Zev Gartner, PhD

Professor
Pharmaceutical Chemistry
[email protected]
+1 415 514-9962

Dr. Zev Gartner is a Professor in the Department of Pharmaceutical Chemistry and is co-Director of the UCSF-based, multi-institution Center for Cellular Construction. He graduated from UC Berkeley and earned his PhD in Chemistry from Harvard University in 2004. He is working to understand how cells assemble into multicellular tissues; how the structure of tissues coordinate the behavior of individual cells; and how changes to tissue structure drive the progression of diseases like cancer. Toward these goals, he and his lab build, perturb, and model human tissues in vitro using techniques from the chemical, engineering, physical and biological sciences.

Publications: 

Patterning and folding of intestinal villi by active mesenchymal dewetting.

bioRxiv : the preprint server for biology

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

Configurational entropy is an intrinsic driver of tissue structural heterogeneity.

bioRxiv : the preprint server for biology

Srivastava V, Hu JL, Garbe JC, Veytsman B, Shalabi SF, Yllanes D, Thomson M, LaBarge MA, Huber G, Gartner ZJ

D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response.

bioRxiv : the preprint server for biology

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

Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation.

Cell systems

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

deMULTIplex2: robust sample demultiplexing for scRNA-seq.

bioRxiv : the preprint server for biology

Zhu Q, Conrad DN, Gartner ZJ

Microfluidics-free single-cell genomics with templated emulsification.

Nature biotechnology

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

Programming the Self-Organization of Endothelial Cells into Perfusable Microvasculature.

Tissue engineering. Part A

Cabral KA, Srivastava V, Graham AJ, Coyle MC, Stashko C, Weaver V, Gartner Z

Adherens junctions organize size-selective proteolytic hotspots critical for Notch signalling.

Nature cell biology

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

Single-cell profiling of environmental enteropathy reveals signatures of epithelial remodeling and immune activation.

Science translational medicine

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, Bramante JT, Uchida AM, Fardoos R, Asowata OE, Herbert N, Yilmaz ?H, Kl?verpris HN, Garber JJ, Ordovas-Monta?es J, Gartner ZJ, Wallach T, Shalek AK, Kelly P

A reductionist approach to determine the effect of cell-cell contact on human epidermal stem cell differentiation.

Acta biomaterialia

Louis B, Tewary M, Bremer AW, Philippeos C, Negri VA, Zijl S, Gartner ZJ, Schaffer DV, Watt FM

Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution.

Cell systems

Murrow LM, Weber RJ, Caruso JA, McGinnis CS, Phong K, Gascard P, Rabadam G, Borowsky AD, Desai TA, Thomson M, Tlsty T, Gartner ZJ

Systematically quantifying morphological features reveals constraints on organoid phenotypes.

Cell systems

Beck LE, Lee J, Coté C, Dunagin MC, Lukonin I, Salla N, Chang MK, Hughes AJ, Mornin JD, Gartner ZJ, Liberali P, Raj A

Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution.

Cell

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

Single cell enhancer activity distinguishes GABAergic and cholinergic lineages in embryonic mouse basal ganglia.

Proceedings of the National Academy of Sciences of the United States of America

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

Bisphenol A replacement chemicals, BPF and BPS, induce protumorigenic changes in human mammary gland organoid morphology and proteome.

Proceedings of the National Academy of Sciences of the United States of America

Winkler J, Liu P, Phong K, Hinrichs JH, Ataii N, Williams K, Hadler-Olsen E, Samson S, Gartner ZJ, Fisher S, Werb Z

Abstract P5-06-02: A gene expression meta-analysis identifies microenvironment differences in cellular composition and cell-cell interactions associated with breast cancer invasion.

