Publications

  1. Coordinated immune dysregulation in Juvenile Dermatomyositis revealed by single-cell genomics.  Gabrielle Rabadam, Camilla Wibrand, Emily Flynn, George C. Hartoularos, Yang Sun, Chun Jimmie Ye, Susan Kim, Zev Gartner, Marina Sirota, Jessica Neely. bioRxiv (2023)

    jdm

    How do broadly dysregulated cellular interactions in the immune system manifest as autoimmune disease? Together with Jessica Neely and Marina Sirota we used an integrative computational and single cell genomics approach to identify a network of immune dysregulation underlying Juvenile Dermatomyositis (JDM). This study points to new strategies for JDM treatment aimed a restoring balance among interacting immune populations, rather than broad immunosuppression.

  2. Patterning and folding of intestinal villi by active mesenchymal dewetting. 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. bioRxiv (2023)

    condensation
    tyler huycke

    The epithelia of many organs initially grow as simple sheets. They must ultimately fold into more complex forms to achieve their adult function. We studied this process during the development of villi: the finger-like structures essential to nutrient absorption in the intestine. Surprisingly, we found that the epithelium does not fold itself. Rather, the sub-epithelial mesenchyme initiates folding by first undergoing a transition to a more fluid-like state. The process is regulated by cell contractility, elevated adhesion, and MMP-dependent remodeling of the ECM. The resulting fluid-like layer of cells is mechanically unstable due to its high surface tension, so it breaks up into a pattern of aggregates that deform the overlying epithelial interface to initiate tissue folding (video above). The entire process is analogous to the dewetting of a thin liquid film into a series of droplets – like water on a windshield.

    condensation
    tyler huycke

    The epithelia of many organs initially grow as simple sheets. They must ultimately fold into more complex forms to achieve their adult function. We studied this process during the development of villi: the finger-like structures essential to nutrient absorption in the intestine. Surprisingly, we found that the epithelium does not fold itself. Rather, the sub-epithelial mesenchyme initiates folding by first undergoing a transition to a more fluid-like state. The process is regulated by cell contractility, elevated adhesion, and MMP-dependent remodeling of the ECM. The resulting fluid-like layer of cells is mechanically unstable due to its high surface tension, so it breaks up into a pattern of aggregates that deform the overlying epithelial interface to initiate tissue folding (video above). The entire process is analogous to the dewetting of a thin liquid film into a series of droplets – like water on a windshield.

  3. Configurational entropy is an intrinsic driver of tissue structural heterogeneity. Srivastava V, Hu JL, Garbe JC, Veytsman B, Shalabi SF, Yllanes D, Thomson M, LaBarge MA, Huber G, Gartner ZJ. bioRxiv (2023)

    Boltzmann distribution
    vasudha srivastava

    A long term goal of the lab is to understand how the measurable properties of tissues derive the individual properties of cells and their interactions. We are particularly interested in tissue structure, a property of tissues that is essential to their function, yet oddly, is highly heterogeneous in most human organs. In this study we identify a fundamental source of this structural heterogeneity: tissues can exist as structural ensembles, the statistics of which follow a Boltzmann’s (maximum entropy) distribution – a function of three measurable parameters – the degeneracy of structural states, interfacial energy, and tissue activity (the energy associated with positional fluctuations). We derive the quantitative relationship between these parameters and use it to engineer the structural ensemble across multiple conditions.

  4. D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response. Jiang J, Chen S, Tsou T, McGinnis CS, Khazaei T, Zhu Q, Park JH, Strazhnik IM, Hanna J, Chow ED, Sivak DA, Gartner ZJ, Thomson M. bioRxiv (2023)

  5. deMULTIplex2: robust sample demultiplexing for scRNA-seq. Zhu Q, Conrad DN, Gartner ZJ. bioRxiv (2023)

    demultiplexing

    Single-cell sample multiplexing technologies increase sample throughput, reduce batch effects, and decrease reagent costs. These methods rely on associated computational tools in order to correctly associate cell-barcodes with sample-barcodes, but their performance deteriorates rapidly when working with datasets that are large, have imbalanced cell numbers across samples, or are noisy due to cross-contamination among sample tags - unavoidable features of many real-world experiments. deMULTIplex2 dramatically improves sample classification accuracy and recovers significantly more cells from noisy, large-scale datasets.

