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Publications

Computational

Kriegman, S., Walker, S., Shah, D. S., Kramer-Bottiglio, R., and Bongard, J., (2019), Automated Shapeshifting for Function Recovery in Damaged Robots, Proceedings of Robotics: Science and Systems XV: 28
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Cervera, C., Pai, V. P., Levin, M., and Mafe, S., (2019), From non-excitable single-cell to multicellular bioelectrical states supported by ion channels and gap junction proteins: electrical potentials as distributed controllers, Progress in Biophysics and Molecular Biology, in press

Kuchling, F., Friston, K., Georgiev, G., and Levin, M., (2019), Morphogenesis as Bayesian Inference: a Variational Approach to Pattern Formation and Control in Complex Biological Systems, Physics of Life Reviews, in press
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Cervera, J., Manzanares, J. A., Mafe, S., and Levin, M., (2019), Synchronization of Bioelectric Oscillations in Networks of Nonexcitable Cells: From Single-Cell to Multicellular States, Journal of Physical Chemistry B, 123: 3924-3934
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Manicka, S., and Levin, M., (2019), The Cognitive Lens: a primer on conceptual tools for analysing information processing in developmental and regenerative morphogenesis, Philosophical Transactions of the Royal Society B, 374: 20180369
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Pietak, A., Bischof, J., LaPalme, J., Morokuma, J., and Levin, M., (2019), Neural control of body-plan axis in regenerating planaria, PLOS Computational Biology, doi: 10.1371/journal.pcbi.1006904
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Hammelman, J., Siegelmann, H., Manicka, S., and Levin, M., (2019), Toward modeling regeneration via adaptable echo state networks, in A. Adamatzky, S. Akl, and G. Sirakoulis (Eds.), From parallel to emergent computing, Chapter 6, pages 117-133, CRC Press: Boca Raton, FL

Churchill, C. D. M., Winter, P., Tuszynski, J. A., and Levin, M., (2019), EDEn – Electroceutical Design Environment: An Ion Channel Database with Small Molecule Modulators, iScience, 11: 42-56
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Minh-Thai, T. N., Aryal, J., Samarasinghe, S., and Levin, M., (2018), A Computational Framework for Autonomous Self-repair Systems, in Mitrovic, T., Xue, B., and Li, X. (Eds.), AI 2018: Advances in Artificial Intelligence, p153-159. Lecture Notes in Computer Science, vol 11320. Springer, Cham
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Moore, D. G., Walker, S. I., and Levin, M., (2018), Pattern Regeneration in Coupled Networks, in T. Ikegami, N. Virgo, O. Witkowski, M. Oka, R. Suzuki and H. Iizuka (Eds.), ALIFE 2018: The 2018 Conference on Artificial Life. MIT Press: Tokyo, p. 204-205.
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Ferreira, G. B. S., Scheutz, M., and Levin, M., (2018), Modeling Cell Migration in a Simulated Bioelectrical Signaling Network for Anatomical Regeneration, in T. Ikegami, N. Virgo, O. Witkowski, M. Oka, R. Suzuki and H. Iizuka (Eds.), ALIFE 2018: The 2018 Conference on Artificial Life. MIT Press: Tokyo, p. 194-201.
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Brodsky, M., and Levin, M., (2018), From Physics to Pattern: Uncovering Pattern Formation in Tissue Electrophysiology, in T. Ikegami, N. Virgo, O. Witkowski, M. Oka, R. Suzuki and H. Iizuka (Eds.), ALIFE 2018: The 2018 Conference on Artificial Life. MIT Press: Tokyo, p. 351-358.
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Cervera, J., Pietak, A., Levin, M., and Mafe, S., (2018), Bioelectrical coupling in multicellular domains regulated by gap junctions: a conceptual approach, Bioelectrochemistry, 123: 45-61
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Pietak, A., and Levin, M., (2018), Bioelectrical control of positional information in development and regeneration: a review of conceptual and computational advances, Progress in Biophysics and Molecular Biology, 137: 52-68
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Moore, D. G., Valentini, G., Walker, S. I., and Levin, M., (2018), Inform: Efficient Information-Theoretic Analysis of Collective Behaviors, Frontiers in Robotics and AI, 5(60): 1-14
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Pezzulo, G., and Levin, M., (2018), Embodying Markov blankets. Comment on 'Answering Schrödinger's question: A free-energy formulation' by Maxwell James Désormeau Ramstead et al., Physics of Life Reviews, 24: 32-36
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Fields, C., and Levin, M., (2018), Are planaria individuals? What regenerative biology is telling us about the nature of multicellularity, Evolutionary Biology, 45(3): 237–247
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Pai, V. P., Pietak, A., Willocq, V., Ye, B., Shi, N-Q., and Levin, M., (2018), HCN2 Rescues brain defects by enforcing endogenous voltage pre-patterns, Nature Communications, 9(998): doi:10.1038/s41467-018-03334-5
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Ferreira, G. B. S., Scheutz, M., and Levin, M., (2018), Introducing Simulated Stem Cells into a Bio-Inspired Cell-Cell Communication Mechanism for Structure Regeneration, Proceedings of the 2017 IEEE Symposium Series on Computational Intelligence (SSCI), p. 2778-2785
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Pietak, A. M., and Levin, M., (2017), Bioelectric Gene and Reaction Networks: Computational Modeling of Genetic, Biochemical, and Bioelectrical Dynamics in Pattern Regulation, J. Royal Society Interface, 14(134): 20170425
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Moore, D., Walker, S., and Levin, M., (2017), Cancer as a Disorder of Patterning Information: computational and biophysical perspectives on the cancer problem, Convergent Science Physical Oncology, in press