Cancer research

Adam Officer, Andre Dempsey, Farnaz Hasteh, Michal Slyper, Asa Segerstolpe, Joanna Klughammer, Judit Jane-Valbuena, Orit Rozenblatt-Rosen, Lyndsay Murrow, Zev Gartner, Aviv Regev, Christina Yau, Pablo Tamayo, Olivier Harismendy

Setting boundaries for tissue patterning.

Science (New York, N.Y.)

Huycke TR, Gartner ZJ

Single-Cell Protein Profiling by Microdroplet Barcoding and Next-Generation Sequencing.

Methods in molecular biology (Clifton, N.J.)

Kim SC, Haliburton JR, Gartner ZJ, Abate AR

Membrane compartmentalization by adherens junctions creates a spatial switch for Notch signaling and function.

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

Human microglia states are conserved across experimental models and regulate neural stem cell responses in chimeric organoids.

Cell stem cell

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

AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data.

Genome biology

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

Roadmap on multiscale coupling of biochemical and mechanical signals during development.

Physical biology

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 BS, Gladfelter AG, Rodrigues A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S

T cell circuits that sense antigen density with an ultrasensitive threshold.

Science (New York, N.Y.)

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

Simple, Affordable, and Modular Patterning of Cells using DNA.

Journal of visualized experiments : JoVE

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.

Journal of Visualized Experiments

Katelyn A. Cabral, David M. Patterson, Olivia J. Scheideler, Russell Cole, Adam R. Abate, David V. Schaffer, Lydia L. Sohn, Zev J. Gartner

High diversity droplet microfluidic libraries generated with a commercial liquid spotter.

Scientific reports

Zhang JQ, Siltanen CA, Dolatmoradi A, Sun C, Chang KC, Cole RH, Gartner ZJ, Abate AR

Identifying Enthalpic Barriers to Entropically-Driven Structural Disruption in Breast Cancers.

Biophysical journal

Vasudha Srivastava, Jennifer L. Hu, James C. Garbe, Martha R. Stampfer, Mark A. LaBarge, Matthew Thomson, Zev J. Gartner

Guiding tissue-scale self-organization.

Nature materials

Gartner ZJ, Hu JL

Abstract 351: Alterations in immune cell signatures during breast cancer metastasis at single cell resolution.

Cancer research

Juliane Winkler, Weilun Tan, Christopher McGinnis, Zev Gartner, Spyros Darmanis, Zena Werb

ZipSeq: barcoding for real-time mapping of single cell transcriptomes.

Nature methods

Hu KH, Eichorst JP, McGinnis CS, Patterson DM, Chow ED, Kersten K, Jameson SC, Gartner ZJ, Rao AA, Krummel MF

Organoid models for mammary gland dynamics and breast cancer.

Current opinion in cell biology

Srivastava V, Huycke TR, Phong KT, Gartner ZJ

2063-P: Quantitative Analysis of Human and Mouse Islet Tissue Structure.

Diabetes

OLIVIA A. CREASEY, JULIE B. SNEDDON, ZEV J. GARTNER

High Throughput Yeast Strain Phenotyping with Droplet-Based RNA Sequencing.

Journal of Visualized Experiments

Jesse Q. Zhang, Kai-Chun Chang, Leqian Liu, Zev J. Gartner, Adam R. Abate

High Throughput Yeast Strain Phenotyping with Droplet-Based RNA Sequencing.

Journal of visualized experiments : JoVE

Zhang JQ, Chang KC, Liu L, Gartner ZJ, Abate AR

Linked optical and gene expression profiling of single cells at high-throughput.

Genome biology

Zhang JQ, Siltanen CA, Liu L, Chang KC, Gartner ZJ, Abate AR

Antibody-Drug Conjugates Targeting the Urokinase Receptor (uPAR) as a Possible Treatment of Aggressive Breast Cancer.

Antibodies (Basel, Switzerland)

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

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices.

Nature methods

McGinnis CS, Patterson DM, Winkler J, Conrad DN, Hein MY, Srivastava V, Hu JL, Murrow LM, Weissman JS, Werb Z, Chow ED, Gartner ZJ

2151-P: Quantification of Tissue Structure in Human and Mouse Islets.