  6. Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains. 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. bioRxiv (2023)

  7. Epithelial TNF controls cell differentiation and CFTR activity to maintain intestinal mucin homeostasis. 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. J Clin Invest. (2023 )

  8. Loss of PPARγ activity characterizes early protumorigenic stromal reprogramming and dictates the therapeutic window of opportunity. Caruso JA, Wang X, Murrow LM, Rodriguez CI, Chen-Tanyolac C, Vu L, Chen YY, Gascard P, Gartner ZJ, Kerlikowske K, Tlsty TD. PNAS (2023)

  9. Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation. 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. Cell Syst. (2023)

  10. Microfluidics-free single-cell genomics with templated emulsification. 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. Nat Biotechnol. (2023)

  11. Programming the Self-Organization of Endothelial Cells into Perfusable Microvasculature. Cabral KA, Srivastava V, Graham AJ, Coyle MC, Stashko C, Weaver V, Gartner ZJ.Tissue Eng Part A. (2023)

  12. A reductionist approach to determine the effect of cell-cell contact on human epidermal stem cell differentiation. Louis B, Tewary M, Bremer AW, Philippeos C, Negri VA, Zijl S, Gartner ZJ, Schaffer DV, Watt FM. Acta Biomater. (2022)

  13. Single-cell profiling of environmental enteropathy reveals signatures of epithelial remodeling and immune activation. Kummerlowe C, Mwakamui S, Hughes TK, Mulugeta N, Mudenda V, Besa E, Zyambo K, Shay JES, Fleming I, Vukovic M, Doran BA, Aicher TP, Wadsworth MH 2nd, Bramante JT, Uchida AM, Fardoos R, Asowata OE, Herbert N, Yilmaz ÖH, Kløverpris HN, Garber JJ, Ordovas-Montañes J, Gartner ZJ, Wallach T, Shalek AK, Kelly P. Sci Transl Med. (2022)

  14. Systematically quantifying morphological features reveals constraints on organoid phenotypes. Beck LE, Lee J, Coté C, Dunagin MC, Lukonin I, Salla N, Chang MK, Hughes AJ, Mornin JD, Gartner ZJ, Liberali P, Raj A. Cell Syst. (2022)

  15. Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution. Yang D, Jones MG, Naranjo S, Rideout WM 3rd, 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. Cell. (2022)

  16. Single cell enhancer activity distinguishes GABAergic and cholinergic lineages in embryonic mouse basal ganglia. Su-Feher L, Rubin AN, Silberberg SN, Catta-Preta R, Lim KJ, Ypsilanti AR, Zdilar I, McGinnis CS, McKinsey GL, Rubino TE Jr, Hawrylycz MJ, Thompson C, Gartner ZJ, Puelles L, Zeng H, Rubenstein JLR, Nord AS. Proc Natl Acad Sci U S A. (2022)

  17. Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution. Murrow LM*, Weber RJ, Caruso J, McGinnis CS, Phong K, Gascard P, Rabadam G, Borowsky AD, Desai TA, Thomson M, Tlsty T, Gartner ZJ*. Cell Systems (2022). PDF icon Mapping... PDF

    *co-corresponding authors

    diagram.

    We developed a method that identifies coordinated cell state transitions in tissues from single cell sequencing data derived from heterogeneous tissue specimens. The method, named DECIPHER-seq, reveals a network of cell state changes in human breast tissue that takes the form of a cycle, and corresponds to the periodic changes in the human breast that occur with the rise and fall of ovarian hormones during the menstrual cycle.

  18. Adherens junctions organize size-selective proteolytic hotspots critical for Notch signalling. Kwak M, Southard KM, Kim WR, Lin A, Kim NH, Gopalappa R, Lee HJ, An M, Choi SH, Jung Y, Noh K, Farlow J, Georgakopoulos A, Robakis NK, Kang MK, Kutys ML, Seo D, Kim HH, Kim YH, Cheon J, *Gartner ZJ, *Jun YW. Nat. Cell Biol. (2022) *co-corresponding authors

    Notch

    We demonstrate that full length Notch is unable to access adherens junctions due to its large extracellular domain. Following force-dependent proteolysis by ADAM proteases, the extracellular domain is shed and Notch can diffuse into adherens junctions where it can engage a reservoir of gamma secretase, which cleaves Notch a second time to release the intracellular domain and activate down stream signaling.

