Selected Publications and Book Chapters


Sorted by year

2020:

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).

2019:

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.

2018:

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.

2017:

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

2016:
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?

2015:
Alicea, B. Animal-oriented Virtual Environments: illusion, dilation, and discovery. F1000 Research, 3:202. doi:10.12688/f1000research.3557.1

2014:
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

2013:
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.

2012:
Alicea, B. Contextual Geometric Structures: modeling the fundamental components of cultural behavior. Proceedings of Artificial Life, 13, 147-154

2011:
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]

2009:
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.

2008:
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]

2007:
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.

2006:
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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