Diabetes

OLIVIA A. CREASEY, DANIEL ELNATAN, JULIE B. SNEDDON, ZEV J. GARTNER

Human organoids: a new dimension in cell biology.

Molecular biology of the cell

Lehmann R, Lee CM, Shugart EC, Benedetti M, Charo RA, Gartner Z, Hogan B, Knoblich J, Nelson CM, Wilson KM

Paracrine costimulation of IFN-? signaling by integrins modulates CD8 T cell differentiation.

Proceedings of the National Academy of Sciences of the United States of America

Krummel MF, Mahale JN, Uhl LFK, Hardison EA, Mujal AM, Mazet JM, Weber RJ, Gartner ZJ, Gérard A

Cell-Specific Chemical Delivery Using a Selective Nitroreductase-Nitroaryl Pair.

ACS chemical biology

Gruber TD, Krishnamurthy C, Grimm JB, Tadross MR, Wysocki LM, Gartner ZJ, Lavis LD

Quanti.us: a tool for rapid, flexible, crowd-based annotation of images.

Nature methods

Hughes AJ, Mornin JD, Biswas SK, Beck LE, Bauer DP, Raj A, Bianco S, Gartner ZJ

An Oil-Free Picodrop Bioassay Platform for Synthetic Biology.

Scientific reports

Siltanen CA, Cole RH, Poust S, Chao L, Tyerman J, Kaufmann-Malaga B, Ubersax J, Gartner ZJ, Abate AR

Characterizing cellular mechanical phenotypes with mechano-node-pore sensing.

Microsystems & nanoengineering

Kim J, Han S, Lei A, Miyano M, Bloom J, Srivastava V, Stampfer MM, Gartner ZJ, LaBarge MA, Sohn LL

Phosphorylated EGFR Dimers Are Not Sufficient to Activate Ras.

Cell reports

Liang SI, van Lengerich B, Eichel K, Cha M, Patterson DM, Yoon TY, von Zastrow M, Jura N, Gartner ZJ

Engineered Tissue Folding by Mechanical Compaction of the Mesenchyme.

Developmental cell

Hughes AJ, Miyazaki H, Coyle MC, Zhang J, Laurie MT, Chu D, Vavrušová Z, Schneider RA, Klein OD, Gartner ZJ

Opportunities for organoids as new models of aging.

The Journal of cell biology

Hu JL, Todhunter ME, LaBarge MA, Gartner ZJ

Single-cell mechanogenetics using monovalent magnetoplasmonic nanoparticles.

Nature protocols

Kim JW, Seo D, Lee JU, Southard KM, Lim Y, Kim D, Gartner ZJ, Jun YW, Cheon J

Printed droplet microfluidics for on demand dispensing of picoliter droplets and cells.

Proceedings of the National Academy of Sciences of the United States of America

Cole RH, Tang SY, Siltanen CA, Shahi P, Zhang JQ, Poust S, Gartner ZJ, Abate AR

A Mechanogenetic Toolkit for Interrogating Cell Signaling in Space and Time.

Cell

Seo D, Southard KM, Kim JW, Lee HJ, Farlow J, Lee JU, Litt DB, Haas T, Alivisatos AP, Cheon J, Gartner ZJ, Jun YW

Unraveling cell-to-cell signaling networks with chemical biology.

Nature chemical biology

Gartner ZJ, Prescher JA, Lavis LD

Dissecting the stem cell niche with organoid models: an engineering-based approach.

Development (Cambridge, England)

Murrow LM, Weber RJ, Gartner ZJ

Non-autonomous cell proliferation in the mammary gland and cancer.

Current opinion in cell biology

Weber RJ, Desai TA, Gartner ZJ

Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding.

