Research Summary

My lab aims to define the rules used by cells to self-organize into structurally ordered tissues, and to reveal how tissue structure guides the flow of chemical, mechanical, and electrical information between cells to coordinate collective decisions and behaviors. A better understanding of these processes will guide the development of new therapies for regenerative medicine and new strategies to block the progression of cancer. My lab’s multidisciplinary approach is uniquely suited to tackling these problems. We apply concepts and methods from chemistry, biology, and engineering, and develop new and enabling technologies when existing methods are insufficient for our experimental needs.

Research Funding

  • September 15, 2020 - June 30, 2025 - The physical and molecular mechanisms of intestinal villus morphogenesis and repair , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01DK126376
  • May 1, 2020 - April 30, 2025 - Understanding breast cancer progression as a defect in the mechanics of tissue self-organization , Principal Investigator . Sponsor: NIH, Sponsor Award ID: U01CA244109
  • May 1, 2021 - April 30, 2024 - Universal Sample Multiplexing for Single Cell Analysis , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R33CA247744
  • September 20, 2019 - June 30, 2023 - MULTIseq: multiplexing massively parallel single cell transcriptional analysis across time, space, and conditions , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01GM135462
  • September 30, 2013 - July 31, 2018 - Total synthesis of the human mammary gland , Principal Investigator . Sponsor: NIH, Sponsor Award ID: DP2HD080351
  • September 18, 2014 - August 31, 2016 - Identifying the intercellular networks regulating estrogen receptor expression with a high definition single cell printer , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R21CA195709
  • March 1, 2014 - February 29, 2016 - Small, modular, and monovalent Quantum Dots for single molecule imaging of Notch , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: R21EB018044

Education

University of California, Berkeley B.S. 1994-1999 Chemistry
Harvard University M.S. Ph.D. 1999-2004 Chemical Biology
University of California, Berkeley Postdoctoral 2005-2008 Chemical Biology

Honors & Awards

  • 2000
    National Science Foundation Graduate Research Fellowship
  • 2003
    Bristol-Myers Squibb Fellowship
  • 2003
    Harvard Merit Fellowship
  • 2005
    IUPAC Prize for Young Chemists
  • 2006
    Jane Coffin Childs Postdoctoral Fellow
  • 2008
    Sandler Opportunity Award
  • 2010
    Kimmel Scholar Award
  • 2010
    Era of Hope Scholar Award
  • 2013
    NIH New Innovator Award
  • 2017
    Named to first cohort of Chan Zuckerberg Biohub Investigators

