DR. XILING SHEN'S LABORATORY

ABOUT DR. XILING SHEN

Dr. Xiling Shen is the chief scientific officer of the Terasaki Institute, responsible for executing its scientific missions. He is also the Scientific Founder of Xilis, Inc, a precision oncology company that raised $70M Series-A financing in July, 2021. Prior to joining Terasaki, he was the Hawkins Family Associate Professor and director of the Woo Center for Big Data and Precision Health at Duke University. He received his BS, MS, and PhD degrees from Stanford University and the NSF junior faculty career award at Cornell University. He was the steering committee chair of the NCI Patient-Derived Model of Cancer Consortium, chair of the NCI Tissue Engineering Consortium 2021 conference, and cancer track chair of BMES 2019. His lab studies precision medicine from a systems biology perspective. Areas of interests include cancer, stem cells, the gut-brain axis, and intravital imaging.

CONTACT ME

xiling.shen@terasaki.org

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RESEARCH OVERVIEW

Dr. Shen’s lab specializes in precision medicine and systems biology. His members integrate biological, engineering, and computational techniques to study cancer, stem cells, and the gut-brain axis.
 

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Precision medicine

Dr. Shen is the Scientific Founder of the company Xilis, which developed a droplet organoid technology termed micro-organospheres (MOS). Several clinical trials are ongoing in both US and Europe to validate the ability of MOS to predict patient outcomes. He founded the company, Xilis Inc., with Drs. Hans Clevers and David Hsu, to develop MOS-based clinical diagnostics that has received a $70M series-A. His lab is further developing this technology for applications including immunotherapy, stem cell regeneration, autoimmune diseases, host-microbe interactome, and infectious diseases.

Cancer Metastasis

Mixed response to chemotherapy between primary tumors and metastases occurs in a significant fraction of patients, supporting the existence of important biological differences between the two. The Shen lab was the first to demonstrate that metastatic colorectal cancer undergo metabolic and epigenetic reprogramming in the liver. New therapeutic development to target the metabolic and epigenetic reprogramming axes have led to clinical trials and pharma partnerships.

Gut-brain axis and Neuromodulation

Dr. Shen leads the Chan-Zuckerberg Human Atlas Along the Gut-Brain Axis program. With deeper understanding of the gut-brain axis using cutting-edge tools such as single-cell sequencing and viral tracing, the Shen lab is developing novel neuromodulation methods to treat a variety of systemic diseases.

Intravital imaging

The Shen lab developed the first intestinal window with scaffold and graphene sensors to measure the enteric nervous system in real time. They then developed the first intravital colon window to study stem cells, inflammation, and peripheral stimulation in the colon. They also developed the very first embryonic window that allowed real-time imaging of embryos and organogenesis. Ongoing projects include improving transplantation and chimeric efficiencies for disease modeling and therapeutic development.

Team

Anders Dohlman

Anders Dohlman

Yanru Wu

Yanru Wu

Shree Bose

Shree Bose

Kun Xiang

Kun Xiang 

Ergang Wang

Ergang Wang

Aliesha O' Raw

Aliesha O' Raw

Tomer Rotstein

Tomer Rotstein

Chi Wut (William) Wong

Chi Wut (William) Wong

RESEARCH PAPERS

  • Wu Y, Wong C, Chiles E, 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. (2022) "Glycerate Production from Intestinal Fructose Metabolism Elevated by Dietary Fat Induces Glucose Intolerance Through β-cell Damage". Cell Metabolism (2022): accepted

  • Bose S, Huang Q, Ma Y, Wang L, Rivera G, Ouyang Y, Whitaker R, Gibson R, Kontos C, Berchuck A, Previs R, Shen X. (2022) "G6PD Inhibition Sensitizes Ovarian Cancer Cells to Oxidative Stress in the Metastatic Omental Microenvironment". Cell Report (2022): accepted

  • 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. (2022) "Patient-derived micro-organospheres enable clinical precision oncology". Cell Stem Cell (2022): https://www.sciencedirect.com/science/article/abs/pii/S193459092200159X?

  • 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. (2022) "Three-dimensional Deep-tissue Functional and Molecular Imaging by Integrated Photoacoustic, Ultrasound, and Angiographic Tomography (PAUSAT)". IEEE Trans Med Imaging (2022): https://ieeexplore.ieee.org/document/9760438

  • 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. (2022) "Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion". Res Sq. (2022): https://www.researchsquare.com/article/rs-1479864/v1

  • 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. (2022) "DAMPs/PAMPs induce monocytic TLR activation and tolerance in COVID-19 patients; nucleic acid binding scavengers can counteract such TLR agonists". Biomaterials. (2022): https://www.sciencedirect.com/science/article/pii/S0142961222000321?

  • Mines RC, Lipniacki T, Shen X. (2022) "Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts". PLOS Computational Biology (2022): https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009811

  • 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. (2022) "Mycobacterial infection aggravates Helicobacter pylori-induced gastric preneoplastic pathology by redirection of de novo induced Treg cells". Cell Reports (2022): https://www.cell.com/cell-reports/fulltext/S2211-1247(22)00080-8?

  • 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. (2022) "Epigenetic basis of oncogenic-Kras-mediated epithelial-cellular proliferation and plasticity". Developmental Cell (2022): https://www.cell.com/developmental-cell/fulltext/S1534-5807(22)00006-5?


  • Micah T. McClain, Florica J. Constantine, Ricardo Henao, Yiling Liu, Ephraim L. Tsalik, Ephraim L. Tsalik, Ephraim L. Tsalik, Thomas W. Burke, Julie M. Steinbrink, Julie M. Steinbrink, Elizabeth Petzold, Bradly P. Nicholson, Robert Rolfe, Bryan D. Kraft, Bryan D. Kraft, Bryan D. Kraft, Matthew S. Kelly, Daniel R. Saban, Chen Yu, Xiling Shen, Emily M. Ko, Gregory D. Sempowski, Thomas N. Denny, Geoffrey S. Ginsburg, Christopher W. Woods, Christopher W. Woods, Christopher W. Woods (2021) "Dysregulated transcriptional responses to SARS-CoV-2 in the periphery". Nature Communications (2021): https://www.scilit.net/article/0ad08a958bee162b6554122632054272?

