Selected Publications and Book Chapters

Sorted by year


Dvoretskii, S., Gong, Z., Gupta, A., Parent, J., and Alicea, B. Braitenberg Vehicles as Developmental Neurosimulation. arXiv, 2003.07689. doi:10.13140/RG.2.2.31149.23526.

Alicea, B. Virtual Reality for Communication Neuroscience..Handbook of Communication Neuroscience (Chapter 32), K. Floyd and R. Weber eds. Routledge Press (2020).


Alicea, B., Gordon, R., Harbich, T., Singh, U., Singh, A., and Varma, V. Towards a Digital Diatom: image processing and deep learning analysis of Bacillaria paradoxa dynamic morphology.bioRxiv, doi:10.1101/2019.12.21.885897.

Alicea, B., Gordon, R. and Portegys, T. Data-theoretical Synthesis of the Early Developmental Process. bioRxiv, doi:10.1101/282004.

Kulkarni, H. and Alicea, B. Cultural association based on machine learning for team formation. arXiv, 1908.00234.


Igamberdiev, A.U., Gordon, R., Alicea, B., and Cherdantsev, V.G. Editorial. Special Issue: Computational, Theoretical, and Experimental Approaches to Morphogenesis. BioSystems, 173, 1-3.

Alicea, B., Portegys, T.E., Gordon, D., and Gordon, R. Morphogenetic processes as data: Quantitative structure in the Drosophila eye imaginal disc. BioSystems, 173, 256-265.

DevoWorm Group and Alicea, B. The Emergent Connectome in Caenorhabditis elegans Embryogenesis. BioSystems, 173, 247-255.

Sarma, G.P., Lee, C-W., Portegys, T., Ghayoomie, V., Jacobs, T., Alicea, B., Cantarelli, M., Currie, M., Gerkin, R.C., Gingell, S., Gleeson, P., Gordon, R., Hasani, R.M., Idili, G., Khayrulin, S., Lung, D., Palyanov, A., Watts, M., Larson, S.D. OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans. Philosophical Transactions of the Royal Society B, 373, 20170382. doi:10.1098/rstb.2017.0382.

Stone, R., Portegys, T., Mikhailovsky, G., and Alicea, B. Origins of the Embryo: self-organization through cybernetic regulation. BioSystems, 173, 73-82.

Weber, R., Alicea, B., Huskey, R., and Mathiak, K. Network Dynamics of Attention During a Naturalistic Behavioral Paradigm. Frontiers in Human Neuroscience, doi:10.3389/fnhum.2018.00182.

Alicea, B. and Gordon R. Cell Differentiation Processes as Spatial Networks: identifying four-dimensional structure in embryogenesis. BioSystems, 173, 235-246.


Alicea, B. The Long Road to Theoretical Synthesis: Review of “Embryogenesis Explained”. International Journal of Developmental Biology, 61, 113-114

Alicea, B. Evolution in Eggs and Phases: experimental selection on fecundity and reproductive timing in Caenorhabditis elegans. Royal Society Open Science, 3, 160496. doi:10.1098/rsos.160496

Portegys, T., Pascualy, G., Gordon, R., McGrew, S., and Alicea, B. Morphozoic: cellular automata with nested neighborhoods as a novel representation for morphogenesis. In "Multi-Agent Based Simulations Applied to Biological and Environmental Systems" Chapter 3. D.F. Adamatti ed. IGI Global, Hershey, PA.

Alicea, B. and Gordon, R. Quantifying Mosaic Development: Towards an Evo-Devo Postmodern Synthesis of the Evolution of Development Via Differentiation Trees of Embryos. Biology, 5(3), 33. SI: Beyond the Modern Evolutionary Synthesis - what have we missed?

Alicea, B. Animal-oriented Virtual Environments: illusion, dilation, and discovery. F1000 Research, 3:202. doi:10.12688/f1000research.3557.1

Alicea, B., McGrew, S., Gordon, R., Larson, S., Warrington, T., and Watts, M. DevoWorm: differentiation waves and computation in C. elegans embryogenesis. bioRxiv, doi:10.1101/009993

Alicea, B. and Gordon, R. Toy Models for Macroevolutionary Patterns and Trends. Biosystems, 122, 25-37 (2014). SI: Patterns of Evolution.

Alicea, B. Modeling Cellular Information Processing Using a Dynamical Approximation of Cellular mRNA. bioRxiv, doi:10.1101/006775

Alicea, B., Murthy, S., Keaton, S.A., Cobbett, P., Cibelli, J.B., and Suhr, S.T. Defining phenotypic respecification diversity using multiple cell lines and reprogramming regimens. Stem Cells and Development, 22(19), 2641-2654

Alicea, B. and Cibelli, J.B. Comparing indirect-derived ES cells and directly-derived iPS cells. In “Principles of Cloning”. Elsevier, Amsterdam.

Alicea, B. Contextual Geometric Structures: modeling the fundamental components of cultural behavior. Proceedings of Artificial Life, 13, 147-154

Bohil, C., Alicea, B., and Biocca, F. Virtual Reality in Neuroscience Research and Therapy. Nature Reviews Neuroscience, 12, 752-762

Alicea, B. The ‘Machinery’ of Biocomplexity: understanding non-optimal architectures in biological systems. arXiv, 1104.3559 [nlin.AO, q-bio.QM, q-bio.PE]

Bohil, C., Owen, C.B., Jeong, E.J., Alicea, B., and Biocca, F. Virtual Reality and Presence. In "21rst Century Communication: a reference book". Sage Publications, Washington, D.C.

Alicea, B. Performance Augmentation in Hybrid Systems: techniques and experiment. arXiv, 0810.4629 [q-bio.NC, q-bio.QM]

Carvallo-Pinto, M.A., Alicea, B., and Rodrigues, J.L.M. Towards a “core” genome: pairwise similarity searches on interspecific genomic data. arXiv, 0807.3353 [q-bio.GN, q-bio.PE]

Alicea, B. Towards a theory of human intraspecific variation for ergonomics and human modeling. Society for Automotive Engineering (SAE) Digital Human Modeling, #2007-01-2461.

Alicea, B. Broad-Spectrum Mitigation and the Cognitive Neurobiological Interface: considering biological rhythms in Augmented Cognition. Proceedings of the Human Factors and Ergonomics Society, 50(16), 1629-1633

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