Prof. dr. J.A. (Jo) Ellis-Monaghan
Faculty of Science
KDV
Visiting address
- Science Park 107
Postal address
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Postbus 94248
1090 GE Amsterdam
Contact details
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Publications
2024
- Almodóvar, L., Ellis-Monaghan, J., Harsy, A., Johnson, C., & Sorrells, J. (2024). Computational complexity and pragmatic solutions for flexible tile based DNA self-assembly. Natural Computing. Advance online publication. https://doi.org/10.1007/s11047-024-09998-x
2023
Ellis-Monaghan, J., & Jonoska, N. (2023). From Molecules to Mathematics. In N. Jonoska, & E. Winfree (Eds.), Visions of DNA Nanotechnology at 40 for the Next 40: A Tribute to Nadrian C. Seeman (pp. 189-206). (Natural Computing Series). Springer. https://doi.org/10.1007/978-981-19-9891-1_11 [details]
2022
- Abrams, L., & Ellis-Monaghan, J. A. (2022). New dualities from old: Generating geometric, Petrie, and Wilson dualities and trialities of ribbon graphs. Combinatorics Probability and Computing, 31(4), 574-597. https://doi.org/10.1017/S096354832100047X [details]
- Ellingham, M. N., & Ellis-Monaghan, J. A. (2022). A Catalog of Enumeration Formulas for Bouquet and Dipole Embeddings under Symmetries. Symmetry, 14(9), Article 1793. https://doi.org/10.3390/sym14091793 [details]
- Ellis-Monaghan, J. A., & Moffatt, I. (2022). Graph theory. In J. A. Ellis-Monaghan, & I. Moffatt (Eds.), Handbook of the Tutte Polynomial and Related Topics (pp. 3-13). CRC Press. https://doi.org/10.1201/9780429161612-1 [details]
- Ellis-Monaghan, J. A., & Moffatt, I. (2022). Skein polynomials and the tutte polynomial when x = y. In J. A. Ellis-Monaghan, & I. Moffatt (Eds.), Handbook of the Tutte Polynomial and Related Topics (pp. 266-283). CRC Press. https://doi.org/10.1201/9780429161612-13 [details]
- Ellis-Monaghan, J. A., & Moffatt, I. (2022). The Tutte polynomial for graphs. In J. A. Ellis-Monaghan, & I. Moffatt (Eds.), Handbook of the Tutte Polynomial and Related Topics (pp. 14-26). CRC Press. https://doi.org/10.1201/9780429161612-2 [details]
- Ellis-Monaghan, J. A., & Moffatt, I. (Eds.) (2022). Handbook of the Tutte Polynomial and Related Topics. CRC Press. https://doi.org/10.1201/9780429161612 [details]
- Ellis-Monaghan, J. A., Goodall, A. J., Moffatt, I., Noble, S. D., & Vena, L. (2022). Irreducibility of the Tutte polynomial of an embedded graph. Algebraic Combinatorics, 5(6), 1337-1351. https://doi.org/10.5802/alco.252 [details]
2020
- Morse, A., Adkisson, W., Greene, J., Perry, D., Smith, B., Ellis-Monaghan, J., & Pangborn, G. (2020). DNA origami and unknotted A-trails in torus graphs. Journal of Knot Theory and its Ramifications, 29(7), Article 2050041. https://doi.org/10.1142/S0218216520500418
2019
- Ellingham, M. N., & Ellis-Monaghan, J. A. (2019). Edge-outer graph embedding and the complexity of the DNA reporter strand problem. Theoretical Computer Science, 785, 117-127. https://doi.org/10.1016/j.tcs.2019.03.019
2018
- Ellis Monaghan, J. A., Kung, J. P. S., & Moffatt, I. (2018). Preface: Special issue on the Tutte polynomial. Advances in Applied Mathematics, 94, 1-2. https://doi.org/10.1016/j.aam.2017.09.005
- Ellis-Monaghan, J., Jonoska, N., & Pangborn, G. (2018). Tile-Based DNA Nanostructures: Mathematical Design and Problem Encoding. In R. Robeva, & M. Macauley (Eds.), Algebraic and Combinatorial Computational Biology (pp. 35-60). (Mathematics in Science an Engineering). Academic Press. https://doi.org/10.1016/B978-0-12-814066-6.00002-7
- Ferrari, M. M., Cook, A., Houlihan, A., Rouleau, R., Seeman, N. C., Pangborn, G., & Ellis-Monaghan, J. (2018). Design formalism for DNA self-assembly of polyhedral skeletons using rigid tiles. Journal of Mathematical Chemistry, 56(5), 1365-1392. https://doi.org/10.1007/s10910-018-0858-9
2017
- Ellis-Monaghan, J. A., Pangborn, G., Seeman, N. C., Blakeley, S., Disher, C., Falcigno, M., Healy, B., Morse, A., Singh, B., & Westland, M. (2017). Design tools for reporter strands and DNA origami scaffold strands. Theoretical Computer Science, 671, 69-78. https://doi.org/10.1016/j.tcs.2016.10.007
2015
- Ellis-Monaghan, J. A., & Moffatt, I. (2015). The Las Vergnas polynomial for embedded graphs. European Journal of Combinatorics, 50, 97-114. https://doi.org/10.1016/j.ejc.2015.03.009
- Ellis-Monaghan, J. A., McDowell, A., Moffatt, I., & Pangborn, G. (2015). DNA origami and the complexity of Eulerian circuits with turning costs. Natural Computing, 14(3), 491-503. https://doi.org/10.1007/s11047-014-9457-2