  • Anders B. Dohlman, Diana Arguijo Mendoza, Shengli Ding, Michael Gao, Holly Dressman, Iliyan D. Iliev, Steven M. Lipkin, Xiling Shen. (2021) "The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants". Cell Host & Microbe (2021): https://www.sciencedirect.com/science/article/abs/pii/S1931312820306636

  • Liuyang Wang, Thomas J Balmat, Alejandro L Antonia, Florica J Constantine, Ricardo Henao, Thomas W Burke, Andy Ingham, Micah T McClain, Micah T McClain, Micah T McClain, Ephraim L Tsalik, Emily R Ko, Emily R Ko, Geoffrey S Ginsburg, Mark R DeLong, Xiling Shen, Christopher W Woods, Christopher W Woods, Christopher W Woods, Elizabeth R Hauser, Elizabeth R Hauser, Dennis C Ko (2021) "An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility". Genome Medicine (2021): https://www.ncbi.nlm.nih.gov/pubmed/34001247

  • Samaneh K. Sarvestani, Steven Signs, Bo Hu, Yunku Yeu, Hao Feng, Ying Ni, David R. Hill, Robert C. Fisher, Sylvain Ferrandon, Reece K. DeHaan, Jennifer Stiene, Michael Cruise, Tae Hyun Hwang, Xiling Shen, Jason R. Spence, Emina H. Huang, Emina H. Huang (2021) "Induced organoids derived from patients with ulcerative colitis recapitulate colitic reactivity". Nature Communications (2021): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7801686/

  • Chen Yu, Sejiro Littleton, Nicholas S. Giroux, Rose Mathew, Shengli Ding, Joan Kalnitsky, Yuchen Yang, Elizabeth Petzold, Hong A. Chung, Grecia O. Rivera, Tomer Rotstein, Rui Xi, Emily R. Ko, Emily R. Ko, Ephraim L. Tsalik, Ephraim L. Tsalik, Ephraim L. Tsalik, Gregory D. Sempowski, Thomas N. Denny, Thomas W. Burke, Micah T. McClain, Micah T. McClain, Micah T. McClain, Christopher W. Woods, Xiling Shen, Daniel R. Saban (2021) "Mucosal Associated Invariant T (MAIT) Cell Responses Differ by Sex in COVID-19". Med (New York, N.Y.) (2021): https://www.sciencedirect.com/science/article/pii/S2666634021001574

  • Qiang Huang, Qiang Huang, Aliesha Garrett, Shree Bose, Stephanie Blocker, Anne C. Rios, Hans Clevers, Xiling Shen (2021) "The Frontier of Live Tissue Imaging Across Space and Time". Cell Stem Cell (2021): https://www.sciencedirect.com/science/article/pii/S1934590921000606

  • Zhuojun Dai, Xiaoyu Yang, Feilun Wu, Lihua Wang, Kun Xiang, Pengcheng Li, Qingqing Lv, Jinhui Tang, Anders Dohlman, Lei Dai, Xiling Shen, Lingchong You (2021) "Living fabrication of functional semi-interpenetrating polymeric materials". Nature Communications (2021): https://www.nature.com/articles/s41467-021-23812-7

  • Zhaohui Wang, Emilio Cortes-Sanchez, Chieh-Hsiang Yang, Daniel Nelson, Daniel Delubac, Shiaowen David Hsu, Alana Welm, Xiling Shen (2021) "Micro-organospheres: An automated patient-derived model platform for rapid drug screening of breast cancer". Journal of Clinical Oncology (2021): https://ascopubs.org/doi/abs/10.1200/JCO.2021.39.15_suppl.e12628

  • Shree Bose, Hans Clevers, Xiling Shen (2021) "Promises and Challenges of Organoid-Guided Precision Medicine". Med (New York, N.Y.) (2021): https://www.sciencedirect.com/science/article/pii/S2666634021002907

  • Lihua Wang, Ergang Wang, Jorge Prado Balcazar, Zhenzhen Wu, Kun Xiang, Yi Wang, Qiang Huang, Marcos Negrete, Kai Yuan Chen, Wei Li, Yujie Fu, Anders Dohlman, Robert Mines, Liwen Zhang, Yoshihiko Kobayashi, Tianyi Chen, Guizhi Shi, John Paul Shen, Scott Kopetz, Purushothama Rao Tata, Victor Moreno, Charles Gersbach, Gregory Crawford, David Hsu, Emina Huang, Pengcheng Bu, Xiling Shen (2021) "Chromatin Remodeling of Colorectal Cancer Liver Metastasis is Mediated by an HGF-PU.1-DPP4 Axis". Advanced Science (2021): https://www.ncbi.nlm.nih.gov/pubmed/34378358

  • Richard C. Davis, Xiang Li, Yuemei Xu, Zehan Wang, Nao Souma, Gina Sotolongo, Jonathan Bell, Matthew Ellis, David Howell, Xiling Shen, Kyle Lafata, Laura Barisoni (2021) "Deep Learning Segmentation of Glomeruli on Kidney Donor Frozen Sections". medRxiv (2021): https://www.medrxiv.org/content/10.1101/2021.09.16.21263707v1

  • Naveen Natesh, Shengli Ding, Golshid Sanati, Shiaowen David Hsu, Scott Joseph Antonia, Xiling Shen (2021) "A micro-organosphere potency assay for adoptive T-cell therapy". Journal of Clinical Oncology (2021): https://ascopubs.org/doi/abs/10.1200/JCO.2021.39.15_suppl.e15027

  • Aliesha Garrett, Nikolai Rakhilin, Nian Wang, Jennifer McKey, Gary Cofer, Robert Bj Anderson, Blanche Capel, G Allan Johnson, Xiling Shen (2021) "Mapping the peripheral nervous system in the whole mouse via compressed sensing tractography". Journal of Neural Engineering (2021): https://www.ncbi.nlm.nih.gov/pubmed/33979784

  • Shengli Ding, Zhaohui Wang, Marcos Negrete Obando, Grecia rivera Palomino, Tomer Rotstein, Ian Williamson, Shiaowen David Hsu, Xiling Shen (2021) "Patient-derived micro-organospheres recapitulate tumor microenvironment and heterogeneity for precision oncology". Journal of Clinical Oncology (2021): https://ascopubs.org/doi/abs/10.1200/JCO.2021.39.15_suppl.3076

  • Z. Wang, E. Cortes-Sanchez, C-H. Yang, D. Nelson, C. Keating, A. Smith, D. Hsu, B. Welm, A. Welm, X. Shen (2021) "1149P An automated platform for rapid drug screening in patient-derived micro-organospheres". Annals of Oncology (2021): https://www.annalsofoncology.org/article/S0923-7534(21)03019-2/fulltext

  • C.H-T. Hsu, Z. Wang, S. Oh, G. Rupprecht, D. Delubac, X. Shen, D. Hsu (2021) "1782P Micro-organospheres as a novel precision oncology platform in colorectal cancer". Annals of Oncology (2021): https://www.annalsofoncology.org/article/S0923-7534(21)03954-5/fulltext

  • Aliesha Danielle O'Raw, Nikolai Rakhilin, Nian Wang, Jennifer McKey, Gary Cofer, Robert Bj Anderson, Blanche Capel, G Allan Johnson, Xiling Shen Author response for "Mapping the peripheral nervous system in the whole mouse via compressed sensing tractography" (2021)

  • Ian A. Williamson, Chi Wut Wong, Yanru Wu, Xiaoyang Su, John F. Rawls, Xiling Shen (2021) "713c Dietary Fat Increases Intestinal Fructose Conversion to Glycerate that Accumlates in Circulation, Driving Glucose Intolerance". Gastroenterology (2021): https://www.gastrojournal.org/article/S0016-5085(21)03147-4/fulltext

  • Qiang Huang, Qiang Huang, Malkiel A. Cohen, Fernando C. Alsina, Garth Devlin, Aliesha Garrett, Jennifer McKey, Patrick Havlik, Nikolai Rakhilin, Ergang Wang, Kun Xiang, Parker Mathews, Lihua Wang, Cheryl Bock, Victor Ruthig, Yi Wang, Marcos Negrete, Chi Wut Wong, Preetish K. L. Murthy, Shupei Zhang, Andrea R. Daniel, David G. Kirsch, Yubin Kang, Blanche Capel, Aravind Asokan, Debra L. Silver, Rudolf Jaenisch, Xiling Shen (2020) "Intravital imaging of mouse embryos". Science (2020): https://www.scilit.net/article/628f5a88bfbbd97e0030215617833abd

