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

  • August 15, 2025 - May 31, 2030 - A Team Science Approach to the Co Development of Oral Mucosa for Therapeutic Purposes , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: RM1DE035338
  • September 15, 2020 - November 30, 2028 - A molecular and physical mechanism for growing and branching the intestinal villus , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01DK126376
  • May 1, 2025 - April 30, 2028 - Increasing organoid reproducibility and complexity for drug testing and disease modeling , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R33CA297969
  • September 20, 2022 - June 30, 2025 - Linking human islet structural heterogeneity to beta cell state , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: U01DK135019
  • 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. 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 regulatory network models from scRNA-seq that reveal organizing principles of perturbation response. Cell. 2026 Jun 25; 189(13):4159-4184.e35. View on PubMed
  2. Phong KT, Song S, Kim EA, Conrad DN, Gartner ZJ. Single cell RNA-sequencing reveals that testosterone reduces estrogen signaling in the healthy human mammary gland. J Mammary Gland Biol Neoplasia. 2026 03 25; 31(1). View on PubMed
  3. Graham AJ, Khoo MWL, Srivastava V, Viragova S, Kim H, Parekh K, Hennick KM, Bird M, Goldhammer N, Yu JZ, Hu G, Brinkley NT, Pardo L, Amaya JS, Morley CD, Chadha N, Lebel P, Kumar S, Rosenbluth JM, Nowakowski TJ, Chaudhuri O, Klein O, Gómez-Sjöberg R, Gartner ZJ. Stress-relaxing granular bioprinting materials enable complex and uniform organoid self-organization. Nat Mater. 2026 Jul; 25(7):1239-1251. View on PubMed
  4. Kalantari A, Klein O, Gartner ZJ, Fattahi F. ENS lineage potential is not intrinsically regionalized but is modulated by PTPRZ1 signaling. bioRxiv. 2026 Mar 07. View on PubMed
  5. Zhu Q, Jiang Z, Zuckerman B, Weinberger L, Thomson M, Gartner ZJ. Revealing a coherent cell-state landscape across single-cell datasets with CONCORD. Nat Biotechnol. 2026 Jan 05. View on PubMed
  6. Phong KT, Song S, Kim E, Conrad D, Gartner Z. Single cell RNA-sequencing reveals an association between testosterone treatment and reduced hormone signaling in the human mammary gland. bioRxiv. 2026 Jan 02. View on PubMed
  7. Hu G, Cebrero KG, Venkataraman N, Ravichandran D, Lin Y, Jin Z, Gartner ZJ, Gu GX. Tuning collagen and collagen-alginate mechanics through extrusion bioprinting process parameters. RSC Adv. 2025 Nov 24; 15(54):46591-46601. View on PubMed
  8. Gray GK, Carlson EG, Lev T, Marshall B, Reed AD, Sánchez-Covarrubias AP, Twigger AJ, Puig-Barbe A, Thennavan A, Omotoso A, Murrow LM, Chatterjee D, He S, Pensa S, Aevermann B, Tavares NK, Chen N, Hilton JA, Blake K, Liu Y, Phong K, Gartner ZJ, Lawson DA, Swarbrick A, Dos Santos CO, George SHL, Brugge JS, LaBarge MA, Nakshatri H, Navin N, Kessenbrock K, Khaled WT. Defining breast epithelial cell types in the single-cell era. Dev Cell. 2025 Sep 08; 60(17):2218-2236. View on PubMed
  9. Graham AJ, Khoo MWL, Srivastava V, Viragova S, Kim H, Parekh K, Hennick KM, Bird M, Goldhammer N, Yu JZ, Hu G, Brinkley NT, Pardo L, Amaya JS, Morley CD, Chadha N, Lebel P, Kumar S, Rosenbluth JM, Nowakowski TJ, Chaudhuri O, Klein O, Gómez-Sjöberg R, Gartner ZJ. Stress relaxing granular bioprinting materials enable complex and uniform organoid self-organization. bioRxiv. 2025 Sep 04. View on PubMed
  10. Zhu Q, Jiang Z, Zuckerman B, Weinberger L, Thomson M, Gartner Z. Revealing a coherent cell state landscape across single cell datasets with CONCORD. bioRxiv. 2025 Aug 28. View on PubMed
  11. Foyt D, Brown D, Zhou S, Moser B, Zhu Q, Gartner ZJ, Huang B. HybriSeq: probe-based device-free single-cell RNA profiling. Commun Biol. 2025 Aug 19; 8(1):1250. View on PubMed
  12. 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. 2025 08 01; 17(8). View on PubMed
  13. Korotkevich E, Conrad DN, Gartner ZJ, O'Farrell PH. Selfish mutations promote age-associated erosion of mtDNA integrity in mammals. Nat Commun. 2025 Jul 01; 16(1):5435. View on PubMed
  14. 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. 2025 May 23. View on PubMed
  15. Foyt D, Brown D, Zhou S, Moser B, Zhu Q, Gartner ZJ, Huang B. HybriSeq: Probe-based Device-free Single-cell RNA Profiling. bioRxiv. 2025 Apr 25. View on PubMed
  16. Conrad DN, Phong KT, Korotkevich E, McGinnis CS, Zhu Q, Chow ED, Gartner ZJ. Reducing batch effects in single cell chromatin accessibility measurements by pooled transposition with MULTI-ATAC. bioRxiv. 2025 Feb 17. View on PubMed
  17. 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
  18. 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
  19. 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 09 03; 134(17). View on PubMed
  20. 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

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