  19. Bisphenol A replacement chemicals, BPF and BPS, induce protumorigenic changes in human mammary gland organoid morphology and proteome. Winkler J, Liu P, Phong K, Hinrichs JH, Ataii N, Williams K, Hadler-Olsen E, Samson S, Gartner ZJ, Fisher S, Werb Z. PNAS (2022)

  20. Setting boundaries for tissue patterning. Huycke TR and Gartner ZJ. Science (2022)

  21. Single-Cell Protein Profiling by Microdroplet Barcoding and Next-Generation Sequencing. Kim SC, Haliburton JR, Gartner ZJ, Abate AR. Single Cell Protein Analysis (book chapter) (2022)

  22. Guiding the formation of tissue structure through self-organization (in "Roadmap for the multiscale coupling of biochemical and mechanical signals during development"). Gartner ZJ. Phys Biol. (2021)

    self-organization concept

    A conceptual model for tissue self-organization involving three key features of living cells: movement and shape changes through active mechanics; communication through paracrine signaling; and information processing through gene regulatory networks.

  23. AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data. 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. Genome Biology (2021)

  24. Human microglia states are conserved across experimental models and regulate neural stem cell responses in chimeric organoids. Popova G, Soliman SS, Kim CN, Keefe MG, Hennick KH, 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. Cell Stem Cell. (2021)

  25. Commitment and oncogene-induced plasticity of human stem cell-derived pancreatic acinar and ductal organoids. Huang L, Desai D, Conrad DN, Leite NC, Akshinthala D, Lim CM, Gonzalez R, Muthuswamy LM, Gartner ZJ, Muthuswamy SK. Cell Stem Cell. (2021)

  26. EPH/EPHRIN regulates cellular organization by actomyosin contractility effects on cell contacts. Kindberg AA, Srivastava V, Muncie JM, Weaver VM, Gartner ZJ, Bush JO. J. Cell Bio. (2021)

  27. Simple, Affordable, and Modular Patterning of Cells using DNA. Cabral KA, Patterson DM, Scheideler OJ, Cole R, Abate AR, Schaffer DV, Sohn LL, Gartner ZJ. J. Vis. Exp. (2021)

  28. T cell circuits that sense antigen density with an ultrasensitive threshold. Hernandez-Lopez RA, Yu W, Cabral KA, Creasey OA, Pazmino MDPL, Tonai Y, Guzman AD, Makela A, Gartner ZJ, Lim WA. Science (2021)

  29. Expanding the Boundaries of Synthetic Development. Martyn I, Gartner ZJ. Developmental Biology (2021)

  30. High diversity droplet microfluidic libraries generated with a commercial liquid spotter. Zhang JQ, Siltanen CA, Dolatmoradi A, Sun C, Chang KC, Cole RH, Gartner ZJ, Abate AR. Scientific Reports (2021)

  31. No detectable alloreactive transcriptional responses during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells. McGinnis CS, Siegel DA, Xie G, Stone M, Gartner ZJ, Roan NR, Lee SA. BMC Biology (2021)

  32. Organoid models for mammary gland dynamics and breast cancer. Srivastava V, Huycke TR, Phong KT, Gartner ZJ. Curr Opin Cell Biol (2020)

  33. ZipSeq: Barcoding for Real-time Mapping of Single Cell Transcriptomes. Hu KH, Eichorst JP, McGinnis CS, Patterson DM, Chow ED, Kersten K, Jameson SC, Gartner ZJ, Rao AA, Krummel MF. Nature Methods (2020). PDF icon ZipSeq... PDF.

  34. High Throughput Yeast Strain Phenotyping with Droplet-Based RNA Sequencing. Zhang JQ, Chang KC, Liu L, Gartner ZJ, Abate AR. JoVE (2020)

  35. Lactoferrin Reverses Methotrexate Driven Epithelial Barrier Defect by Inhibiting TGF-β Mediated Epithelial to Mesenchymal Transition. Wallach TE, Srivastava V, Reyes E, Klein OD, Gartner ZJ. (submitted)

  36. Linked optical and gene expression profiling of single cells at high-throughput. Zhang JQ, Siltanen CA, Liu L, Chang KC, Gartner ZJ, Abate AR. Genome Bio. (2020)

