University of Notre Dame College of Engineering

Publications

An updated list of publications (including published to the preprint server) also can be found on Google Scholar.

* Co-equal contributions, # (co-)corresponding author

27.Wu, Q., Bodskiy, P.A., Huizar, F., Jangula, J.J., Narciso, C., Levis, M., Brito-Robinson, T., Zartman, J.J. “In vivo relevance of intercellular calcium signaling in Drosophila wing development.”bioRxiv. 2017, 187401. doi.org/10.1101/187401.

26. Höök*, P., Brito-Robinson*, T., Narciso, C., Kim, O., Goodson, R.I., Weisel, J.W.#, Alber, M.S.#, and Zartman, J.J.#. “Whole blood clot optical clearing for nondestructive 3D imaging and quantitative analysis”. Biomedical Optics Express. Vol. 8, Issue 8, pp. 3671-3686 (2017). doi.org/10.1364/BOE.8.003671.

* This work has been highlighted at EurekAlert and Science Daily.

25. Narciso, Cody E., Nicholas M. Contento, Thomas J. Storey, David J. Hoelzle, and Jeremiah J. Zartman. "Release of Applied Mechanical Loading Stimulates Intercellular Calcium Waves in Drosophila Wing Discs." Biophysical Journal 113, no. 2 (2017): 491-501. doi: 10.1016/j.bpj.2017.05.051.

* This work was highlighted as a "New and Notable" by the journal:

Kinzer-Ursem T. "Relieving the Pressure on Tissue Developmen.t" Biophys J. 2017 Jul 25;113(2):360-361. doi: 10.1016/j.bpj.2017.06.006.

* Preprint available at: Link.

24. Wu, Q.*, Brodskiy, P.*, Narciso, C., Levis, M., Chen, J., Liang, P., Arredondo-Walsh, N., Chen, D. Z., and Zartman, J. J.# “Intercellular Calcium Waves Are Controlled by Morphogen Signaling during Organ Development” bioRxiv (2017): 104745. doi: https://doi.org/10.1101/104745 Link (current status: preprint).

23. Nematbakhsh, A.*, Sun, W.*, Brodskiy, P. A.*, Amiri, A.*, Narciso, C., Xu, Z., Zartman, J. J.#, and Alber, M. S.* “Multi-scale computational study of the mechanical regulation of cell mitotic rounding in epithelia.” PLOS Computational Biology 2017;13:e1005533.

* Preprint available on bioRxiv (2016): 037820.

22. Brodskiy, P. A., Eberts, P. M.#, Narciso, C., Kursawe, J., Fletcher, A., and Zartman, J. J. “QuickStitch for Seamless Stitching of Confocal Mosaics through High-Pass Filtering and Recursive Normalization” bioRxiv (2016): 075440. doi:10.1101/075440. (current status: preprint).

21. Kursawe, J., Bardenet, R., Zartman, J.J. , Baker, R. E., and Fletcher, A. G. “Robust Cell Tracking in Epithelial Tissues through Identification of Maximum Common Subgraphs” Journal of The Royal Society Interface 13, no. 124 (2016): 20160725.

* Post-print available: bioRxiv (2016): 049551. doi:10.1101/049551. Link.

20. Narciso C, Cowdrick KR, Zellmer V, Brito-Robinson T, Brodskiy P, Hoelzle DJ, Zhang S, Zartman JJ#. On-chip three-dimensional tissue histology for microbiopsies. Biomicrofluidics. 2016 Mar 10 (2): 021101. Link.

19. Kursawe J, Brodskiy PA, Zartman JJ# , Baker RE, Fletcher AG. Capabilities and Limitations of Tissue Size Control Through Passive Mechanical Forces. PLOS Comput Biol 11, no. 12 (2015): e1004679. doi:10.1371/journal.pcbi.1004679.

* Postprint available on bioRxiv. 2015 Jul 24;023184. doi:10.1101/023184 Link

18. Burnette M, Zartman JJ#. (2015) Spatiotemporal patterning of polyamines in Drosophila development. Amino acids, 1-6. DOI: 10.1007/s00726-015-2093-z. Link.

17. Narciso C, Wu Q, Brodskiy P, Garston G, Baker R, Fletcher A, Zartman J#. Patterning of wound-induced intercellular Ca2+ flashes in a developing epithelium. Phys Biol. 2015 Oct 1;12(5):056005. DOI: http://dx.doi.org/10.1088/1478-3975/12/5/056005. Link.

