Our Publications

Molecular Systems Biology • 2026

Engineered E. coli swarming for binary and analog input recording

Shaw, M., Garg, S., Kirby, J., Schmidgall, S., Liguori, F., Doshi, A., Tu, T., Danino, T.

(2026) doi:10.1038/s44320-026-00232-7

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BioDesign Research • 2026

Toward development of soil-derived Bacillus isolates as lung cancer cytotoxic agents.

Dhru, D., Liguori, F., Shuster, B.M., Huang, R., Shoreibah, S., Wang, S., Rojas Ocampo, N.E., Murray, K.P., Danino, T.

(2026) doi.org/10.1016/j.bidere.2026.100074

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ACS Synthetic Biology • 2025

Design and modeling of biosensor-driven encapsulation systems for systemic delivery of bacterial cancer therapy

Hahn, J.*, Harimoto, T.*, Chen, Y-Y., Liguori, F., Leong, K.W.*, Danino, T.*

(2025) doi.org/10.1021/acssynbio.5c00598

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International Forum of Allergy & Rhinology • 2025

Engineered Microbial-Based Therapeutics Nose No Bounds: Extending Innovation to Rhinologic Disease Management

Pabón, J., Danino, T, Gudis, G.A., Overdevest, J.

(2025) doi.org/10.1002/alr.23619

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Nature Biomedical Engineering • 2025

Engineered bacteria launch and control an oncolytic virus

Singer, Z.S.*, Pabón, J.*, Huang, H., Sun, W., Luo H., Grant, K.R., Obi, I., Coker, C., Rice, C.M., Danino, T.

(2025) doi.org/10.1038/s41551-025-01476

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Using bacteria to sneak viruses into tumorsEurekAlert!Cancer-killing virus becomes more effective when shielded by bacteriaNew ScientistHarnessing Bacteria to Deliver Viruses Directly into TumorsBioengineer.org

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Nature Biotechnology • 2025

The emerging landscape of engineered bacteria cancer therapies

Ballister, E.R.*, Michels, A.*, Vincent, R.L.,Kreindler, L., Chowdhury, S., Upadhaya, S., Saez-Ibañez, A.R., Tu, T., Gottweis, J., Danino, T.

(2025) doi.org/10.1038/s41587-025-02623-x

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ACS Synthetic Biology • 2024

Iron-tannin coating reduces clearance and increases tumor colonization of systemically delivered bacteria

Windemuth, S., Hahn, J., You, J., Wang, Z., Ding, S., Tarrab, S., Coker, C., Leong, K. W.*, Danino, T*.

13:0012 (2024)

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Hacking bacteria to attack cancerColumbia University Irving Medical CenterEngineering immunity: bacterial delivery of cancer neoantigen vaccinesTrends in ImmunologyA bacterial neoantigen cancer vaccineNature BiotechnologyA “living medicine”: Engineered E. coli shrink tumors in miceNational Cancer Institute

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Nature • 2024

Probiotic neoantigen delivery vectors for precision cancer immunotherapy

Redenti, A.*, Im, J.*, Redenti, B,, Li, F., Rouanne, M., Sheng, Z., Sun, W., Gubatri, C.R., Huang, S., Komaranchath, M., Jang, Y., Hahn, J., Ballister, E., Vincent, R.L., Vardoshivilli, A., Danino, T.*, Arpaia, N*.

(2024) https://doi.org/10.1038/s41586-024-08033-4

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Hacking bacteria to attack cancerColumbia University Irving Medical CenterEngineering immunity: bacterial delivery of cancer neoantigen vaccinesTrends in ImmunologyA bacterial neoantigen cancer vaccineNature BiotechnologyA “living medicine”: Engineered E. coli shrink tumors in miceNational Cancer Institute

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Biodesign Research • 2024

Dynamic gene expression mitigates mutational escape in lysis-driven bacteria cancer therapy

Liguori, F., Pellicciotta, N., Milanetti, E., Windemuth, S.X., Ruocco, G., Di Leonardo, R., Danino, T.