  37. Antibody-Drug Conjugates Targeting the Urokinase Receptor (uPAR) as a Possible Treatment of Aggressive Breast Cancer. Harel ET, Drake PM, Barfield RM, Lui I, Farr-Jones S, Van’t Veer L, Gartner ZJ, Green EM, Lourenço AL, Cheng Y, Hann BC, Rabuka D, Craik CS. Antibodies (2019)

  38. Balancing Act: Cell Polarity and Shape Compete to Ensure Robust Development. Murrow LM, Gartner ZJ. Dev. Cell (2019)

  39. Bioprinting in Space and Time. *Gartner Z, *Hughes A. Nature (2019). PDF icon Bioprinting... PDF.

    *co-corresponding authors

  40. Human organoids: a new dimension in cell biology. Lehmann R, Lee CM, Shugart EC, Benedetti M, Charo RA, Gartner Z, Hogan B, Knoblich J, Nelson CM, Wilson KM. Mol Biol Cell. (2019). PDF icon Human... PDF.

  41. MULTI-seq: scalable sample multiplexing for single-cell RNA sequencing using lipid-tagged indices. McGinnis CS, Patterson DM, Winkler J, Hein MY, Srivastava S, Hu JL, Conrad DN, Murrow LM, Weissman JS, Werb Z, *Chow ED, *Gartner ZJ. Nature Methods (2019). PDF icon MULTI-seq... PDF.

    *co-corresponding authors

  42. DoubletFinder: Doublet detection in single-cell RNA sequencing data using artificial nearest neighbors. McGinnis CS, Murrow LM, Gartner ZJ. Cell Systems (2019). PDF icon DoubletFinder... PDF.

  43. Paracrine costimulation of IFN-γ signaling by integrins modulates CD8 T cell differentiation. select Krummel MF, Mahale JN, Uhl LFK, Hardison EA, Mujal AM, Mazet JM, Weber RJ, Gartner ZJ, Gérard A. Proc Natl Acad Sci U S A (2018). PDF icon Paracrine... PDF.

  44. Cell-specific chemical delivery using a selective nitroreductase-nitroaryl pair. Gruber TD, Krishnamurthy C, Grimm JB, Tadross MR, Wysocki LM, Gartner ZJ, Lavis LD. ACS Chem. Bio. (2018)

  45. 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 icon Phosphorylated... PDF.

  46. An Oil-Free Picodrop Bioassay Platform for Synthetic Biology. Siltanen CA, Cole RH, Poust S, Chao L, Tyerman J, Kauffman-Malaga B, Ubersax J, Gartner ZJ, Abate A. Sci Rep (2018). PDF icon Oil-Free... PDF.

  47. 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 icon Characterizing... PDF.

  48. 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 icon Engineered... PDF.

    Video, 5 seconds, no audio. Tissue origami: groups of mesenchymal cells dispersed in a loose and fibrous ECM compact to form condensates. We use this fundamental cell behavior to engineer tissues that fold up along specific trajectories, in a manner analogous to self-folding origami. Fibroblasts (green) generate forces that transform a collagen-rich gel (black) into an origami-like four-fold junction.

  49. Quantius: a tool for rapid, flexible, crowd-based annotation of images. Hughes AJ, Mornin JD, Biswas SK, Beck LE, Bauer DP, Raj A, Bianco S, Gartner ZJ. Nat. Meth. (2018)

  50. Unraveling cell-to-cell signaling networks with chemical biology. *Gartner ZJ, *Prescher JA, *Lavis LD. Nat. Chem. Biol.(2017)

    *co-corresponding authors

  51. Opportunities for organoids as new models of aging. Hu JH, Todhunter ME, *Labarge MA, *Gartner ZJ. J Cell Bio (2017). PDF icon Opportunities... PDF.

    *co-corresponding authors

  52. 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

    a grid of black circles, each with a green and red dot in various positions.

    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.