Scientific reports

Shahi P, Kim SC, Haliburton JR, Gartner ZJ, Abate AR

192 Diagnosis and therapy of aggressive breast cancers by targeting urokinase receptor.

European Journal of Cancer

E. Harel, S. Liang, S. Brain, Z. Gartner, L. Van't Veer, C. Craik

Effects of cell type and configuration on anabolic and catabolic activity in 3D co-culture of mesenchymal stem cells and nucleus pulposus cells.

Journal of orthopaedic research : official publication of the Orthopaedic Research Society

Ouyang A, Cerchiari AE, Tang X, Liebenberg E, Alliston T, Gartner ZJ, Lotz JC

Rapid Organoid Reconstitution by Chemical Micromolding.

ACS biomaterials science & engineering

Weber RJ, Cerchiari AE, Delannoy LS, Garbe JC, LaBarge MA, Desai TA, Gartner ZJ

Fabrication of 3-D Reconstituted Organoid Arrays by DNA-Programmed Assembly of Cells (DPAC).

Current protocols in chemical biology

Todhunter ME, Weber RJ, Farlow J, Jee NY, Cerchiari AE, Gartner ZJ

Probing the luminal microenvironment of reconstituted epithelial microtissues.

Scientific reports

Cerchiari AE, Samy KE, Todhunter ME, Schlesinger E, Henise J, Rieken C, Gartner ZJ, Desai TA

A Mechanogenetic Toolkit for Interrogating Cell Signaling in Space and Time.

Cell

Seo D, Southard KM, Kim JW, Lee HJ, Farlow J, Lee JU, Litt DB, Haas T, Alivisatos AP, Cheon J, Gartner ZJ, Jun YW

Multicolor Fluorescence Detection for Droplet Microfluidics Using Optical Fibers.

Journal of visualized experiments : JoVE

Cole RH, Gartner ZJ, Abate AR

Multicolor Fluorescence Detection for Droplet Microfluidics Using Optical Fibers.

Journal of Visualized Experiments

Russell H. Cole, Zev J. Gartner, Adam R. Abate

Mysteries in a Minimal Genome.

ACS central science

Coyle M, Hu J, Gartner Z

Interrogating cellular fate decisions with high-throughput arrays of multiplexed cellular communities.

Nature communications

Chen S, Bremer AW, Scheideler OJ, Na YS, Todhunter ME, Hsiao S, Bomdica PR, Maharbiz MM, Gartner ZJ, Schaffer DV

Coupling between apical tension and basal adhesion allow epithelia to collectively sense and respond to substrate topography over long distances.

Integrative biology : quantitative biosciences from nano to macro

Broaders KE, Cerchiari AE, Gartner ZJ

Programmed synthesis of three-dimensional tissues.

Nature methods

Todhunter ME, Jee NY, Hughes AJ, Coyle MC, Cerchiari A, Farlow J, Garbe JC, LaBarge MA, Desai TA, Gartner ZJ

Compact and modular multicolour fluorescence detector for droplet microfluidics.

Lab on a chip

Cole RH, de Lange N, Gartner ZJ, Abate AR

A strategy for tissue self-organization that is robust to cellular heterogeneity and plasticity.

Proceedings of the National Academy of Sciences of the United States of America

Cerchiari AE, Garbe JC, Jee NY, Todhunter ME, Broaders KE, Peehl DM, Desai TA, LaBarge MA, Thomson M, Gartner ZJ

Formation of spatially and geometrically controlled three-dimensional tissues in soft gels by sacrificial micromolding.

Tissue engineering. Part C, Methods

Cerchiari A, Garbe JC, Todhunter ME, Jee NY, Pinney JR, LaBarge MA, Desai TA, Gartner ZJ

Production and Targeting of Monovalent Quantum Dots.

Journal of Visualized Experiments

Daeha Seo, Justin Farlow, Kade Southard, Young-wook Jun, Zev J. Gartner

Production and targeting of monovalent quantum dots.