- Ellis-Monaghan, J., & Moffatt, I. (2015). Evaluations of topological Tutte polynomials. Combinatorics Probability and Computing, 24(3), 556-583. https://doi.org/10.1017/S0963548314000571
2014
- Ellis-Monaghan, J. A., & Moffatt, I. (2014). A note on recognizing an old friend in a new place: List coloring and the zero-temperature potts model. Annales de l'Institut Henri Poincare (D) Combinatorics, Physics and their Interactions, 1(4), 429-442. https://doi.org/10.4171/AIHPD/12
- Ellis-Monaghan, J., Pangborn, G., Beaudin, L., Miller, D., Bruno, N., & Hashimoto, A. (2014). Minimal tile and bond-edge types for self-assembling DNA graphs. In N. Jonoska, & M. Saito (Eds.), Discrete and Topological Models in Molecular Biology (pp. 241-270). (Natural Computing Series; Vol. 48). Springer. https://doi.org/10.1007/978-3-642-40193-0_11
2013
- Ellis-Monaghan, J. A., & Moffatt, I. (2013). A Penrose polynomial for embedded graphs. European Journal of Combinatorics, 34(2), 424-445. https://doi.org/10.1016/j.ejc.2012.06.009
- Ellis-Monaghan, J., & Pangborn, G. (2013). An example of practical organization for undergraduate research experiences. PRIMUS, 23(9), 805-814. https://doi.org/10.1080/10511970.2012.758680
2012
- Ellis-Monaghan, J. A., & Moffatt, I. (2012). Twisted duality for embedded graphs. Transactions of the American Mathematical Society, 364(3), 1529-1569. https://doi.org/10.1090/S0002-9947-2011-05529-7
2011
- Ellis-Monaghan, J. A., & Merino, C. (2011). Graph polynomials and their applications I: The Tutte polynomial. In M. Dehmer (Ed.), Structural Analysis of Complex Networks (pp. 219-255). Birkhäuser. https://doi.org/10.1007/978-0-8176-4789-6_9
- Ellis-Monaghan, J. A., & Merino, C. (2011). Graph polynomials and their applications II: Interrelations and interpretations. In M. Dehmer (Ed.), Structural Analysis of Complex Networks (pp. 257-292). Birkhäuser. https://doi.org/10.1007/978-0-8176-4789-6_10
- Ellis-Monaghan, J. A., & Moffatt, I. (2011). The Tutte-Potts connection in the presence of an external magnetic field. Advances in Applied Mathematics, 47(4), 772-782. https://doi.org/10.1016/j.aam.2011.02.004
- Ellis-Monaghan, J. A., & Sarmiento, I. (2011). A recipe theorem for the topological Tutte polynomial of Bollobás and Riordan. European Journal of Combinatorics, 32(6), 782-794. https://doi.org/10.1016/j.ejc.2011.01.019
- Ellis-Monaghan, J., & Boelkins, M. (2011). Twenty years of PRIMUS: A tribute to Brian J. Winkel. PRIMUS, 21(2), 99-100. https://doi.org/10.1080/10511970.2011.537502
- Ellis-Monaghan, J., & Pangborn, G. (2011). Using DNA self-assembly design strategies to motivate graph theory concepts. Mathematical Modelling of Natural Phenomena, 6(6), 96-107. https://doi.org/10.1051/mmnp/20116606
2010
- Beaudin, L., Ellis-Monaghan, J., Pangborn, G., & Shrock, R. (2010). A little statistical mechanics for the graph theorist. Discrete mathematics, 310(13-14), 2037-2053. https://doi.org/10.1016/j.disc.2010.03.011
- Ellis-Monaghan, J. A. (2010). Considering the chalkless classroom. PRIMUS, 20(4), 332-343. https://doi.org/10.1080/10511970802342191
- Ellis-Monaghan, J. A., & Boelkins, M. (2010). PRIMUS: Sharing ideas in changing times. PRIMUS, 21(1), 1-3. https://doi.org/10.1080/10511970.2010.515546
2008
- Cox, M. A., Hughes, T. S., Ellis-Monaghan, J. A., & Mondanaro, K. R. (2008). Hydrocarbon links in an octet truss. Journal of Mathematical Chemistry, 43(2), 874-891. https://doi.org/10.1007/s10910-007-9323-x
- Dean, A. M., Ellis-Monaghan, J. A., Hamilton, S., & Pangborn, G. (2008). Unit rectangle visibility graphs. Electronic Journal of Combinatorics, 15(1), Article R79. https://doi.org/10.37236/803
2007
- Archdeacon, D., Bonnington, C. P., & Ellis-Monaghan, J. A. (2007). How to exhibit toroidal maps in space. Discrete and Computational Geometry, 38(3), 573-594. https://doi.org/10.1007/s00454-007-1354-3
- Ellis-Monaghan, J. A., & Sarmiento, I. (2007). Distance hereditary graphs and the interlace polynomial. Combinatorics Probability and Computing, 16(6), 947-973. https://doi.org/10.1017/S0963548307008723
2006
- Ashline, G., & Ellis-Monaghan, J. (2006). How high? How fast? How long? Modeling water rocket flight with calculus. PRIMUS, 16(2), 121-137. https://doi.org/10.1080/10511970608984140
- Ellis-Monaghan, J. A., & Traldi, L. (2006). Parametrized Tutte polynomials of graphs and matroids. Combinatorics Probability and Computing, 15(6), 835-854. https://doi.org/10.1017/S0963548306007656
- Ellis-Monaghan, J. A., Pike, D. A., & Zor, Y. (2006). Decycling of Fibonacci cubes. Australasian Journal of Combinatorics, 35, 31-40.