Selected Publications

  1. Saraswathibhatla A, Rabbi MF, Varma S, Srivastava V, Ilina O, Alyafei NHK, Hodgson L, Gartner Z, Friedl P, West R, Kim T, Chaudhuri O. Swirling motion of breast cancer cells radially aligns collagen fibers to enable collective invasion. bioRxiv. 2025 Feb 06.  View on PubMed
  2. Kim H, Hu G, Graham AJ, Gu GX, Gartner ZJ. Four-Dimensional Bioprinting: Harnessing Active Mechanics to Build with Living Inks. Cold Spring Harb Perspect Biol. 2024 Nov 25.  View on PubMed
  3. Graham AJ, Khoo MWL, Srivastava V, Viragova S, Kim H, Parekh K, Hennick KM, Bird M, Goldhammer N, Yu JZ, Morley CD, Lebel P, Kumar S, Rosenbluth JM, Nowakowski TJ, Klein O, Gómez-Sjöberg R, Gartner ZJ. MAGIC matrices: freeform bioprinting materials to support complex and reproducible organoid morphogenesis. bioRxiv. 2024 Oct 09.  View on PubMed
  4. Korotkevich E, Conrad DN, Gartner ZJ, O'Farrell PH. Selection promotes age-dependent degeneration of the mitochondrial genome. bioRxiv. 2024 Sep 28.  View on PubMed
  5. Winkler J, Tan W, Diadhiou CM, McGinnis CS, Abbasi A, Hasnain S, Durney S, Atamaniuc E, Superville D, Awni L, Lee JV, Hinrichs JH, Wagner PS, Singh N, Hein MY, Borja M, Detweiler AM, Liu SY, Nanjaraj A, Sitarama V, Rugo HS, Neff N, Gartner ZJ, Oliveira Pisco A, Goga A, Darmanis S, Werb Z. Single-cell analysis of breast cancer metastasis reveals epithelial-mesenchymal plasticity signatures associated with poor outcomes. J Clin Invest. 2024 Sep 03; 134(17).  View on PubMed
  6. Jiang J, Chen S, Tsou T, McGinnis CS, Khazaei T, Zhu Q, Park JH, Strazhnik IM, Vielmetter J, Gong Y, Hanna J, Chow ED, Sivak DA, Gartner ZJ, Thomson M. D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response. bioRxiv. 2024 Jun 04.  View on PubMed
  7. Huycke TR, Häkkinen TJ, Miyazaki H, Srivastava V, Barruet E, McGinnis CS, Kalantari A, Cornwall-Scoones J, Vaka D, Zhu Q, Jo H, Oria R, Weaver VM, DeGrado WF, Thomson M, Garikipati K, Boffelli D, Klein OD, Gartner ZJ. Patterning and folding of intestinal villi by active mesenchymal dewetting. Cell. 2024 Jun 06; 187(12):3072-3089.e20.  View on PubMed
  8. Rabadam G, Wibrand C, Flynn E, Hartoularos GC, Sun Y, Madubata C, Fragiadakis GK, Ye CJ, Kim S, Gartner ZJ, Sirota M, Neely J. Coordinated immune dysregulation in juvenile dermatomyositis revealed by single-cell genomics. JCI Insight. 2024 May 14; 9(12).  View on PubMed
  9. Zwick RK, Kasparek P, Palikuqi B, Viragova S, Weichselbaum L, McGinnis CS, McKinley KL, Rathnayake A, Vaka D, Nguyen V, Trentesaux C, Reyes E, Gupta AR, Gartner ZJ, Locksley RM, Gardner JM, Itzkovitz S, Boffelli D, Klein OD. Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains. Nat Cell Biol. 2024 Feb; 26(2):250-262.  View on PubMed
  10. Zhu Q, Conrad DN, Gartner ZJ. deMULTIplex2: robust sample demultiplexing for scRNA-seq. Genome Biol. 2024 01 30; 25(1):37.  View on PubMed
  11. Rabadam G, Wibrand C, Flynn E, Hartoularos GC, Sun Y, Ye CJ, Kim S, Gartner Z, Sirota M, Neely J. Coordinated immune dysregulation in Juvenile Dermatomyositis revealed by single-cell genomics. bioRxiv. 2023 Nov 10.  View on PubMed
  12. Reyes EA, Castillo-Azofeifa D, Rispal J, Wald T, Zwick RK, Palikuqi B, Mujukian A, Rabizadeh S, Gupta AR, Gardner JM, Boffelli D, Gartner ZJ, Klein OD. Epithelial TNF controls cell differentiation and CFTR activity to maintain intestinal mucin homeostasis. J Clin Invest. 2023 10 16; 133(20).  View on PubMed
  13. Caruso JA, Wang X, Murrow LM, Rodriguez CI, Chen-Tanyolac C, Vu L, Chen YY, Gascard P, Gartner ZJ, Kerlikowske K, Tlsty TD. Loss of PPARγ activity characterizes early protumorigenic stromal reprogramming and dictates the therapeutic window of opportunity. Proc Natl Acad Sci U S A. 2023 10 17; 120(42):e2303774120.  View on PubMed
  14. Zwick RK, Kasparek P, Palikuqi B, Viragova S, Weichselbaum L, McGinnis CS, McKinley KL, Rathnayake A, Vaka D, Nguyen V, Trentesaux C, Reyes E, Gupta AR, Gartner ZJ, Locksley RM, Gardner JM, Itzkovitz S, Boffelli D, Klein OD. Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains. bioRxiv. 2023 Sep 22.  View on PubMed
  15. Huycke TR, Miyazaki H, Häkkinen TJ, Srivastava V, Barruet E, McGinnis CS, Kalantari A, Cornwall-Scoones J, Vaka D, Zhu Q, Jo H, DeGrado WF, Thomson M, Garikipati K, Boffelli D, Klein OD, Gartner ZJ. Patterning and folding of intestinal villi by active mesenchymal dewetting. bioRxiv. 2023 Aug 15.  View on PubMed
  16. Srivastava V, Hu JL, Garbe JC, Veytsman B, Shalabi SF, Yllanes D, Thomson M, LaBarge MA, Huber G, Gartner ZJ. Configurational entropy is an intrinsic driver of tissue structural heterogeneity. bioRxiv. 2023 Jul 02.  View on PubMed
  17. Adler FR, Anderson ARA, Bhushan A, Bogdan P, Bravo-Cordero JJ, Brock A, Chen Y, Cukierman E, DelGiorno KE, Denis GV, Ferrall-Fairbanks MC, Gartner ZJ, Germain RN, Gordon DM, Hunter G, Jolly MK, Karacosta LG, Mythreye K, Katira P, Kulkarni RP, Kutys ML, Lander AD, Laughney AM, Levine H, Lou E, Lowenstein PR, Masters KS, Pe'er D, Peyton SR, Platt MO, Purvis JE, Quon G, Richer JK, Riddle NC, Rodriguez A, Snyder JC, Lee Szeto G, Tomlin CJ, Yanai I, Zervantonakis IK, Dueck H. Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation. Cell Syst. 2023 04 19; 14(4):252-257.  View on PubMed
  18. Zhu Q, Conrad DN, Gartner ZJ. deMULTIplex2: robust sample demultiplexing for scRNA-seq. bioRxiv. 2023 Apr 12.  View on PubMed
  19. Clark IC, Fontanez KM, Meltzer RH, Xue Y, Hayford C, May-Zhang A, D'Amato C, Osman A, Zhang JQ, Hettige P, Ishibashi JSA, Delley CL, Weisgerber DW, Replogle JM, Jost M, Phong KT, Kennedy VE, Peretz CAC, Kim EA, Song S, Karlon W, Weissman JS, Smith CC, Gartner ZJ, Abate AR. Microfluidics-free single-cell genomics with templated emulsification. Nat Biotechnol. 2023 Nov; 41(11):1557-1566.  View on PubMed
  20. Cabral KA, Srivastava V, Graham AJ, Coyle MC, Stashko C, Weaver V, Gartner ZJ. Programming the Self-Organization of Endothelial Cells into Perfusable Microvasculature. Tissue Eng Part A. 2023 02; 29(3-4):80-92.  View on PubMed

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