  • Tianyi Chen, Sehhoon Oh, Simon Gregory, Xiling Shen, Anna Mae Diehl (2020) "Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration". JCI insight (2020): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7710279

  • Anil Dangi, Naveen R. Natesh, Irma Husain, Zhicheng Ji, Laura Barisoni, Jean Kwun, Xiling Shen, Edward B. Thorp, Xunrong Luo (2020) "Single cell transcriptomics of mouse kidney transplants reveals a myeloid cell pathway for transplant rejection". JCI insight (2020): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7605544

  • Michael Bauer, Zuzana Nascakova, Zuzana Nascakova, Anca-Irina Mihai, Phil F. Cheng, Mitchell P. Levesque, Simon Lampart, Robert Hurwitz, Lennart Pfannkuch, Jana Dobrovolna, Melanie Jacobs, Sina Bartfeld, Anders Dohlman, Xiling Shen, Alevtina A. Gall, Nina R. Salama, Antonia Töpfer, Achim Weber, Thomas F. Meyer, Pavel Janscak, Pavel Janscak, Anne Müller (2020) "The ALPK1/TIFA/NF-κB axis links a bacterial carcinogen to R-loop-induced replication stress". Nature Communications (2020): https://www.zora.uzh.ch/id/eprint/190954/

  • Samaneh Kamali Sarvestani, Reece K. DeHaan, Paula G. Miller, Shree Bose, Xiling Shen, Michael L. Shuler, Emina H. Huang (2020) "A Tissue Engineering Approach to Metastatic Colon Cancer". iScience (2020): https://www.sciencedirect.com/science/article/pii/S2589004220309160

  • Erdem Altunel, Roham S. Roghani, Kai-Yuan Chen, So Young Kim, Shannon McCall, Kathryn E. Ware, Xiling Shen, Jason A. Somarelli, David S. Hsu (2020) "Development of a precision medicine pipeline to identify personalized treatments for colorectal cancer". BMC Cancer (2020): https://www.researchsquare.com/article/rs-18273/v1

  • Liuyang Wang, Thomas J Balmat, Alejandro L Antonia, Florica J Constantine, Ricardo Henao, Thomas W Burke, Andy Ingham, Micah T McClain, Micah T McClain, Micah T McClain, Ephraim L Tsalik, Emily R Ko, Emily R Ko, Geoffrey S Ginsburg, Mark R DeLong, Xiling Shen, Christopher W Woods, Christopher W Woods, Christopher W Woods, Elizabeth R Hauser, Elizabeth R Hauser, Dennis C Ko (2020) "An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility". medRxiv (2020): https://www.ncbi.nlm.nih.gov/pubmed/33398303

  • Nicholas S. Giroux, Shengli Ding, Micah T. McClain, Thomas W. Burke, Elizabeth W. Petzold, Hong A. Chung, Grecia R. Palomino, Ergang Wang, Rui Xi, Shree Bose, Tomer Rotstein, Bradly P. Nicholson, Tianyi Chen, Ricardo Henao, Gregory D. Sempowski, Thomas N. Denny, Emily R. Ko, Geoffrey S. Ginsburg, Bryan D. Kraft, Ephraim L. Tsalik, Christopher W. Woods, Christopher W. Woods, Christopher W. Woods, Xiling Shen (2020) "Chromatin remodeling in peripheral blood cells reflects COVID-19 symptom severity" bioRxiv (2020): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7724678

  • Jason A. Somarelli, Roham Salman Roghani, Ali Sanjari Moghaddam, Beatrice C. Thomas, Gabrielle Rupprecht, Kathryn E. Ware, Erdem Altunel, John B. Mantyh, So Young Kim, Shannon J. McCall, Xiling Shen, Christopher R. Mantyh, David S. Hsu (2020) "A Precision Medicine Drug Discovery Pipeline Identifies Combined CDK2 and 9 Inhibition as a Novel Therapeutic Strategy in Colorectal Cancer". Molecular Cancer Therapeutics (2020) https://www.scilit.net/article/4e580b576942f76f67fe5a8c697d9ef0

  • Chen Yu, Sejiro Littleton, Nicholas Giroux, Rose Mathew, Shengli Ding, Joan Kalnitsky, Elizabeth W. Petzold, Hong Chung, Grecia Rivera Palomino, Tomer Rotstein, Rui Xi, Emily R. Ko, Emily R. Ko, Ephraim L. Tsalik, Ephraim L. Tsalik, Ephraim L. Tsalik, Gregory D. Sempowski, Thomas N. Denny, Thomas W. Burke, Micah T. McClain, Micah T. McClain, Micah T. McClain, Christopher W. Woods, Xiling Shen, Daniel R. Saban (2020) "Mucosal Associated Invariant T (MAIT) Cell Responses Differ by Sex in COVID-19". bioRxiv (2020) https://www.biorxiv.org/content/10.1101/2020.12.01.407148v1

  • Grill Warren M, Barth Bradley, Henriquez Craig, Shen Xiling (2020) "SYSTEMS AND METHODS FOR THE MODULATION OF GUT MOTILITY". https://www.freepatentsonline.com/y2020/0306532.html

  • Xiling Shen (2020) "An imprecise path to precision medicine". Nature Medicine (2020): https://www.ncbi.nlm.nih.gov/pubmed/31932784

  • J. Yang, H. Zhang, D. Huang, X. Shen, X. She (2020) "115P PD-L1 expression landscape and microsatellite instability status in Chinese endometrial and cervical cancer patients". Annals of Oncology (2020): https://www.annalsofoncology.org/article/S0923-7534(20)40232-7/fulltext

  • Xiling Shen, Shengli Ding, Holly Dressman, Anders B. Dohlman, Michael Gao, Diana Arguijo-Mendoza, Steven M. Lipkin, Iliyan D. Iliev (2020) "Data from: The Cancer Microbiome Atlas (TCMA): A Pan-Cancer Comparative Analysis to Distinguish Organ-Associated Microbiota from Equiprevalent Contaminants". Research Data Repository, Duke University (2020): https://dx.doi.org/10.7924/r4rn36833

  • M. Chen, D. Huang, X. She, X. Shen, H. Zhang, Z. Luo (2020) "1408P The landscape of ROS1 fusion in patients with non-small cell lung cancer in China". Annals of Oncology (2020): https://www.annalsofoncology.org/article/S0923-7534(20)41718-1/fulltext

  • Shen Xiling, Hsu David, Motschman Jeffrey, Delubac Daniel, Wang Zhaouhui (2020) "METHODS AND APPARATUSES FOR PATIENT-DERIVED MICRO-ORGANOSPHERES".