16. Burnette M., Brito-Robinson T., Li J.#, Zartman J# (2014). An inverse small molecule screen to design a chemically defined medium supporting long-term growth of Drosophila cell lines. Mol BioSyst, DOI: 10.1039/C4MB00155A. Link

15. Buchmann, A., Alber, M#. and Zartman, J.J#. (2014). Sizing it up: The mechanical feedback hypothesis of organ growth regulation. Seminars in Cell & Developmental Biology, DOI: 10.1016/j.semcdb.2014.06.018. Link

14. Restrepo, S., Zartman, J.J., and Basler, K. “Cultivation and Live Imaging of Drosophila Imaginal Discs” Methods in Molecular Biology (Clifton, N.J.) 1478, (2016): 203–213. doi:10.1007/978-1-4939-6371-3_11.

13. Restrepo, S.*, Zartman, J. J.* and Basler, K. (2014). Coordination of Patterning and Growth by the Morphogen DPP. Current Biology 24, R245–R255. DOI: 10.1016/j.cub.2014.01.055. Link

12. Zartman J*, Restrepo S*, Basler K. (2013). A high-throughput template for optimizing Drosophila organ culture with response-surface methods. Development 140(3):667–674. Link

11. Zartman JJ*, Cheung LS*, Niepielko MG, Bonini C, Haley B, Yakoby N, Shvartsman SY (2011). Pattern formation by a moving morphogen source. Phys Biol. 2011 Aug;8(4):045003

10. Zartman JJ and Shvartsman SY (2010). Unit Operations of Tissue Development: Epithelial Folding. Annual Review of Chemical and Biomolecular Engineering 1:231-46.

9. Zartman JJ, Kanodia JS, Cheung LS, Shvartsman SY (2009) Feedback control of the EGFR signaling gradient: superposition of domain-splitting events in Drosophila oogenesis. Development 136(17):2903-2911

8. Yan S-J, Zartman JJ, Zhang M, Scott A, Shvartsman SY, Li WX. 2009 Bistability coordinates activation of the EGFR and DPP pathways in Drosophila vein differentiation. Molecular Systems Biology 5:278.

7. Zartman JJ, Kanodia JS, Yakoby N, Schafer X, Watson C, Schlichting K, Dahmann C, Shvartsman SY (2009) Expression patterns of cadherin genes in Drosophila oogenesis. Gene Expr Patterns 9(1):31-36.

6. Yakoby N, Bristow CA, Gong D, Schafer X, Lembong J, Zartman JJ, Halfon MS, Schupbach T, Shvartsman SY (2008) A Combinatorial Code for Pattern Formation in Drosophila Oogenesis. Developmental Cell 15(5):725-737.

5. Zartman JJ, Yakoby N, Bristow CA, Zhou X, Schlichting K, Dahmann C and Shvartsman, SY (2008) Cad74A is regulated by BR and is required for robust dorsal appendage formation in Drosophila oogenesis. Developmental Biology 322:289-301.

4. Zartman JJ, and Shvartsman SY (2007) Enhancer organization: transistor with a twist or something in a different vein? Current Biology 17(24):R1048-1050.

3. Pekny M, Zartman J, Krantz W, Greenberg A, Todd, P. (2003) Flow-visualization during macrovoid pore formation in dry-cast cellulose acetate membranes. J Memb Sci 211:71-90.

2. Khare V, Greenberg A, Zartman J, Krantz W, Todd P (2002) Macrovoid growth during polymer membrane casting. Desalination 145:17-23

1. Pekny MR, Zartman J, Greenberg AR, Krantz, WB, Todd P (2002) Macrovoid pore formation in dry-east cellulose acetate membranes: buoyancy studies. J Memb Sci 205:11-21.

Patents

2. Zartman, J., Burnette, M., Li, J., and Brito-Robinson, T. “Cell Culture Medium and Bioprocess Optimization” WO2015066631 A9, 2015 (2015). Link

1. Amodei DG, Bangera MG, Bao XR, Bershteyn A, Bethke B, Eckhoff PA, Esvelt KM, Gustafson KB, Jung EKY, Kaminsky WM, Kare JT, Kim LY, Leuthardt EC, Lieberman E, Moitra A, Somogyi C, Tegreene CT, JR LLW, Zartman JJ. Device including altered microorganisms, and methods and systems of use . US8734823 B2, 201. Link

Other Products and Protocols

1. Lake, M., Narciso, C., Cowdrick, K., Storey, T., Zhang, S., Zartman, J., and Hoelzle, D. “Microfluidic Device Design, Fabrication, and Testing Protocols” Protocol Exchange (2015): doi:10.1038/protex.2015.069, Link.