(26069). doi: 10.1038/srep26069.

Srinivasan T, Walters J, Bu P, Than EB, Tung KL, Chen KY, Panarelli N, Milsom J, Augenlicht L, Lipkin SM, Shen X. (2016) NOTCH Signaling Regulates Asymmetric Cell Fate of Fast- and Slow-Cycling Colon Cancer Initiating Cells. Cancer Research, 10.1158/0008-5472.CAN-15-3198.

Bu P, Wang L, Chen KY, Srinivasan T, Murthy PKL, Varanko AK, Chen HJ, Ai Y, King S, Lipkin SM, Shen X. (2016) A miR-34a-Numb feed-forward loop triggered by inflammation regulates asymmetric stem cell division in intestine and colon cancer. Cell Stem Cell, 18(2), 189-202. doi: 10.1016/j.stem.2016.01.006

Rothschild DE, Srinivasan T, Aponte-Santiago AL, Shen X, Allen IC. The Ex Vivo Culture and Pattern Recognition Receptor Stimulation of Mouse Intestinal Organoids. J. Vis. Exp., no. 111 (2016).

Joe DJ, Hwang J, Johnson C, Cha H-Y, Lee J-W, Shen X, Spencer MG, Tiwari S, Kim M. Surface Functionalized Graphene Biosensor on Sapphire for Cancer Cell Detection. Journal of Nanoscience and Nanotechnology 16, no. 1 (2016): 144-151.

Cao Y, Rakhilin N, Gordon PH, Shen X, Kan EC. (2016)  A real-time spike classification method based on dynamic time warping for extracellular enteric neural recording with large waveform variability. J Neurosci Methods. 2015 Dec 21. pii: S0165-0270(15)00446-X. doi: 10.1016/j.jneumeth.2015.12.006.

Li J, Ai Y, Wang L, Bu P, Sharkey CC, Wu Q, Wun B, Roy S, Shen X, King MR. (2016) Targeted drug delivery to circulating tumor cells via platelet membrane-functionalized particles. Biomaterials. 76:52-65. doi: 10.1016/j.biomaterials.2015.10.046.Shengyi

Chen HJ, Sun J, Huang Z, Hou H, Arcilla M, Rakhilin N, Joe D, 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, Gümüş ZH, Shuler M, Nishimura N, Edelmann W, Shen X*, Lipkin SM. (2015) Comprehensive models of human primary and metastatic colorectal tumors in immunodeficient and immunocompetent mice by chemokine targeting. Nature Biotechnology, 33,656–660 doi:10.1038/nbt.3239. *equal corresponding author.

Bu P, Wang L, Chen KY, Sun J, Rakhilin N, Closa A, Tung KL, Xu Y, Cummings B, Hsu D, Lipkin SM, Moreno V, Gümüş ZH, Shen X. (2015) miR-1269 promotes metastasis and forms a positive feedback loop with TGF-β. Nature Communications, 6:6879. doi: 10.1038/ncomms7879.

Chen K-Y, Joe DJ, Shealy JB, Land BR, Shen X. (2014) A Bio-inspired spatial patterning circuit., IEEE Eng. Med Biol., 2014 Aug;2014:86-9. doi:10.1109/EMBC.2014.6943535.

Chen K-Y, Liu X, Bu P, Lin CS, Rakhilin N, Locasale JW, Shen X. (2014) A Metabolic Signature of Colon Cancer Initiating Cells. IEEE Eng Med Biol., 4759-4762 doi: 10.1109/EMBC.2014.6944688.

Johnson C, Warmoes MO, Shen X, Locasale JW. Epigenetics and cancer metabolism. (2013) Cancer Letters, 0304-3835.

Shin YJ, Chen KY, Hencey B, Lipkin S, Sayed AH, Shen X. (2013) Post-translational regulation enables robust p53 regulation. BMC Systems Biology, 7:83.

Bu P, Chen KY, Lipkin SM, Shen X. (2013). Asymmetric division: a marker for cancer stem cells in early stage tumors? Oncotarget, 4, 948.

Bu P, Chen KY, Chen JK, 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, Gümüş ZH, Lipkin SM, Shen X. (2013). A microRNA miR-34a Regulated Bimodal Switch targets Notch in Colon Cancer Stem Cells. Cell Stem Cell, 12, 602-615.

Shin YJ, Sayed AH, Shen X. (2012). Using an adaptive gene network model for self-organizing multicellular behavior. IEEE Eng Med Biol. 2012:5449-53

Li J, Bu P, Chen K, Shen X. (2013) Spatial perturbation with synthetic protein scaffold reveals robustness of asymmetric cell division. Journal of Biomedical Science and Engineering, 6, 134-143.