  • Xiling Shen (2020) "Duke - Isolation, Culture, and Maintenance of Patient-Derived Tumor Biopsy": https://www.protocols.io/view/isolation-culture-and-maintenance-of-patient-deriv-bh2pj8dn

  • Nikolai Rakhilin, Aliesha Garrett, Chi-Yong Eom, Katherine Ramos Chavez, David M. Small, Andrea R. Daniel, Melanie M. Kaelberer, Menansili A. Mejooli, Qiang Huang, Shengli Ding, David G. Kirsch, Diego V. Bohórquez, Nozomi Nishimura, Bradley B. Barth, Xiling Shen (2019) "An intravital window to image the colon in real time". Nature Communications (2019): https://www.ncbi.nlm.nih.gov/pubmed/31827103

  • Anders B Dohlman, Xiling Shen (2019) "Mapping the microbial interactome: Statistical and experimental approaches for microbiome network inference". Experimental Biology and Medicine (2019): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547001

  • Yitian Xu, Lu Huang, Jonathan L. Kirschman, Daryll A. Vanover, Pooja M. Tiwari, Philip J. Santangelo, Xiling Shen, Xiling Shen, David G. Russell (2019) "Exploitation of Synthetic mRNA To Drive Immune Effector Cell Recruitment and Functional Reprogramming In Vivo". Journal of Immunology (2019): https://www.ncbi.nlm.nih.gov/pubmed/30541883

  • Rui Xi, Preetish Kadur Lakshminarasimha Murthy, Preetish Kadur Lakshminarasimha Murthy, Kuei Ling Tung, Kuei Ling Tung, Cynthia D. Guy, Ji Wan, Feng Li, Zhuo Wang, Xiaodong Li, Anastasia Varanko, Nikolai Rakhilin, Nikolai Rakhilin, Yongning Xin, Botao Liu, Shu Bing Qian, Lishan Su, Yan Han, Xiling Shen (2019) "SENP3-mediated host defense response contains HBV replication and restores protein synthesis". PLOS ONE (2019): https://www.ncbi.nlm.nih.gov/pubmed/30640896

  • Huanhuan Joyce Chen, Zhubo Wei, Jian Sun, Asmita Bhattacharya, David J. Savage, Rita Serda, Yuri Mackeyev, Steven A. Curley, Pengcheng Bu, Lihua Wang, Shuibing Chen, Leona Cohen-Gould, Emina Huang, Xiling Shen, Steven M. Lipkin, Neal G. Copeland, Nancy A. Jenkins, Michael L. Shuler (2019) "Author Correction: A recellularized human colon model identifies cancer driver genes". Nature Biotechnology (2019): https://www.ncbi.nlm.nih.gov/pubmed/31160724

  • Kuei-Ling Tung, Kuei-Ling Tung, Kai-Yuan Chen, Marcos Negrete, Tianyi Chen, Alexias Safi, Abed Alhalim Aljamal, Lingyun Song, Gregory E. Crawford, Shengli Ding, David S. Hsu, Xiling Shen (2019) "Integrated chromatin and transcriptomic profiling of patient-derived colon cancer organoids identifies personalized drug targets to overcome oxaliplatin resistance". Genes and Diseases (2019): https://www.scienceopen.com/document?vid=899acac1-d18e-4eb1-91de-2922b25cee3e

  • Xiling Shen (2019) "COMPOSITIONS AND METHODS FOR TARGETING FRUCTOSE ENZYMES AND TRANSPORTERS FOR THE TREATMENT OF CANCER". https://www.freepatentsonline.com/y2019/0231761.html

  • Jatin Roper, Xiling Shen (2019) "Novel Three-Dimensional Cultures of Patient-Derived Cancer and Tumor Immune Cells". Gastroenterology (2019): https://www.sciencedirect.com/science/article/pii/S0016508519409177

  • Jiahn Choi, Nikolai Rakhilin, Poornima Gadamsetty, Daniel J. Joe, Tahmineh Tabrizian, Steven M. Lipkin, Derek M. Huffman, Xiling Shen, Nozomi Nishimura (2019) "Author Correction: Intestinal crypts recover rapidly from focal damage with coordinated motion of stem cells that is impaired by aging". Scientific Reports (2019): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6768855

  • Robert Mines, Kai-Yuan Chen, Xiling Shen (2019) "Agent-Based Modelling to Delineate Spatiotemporal Control Mechanisms of the Stem Cell Niche". Methods of Molecular Biology (2019): https://www.ncbi.nlm.nih.gov/pubmed/31062303

  • Shen Xiling, Hsu Shiaowen David (2019) "PATIENT SPECIFIC CLINICAL TRIALS AND ASSOCIATED METHODS OF TREATMENT"

  • Melanie Maya Kaelberer, Kelly L. Buchanan, Marguerita E. Klein, Bradley B. Barth, Marcia M. Montoya, Xiling Shen, Diego V. Bohórquez (2018) "A gut-brain neural circuit for nutrient sensory transduction". Science (2018): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417812/

  • Pengcheng Bu, Pengcheng Bu, Kai Yuan Chen, Kun Xiang, Christelle Johnson, Scott B. Crown, Nikolai Rakhilin, Nikolai Rakhilin, Yiwei Ai, Lihua Wang, Rui Xi, Inna Astapova, Yan Han, Jiahe Li, Bradley B. Barth, Min Lu, Ziyang Gao, Robert Mines, Liwen Zhang, Mark Herman, David Hsu, Guofang Zhang, Xiling Shen (2018) "Aldolase B-Mediated Fructose Metabolism Drives Metabolic Reprogramming of Colon Cancer Liver Metastasis". Cell Metabolism (2018): https://www.sciencedirect.com/science/article/pii/S1550413118302444

  • Yitian Xu, Lihua Wang, Matthew D. Zimmerman, Kai-Yuan Chen, Kai-Yuan Chen, Lu Huang, Dah-Jiun Fu, Firat Kaya, Nikolai Rakhilin, Nikolai Rakhilin, Evgeniya V. Nazarova, Pengcheng Bu, Veronique Dartois, David G. Russell, Xiling Shen, Xiling Shen (2018) "Matrix metalloproteinase inhibitors enhance the efficacy of frontline drugs against Mycobacterium tuberculosis". PLOS Pathogens (2018): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5919409

  • Kai-Yuan Chen, Tara Srinivasan, Christopher Lin, Kuei-Ling Tung, Ziyang Gao, David S. Hsu, Steven M. Lipkin, Xiling Shen (2018) "Single-Cell Transcriptomics Reveals Heterogeneity and Drug Response of Human Colorectal Cancer Organoids". International Conference of the IEEE Engineering in Medicine and Biology Society (2018): https://www.ncbi.nlm.nih.gov/pubmed/30440885

  • Lihua Wang, Ergang Wang, Yi Wang, Yi Wang, Robert Mines, Kun Xiang, Zhiguo Sun, Gaiting Zhou, Kai-Yuan Chen, Nikolai Rakhilin, Nikolai Rakhilin, Shanshan Chao, Gaoqi Ye, Zhenzhen Wu, Huiwen Yan, Hong Shen, Jeffrey Everitt, Pengcheng Bu, Xiling Shen, Xiling Shen (2018) "miR-34a is a microRNA safeguard for Citrobacter-induced inflammatory colon oncogenesis". eLife (2018): https://www.ncbi.nlm.nih.gov/pubmed/30543324

  • Jiahn Choi, Nikolai Rakhilin, Poornima Gadamsetty, Daniel J. Joe, Tahmineh Tabrizian, Steven M. Lipkin, Derek M. Huffman, Xiling Shen, Nozomi Nishimura (2018) "Intestinal crypts recover rapidly from focal damage with coordinated motion of stem cells that is impaired by aging". Scientific Reports (2018): https://www.ncbi.nlm.nih.gov/pubmed/30030455