6:0049 (2024)

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Nature Communications • 2024

Colorectal cancer detection and treatment with engineered probiotics

Gurbatri, C.R.*, Radford, G.*, Vrbanac, L., Coker, C., Im, J., Taylor, S.R., Jang, Y., Sivan, A., Rhee, K., Saleh, A.A., Chien, T., Zandkarimi, F., Lia, I., Lannagan, T.R., Wang, T., Wright, J.A., Thomas, E., Kobayashi, H., Ng, J.Q., Lawrence, M., Sammour, T., Thomas, M., Lewis, M., Papanicolas, L., Perry, J., Fitzsimmons, T., Kaazan, P., Lim, A., Marker, J., Ostroff, C., Rogers, G., Arpaia, N., Worthley, D.L., Woods, S.L.*, Danino, T.*

15:646 (2024)

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Science • 2023

Probiotic-guided CAR-T cells for solid tumor targeting

Vincent, R.L.*, Gurbatri, C.R.*, Li, F., Vardoshvili, A., Coker, C., Im, J., Ballister, E.R., Rouanne, M., Savage, T., de los Santos-Alexis, K., Redenti, A., Brockmann, L., Komaranchath, M., Arpaia, N., Danino, T.

382(6667), 211-218 (2023)

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Bacteria tag tumours for CAR-T cell attackNature Reviews Drug DiscoveryA bacterial assist for CAR-T cellsNature BiotechnologyEngineered bacteria + CAR-T cells: A dynamic duo to crush cancer?ScienceEngineered bacteria guide T cells to tumorsDanino LabEngineered Bacteria Paint Targets on Tumors for Cancer-killing T Cells to SeeColumbia Engineering

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Nature Reviews Bioengineering • 2023

Bacterial therapies at the interface of synthetic biology and nanomedicine

Hahn, J., Ding, S., Im, J., Harimoto, T., Leong, K.W., Danino, T.

(2023). doi 10.1038/s44222-023-00119-4

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Nature Chemical Biology • 2023

Engineered bacterial swarm patterns as spatial records of environmental inputs

Doshi, A., Shaw, M., Tonea, R., Moon, S., Minyety, R., Doshi, A., Laine, A., Guo, J., Danino, T.

19(7), 878–886 (2023)

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Microbiology Spectrum • 2023

Engineered bacteria for short-chain-fatty-acid-repressed expression of biotherapeutic molecules

Serebrinsky-Duek, K., Barra, M., Danino, T., Garrido, D.

11(2), (2023)

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Science Advances • 2023

Chemokines expressed by engineered bacteria recruit and orchestrate antitumor immunity

Savage, T.M., Vincent, R.L., Rae, S.S., Huang, L.H., Ahn, A., Pu, K., Li, F., de Los Santos-Alexis, K., Coker, C., Danino, T., Arpaia, N.

9(10), (2023)

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Scientific Reports • 2022

Design of combination therapy for engineered bacterial therapeutics in non-small cell lung cancer

Deb, D., Wu, Y., Coker, C., Harimoto, T., Huang, R., Danino, T.

12:21551 (2022)

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Science • 2022

Engineering bacteria as interactive cancer therapies

Gurbatri, C.R., Arpaia, N., Danino, T.

378(6622), 858-864 (2022)

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Frontiers in Oncology • 2022

Assessing chemotherapy dosing strategies in a spatial cell culture model

Deb, D.*, Zhu, S.*, Leblanc, M.J., Danino, T.

12:980770 (2022)

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IEEE Engineering in Medicine & Biology Society (EMBC) • 2022

Segmentation with residual attention U-Net and an edge-enhancement approach preserves cell shape features

Zhu, N.*, Liu, C.*, Forsyth, B., Singer, Z., Laine, A., Danino, T., Guo, J.

2115-2118 (2022)

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Nature Protocols • 2022

A rapid screening platform to coculture bacteria within tumor spheroids

Harimoto, T., Deb, D., Danino, T.

17(10), 2216-2239 (2022)

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Nature Biotechnology • 2022

A programmable encapsulation system improves delivery of therapeutic bacteria in mice

Harimoto, T., Hahn, J., Chen, Y., Im, J., Zhang, J., Hou, N., Coker, C., Gray, K., Harr, N., Chowdhury, C., Pu, K., Nimura, C., Arpaia, N., Leong, K.*, Danino, T.*

40, 1259-1269 (2022)

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Bacteria deliver the goodsNature Reviews Drug DiscoveryEngineering an “Invisible Cloak” for Bacteria to Deliver Cancer DrugsColumbia Engineering

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Nature Reviews Cancer • 2022

Reimagining cancer research with art

Deb, D., Shoreibah, S., Danino, T.

22, 191(2022)

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Nature Biomedical Engineering • 2022

Bacterial couriers as cancer vaccines

Redenti, A., Hahn, J., Danino, T.

6, 3-5 (2022)

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IEEE International Symposium on Biomedical Imaging (ISBI) • 2022

A deep learning pipeline for segmentation of Proteus mirabilis colony patterns

Doshi, A.*, Shaw, M.*, Tonea, R., Minyety, R., Moon, S., Laine, A., Guo, J.*, Danino, T.*

1-5 (2022)

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Nature Chemical Biology • 2022

CAR-T cells SEAK help from enzymes

Vincent, R., Danino, T.