2004
- Archdeacon, D., Ellis-Monaghan, J., Fisher, D., Froncek, D., Lam, P. C. B., Seager, S., Wei, B., & Yuster, R. (2004). Some remarks on domination. Journal of Graph Theory, 46(3), 207-210. https://doi.org/10.1002/jgt.20000
- Ashline, G., & Ellis-Monaghan, J. (2004). The lottery: A dream come true or a tax on people who are bad at math? PRIMUS, 14(4), 303-314. https://doi.org/10.1080/10511970408984095
- Ellis-Monaghan, J. A. (2004). Exploring the Tutte-Martin connection. Discrete mathematics, 281(1-3), 173-187. https://doi.org/10.1016/j.disc.2003.10.018
- Ellis-Monaghan, J. A. (2004). Identities for circuit partition polynomials, with applications to the Tutte polynomial. Advances in Applied Mathematics, 32(1-2), 188-197. https://doi.org/10.1016/S0196-8858(03)00079-4
2001
- Ashline, G., & Ellis-Monaghan, J. (2001). Home sweet home: A financial incentive for the lower level mathematics course. PRIMUS, 11(1), 16-26. https://doi.org/10.1080/10511970108965976
1999
- Ashline, G., & Ellis-Monaghan, J. (1999). Interdisciplinary population projects in a first semester calculus course. PRIMUS, 9(1), 39-55. https://doi.org/10.1080/10511979908965915
1998
- Ellis-Monaghan, J. A. (1998). New Results for the Martin Polynomial. Journal of Combinatorial Theory. Series B, 74(2), 326-352. https://doi.org/10.1006/jctb.1998.1853
2022
- Ellis-Monaghan, J. A., & Moffatt, I. (2022). Preface. In J. A. Ellis-Monaghan, & I. Moffatt (Eds.), Handbook of the Tutte Polynomial and Related Topics (pp. xv). CRC Press. https://doi.org/10.1201/9780429161612 [details]
Prize / grant
- Ellis-Monaghan, J., Bolhuis, P. & Candian, A. (2024). MMD hub grant: MMD Theoretical and Technical Supports Workshops. https://hims.uva.nl/shared/faculteiten/en/faculteit-der-natuurwetenschappen-wiskunde-en-informatica/news/2024/07/nine-research-projects-chos…
- Groot, A., Ellis-Monaghan, J., Forré, P. & Samanipour, S. (2024). MMD hub grant: Predicting and designing olfactory molecules. https://hims.uva.nl/shared/faculteiten/en/faculteit-der-natuurwetenschappen-wiskunde-en-informatica/news/2024/07/nine-research-projects-chos…
Journal editor
- Ellis-Monaghan, J. (editor) (2021-2025). Annales de l'Institut Henri Poincaré D (Journal).
Others
- Ellis-Monaghan, J. (organiser) (20-6-2021 - 26-6-2021). European Congress of Mathematics (organising a conference, workshop, ...). https://www.8ecm.si/
- Ellis-Monaghan, J. (organiser) (2020 - 2025). Dutch Combinatorics Network (organising a conference, workshop, ...).
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Ancillary activities
- No ancillary activities
Ellis-Monaghan, J., & Jonoska, N. (2023). From Molecules to Mathematics. In N. Jonoska, & E. Winfree (Eds.), Visions of DNA Nanotechnology at 40 for the Next 40: A Tribute to Nadrian C. Seeman (pp. 189-206). (Natural Computing Series). Springer.