  • Preetish Kadur Lakshminarasimha Murthy, Preetish Kadur Lakshminarasimha Murthy, Tara Srinivasan, Matthew S Bochter, Rui Xi, Anastasia Kristine Varanko, Kuei-Ling Tung, Kuei-Ling Tung, Fatih Semerci, Keli Xu, Mirjana Maletic-Savatic, Susan E Cole, Xiling Shen, Xiling Shen (2018) "Radical and lunatic fringes modulate notch ligands to support mammalian intestinal homeostasis". eLife (2018): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5896954
  • Bradley B Barth, Hsin-I Huang, Gianna E Hammer, Xiling Shen (2018) "Opportunities and Challenges for Single-Unit Recordings from Enteric Neurons in Awake Animals". Micromachines (2018): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6187697/

  • Bradley B. Barth, Xiling Shen (2018) "Computational motility models of neurogastroenterology and neuromodulation". Brain Research (2018): https://www.sciencedirect.com/science/article/pii/S0006899318301082

  • Ziyang Gao, Kai-Yuan Chen, Olaf Mueller, Han Zhang, Nikolai Rakhilin, Jiande Chen, Xiling Shen (2018) "Microbiota of Inflammatory Bowel Disease Models". International Conference of the IEEE Engineering in Medicine and Biology Society (2018): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6709594/

  • Lihua Wang, Ergang Wang, Yi Wang, Yi Wang, Robert Mines, Kun Xiang, Zhiguo Sun, Gaiting Zhou, Kai-Yuan Chen, Nikolai Rakhilin, Nikolai Rakhilin, Shanshan Chao, Gaoqi Ye, Zhenzhen Wu, Huiwen Yan, Hong Shen, Jeffrey Everitt, Pengcheng Bu, Xiling Shen, Xiling Shen (2018) "Author response: miR-34a is a microRNA safeguard for Citrobacter-induced inflammatory colon oncogenesis". eLife (2018)

  • Robert C. Mines, Anders Dohlman, Sze-Xian Lim, Kuei-Ling Tung, Ergang Wang, Xiling Shen (2018) "Spatial Patterning from an Integrated Wnt/β-catenin and Notch/Delta Gene Circuit". International Conference of the IEEE Engineering in Medicine and Biology Society (2018): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7081632

  • Bradley Barth, Hsin-I Huang, Gianna Hammer, Xiling Shen (2018) "Opportunities and Challenges for Single-Unit Recordings from Enteric Neurons in Awake Animals". (2018) https://www.preprints.org/manuscript/201807.0631/v1

  • Erik A. Zavrel, Michael L. Shuler, Xiling Shen (2018) "A Simple Aspect Ratio Dependent Method of Patterning Microwells for Selective Cell Attachment". 2018 Design of Medical Devices Conference : April 9-12, 2018, Minneapolis, Minnesota, USA. Design of Medical Devices Conference (2018 : Minneapolis, Minn.) (2018): https://www.ncbi.nlm.nih.gov/pubmed/30854173

  • Preetish Kadur Lakshminarasimha Murthy, Preetish Kadur Lakshminarasimha Murthy, Tara Srinivasan, Matthew S Bochter, Rui Xi, Anastasia Kristine Varanko, Kuei-Ling Tung, Kuei-Ling Tung, Fatih Semerci, Keli Xu, Mirjana Maletic-Savatic, Susan E Cole, Xiling Shen, Xiling Shen (2018) "Author response: Radical and lunatic fringes modulate notch ligands to support mammalian intestinal homeostasis". eLife (2018)

  • Erik A. Zavrel, Xiling Shen (2018) "TOWARD A MICROFLUIDIC IMPLEMENTATION OF A DIGITAL POTENTIOMETER". 2018 Design of Medical Devices Conference : April 9-12, 2018, Minneapolis, Minnesota, USA. Design of Medical Devices Conference (2018 : Minneapolis, Minn.) (2018): https://www.ncbi.nlm.nih.gov/pubmed/30854172

  • Xiling Shen (2018) "Abstract 5479: Targeting fructose-induced metabolic reprogramming in liver metastasis". Cancer Research (2018): https://cancerres.aacrjournals.org/content/78/13_Supplement/5479

  • Melanie M. Kaelberer, Kelly Buchanan, Marguerita Klein, Marcia Montoya, Bradley Barth, Xiling Shen, Diego V. Bohórquez (2018) "725 - Sensory Synaptic Transduction from Gut to Brain". Gastroenterology (2018): https://www.gastrojournal.org/article/S0016-5085(18)30915-6/abstract

  • Xiling Shen (2018) "P076 MICRORNA SAFEGUARDING THE INFLAMMATORY COLON STEM CELL NICHE". Gastroenterology (2018): https://www.gastrojournal.org/article/S0016-5085(17)36474-0/fulltext

  • Christoph S.N. Klose, Tanel Mahlakõiv, Jesper B. Moeller, Jesper B. Moeller, Lucille C. Rankin, Anne Laure Flamar, Hiroki Kabata, Laurel A. Monticelli, Saya Moriyama, Gregory Garbès Putzel, Nikolai Rakhilin, Nikolai Rakhilin, Xiling Shen, Xiling Shen, Evi Kostenis, Gabriele M. König, Takashi Senda, Dustin Carpenter, Donna L. Farber, David Artis (2017) "The neuropeptide neuromedin U stimulates innate lymphoid cells and type 2 inflammation". Nature (2017): https://www.ncbi.nlm.nih.gov/pubmed/28869965

  • Subhash Kulkarni, Maria Adelaide Micci, Jenna Leser, Changsik Shin, Shiue Cheng Tang, Ya Yuan Fu, Liansheng Liu, Qian Li, Monalee Saha, Cuiping Li, Grigori Enikolopov, Grigori Enikolopov, Laren Becker, Nikolai Rakhilin, Nikolai Rakhilin, Michael Anderson, Xiling Shen, Xiling Shen, Xinzhong Dong, Manish J. Butte, Hongjun Song, E. Michelle Southard-Smith, Raj P. Kapur, Milena Bogunovic, Pankaj J. Pasricha (2017) "Adult enteric nervous system in health is maintained by a dynamic balance between neuronal apoptosis and neurogenesis". Proceedings of the National Academy of Sciences of the United States of America (2017): https://www.pnas.org/content/114/18/E3709

  • Kai-Yuan Chen, Kai-Yuan Chen, Tara Srinivasan, Kuei-Ling Tung, Julio M Belmonte, Lihua Wang, Lihua Wang, Preetish Kadur Lakshminarasimha Murthy, Jiahn Choi, Nikolai Rakhilin, Nikolai Rakhilin, Sarah King, Anastasia Kristine Varanko, Mavee Witherspoon, Nozomi Nishimura, James A Glazier, Steven M Lipkin, Pengcheng Bu, Pengcheng Bu, Xiling Shen, Xiling Shen (2017) "A Notch positive feedback in the intestinal stem cell niche is essential for stem cell self-renewal". Molecular Systems Biology (2017): https://www.ncbi.nlm.nih.gov/pubmed/28455349