18, 122-123 (2022)

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Gastroenterology • 2022

The Origin and Contribution of Cancer-Associated Fibroblasts in Colorectal Carcinogenesis Gastroenterology

Kobayashi H*, Gieniec KA*, Lannagan TRM*, Wang T, Asai N, Mizutani Y, Iida T, Ando R, Thomas EM, Sakai A, Suzuki N, Ichinose M, Wright JA, Vrbanac L, Ng JQ, Goyne J, Radford G, Lawrence MJ, Sammour T, Hayakawa Y, Klebe S, Shin AE, Asfaha S, Bettington ML, Rieder F, Arpaia N, Danino T, Butler LM, Burt AD, Leedham SJ, Rustgi AK, Mukherjee S, Takahashi M, Wang TC, Enomoto A, Woods SL, Worthley DL.

162(3), 890-906 (2022)

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Nature Biomedical Engineering • 2021

Enhancing the tropism of bacteria via genetically programmed biosensors

Chien, T.*, Harimoto, T.*, Kepecs, BGray, K., Coker, C., Hou, N., Pu, K., Azad, T., Nolasco, A., Pavlicova, M., Danino, T.

6, 94-104 (2021)

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Genetic Circuit Could Help Engineered Bacteria Hunt Down TumorsColumbia Engineering

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Cell Systems • 2021

Quantitative measurements of early alphaviral replication dynamics in single cells reveals the basis for superinfection exclusion

Singer, Z.S., Ambrose, P.M., Danino, T.*, Rice, C.M.*

12(3), 210-219 (2021)

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ACS Synthetic Biology • 2020

Engineered Bacterial Production of Volatile Methyl Salicylate

Chien, T., Jones, D.R. , and Danino, T.

10(1), 204-208 (2020)

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Frontiers in bioengineering and biotechnology • 2020

Engineered Probiotics for Detection and Treatment of Inflammatory Intestinal Diseases

Barra, M., Danino, T., Garrido, D.

, 8, 265 (2020)

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Science Translational Medicine • 2020

Engineered probiotics for local tumor delivery of checkpoint blockade nanobodies

Gurbatri, C., Iona, L., Vincent, R., Coker, C., Castro, S., Treuting, P., Hinchliffe, T.E., Arpaia, N., Danino, T.

12(530):eaax0876 (2020)

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Delivering immunotherapy with bacteriaNature MedicineDesigner Probiotic Treatment for Cancer ImmunotherapyColumbia EngineeringBacteria producing checkpoint inhibitors shrink tumors in miceChemical & Engineering NewsEngineered Probiotic Bacteria Deliver Anticancer Nanobodies to Regress Tumors in MiceGenetic Engineering & Biotechnology NewsSeek and destroy: beneficial bacteria programmed to fight cancerBBC Science Focus

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Emerging Topics In Life Science • 2019

Engineering Bacteria For Cancer Therapy

Harimoto, T., Danino, T.

3(5), 623-629(2019)

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Nature Medicine • 2019

Programmable bacteria induce durable tumor regression and systemic antitumor immunity

Chowdhury, S., Castro, S., Coker, C., Hinchliffe, T.E., Arpaia, N.*, Danino, T.*

25(7), 1057–1063 (2019)

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Programmable bacteria as cancer therapyDanino LabNew Weapons Against Cancer: Millions of Bacteria Programmed to KillThe New York TimesF1000F1000Prime

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PNAS • 2019

Rapid screening of engineered microbial therapies in a 3-D multicellular model

Harimoto, T., Singer, Z.S., Velazquez, O.S., Zhang, J., Castro, S., Hinchliffe, T.E., Mather, W., Danino, T.

116(18), 9002-9007(2019)

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Bacterial Therapy in a DishColumbia Engineering

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iScience • 2019

Two new plasmid post-segregational killing mechanisms for the implementation of synthetic gene networks in E. coli

Fedorec, A J.H., Ozdemir, T., Doshi, A., Rosa, L., Velazquez, O., Danino, T., Barnes, C P.

14, 323-334 (2019)

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Cell Systems • 2018

Synthetic Biology and Engineered Live Biotherapeutics: Toward Increasing System Complexity

Ozdemir, T., Fedorec, A J.H., Danino, T., Barnes, C P.

