Our Publications

  • "DoubletFinder: Doublet detection in single-cell RNA sequencing data using artificial nearest neighbors" McGinnis CS, Murrow LM, Gartner ZJ. (submitted)
  • "Phosphorylated EGFR dimers are not sufficient to activate Ras" Liang SI, van Lengerich B, Eichel K, Cha M, Patterson DM, Yoon T-Y, von Zastrow M, Jura N, Gartner ZJ. Cell Reports (2018) [pdf]
  • "An Oil-Free Picodrop Bioassay Platform for Synthetic Biologys" Siltanen CA, Cole RH, Poust S, Chao L, Tyerman J, Kauffman-Malaga B, Ubersax J, Gartner ZJ, Abate A. Sci Rep (2018) [pdf]
  • "Characterizing cellular mechanical phenotypes with mechano-node-pore sensing" Kim J, Han S, Lei A, Miyano M, Bloom J, Srivastava V, Stampfer MM, LaBarge MA, Sohn LL. Microsys Nanoeng (2018) [pdf]
  • "Engineered tissue folding by mechanical compaction of the mesenchyme" Hughes AJ, Miyazaki H, Coyle MC, Zhang J, Laurie MT, Chu D, Vavrusova Z, Schneider RA, Klein OD, Gartner ZJ. Developmental Cell (2018) [pdf]

    Groups of mesenchymal cells dispersed in a loose and fibruous ECM compact to form condensates. We use this fundamental cell behavior to engineer tissues that fold up along specific trajectories, in a manner analagous to self-folding origami.

  • "Quantius: generic, high-fidelity human annotation of scientific images at 10^5-clicks-per-hour" Hughes AJ, Mornin JD, Biswas SK, Bauer DP, Bianco S, Gartner ZJ. (submitted)
  • "Unravelng cell-to-cell signaling networks with chemical biology" *Gartner ZJ, *Prescher JA, *Lavis LD. Nat. Chem. Biol.(2017)
    *co-corresponding authors
  • "Opportunities for organoids as new models of aging" Hu JH, Todhunter ME, *Labarge MA, *Gartner ZJ. J Cell Bio (2017) [pdf]
    *co-corresponding authors
  • "Printed Droplet Microfluidics for on demand dispensing of picoliter droplets and cells" Cole R, Tang S, Siltanen C, Shahi P, Zhang J, Poust S, *Gartner ZJ, *Abate AR. Proc. Nat. Acad. Sci. USA (2017)
    *co-corresponding authors

    We describe a technology that enables deterministic printing of tailored groups of cells and reagents to arrays exceeding 10,000 features. In this image we printed exactly one green cell and one red cell to each feature in an array.

  • "A DNA-Based T Cell Receptor Reveals a Role for Receptor Clustering in Ligand Discrimination" Taylor MJ, Husain, K, Gartner ZJ, Mayor S, Vale RD. Cell (2017)
  • "Non-autonomous cell proliferation in the mammary gland and cancer." Weber RJ, Desai TA, Gartner ZJ. Curr Opin Cell Biol (2017)
  • "Dissecting the stem cell niche with organoid models: an engineering-based approach." Murrow LM, Weber RJ, Gartner ZJ. Development (2017)
  • "Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding" Shahi P, Kim SC, Haliburton JR, Gartner ZJ, Abate AR. Sci Rep. (2017)
  • "Effects of cell type and configuration on anabolic and catabolic activity in 3D coculture of mesenchymal stem cells and nucleus pulposus cells" Ouyang A, Cerchiari AE, Tang X, Liebenberg E, Alliston T, Gartner ZJ, Lotz JC. J Orthop Res (2016)
  • "Fabrication of 3-D Reconstituted Organoid Arrays by DNA-Programmed Assembly of Cells (DPAC)" Todhunter ME, Weber RJ, Farlow J, Jee NY, Cerchiari AE, Gartner ZJ. Curr Protoc Chem Biol (2016)
  • "Probing the luminal microenvironment of reconstituted epithelial microtissues" Cerchiari AE, Samy KE, Todhunter ME, Schlesinger E, Henise J, Rieken C, Gartner ZJ, Desai TA. Sci Rep (2016)
  • "Mysteries in a Minimal Genome" Coyle M, Hu J, Gartner ZJ. ACS Cent Sci (2016)
  • "Multicolor Fluorescence Detection for Droplet Microfluidics Using Optical Fibers" Cole RH, Gartner ZJ, Abate AR. J Vis Res (2016)
  • "A Mechanogenetic Toolkit for Interrogating Cell Signaling in Space and Time." Seo D**, Southard KM**, Kim JW, Farlow J, Lee JU, Litt DB, Haas T, Cheon J, Alivisatos PA, Gartner ZJ*, Jun YW*. Cell (2016) [pdf]
    *co-corresponding authors
    **equal contributions

    We describe monovalent nanoparticles that can be used to independently localize or deliver quantitative mechanical loads to single cell surface receptors.

