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

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. Beck LE, Lee J, Coté C, Dunagin MC, Lukonin I, Salla N, Chang MK, Hughes AJ, Mornin JD, Gartner ZJ, Liberali P, Raj A. Systematically quantifying morphological features reveals constraints on organoid phenotypes. Cell Syst. 2022 Jun 08.  View on PubMed
  2. Yang D, Jones MG, Naranjo S, Rideout WM, Min KHJ, Ho R, Wu W, Replogle JM, Page JL, Quinn JJ, Horns F, Qiu X, Chen MZ, Freed-Pastor WA, McGinnis CS, Patterson DM, Gartner ZJ, Chow ED, Bivona TG, Chan MM, Yosef N, Jacks T, Weissman JS. Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution. Cell. 2022 Apr 28.  View on PubMed
  3. Su-Feher L, Rubin AN, Silberberg SN, Catta-Preta R, Lim KJ, Ypsilanti AR, Zdilar I, McGinnis CS, McKinsey GL, Rubino TE, Hawrylycz MJ, Thompson C, Gartner ZJ, Puelles L, Zeng H, Rubenstein JLR, Nord AS. Single cell enhancer activity distinguishes GABAergic and cholinergic lineages in embryonic mouse basal ganglia. Proc Natl Acad Sci U S A. 2022 Apr 12; 119(15):e2108760119.  View on PubMed
  4. Winkler J, Liu P, Phong K, Hinrichs JH, Ataii N, Williams K, Hadler-Olsen E, Samson S, Gartner ZJ, Fisher S, Werb Z. Bisphenol A replacement chemicals, BPF and BPS, induce protumorigenic changes in human mammary gland organoid morphology and proteome. Proc Natl Acad Sci U S A. 2022 03 15; 119(11):e2115308119.  View on PubMed
  5. Huycke TR, Gartner ZJ. Setting boundaries for tissue patterning. Science. 2022 Jan 07; 375(6576):26-27.  View on PubMed
  6. Kim SC, Haliburton JR, Gartner ZJ, Abate AR. Single-Cell Protein Profiling by Microdroplet Barcoding and Next-Generation Sequencing. Methods Mol Biol. 2022; 2386:101-111.  View on PubMed
  7. Minsuk Kwak, Kaden Southard, Woon Ryoung Kim, Annie Lin, Nam Hyeong Kim, Ramu Gopalappa, Minji An, Hyun Jung Lee, Seo Hyun Choi, Justin Farlow, Anastasios Georgakopoulos, Nikolaos Robakis, Min Kang, Matthew Kutys, Daeha Seo, Hyongbum Henry Kim, Yong Ho Kim, Jinwoo Cheon, Zev Gartner, Young-wook Jun. Membrane compartmentalization by adherens junctions creates a spatial switch for Notch signaling and function. . 2021 Nov 1.  View on PubMed
  8. Popova G, Soliman SS, Kim CN, Keefe MG, Hennick KM, Jain S, Li T, Tejera D, Shin D, Chhun BB, McGinnis CS, Speir M, Gartner ZJ, Mehta SB, Haeussler M, Hengen KB, Ransohoff RR, Piao X, Nowakowski TJ. Human microglia states are conserved across experimental models and regulate neural stem cell responses in chimeric organoids. Cell Stem Cell. 2021 12 02; 28(12):2153-2166.e6.  View on PubMed
  9. Thibodeau A, Eroglu A, McGinnis CS, Lawlor N, Nehar-Belaid D, Kursawe R, Marches R, Conrad DN, Kuchel GA, Gartner ZJ, Banchereau J, Stitzel ML, Cicek AE, Ucar D. AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data. Genome Biol. 2021 09 01; 22(1):252.  View on PubMed
  10. Kindberg AA, Srivastava V, Muncie JM, Weaver VM, Gartner ZJ, Bush JO. EPH/EPHRIN regulates cellular organization by actomyosin contractility effects on cell contacts. J Cell Biol. 2021 06 07; 220(6).  View on PubMed
  11. Huang L, Desai R, Conrad DN, Leite NC, Akshinthala D, Lim CM, Gonzalez R, Muthuswamy LB, Gartner Z, Muthuswamy SK. Commitment and oncogene-induced plasticity of human stem cell-derived pancreatic acinar and ductal organoids. Cell Stem Cell. 2021 06 03; 28(6):1090-1104.e6.  View on PubMed
  12. Lenne PF, Munro E, Heemskerk I, Warmflash A, Bocanegra-Moreno L, Kishi K, Kicheva A, Long Y, Fruleux A, Boudaoud A, Saunders TE, Caldarelli P, Michaut A, Gros J, Maroudas-Sacks Y, Keren K, Hannezo E, Gartner ZJ, Stormo B, Gladfelter A, Rodrigues A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Phys Biol. 2021 04 14; 18(4).  View on PubMed
  13. Hernandez-Lopez RA, Yu W, Cabral KA, Creasey OA, Lopez Pazmino MDP, Tonai Y, De Guzman A, Mäkelä A, Saksela K, Gartner ZJ, Lim WA. T cell circuits that sense antigen density with an ultrasensitive threshold. Science. 2021 03 12; 371(6534):1166-1171.  View on PubMed
  14. Cabral KA, Patterson DM, Scheideler OJ, Cole R, Abate AR, Schaffer DV, Sohn LL, Gartner ZJ. Simple, Affordable, and Modular Patterning of Cells using DNA. J Vis Exp. 2021 02 24; (168).  View on PubMed
  15. Zhang JQ, Siltanen CA, Dolatmoradi A, Sun C, Chang KC, Cole RH, Gartner ZJ, Abate AR. High diversity droplet microfluidic libraries generated with a commercial liquid spotter. Sci Rep. 2021 02 23; 11(1):4351.  View on PubMed
  16. Martyn I, Gartner ZJ. Expanding the boundaries of synthetic development. Dev Biol. 2021 06; 474:62-70.  View on PubMed
  17. Vasudha Srivastava, Jennifer L. Hu, James C. Garbe, Martha R. Stampfer, Mark A. LaBarge, Matthew Thomson, Zev J. Gartner. Identifying Enthalpic Barriers to Entropically-Driven Structural Disruption in Breast Cancers. Biophysical Journal. 2021 Feb 1; 120(3):196a.  View on PubMed
  18. McGinnis CS, Siegel DA, Xie G, Hartoularos G, Stone M, Ye CJ, Gartner ZJ, Roan NR, Lee SA. No detectable alloreactive transcriptional responses under standard sample preparation conditions during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells. BMC Biol. 2021 01 20; 19(1):10.  View on PubMed
  19. Gartner ZJ, Hu JL. Guiding tissue-scale self-organization. Nat Mater. 2021 01; 20(1):2-3.  View on PubMed
  20. Hu KH, Eichorst JP, McGinnis CS, Patterson DM, Chow ED, Kersten K, Jameson SC, Gartner ZJ, Rao AA, Krummel MF. ZipSeq: barcoding for real-time mapping of single cell transcriptomes. Nat Methods. 2020 08; 17(8):833-843.  View on PubMed

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