7(1), 5-16 (2018)

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Science • 2017

Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine

Geller, L.*, Barzily-Rokni, M.*, Danino, T., Jonas, O.H., Shental, N., Nejman, D., Gavert, N., Zwang, Y., Cooper, Z., A., Shee, K., Thaiss, C., A., Reuben, A., Livny, J., Avraham, R., Frederick, D., T., Ligorio, M., Chatman, K., Johnston, S., E., Mosher, C., M., Brandis, A., Fuks, G., Gurbatri, C., Gopalakrishnan, V., Kim, M., Hurd, M., W., Katz, M., Fleming, J., Maitra, A., Smith, D., A., Skalak, M., Bu, J., Michaud, M., Trauger, S., A., Barshack, I., Golan, T., Sandbank, J., Flaherty, K., T., Mandinova, A., Garrett, W., S., Thayer, S., P., Ferrone, C., R., Huttenhower, C., Bhatia, S., N., Gevers, D., Wargo, J., A., Golub, T., R. Straussman, R.

357(6356), 1156-1160 (2017)

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Current Opinions in Systems Biology • 2017

Advances in bacterial cancer therapies using synthetic biology

Chien, T.*, Doshi, A.*, Danino, T.

5, 1-8 (2017)

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3D Printing and Additive Manufacturing • 2016

Spatial Control of Bacteria Using Screen Printing

Moon, S.*, Fritz, I.*, Singer, Z.*, Danino, T.

3(4), 194-203 (2016)

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Nature • 2016

Synchronized cycles of bacterial lysis for in vivo delivery

Din, O.*, Danino, T.*, Prindle, A., Skalak, M., Selimkhanov, J., Allen, K., Julio, E., Atolia, A., Tsimring, L., Bhatia, S., Hasty, J.

536(7614), 81-85 (2016)

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Cell • 2015

Hepatitis C virus RNA functionally sequesters miR-122

Luna, J., Scheel, T., Danino, T., Shaw, K., Takacs, C., Mele, A., Fak, J., Nishiuchi, E., Cantanese, M., Rice, C., Darnell, R.

160(6), 1099–1110 (2015)

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Science Translational Medicine • 2015

Programmable probiotics for detection of cancer in urine

Danino, T.*, Prindle, A.*, Kwong, G., Skalak, M., Li, H., Allen, K., Hasty, J., and Bhatia, S.

7, 289ra84 (2015)

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Journal of Visualized Experiments • 2013

Measuring growth and gene expression dynamics of tumor-targeted S. typhimurium bacteria

Danino, T.*, Prindle, A.*, Hasty, J., and Bhatia, S.

77, e50540 (2013)

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ACS Synthetic biology • 2012

Genetic Circuits in Salmonella typhimurium

Prindle, A., Selimkhanov, J.S., Danino, T., Samayoa, P., Goldberg, A., Bhatia, S., and Hasty, J.

1(10), 458-464 (2012)

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ACS Synthetic biology • 2012

In vivo gene expression dynamics from tumor-targeted bacteria

Danino, T., Lo, J., Prindle, A., Hasty, J., and Bhatia, S.

1(10), 465-470 (2012)

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Molecular Systems Biology • 2011

Queueing up for enzymatic processing: Correlated signaling through coupled degradation

Cookson, N.A.*, Mather, W.H.*, Danino, T., Mondragón-Palomino, O., Williams, R. J., Tsimring, L. S., and Hasty, J.

7:561, (2011)

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Nature • 2011

A sensing array of radically coupled genetic ‘biopixels’

Prindle, A.*, Samayoa, P.*, Razinkov, I., Danino, T., Tsimring, L.S. and Hasty, J.

481, 39-44 (2011)

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Science • 2011

Entrainment of a population of synthetic genetic oscillators

Mondragon-Palomino, O., Danino, T., Selimkhanov, J., Tsimring, L.S., and Hasty, J.

333(6047), 1315-1319 (2011)

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Physical Biology • 2011

Buckling instability in ordered bacterial colonies

Boyer, D., Mather, W., Mondragon-Palomino, O., Orozco-Fuentes, S., Danino, T., Hasty, J., and Tsimring, L. S.

8, 026008 (2011)

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PLoS ONE • 2011

In-silico pattern formation of vascular mesenchymal stem-cells in three-dimensions

Danino,T., Volfson, D., Bhatia, S., Tsimring, L., and Hasty, J.

6(5), e20182 (2011)

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Physical Review Letters • 2010

Streaming instability in growing cell populations

Mather, W., Mondragon-Palomino, O., Danino, T., Hasty, J., and Tsimring, L.S.

104(20), 208101 (2010)

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Nature • 2010

A synchronized quorum of genetic clocks

Danino, T.*, Mondragon-Palomino, O.*, Tsimring, L., and Hasty, J.

463, 326-330 (2010)

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