  • "Multicolor fluorescence detection for droplet microfluidics using optical fibers." Cole RH, Gartner ZJ, Abate AR. Journal of Visualized Experiments (2016)
  • "Interrogating Stem Cell Fate Decisions with High-Throughput Arrays of Cellular Communities." Chen S, Na YS, Todhunter M, Hsiao S, Scheideler OJ, Bremer AW, Bomdica P, Maharbiz MM, Gartner ZJ*, Schaffer DV*. Nature Communication (2016) [pdf]
    *co-corresponding authors
  • "Compact and modular multicolor fluorescence detector for droplet microfluidics" Cole RH, de Lange N, Gartner ZJ, Abate AR. Lab Chip (2015) [pdf]
  • "Coupling between apical tension and basal adhesion allow epithelia to sense and respond to substrate topography over long distances." Broaders KE, Cerchiari AE, Gartner ZJ Integrative Biology (2015) [pdf]
  • "Programmed Synthesis of Three-Dimensional Tissues." Todhunter ME*, Jee NY*, Hughes AJ, Coyle MC, Cerchiari A, Farlow J, Garbe JC, LaBarge MA, Desai TA, Gartner ZJ. Nature Methods (2015) [pdf]
    *equal contributions

    Three-dimensional image of a tissue constructed using DNA-programmed assembly of cells (DPAC). We aimed to synthesize a tissue with a structure similar to the Terminal Ductal Lobular Unit (TDLU) of the breast.

  • "Formation of spatially and geometrically controlled 3D tissues in soft gels via sacrificial micro molding." Cerchiari A, Garbe JC, Todhunter ME, Jee NY, LaBarge MA, Desai T*, Gartner ZJ. Tiss. Eng. Part C (2015) [pdf]
    *co-corresponding authors
  • "A strategy for tissue self-organization that is robust to cellular heterogeneity and plasticity." Cerchiari A, Garbe JC, Todhunter ME, Jee NY, Broaders K, Peehl D, LaBarge MA, Desai T, Thomson M, Gartner ZJ. Proc. Natl. Acad. Sci. USA (2015) [pdf]

  • We investigate how the mammary gland maintains a single three-dimensional structure through a robust program of self-organization. In the movie, luminal (green) and myoepithelial (red) cells self-organize correctly in extracellular matrix (left), but into an inverted structure in non-adhesive microenvironments such as agarose (right).

  • "Efficient targeting of fatty-acid modified oligonucleotides to live cell membranes through step-wise assembly." Weber RJ, Liang SI, Selden NS, Desai TA, Gartner ZJ. BioMacroMolecules (2014) [pdf]
  • "Production & Targeting of Monovalent Quantum Dots." Seo D, Farlow J, Southard K , Jun YW* Gartner ZJ*. J. Vis. Exp. (2014)
    *co-corresponding authors
  • “A Modular Approach for Assembling Aldehyde-Tagged Proteins on DNA Scaffolds.” Liang SI, McFarland J, Rabuka D, Gartner ZJ. J. Am. Chem. Soc. (2014) [pdf]

  • A simple method for generating site-specific DNA-protein conjugates is presented. This method provides a means of assembling antibody fragments on DNA scaffolds in precisely defined nanoscale geometries. These constructs will find utility as nanoscale probes of receptor organization at the cell surface.

  • "Cells: Shaping tissues and organs." Rosenblatt J, Gartner ZJ. Mol. Bio. Cell (2014)
  • “Mycobacterium tuberculosis Rv3406 is a type II alkyl sulfatase capable of sulfate scavenging.” Sogi KM, Gartner ZJ, Breidenbach MA, Appel MJ, Schelle MW, Bertozzi CR. PLOS One (2013)

  • "Formation of targeted monovalent quantum dot by steric exclusion.” Farlow J, Seo D, Broaders KE, Taylor M, Gartner ZJ*, Jun YW*. Nature Methods (2013) [pdf]
    *co-corresponding authors

  • Controlling the valency of targeting elements on nanoparticles is a major challenge. Here we describe a modular and scalable synthetic strategy to generate monovalent semiconductor quantum dots by steric exclusion. Phosphorothioate DNA is mixed with ZnS coated CdSe QDs to produce targetable and highly fluorescent nanoparticles of a single valency.