  53. 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)

  54. Non-autonomous cell proliferation in the mammary gland and cancer. Weber RJ, Desai TA, Gartner ZJ. Curr Opin Cell Biol (2017)

  55. Dissecting the stem cell niche with organoid models: an engineering-based approach. Murrow LM, Weber RJ, Gartner ZJ. Development (2017)

  56. Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding. Shahi P, Kim SC, Haliburton JR, Gartner ZJ, Abate AR. Sci Rep. (2017)

  57. 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)

  58. 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)

  59. 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)

  60. Mysteries in a Minimal Genome. Coyle M, Hu J, Gartner ZJ. ACS Cent Sci (2016)

  61. Multicolor Fluorescence Detection for Droplet Microfluidics Using Optical Fibers. Cole RH, Gartner ZJ, Abate AR. J Vis Res (2016)

  62. 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)

    *co-corresponding authors

    **equal contributions

    Video, 16 seconds, no audio. We describe monovalent nanoparticles that can be used to independently localize or deliver quantitative mechanical loads to single cell surface receptors. Notch receptors concentrated to a targeted spatial location on the cell surface using monovalent magnetoplasmonic nanoparticles (MPN).

  63. Multicolor fluorescence detection for droplet microfluidics using optical fibers. Cole RH, Gartner ZJ, Abate AR. Journal of Visualized Experiments (2016)

  64. 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 icon Interrogating... PDF.

    *co-corresponding authors

  65. Compact and modular multicolor fluorescence detector for droplet microfluidics. Cole RH, de Lange N, Gartner ZJ, Abate AR. Lab Chip (2015). PDF icon Compact... PDF.

  66. 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 icon Coupling... PDF.

  67. 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 icon Programmed... PDF.

    *equal contributions

    Video, 6 seconds, no audio. A three-dimensional tissue prepared from two populations of human mammary epithelial cells and 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. One cell population (red) expresses wild type Ras, the other cell type (green) expressed oncogenic Ras.

  68. 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 icon Formation of spatially... PDF.

    *co-corresponding authors

  69. 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 icon Strategy... PDF.

    Video, 10 seconds, no audio. We investigate how the mammary gland maintains a single three-dimensional structure through a robust program of self-organization. Luminal (green) and myoepithelial (red) cells self-organize correctly in extracellular matrix (IrECM, left) but into an inverted structure in non-adhesive microenvironments such as agarose (right).

  70. 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 icon Efficient... PDF.

  71. Production & Targeting of Monovalent Quantum Dots. Seo D, Farlow J, Southard K , Jun YW* Gartner ZJ*. J. Vis. Exp. (2014)

    *co-corresponding authors

  72. 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 icon Modular... PDF.

    diagrams.

    A simple method for generating site-specific DNA-protein conjugates. 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.

  73. Cells: Shaping tissues and organs. Rosenblatt J, Gartner ZJ. Mol. Bio. Cell (2014)

  74. 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)

  75. 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 icon Formation of targeted... PDF.

    *co-corresponding authors

    diagram.

    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.

  76. 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)

    Video, 4 seconds, no audio. Variability in cell state can arise as a consequence of noisy gene expression, microenvironmental heterogeneity, or somatic mutations. Heterogeneity can become accentuated in tumors. 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.

  77. Directing the assembly of multiple cell types into spatially organized tissues. Liu, J.; Gartner, Z. J. Trends in Cell Biology (2012). PDF icon Directing... PDF.

  78. 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)

  79. 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)

  80. 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).

    This work was featured in MIT’s Technology Review, a Science and Technology Concentrates in C and E news, and in the August 2009 issue of the HHMI Bulletin.

    grid of two rows and three columns with cellular activity.

    IL-3 producing cells (green, top row) but not controls (green, bottom row) rescue the growth of IL-3 dependent hematopoietic progenitors (Phase) across 0, 16, and 44 hours (columns). This paracrine signaling network mimics certain aspects of immune system function.

  81. 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).

  82. 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).

  83. Evolutionary Approaches for the Discovery of Functional Synthetic Small Molecules. Gartner, Z. J. Pure and Applied Chemistry 78[1] 1-14 (2006).

  84. 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).

    molecular structure.

    A library of macrocyclic peptide fumaramides.

  85. 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).

  86. 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).

  87. 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).

  88. 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).

  89. Multistep Small-Molecule Synthesis Programmed by DNA Templates. Gartner, Z. J.; Kanan, M. W.; Liu, D. R. J. Am. Chem. Soc. 124, 10304 (2002).

  90. Expanding the Reaction Scope of DNA-Templated Synthesis. Gartner, Z, J.; Kanan, M. W.; Liu, D. R. Angew. Chem. Int. Ed., 41, 1796 (2002).

  91. 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).