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Publications

Regeneration

McLaughlin, K. A., Levin, M., (2017), Bioelectric Signaling in Regeneration: Mechanisms of Ionic Controls of Growth and Form, Developmental Biology, in press

Bryant, D. M., Sousounis, K., Farkas, J. E., Bryant, S., Thao, N., Guzikowski, A. R., Monaghan, J. R., Levin, M., and Whited, J. L., (2017), Repeated removal of developing limb buds permanently reduces appendage size in the highly-regenerative axolotl, Developmental Biology, 424: 1-9
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Durant, F., Morokuma, J., Fields, C., Williams, K., Adams, D. S., and Levin, M., (2017), Long-Term, Stochastic Editing of Regenerative Anatomy via Targeting Endogenous Bioelectric Gradients, Biophysical Journal, 112: 2231-2243
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Garcia-Quismondo, M., Levin, M., Lobo, D. (2017), Modeling regenerative processes with Membrane Computing, Information Sciences, 381: 229-249
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Neuhof, M., Levin, M., and Rechavi, O., (2016), Vertically and horizontally-transmitted memories – the fading boundaries between regeneration and inheritance in planaria, Biology Open, 5, 1177-1188
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Ferreira, G. B. S., Smiley, M., Scheutz, M., and Levin, M., (2016), Dynamic structure discovery and repair for 3D cell assemblages, Proceedings of the Artificial Life Conference 2016, 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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Golding, A., Guay, J. A., Herrera-Rincon, C., Levin, M., and Kaplan, D. L., (2016), A Tunable Silk Hydrogel Device for Studying Limb Regeneration in Adult Xenopus laevis, PLoS One 11, e0155618
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Sullivan, K. G., Emmons-Bell, M., and Levin, M., (2016), Physiological Inputs Regulate Species-Specific Anatomy During Embryogenesis And Regeneration, Communicative and Integrative Biology, 9:4, e1192733
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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, doi: 10.1093/bioinformatics/btw299
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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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Durant, F., Lobo, D., Hammelman, J., and Levin, M., (2016), Physiological controls of large-scale patterning in planarian regeneration: a molecular and computational perspective on growth and form, Regeneration, 3(2): 78-102
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Lobo, D., and Levin, M., (2016), Computing a worm: reverse-engineering planarian regeneration, Advances in Unconventional Computing, Andrew Adamatzky ed., Springer, in press

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) Modelling, S. Shanmuganathan and S. Samarasinghe editors, in press