Ferreira, G. B., Scheutz, M., and Levin, M., (2017), Investigating the Effects of Noise on a Cell-to-Cell Communication Mechanism for Structure Regeneration, in C. Knibbe, D. Parsons, D. Misevic, J. Rouzaud-Cornaba, N. Bredèche, S. Hassas, O. Simonin, and H. Soula. (Eds.), Proceedings of the 14th European Conference on Artificial Life (ECAL 2017), Lyon, France
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Lobo, D., Lobikin, M., and Levin, M., (2017), Discovering novel phenotypes with automatically inferred dynamic models: partial melanocyte conversion in Xenopus, Scientific Reports, 7: 41339
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Garcia-Quismondo, M., Levin, M., and Lobo, D., (2017), Modeling regenerative processes with Membrane Computing, Information Sciences, 381: 229-249
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Pezzulo, G., and Levin, M., (2016), Top-down Models in biology: Explanation and control of complex living systems above the molecular level, Journal of the Royal Society Interface, 13: 20160555
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Ferreira, G., Smiley, M., Scheutz, M., and Levin, M., (2016), Dynamic structure discovery and repair for 3D cell assemblages, Proceedings of the Fifteenth International Conference on the Synthesis and Simulation of Living Systems (ALIFEXV), p. 352-359
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Serlin, Z., Rife, J., and Levin, M., (2016), A Level Set Approach to Simulating Xenopus laevis Tail Regeneration, Proceedings of the Artificial Life Conference 2016, p. 528-535
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Pietak, A., and Levin, M., (2016), Exploring Instructive Physiological Signaling with the Bioelectric Tissue Simulation Engine (BETSE), Frontiers in Bioengineering and Biotechnology, 4(55): doi 10.3389/fbioe.2016.00055
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Lobo, D., Morokuma, J., and Levin, M., (2016), Computational discovery and in vivo validation of hnf4 as a regulatory gene in planarian re-generation, Bioinformatics, 32(17): 2681-2685
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De, Abhishek, Chakravarthy, V. Srinivasa , and Levin, M., (2016), A Computational Model of Planarian Regeneration, International Journal of Parallel, Emergent, and Distributed Systems, 32(4): 331-347
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Lobo, D., Hammelman, J., and Levin, M., (2016), MoCha: molecular characterization of unknown pathways, Journal of Computational Biology, 23(4): 291-297
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Whiting, J. G. H., Jones, J., Bull, L., Levin, M., and Adamatzky, A., (2016), Towards a physarum learning chip, Scientific Reports, 6:19948 (1-14)

Hammelman, J., Lobo, D., and Levin, M., (2016), Artificial neural networks as models of robustness in development and regeneration: stability of memory during morphological remodeling, in Artificial Neural Network (ANN) Modeling, S. Shanmuganathan and S. Samarasinghe (Eds.) , p. 45-65
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Pang, J., Ozkucur, N., Ren, M., Kaplan, D. L., Levin, M., and Miller, E. L., (2015), Automatic neuron segmentation and neural network analysis method for phase contrast microscopy images, Biomedical Optics Express, 6(11) 4395-4416
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Lobo, D., and Levin, M., (2016), Computing a worm: reverse-engineering planarian regeneration, Advances in Unconventional Computing, Andrew Adamatzky ed., Vol. 2, Springer, p. 637-654