  • Yiwei Wang, Dan Huang, Kai Yuan Chen, Min Cui, Weihuan Wang, Xiaoran Huang, Amad Awadellah, Qing Li, Ann Friedman, William W. Xin, Luca Di Martino, Fabio Cominelli, Alexander Miron, Ricky Chan, James G. Fox, Yan Xu, Xiling Shen, Matthew F Kalady, Sanford D Markowitz, Ivan Maillard, John B. Lowe, Wei Xin, Lan Zhou (2017) "Fucosylation Deficiency in Mice Leads to Colitis and Adenocarcinoma". Gastroenterology (2017): https://www.sciencedirect.com/science/article/pii/S0016508516350296

  • Bradley B Barth, Craig S Henriquez, Warren M Grill, Xiling Shen (2017) "Electrical stimulation of gut motility guided by an in silico model". Journal of Neural Engineering (2017): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5724779

  • Jianjun Yu, Xiaosheng Qin, Yee Meng Chiew, Rui Min, Xiling Shen (2017) "Stochastic Optimization Model for Supporting Urban Drainage Design under Complexity". Journal of Water Resources Planning and Management (2017): https://ascelibrary.org/doi/pdf/10.1061/%28ASCE%29WR.1943-5452.0000806

  • C. Petritsch, X. Shen (2017) "Asymmetric Division of Cancer Stem Cells". Cancer Stem Cells#R##N#Targeting the Roots of Cancer, Seeds of Metastasis, and Sources of Therapy Resistance (2017): https://www.sciencedirect.com/science/article/pii/B9780128038925000115

  • Jiahn Choi, Nikolai Rakhilin, Poornima Gadamsetty, Daniel J. Joe, Tahmineh Tabrizian, Steven M. Lipkin, Derek M. Huffman, Xiling Shen, Nozomi Nishimura (2017) "Intestinal crypts recover rapidly from focal damage with coordinated motion of stem cells that is impaired by aging". bioRxiv (2017): https://www.biorxiv.org/content/10.1101/218685v1

  • Jiahe Li, Yiwei Ai, Lihua Wang, Pengcheng Bu, Charles C. Sharkey, Qianhui Wu, Brittany Wun, Sweta Roy, Xiling Shen, Michael R. King (2016) "Targeted drug delivery to circulating tumor cells via platelet membrane-functionalized particles". Biomaterials (2016): https://www.sciencedirect.com/science/article/pii/S014296121500856X

  • Pengcheng Bu, Lihua Wang, Kai-Yuan Chen, Tara Srinivasan, Preetish Kadur Lakshminarasimha Murthy, Kuei-Ling Tung, Anastasia Kristine Varanko, Huanhuan Joyce Chen, Yiwei Ai, Sarah King, Steven M. Lipkin, Xiling Shen (2016) "A miR-34a-Numb Feedforward Loop Triggered by Inflammation Regulates Asymmetric Stem Cell Division in Intestine and Colon Cancer". Cell Stem Cell (2016): https://www.sciencedirect.com/science/article/pii/S1934590916000072

  • Lihua Wang, Pengcheng Bu, Pengcheng Bu, Yiwei Ai, Tara Srinivasan, Huanhuan Joyce Chen, Kun Xiang, Steven M Lipkin, Xiling Shen (2016) "A long non-coding RNA targets microRNA miR-34a to regulate colon cancer stem cell asymmetric division". eLife (2016): https://www.ncbi.nlm.nih.gov/pubmed/27077950

  • Huanhuan Joyce Chen, Zhubo Wei, Jian Sun, Asmita Bhattacharya, David J Savage, Rita Serda, Yuri Mackeyev, Steven A Curley, Pengcheng Bu, Lihua Wang, Shuibing Chen, Leona Cohen-Gould, Emina Huang, Xiling Shen, Steven M Lipkin, Neal G Copeland, Nancy A Jenkins, Michael L Shuler (2016) "A recellularized human colon model identifies cancer driver genes". Nature Biotechnology (2016): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4980997

  • Nikolai Rakhilin, Bradley Barth, Jiahn Choi, Nini L. Muñoz, Subhash Kulkarni, Jason S. Jones, David M. Small, Yu Ting Cheng, Yingqiu Cao, Colleen Lavinka, Edwin Kan, Xinzhong Dong, Xinzhong Dong, Michael Spencer, Pankaj Pasricha, Nozomi Nishimura, Xiling Shen, Xiling Shen (2016) "Simultaneous optical and electrical in vivo analysis of the enteric nervous system". Nature Communications (2016): https://www.ncbi.nlm.nih.gov/pubmed/27270085

  • Tara Srinivasan, Jewell Walters, Pengcheng Bu, Elaine Bich Than, Kuei Ling Tung, Kai Yuan Chen, Nicole Panarelli, Jeff Milsom, Leonard Augenlicht, Steven M. Lipkin, Xiling Shen, Xiling Shen (2016) "NOTCH Signaling Regulates Asymmetric Cell Fate of Fast- and Slow-Cycling Colon Cancer-Initiating Cells". Cancer Research (2016): https://www.ncbi.nlm.nih.gov/pubmed/27197180

  • Tara Srinivasan, Elaine Bich Than, Pengcheng Bu, Kuei Ling Tung, Kai Yuan Chen, Leonard Augenlicht, Steven M. Lipkin, Xiling Shen, Xiling Shen (2016) "Notch signalling regulates asymmetric division and inter-conversion between lgr5 and bmi1 expressing intestinal stem cells". Scientific Reports (2016): https://www.ncbi.nlm.nih.gov/pubmed/27181744

  • Daniel J. Joe, Jeonghyun Hwang, Christelle Johnson, Ho-Young Cha, Jo-Won Lee, Xiling Shen, Michael G. Spencer, Sandip Tiwari, Moonkyung Kim (2016) "Surface Functionalized Graphene Biosensor on Sapphire for Cancer Cell Detection". Journal of Nanoscience and Nanotechnology (2016): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5724034

  • Yingqiu Cao, Nikolai Rakhilin, Philip H. Gordon, Xiling Shen, Edwin C. Kan (2016) "A real-time spike classification method based on dynamic time warping for extracellular enteric neural recording with large waveform variability". Journal of Neuroscience Methods (2016): https://www.sciencedirect.com/science/article/pii/S016502701500446X

  • Lihua Wang, Pengcheng Bu, Xiling Shen (2016) "Asymmetric division: An antitumor player?". Molecular and Cellular Oncology (2016): https://www.tandfonline.com/doi/full/10.1080/23723556.2016.1164279

  • Daniel E Rothschild, Tara Srinivasan, Linette A Aponte-Santiago, Xiling Shen, Irving C Allen (2016) "The Ex Vivo Culture and Pattern Recognition Receptor Stimulation of Mouse Intestinal Organoids". Journal of Visualized Experiments (2016): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4927701

  • Yiwei Wang, Dan Huang, Kai-Yuan Chen, Min Cui, Weihuan Wang, Xiaoran Huang, Amad Awadellah, Qing Li, Ann Friedman, William W. Xin, Luca Di Martino, Fabio Cominelli, Alex Miron, Ricky Chan, James G. Fox, Yan Xu, Xiling Shen, Mathew F. Kalady, Sanford Markowitz, Ivan Maillard, John B. Lowe, Wei Xin, Lan Zhou (2016) "Fucosylation Deficiency in Mice Leads to Colitis and Adenocarcinoma". PMC (2016): https://dspace.mit.edu/openaccess-disseminate/1721.1/117652