Emmons-Bell, M., Durant, F., Hammelman, J., Bessonov, N., Volpert, V., Morokuma, J., Pinet, K., Adams, D. S., Pietak, A., Lobo, D., and Levin, M., (2015), Gap junctional blockade stochastically induces different species-specific head anatomies in genetically wild-type Girardia dorotocephala flatworms, International Journal of Molecular Sciences, 16: 27865–27896
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Pezzulo, G., and Levin, M., (2015), Re-membering the body: applications of computational neuroscience to the top-down control of regeneration of limbs and other complex organs, Integrative Biology, 7: 1487-1517
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Pai, V. P., Martyniuk, C. J., Echeverri, K., Sundelacruz, S., Kaplan, D. L., and Levin, M., (2015), Genome-wide analysis reveals conserved transcriptional responses downstream of resting potential change in Xenopus embryos, axolotl regeneration, and human mesenchymal cell differentiation, Regeneration, 3(1): 3-25
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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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Blackiston, D. J., Shomrat, T., and Levin, M., (2015), The Stability of Memories During Brain Remodeling: a Perspective, Communicative and Integrative Biology, 8(5): e1073424
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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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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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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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Levin, M., (2014), Endogenous bioelectrical networks store non-genetic patterning information during development and regeneration, Journal of Physiology, 592(11): 2295–2305.
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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: 20130918
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Daniel Lobo; Taylor J. Malone; Michael Levin, (2013), Planform: an application and database of graph-encoded planarian regenerative experiments, Bioinformatics, 29(8): 1098-1100, doi: 10.1093/bioinformatics/btt088
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Adams, D. S., Tseng, A-S. and M. Levin, (2013), Light-activation of the Archaerhodopsin H+ pump reverses age-dependent loss of vertebrate regeneration: sparking system-level controls in vivo, Biology Open, 2(3): 306-313
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Beane, W. S., Morokuma, J., Lemire, J. M., and Levin, M., (2013), Bioelectric signaling regulates head and organ size during planarian regeneration, Development, 140:313-322
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Tseng, A-S., and M. Levin, (2012), Transducing bioelectrical signals into epigenetic pathways during tadpole tail regeneration, Anatomical Record, 295:1541-1551
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Levin, M., (2012), Morphogenetic fields in embryogenesis, regeneration, and cancer: non-local control of complex patterning, BioSystems, 109 (2012) 243­-261
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Beane, W. S., Tseng, A-S, Morokuma, J., and M. Levin, (2012), Inhibition of planar cell polarity extends neural growth during regeneration, homeostasis, and development, Stem Cells and Development, 21(12): 2085-2094
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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, doi: 10.1371/journal.pcbi.1002481
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Beane, W. S., Morokuma, J., Adams, D. S., and Levin, M., (2011), A chemical genetics approach reveals H,K-ATPase-mediated membrane voltage is required for planarian head regeneration. Cell Chemistry and Biology, 18: 77-89
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Tseng, A-S., Beane, W. S., Lemire, J. M., Masi, A., and M. Levin, (2010), Induction of vertebrate regeneration by a transient sodium current, Journal of Neuroscience, 30(39): 13192-13200
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Hechavarria, D., Dewilde, A., Braunhut, S., Levin, M., and Kaplan, D. K., (2010), BioDome regenerative sleeve for biochemical and biophysical stimulation of tissue regeneration. Medical Engineering and Physics, 32: 1065-1073
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Levin, M. (2009), Bioelectric mechanisms in regeneration: Unique aspects and future perspectives. Seminars in Cell and Developmental Biology, 20: 543-556
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Levin, M., (2009), Errors of Geometry: regeneration in a broader perspective. Seminars in Cell and Developmental Biology, 20(6): 643-645
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Levin, M., (2009), Regeneration: recent advances, major puzzles, and biomedical opportunities. Seminars in Cell and Developmental Biology, 20(5): 515-516
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Oviedo, N. J., B. J. Pearson, M. Levin, and A. S. Alvarado, (2008), Planarian PTEN homologs regulate stem cells and regeneration through TOR signaling, Disease Models and Mechanisms, 1: 131-143
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Oviedo, N., and Levin, M., (2008), The planarian regeneration model as a context for the study of drug effects and mechanisms, in Planaria: A Model for Drug Action and Abuse, Raffa RB & Rawls SM (eds), RG Landes Co.: Austin, pp. 95-104

Oviedo, N., Nicolas, C. L., Adams, D. S., and Levin, M. (2008), Planarians: a versatile and powerful model system for molecular studies of regeneration, adult stem cell regulation, aging, and behavior, in Emerging Model Organisms, Cold Spring Harbor Press
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Tseng, A-S., and Levin, M., (2008), Tail regeneration in Xenopus laevis as a model for understanding tissue repair, Journal of Dental Research, 87(9): 806-816
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Tseng, A-S., Adams, D. S., Qiu, D., Koustubhan, P., (2007), Apoptosis is required during early stages of tail regeneration in Xenopus laevis. Developmental Biology, 301: 62-69
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Adams, D. S., Masi, A., and Levin, M. (2007), H+ Pump-dependent changes in membrane voltage are an early mechanism necessary and sufficient to induce tail regeneration. Development, 134: 1323-1335
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Oviedo, N. J., Levin, M., (2007), smedxin-11 is a Planarian Stem Cell Gap Junction Gene Required for Regeneration and Homeostasis. Development, 134: 3121-3131
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Levin, M., (2007), Large-Scale Biophysics: Ion Flows and Regeneration. Trends in Cell Biology, 17(6): 262-271 PDF

Ingber, D., and Levin, M. (2007), What lies at the interface of regenerative medicine and developmental biology?. Development, 134: 2541-2547
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