Lobikin, M., Lobo, D., Blackiston, D. J., Martyniuk, C. J., Tkachenko, E., and Levin, M., (2015), Serotonergic regulation of melanocyte conversion: A bioelectrically regulated network for stochastic all-or-none hyperpigmentation, Science Signaling, 8(397): ra99
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Law, R., and Levin, M., (2015), Bioelectric memory: modeling resting potential bistability in amphibian embryos and mammalian cells, Theoretical Biology and Medical Modelling, 12: (1): 22
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Bessonov, N., Levin, M., Morozova, N., Reinberg, N., Tosenberger, A., Volpert, V., (2015), Target morphology and cell memory: a model of regenerative pattern formation, Neural Regeneration Research, 10(12): 1901-1905
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Lobo, D., and Levin, M., (2015), Inferring regulatory networks from experimental morphological phenotypes: a computational method reverse-engineers planarian regeneration, PLoS Computational Biology, 11(6): e1004295
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A. Tosenberger, N. Bessonov, M. Levin, N. Reinberg, V.Volpert, N. Morozova, (2015), A conceptual model of morphogenesis and regeneration, Acta Biotheoretica, 63: 283-294
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Friston, K., Levin, M., Sengupta B., and Pezzulo, G., (2015), 'Knowing one's place' a free energy approach to pattern regulation, Journal of the Royal Society Interface, 12: 20141383
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Bessonov, N., Levin, M., Morozova, N., Reinberg, N., Tosenberger, A., and Volpert, V., (2015), On a model of pattern recognition based on cell memory, PLoS One, 10(2): e0118091
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Chernet, B. T., Fields, C., and Levin, M., (2015), Long-range gap junctional signaling controls oncogene-mediated tumorigenesis in Xenopus laevis embryos, Frontiers in Physiology, 5(519); 1-15, doi: 10.3389/fphys.2014.00519
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Lobo, D., Feldman, E. B., Shah, M., Malone, T. J., and Levin, M., (2014), Limbform: a functional ontology-based database of limb regeneration experiments, Bioinformatics, 30(24): 3598-3600
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Mustard, J., and Levin, M., (2014), Bioelectrical mechanisms for programming growth and form: taming physiological networks for soft body robotics, Soft Robotics, 2(3): 1-23
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Lobo, D., Feldman, E. B., Shah, M., Malone, T., and Levin, M., (2014), A bioinformatics expert system linking functional data to anatomical outcomes in limb regeneration, Regeneration, 1(2): 37-56
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Budnikova, M., Habig, J. W., Cornia, N., Levin. M., Lobo, D., and Andersen, T., (2014), Design of a flexible component gathering algorithm for converting cell-based models to graph representations for use in evolutionary search, BMC Bioinformatics, 15: 178, doi: 10.1002/reg2.13
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Lobo, D., Solano, M., Bubenik, G. A., and Levin, M., (2014), A linear-encoding model explains the variability of the target morphology in regeneration, Journal of the Royal Society Interface, 11(92): 20130918
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Lobo, D., Malone, T. J., and Levin, M., (2013), Towards a bioinformatics of patterning: a computational approach to understanding regulative morphogenesis, Biology Open, 2(2): 156-169
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Lobo, D., Malone, T.J., and Levin, M., (2013), Planform: an application and database of graph-encoded planarian regenerative experiments, Bioinformatics, 29(8): 1098-1100
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Lobo, D., Beane, W., and Levin, M., (2012), Modeling planarian regeneration: a primer for reverse-engineering the worm, PLoS Computational Biology, 8(4): e1002481 [cover]
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Mondia, J. P., Levin, M., Omenetto, F. G., Orendorff, R. D., Branch, M. R., and Adams, D. S., (2011), Long-distance signals are required for morphogenesis of the regenerating Xenopus tadpole tail, PLoS One, 6(9): e24953
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Levin, M., (2011), The wisdom of the body: future techniques and approaches to morphogenetic fields in regenerative medicine, developmental biology, and cancer. Regenerative Medicine, 6(6): 667-673
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Zhang, Y., and M. Levin, (2009), Particle tracking model of electrophoretic morphogen movement reveals stochastic dynamics of embryonic gradient, Developmental Dynamics, 238(8): 1923-1935
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Esser, A. T., Smith, K. C., Weaver, J. C., and Levin, M., (2006), Mathematical Model of Morphogen Electrophoresis through Gap Junctions. Developmental Dynamics, 235(8): 2144-2159
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Levin, Michael, (1995), Use of Genetic Algorithms to solve biomedical Problems. M.D. Computing, 12(3): 193-198
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Levin, Michael, (1995), The evolution of understanding: A genetic algorithm model of the evolution of animal communication. BioSystems, 36: 167-178
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Levin, Michael, (1995), Locating putative protein signal sequences, in The Practical Handbook of Genetic Algorithms: New Frontiers, Vol. 2, pp. 53-66, CRC Press: FL
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Levin, Michael, A Julia set model of field-directed morphogenesis, (1994), Computer Applications in the Biosciences, 10(2): 85-103
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Levin, Michael, (1994), Discontinuous and alternate q-system fractals. Computers and Graphics, 18(6): 873-884
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