  • Lihua Wang, Pengcheng Bu, Pengcheng Bu, Yiwei Ai, Tara Srinivasan, Huanhuan Joyce Chen, Kun Xiang, Steven M Lipkin, Xiling Shen (2016) "Author response: A long non-coding RNA targets microRNA miR-34a to regulate colon cancer stem cell asymmetric division". eLife (2016)

  • Kai Wang, Youjin Zhao, Qingyu Xiong, Xiling Shen, Min Fan, Min Gao (2016) "Video Recognition of Human Fall Based on Spatiotemporal Features". Intelligent Automation and Soft Computing (2016): https://www.tandfonline.com/doi/full/10.1080/10798587.2015.1095487

  • Shengyi Sun, Guojun Shi, Haibo Sha, Yewei Ji, Xuemei Han, Xin Shu, Hongming Ma, Takamasa Inoue, Beixue Gao, Hana Kim, Pengcheng Bu, Robert D. Guber, Xiling Shen, Xiling Shen, Ann Hwee Lee, Takao Iwawaki, Adrienne W. Paton, James C. Paton, Deyu Fang, Billy Tsai, John R. Yates, Haoquan Wu, Sander Kersten, Qiaoming Long, Gerald E. Duhamel, Kenneth W. Simpson, Ling Qi (2015) "IRE1α is an endogenous substrate of endoplasmic-reticulum-associated degradation". Nature Cell Biology (2015): https://www.scholars.northwestern.edu/en/publications/ire1%CE%B1-is-an-endogenous-substrate-of-endoplasmic-reticulum-associa

  • Pengcheng Bu, Lihua Wang, Kai-Yuan Chen, Nikolai Rakhilin, Jian Sun, Adria Closa, Kuei-Ling Tung, Sarah King, Anastasia Kristine Varanko, Yitian Xu, Joyce Huan Chen, Amelia S Zessin, James Shealy, Bethany Cummings, David Hsu, Steven M Lipkin, Victor Moreno, Zeynep H Gümüş, Xiling Shen (2015) "miR-1269 promotes metastasis and forms a positive feedback loop with TGF-β". Nature Communications (2015): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4399006/

  • Christelle Johnson, Marc O. Warmoes, Xiling Shen, Jason W. Locasale (2015) "Epigenetics and Cancer Metabolism". Cancer Letters (2015): https://www.sciencedirect.com/science/article/abs/pii/S0304383513007155

  • Huanhuan Joyce Chen, Jian Sun, Zhiliang Huang, Harry Hou, Myra Arcilla, Nikolai Rakhilin, Daniel J Joe, Jiahn Choi, Poornima Gadamsetty, Jeff Milsom, Govind Nandakumar, Randy Longman, Xi Kathy Zhou, Robert Edwards, Jonlin Chen, Kai Yuan Chen, Pengcheng Bu, Lihua Wang, Yitian Xu, Robert Munroe, Christian Abratte, Andrew D Miller, Zeynep H Gümüş, Michael Shuler, Nozomi Nishimura, Winfried Edelmann, Xiling Shen, Steven M Lipkin (2015) "Comprehensive models of human primary and metastatic colorectal tumors in immunodeficient and immunocompetent mice by chemokine targeting". Nature Biotechnology (2015): https://www.ncbi.nlm.nih.gov/pubmed/26006007

  • Feng Yating, Si Gaofeng, Shen Xiling, Wen Rujun (2015) "Power transmission line tower detects with dismantling ladder". (2015)
  • Feng Yating, Si Gaofeng, Shen Xiling, Wen Rujun (2015) "Detachable ladder for electric power pylon detection". (2015)

  • Steven M. Lipkin, Huanhuan Joyce Chen, Jian Sun, Zhiliang Huang, Harry Hou, Myra Arcilla, Nikolai Rakhilin, Daniel Joe, Jiahn Choi, Poornima Gadamsetty, Jeff Milsom, Govind Nandakumar, Randy Longman, Kathy Zhou, Robert Edwards, Kai Yuan Chen, Pengcheng Bu, Lihua Wang, Yitian Xu, Robert Munroe, Christian Abratte, Andrew Miller, Zeynep Gümüş, Michael Shuler, Nozomi Nishimura, Winfried Edelmann, Xiling Shen (2015) "Abstract 2891: Chemokine-targeted models of human orthotopic colorectal cancer in immunocompetant mice". Cancer Research (2015): https://cancerres.aacrjournals.org/content/75/15_Supplement/2891
  • Jiahn Choi, Daniel J. Joe, Poornima Gadamsetty, Nikolai Rakhilin, Pengcheng Bu, Steven Lipkin, Xiling Shen, Nozomi Nishimura (2015) "Understanding the Dynamics of the Stem Cell Niche in the Small Intestine with Femtosecond Laser Photodisruption". Frontiers in Optics (2015): https://www.osapublishing.org/abstract.cfm?uri=FiO-2015-FTu2D.2

  • Xiling Shen (2015) "Hybrid Microrna Control of Colon Cancer Stem Cell Asymmetric Division". Biophysical Journal (2015): https://www.cell.com/biophysj/fulltext/S0006-3495(14)03740-0

  • Kai-Yuan Chen, Xiaojing Liu, Pengcheng Bu, Chieh-Sheng Lin, Nikolai Rakhilin, Jason W. Locasale, Xiling Shen (2014) "A metabolic signature of colon cancer initiating cells". International Conference of the IEEE Engineering in Medicine and Biology Society (2014): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302416/
  • Zhao Qu, Xiling Shen, Kun Ding (2014) "Comparative analysis on technologies between Chinese and American large-sized oil companies based on patentometrics". Journal of Scientific Research (2014): https://www.jscires.org/article/75

  • Huanhuan Joyce Chen, Jian Sun, Harry Hou, Winfried Edelmann, Xiling Shen, Steven M. Lipkin (2014) "Abstract 3118: Chemokine-targeted colorectal cancer: improved models of human primary tumor formation, liver metastasis and chemoresistance". Cancer Research (2014): https://cancerres.aacrjournals.org/content/74/19_Supplement/3118

  • Christelle Johnson, Kai-Yuan Chen, Xiaojing Liu, Pengcheng Bu, Jason Locasale, Xiling Shen (2014) "A metabolic signature of colon cancer initiating cells". Cancer and Metabolism (2014): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4072946/

  • Kai-Yuan Chen, Danial J. Joe, James B. Shealy, Bruce R. Land, Xiling Shen (2014) "A bio-inspired spatial patterning circuit". International Conference of the IEEE Engineering in Medicine and Biology Society (2014): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4304701

  • Pengcheng Bu, Kai-Yuan Chen, Joyce Huan Chen, Lihua Wang, Jewell Walters, Yong Jun Shin, Julian P. Goerger, Jian Sun, Mavee Witherspoon, Nikolai Rakhilin, Jiahe Li, Herman Yang, Jeff Milsom, Sang Lee, Warren Zipfel, Moonsoo M. Jin, Zeynep H. Gümüş, Steven M. Lipkin, Xiling Shen (2013) "A microRNA miR-34a-Regulated Bimodal Switch Targets Notch in Colon Cancer Stem Cells". Cell Stem Cell (2013): https://www.sciencedirect.com/science/article/pii/S1934590913000970