  • “Programmed Cell-to-Cell Variability in Ras Activity Triggers Emergent Behaviors during Mammary Epithelial Morphogenesis.” Liu J; Farlow J; Paulson AK; Labarge MA; Gartner ZJ Cell Reports (2012) (pdf)

  • Variability in cell state can arise as a consequence of noisy gene expression, microenvironmental heterogeneity, or somatic mutations. Heterogeneity can become accentuated in tumors. In this paper, we find that tissues exhibiting heterogeneity in signaling through the Ras oncogene can drive the emergence of more invasive collective cell behaviors when compared to tissue with more homogeneous signaling through Ras.

  • “Directing the assembly of multiple cell types into spatially organized tissues.” Liu, J.; Gartner, Z. J. Trends in Cell Biology (2012) (pdf)

  • “Cellular Microfabrication: Observing Intercellular Interactions Using Lithographically-Defined DNA Capture Sequences.” Onoe, H.; Hsiao, S. C.; Douglas, E. S.; Gartner, Z. J.; Bertozzi, C. R.; Francis, M. B.; Mathies, R. A. Langmuir. (2012)
  • “Chemically Programmed Cell Adhesion with Membrane-Anchored Oligonucleotides.” Selden, N. S.; Todhunter, M. E.; Jee, N. Y.; Liu J. S.; Broaders, K. E.; Gartner, Z. J. J. Am. Chem. Soc. (2011)
  • "Programmed assembly of three-dimensional microtissues with defined cellular connectivity.” Gartner, Z. J.; Bertozzi, C. R. Proc. Natl. Acad. Sci. USA 106, 4606-4610 (2009).
  • Read a review of this work in MIT's Technology Review. This work was also featured in a C&E news Science and Technology Concentrates and in the August 2009 issue of the HHMI Bulletin.

    IL-3 producing cells (green, top), but not controls (green, bottom) rescue the growth of IL-3 dependent hematopoietic progenitors (Phase). This paracrine signaling network mimics certain aspects of immune system function.


  • "Boron Nitride Nanotubes Are Noncytotoxic and Can Be Functionalized for Interaction with Proteins and Cells." Chen, X; Wu, P; Rousseas, M; Okawa, D; Gartner, Z. J.; Zettl, A; Bertozzi, C. R. J. Am. Chem. Soc. 131, 890-891 (2009).
  • "Direct cell surface modification with DNA for the capture of primary cells and the investigation of myotube formation on defined patterns." Hsiao, H.C.; Shum, B.J.; Onoe, H; Douglas, E.S.; Gartner, Z.J.; Mathies, R.A.; Bertozzi, C.R.; Francis, M.B. Langmuir 25, 6985-6991 (2009).
  • “Evolutionary Approaches for the Discovery of Functional Synthetic Small Molecules.” Gartner, Z. J. Pure and Applied Chemistry 78[1] 1-14 (2006).
  • “DNA-Templated Organic Synthesis and Selection of a Library of Macrocycles.” Gartner, Z. J.; Tse, B. N.; Grubina, R.; Doyon, J. B.; Snyder, T. M.; Liu, D. R. Science 305, 1601-1605 (2004).
  • A library of macrocyclic peptide fumaramides.


  • “Directed Evolution of Ligand Dependence: Small Molecule-Activated Protein Splicing.” Buskirk, A. R.; Ong, Y.; Gartner, Z. J.; Liu, D. R. Proc. Natl. Acad. Sci. USA 101 , 10505-10510 (2004).
  • “Translation of DNA into Synthetic N-Acyloxazolidines.” Li, X.; Gartner, Z. J.; Tse, B. N.; Liu, D. R. J. Am. Chem. Soc. 126, 5090-5092 (2004).
  • “Two Enabling New Architectures for DNA-Templated Synthesis.” Gartner, Z. J.; Grubina, R.; Calderone, C. T.; Liu, D.R. Angew. Chem. Int. Ed. 42, 1370 (2002).
  • “Directing Otherwise Incompatible Reactions in a Single Solution Using DNA-Templated Organic Synthesis.” Calderone, C. T.; Puckett, J. W.; Gartner, Z. J.; Liu, D. R. Angew. Chem. Int. Ed. 41, 4104 (2002).
  • “Multistep Small-Molecule Synthesis Programmed by DNA Templates.” Gartner, Z. J.; Kanan, M. W.; Liu, D. R. J. Am. Chem. Soc. 124, 10304 (2002).
  • “Expanding the Reaction Scope of DNA-Templated Synthesis.” Gartner, Z, J.; Kanan, M. W.; Liu, D. R. Angew. Chem. Int. Ed., 41, 1796 (2002).
  • “The Generality of DNA-Templated Synthesis as a Basis for Evolving Non-Natural Small Molecules.” Gartner, Z. J. and Liu, D. R. J. Am. Chem. Soc. 123, 6961-6963 (2001).