Shin YJ, Sayed AH, Shen X. (2012). Adaptive Models for Gene Networks. PLoS One, 7:1-6. E31657

Chen HJ, Edwards R, Tucci S, Bu P, Milsom J, Lee S, Edelmann W, Gumus ZH, Shen X^*, Lipkin S. (2012). Chemokine 25-induced signaling suppresses colon cancer invasion and metastasis. The Journal of Clinical Investigation, 122:3184-96. *equal corresponding author.

Shin YJ, Hencey B, Lipkin S, Shen X. (2011). Frequency domain analysis reveals external periodic fluctuations can generate sustained p53 oscillation. PLoS One, 6:1-13. PMID: 21829536.

Sikandar S, Dizon D, Shen X, Li Z, Besterman J, Lipkin S. (2010). 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: 596-605.

Tan M, Kozden JB, Shen X, Shapiro L, McAdams H. (2010). An essential transcription factor, SciP, enhances robustness of Caulobacter cell cycle regulation. Proc. Natl. Acad. Sci. USA 107: 18985-18990.

Shen X, Collier J, Shapiro L, Dill D, Horowitz MA, McAdams HH. (2008). Architecture and Inherent Robustness of a Bacterial Cell-Cycle Control System. Proc. Natl. Acad. Sci. USA 105-32: 11340-11345.

Shen X, Kahn JM, Horowitz MA. (2005). Compensation for Multimode Fiber Dispersion by Adaptive Optics. Optics Letters, 30: 2985-2987.

Book Chapters

Mines R, Chen K-Y, Shen X. "Agent-Based Modelling to Delineate Spatiotemporal Control Mechanisms of the Stem Cell Niche." Methods in Molecular Biology (Clifton, N.J.) 1975 (2019): 3-35.

Petritsch C, Shen X. “Asymmetric Division of Cancer Stem Cells”. Cancer Stem Cells: Targeting the Roots of Cancer, Seeds of Metastasis, and Sources of Therapy Resistance. 285-315 (ISBN-13) 10.1016/B978-0-12-803892-5.00011-5.

Patents

US6789246: M. Sunderarjan and X. Shen, “Method and apparatus for automatic layout of circuit structures”

US6802050: X. Shen and M. Sunderarja, “Efficient layout strategy for automated design layout tools”

US20150164053A1: J.H. Chen, J.M. Lipkin, and X. Shen, “Compositions and methods useful for making orthotopic tumors with controllable metastasis”

US20080072215: S. Boyd, X. Shen, M. Hershenson, L. Vandenberghe, C. Crucius, D. Colleran, and S. Mohan, “Parser for signomial and geometric programs”

US9681647: J.H. Chen, J.M. Lipkin, and X. Shen, “Mammal with an orthotopic tumor capable of metastasis, a method of making and a method of using”

WO2019067795: D. Hsu and X. Shen, “Patient specific clinical trials and associated methods of treatment”

US20190231761: X. Shen, “Compositions and methods for targeting fructose enzymes and transporters For The Treatment Of Cancer”

WO2018236880: B. Barth, W. Grill, and X. Shen, “Systems and methods for the modulation of gut motility”

US2023/0002737: X. Shen, D. Hsu, Z. Wang, J. Motschman, and D. Delubac, “Methods and apparatuses for patient-derived micro-organospheres”

US20210285054: X. Shen and S. Ding “Precision drug screening for personalized cancer therapy”

WO2023042156: N. Natesh and X. Shen, “Droplet organoid-based immuno-oncology assays and methods of using same”

WO2023042156: X. Shen and S. Ding, “Methods and apparatus for testing immuno-oncology drugs and biologics using microorganospheres”

US11628382: Z. Wang and X. Shen, “methods and apparatuses for purification of gel droplets supporting biological tissue”

EP4178666: X. Shen, A. O'Raw, J. Morizio, A. Deshmukh, A. Erez, and S. Ezagouri, “Compositions and methods for treating cancer-associated cachexia”

WO2023215793A2: X. Shen, “Patient-derived microorganospheres (mos) enable clinical precision oncology”

WO2023212732A2: X. Shen and Z. Wang, “Methods and apparatuses for testing hepatocyte toxicity using microorganospheres”

US20240062365A1: X. Shen, Z. Wang, W. Quayle, and G. Jenkinson, “Imaging-based microorganosphere drug assays”

WO2024054564A2: X. Shen and S. Ding, “Multiple myeloma microorganospheres”

WO2024035638A1: I. Iliev, A. Dohlman, and X. Shen, “Methods for classifying and treating gastrointestinal tumors based on mycobiome analysis”

US12100151B2: X. Shen, Z. Wang, W. Quayle, and G. Jenkinson, “Droplet imaging pipeline”

WO2024191617A1: Z. Wang, X. Shen, E. Bankaitis, and S. Steele, “Cell labeling and annotation in micro-organospheres”