Journal of visualized experiments : JoVE

Seo D, Farlow J, Southard K, Jun YW, Gartner ZJ

A modular approach for assembling aldehyde-tagged proteins on DNA scaffolds.

Journal of the American Chemical Society

Liang SI, McFarland JM, Rabuka D, Gartner ZJ

Cells: Shaping tissues and organs.

Molecular biology of the cell

Rosenblatt J, Gartner Z

Regulating Spatiotemporal Dynamics of Notch Signaling in Live Cells via Magnetoplasmonic Nanoprobes.

Biophysical journal

Daeha Seo, Jiwook Kim, Justin Farlow, Hyunjung Lee, Paul Alivisatos, Jinwoo Cheon, Zev Gartner, Young-wook Jun

Formation of targeted monovalent quantum dots by steric exclusion.

Nature methods

Farlow J, Seo D, Broaders KE, Taylor MJ, Gartner ZJ, Jun YW

Mycobacterium tuberculosis Rv3406 is a type II alkyl sulfatase capable of sulfate scavenging.

PloS one

Sogi KM, Gartner ZJ, Breidenbach MA, Appel MJ, Schelle MW, Bertozzi CR

Cellular microfabrication: observing intercellular interactions using lithographically-defined DNA capture sequences.

Langmuir : the ACS journal of surfaces and colloids

Onoe H, Hsiao SC, Douglas ES, Gartner ZJ, Bertozzi CR, Francis MB, Mathies RA

Chemically programmed cell adhesion with membrane-anchored oligonucleotides.

Journal of the American Chemical Society

Selden NS, Todhunter ME, Jee NY, Liu JS, Broaders KE, Gartner ZJ

Direct cell surface modification with DNA for the capture of primary cells and the investigation of myotube formation on defined patterns.

Langmuir : the ACS journal of surfaces and colloids

Hsiao SC, Shum BJ, Onoe H, Douglas ES, Gartner ZJ, Mathies RA, Bertozzi CR, Francis MB

Programmed assembly of 3-dimensional microtissues with defined cellular connectivity.

Proceedings of the National Academy of Sciences of the United States of America

Gartner ZJ, Bertozzi CR

Boron nitride nanotubes are noncytotoxic and can be functionalized for interaction with proteins and cells.

Journal of the American Chemical Society

Chen X, Wu P, Rousseas M, Okawa D, Gartner Z, Zettl A, Bertozzi CR

DNA-templated organic synthesis and selection of a library of macrocycles.

Science (New York, N.Y.)

Gartner ZJ, Tse BN, Grubina R, Doyon JB, Snyder TM, Liu DR

Directed evolution of ligand dependence: small-molecule-activated protein splicing.

Proceedings of the National Academy of Sciences of the United States of America

Buskirk AR, Ong YC, Gartner ZJ, Liu DR

Translation of DNA into synthetic N-acyloxazolidines.

Journal of the American Chemical Society

Li X, Gartner ZJ, Tse BN, Liu DR

Two Enabling Architectures for DNA-Templated Organic Synthesis.

Angewandte Chemie

Zev J. Gartner, Rozalina Grubina, Christopher T. Calderone, David R. Liu

Two enabling architectures for DNA-templated organic synthesis.

Angewandte Chemie (International ed. in English)

Gartner ZJ, Grubina R, Calderone CT, Liu DR

Directing Otherwise Incompatible Reactions in a Single Solution by Using DNA-Templated Organic Synthesis.

Angewandte Chemie

Christopher T. Calderone, James W. Puckett, Zev J. Gartner, David R. Liu

Expanding the Reaction Scope of DNA-Templated Synthesis .

Angewandte Chemie

Zev J. Gartner, Matthew W. Kanan, David R. Liu

Expanding the reaction scope of DNA-templated synthesis.

Angewandte Chemie (International ed. in English)

Gartner ZJ, Kanan MW, Liu DR