  • Pengcheng Bu, Kai-Yuan Chen, Steven M Lipkin, Xiling Shen (2013) "Asymmetric division: a marker for cancer stem cells?". Oncotarget (2013): https://www.oncotarget.com/index.php?journal=oncotarget&page=article&op=view&path%5B%5D=1029&path%5B%5D=1317

  • Yong-Jun Shin, Kai-Yuan Chen, Ali H Sayed, Brandon Hencey, Xiling Shen (2013) "Post-translational regulation enables robust p53 regulation". BMC Systems Biology (2013): https://www.ncbi.nlm.nih.gov/pubmed/23992617

  • Jiahe Li, Pengcheng Bu, Kai-Yuan Chen, Xiling Shen (2013) "Spatial perturbation with synthetic protein scaffold reveals robustness of asymmetric cell division". Journal of Biomedical Science and Engineering (2013): https://www.scirp.org/journal/PaperInformation.aspx?PaperID=28256

  • Huanhuan Chen, Steven M. Lipkin, Xiling Shen (2013) "Mammal with an orthotopic tumor capable of metastasis, a method of making and a method of using".(2013): https://www.freepatentsonline.com/9681647.html

  • Huanhuan Chen, Steven M. Lipkin, Xiling Shen (2013). "Compositions and methods useful for making orthotopic tumors with controllable metastasis". (2013): https://www.freepatentsonline.com/y2015/0164053.html

  • Xi-ling Shen, Jia Zhao, Xiao-li Zhang, Kun Tian (2013) "Ultrasonographic features of aortic dissection". Central Plains Medical Journal (2013)

  • Huanhuan Joyce Chen, Robert Edwards, Serena Tucci, Pengcheng Bu, Jeff Milsom, Sang Lee, Winfried Edelmann, Zeynep H. Gümüs, Xiling Shen, Steven Lipkin (2012) "Chemokine 25-induced signaling suppresses colon cancer invasion and metastasis". Journal of Clinical Investigation (2012): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3428084

  • Yong-Jun Shin, Ali H. Sayed, Xiling Shen (2012) "Adaptive models for gene networks". PLOS ONE (2012): https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031657

  • Yong-Jun Shin, Ali H. Sayed, Xiling Shen (2012) "Using an adaptive gene network model for self-organizing multicellular behavior". International Conference of the IEEE Engineering in Medicine and Biology Society (2012): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4310473/

  • Huanhuan Chen, Serena Tucci, Zeynep Gümüs, Xiling Shen, Steven M. Lipkin (2012) "Abstract 5207: The chemokine 25 and chemokine receptor 9 axis suppresses colon cancer invasion and metastasis". Cancer Research (2012): https://cancerres.aacrjournals.org/content/72/8_Supplement/5207

  • Yong-Jun Shin, Ali H. Sayed, Brandon Hencey, Xiling Shen (2012) "Feedback Control Theory Reveals Tradeoff between Robustness and Stability in the p53-MDM2 Network". 2012 q-bio Conference, Santa Fe, NM (2012): https://infoscience.epfl.ch/record/233402/files/Shin_YongJun_Talk.pdf

  • Xi-ling Shen, Jia Zhao, Xiao-li Zhang, Pu-nan Li, Kun Tian (2012) "Application of three-dimensional SRI to study myocardial PSS on the significance of ischemic cardiomyopathy". Central Plains Medical Journal (2012)

  • Yong-Jun Shin, Brandon Hencey, Steven M. Lipkin, Xiling Shen (2011) 'Frequency domain analysis reveals external periodic fluctuations can generate sustained p53 oscillation". PLOS ONE (2011): https://www.ncbi.nlm.nih.gov/pubmed/21829536

  • Yong-Jun Shin, Steven M. Lipkin, Brandon Hencey, Xiling Shen (2011) "Disturbance Rejection Helps Modulate the p53 Oscillation". ASME 2011 Dynamic Systems and Control Conference and Bath/ASME Symposium on Fluid Power and Motion Control, Volume 2 (2011): https://proceedings.asmedigitalcollection.asme.org/proceeding.aspx?articleid=1638828

  • Xiling Shen (2011) "Silencing trumpet capable of being used for abreacting".

  • Douglas Densmore, Mark Horowitz, Smita Krishnaswamy, Xiling Shen, Adam Arkin, Erik Winfree, Chris Voigt (2011) "Joint DAC/IWBDA special session design and synthesis of biological circuits". Design Automation Conference (2011): https://ieeexplore.ieee.org/document/5981926/

  • Xiling Shen (2011) "Test paper sorting box".

  • Meng How Tan, Jennifer B. Kozdon, Xiling Shen, Lucy Shapiro, Harley H. McAdams (2010) "An essential transcription factor, SciP, enhances robustness of Caulobacter cell cycle regulation". Proceedings of the National Academy of Sciences of the United States of America (2010): https://www.pnas.org/content/107/44/18985

  • Shaheen Sikandar, Diana Dizon, Xiling Shen, Zuomei Li, Jeffery Besterman, Steven M. Lipkin (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 (2010): https://www.oncotarget.com/index.php?journal=oncotarget&page=article&op=view&path%5B%5D=194&path%5B%5D=273

  • Shen X, Collier J, Dill D, Shapiro L, Horowitz M, McAdams H. (2008) "Architecture and inherent robustness of a bacterial cell-cycle control system". Proceedings of the National Academy of Sciences (2005): https://www.pnas.org/doi/abs/10.1073/pnas.0805258105

  • Shen X, Kahn J, and Horowitz M. (2005) "Compensation for multimode fiber dispersion by adaptive optics". COpt. Lett. 30, 2985-2987. (2005): https://opg.optica.org/ol/abstract.cfm?uri=ol-30-22-2985

ALUMNI

Shengli Ding (Senior scientist, Xilis Inc)
Kendall Lough (postdoc, UNC)
Ian Williamson (postdoc, Duke)
Yanru Wu (postdoc, Duke)
LIhua Wang (staff scientist, Xilis Inc)
Zhiguo Sun
Robert Mines
Rui Xi (scientist, Xilis Inc)
Kuei-Ling Tung (postdoc, University of California San Francisco)
Preetish K. L. Murthy (postdoc, Duke University)
Nikolai Rakhilin (Post-doc, Pfizer)
Yong-Jun Shin (Assistant Professor, BME, UConn)
Christelle Haibi-Johnson (Field Application Scientist, Personalis Inc)
Huanhuan Joyce Chen (Assistant Professor, Pritzker School of Molecular Engineering and Comprehensive Cancer Center, University of Chicago)
Kim Heiman Chow (Assistant Professor, School of Life Science, The Chinese University of Hong Kong (CUHK))
Daniel Jo (R&D engineer, Samsung)
Tara Srinivasan (R&D scientist, Sangamo Biosciences)
Yan Han (Principle Scientist, Curacloud Inc)
Pengcheng Bu (Assistant Professor, Institute of Biophysics of Chinese Academy of Sciences)
Kai-Yuan Chen (Research scientist, Intellia Therapeutics)
Yitian Xu (postdoc, Baylor College of Medicine)