Selected Publications and Book Chapters
Sorted by Year, Reverse Chronological Order
2024
Alicea, B., Chakrabarty, R., Dvoretskii, S., Gopiiswaminathan, A.V., Lim, A., and Parent, J.
Continual Developmental Neurosimulation Using Embodied Computational Agents. IOP Conference Series: Materials Science and Engineering, 1321, 012013.
Alicea, B.
Allostasis Machines as Continuous Cognitive Modeling. Studies in Computational Intelligence, 477, 9-18.
Alicea, B.
Book Review: New Directions (and Insights) in Braitenberg Vehicles and Cognitive Science. Artificial Life, 30, 4.
Alicea, B., Bastani, S., Gordon, N.K., Crawford-Young, S., and Gordon, R.
The Molecular Basis of Differentiation Wave Activity in Embryogenesis. BioSystems, 105272.
Alicea, B.
Super-performance: sampling, planning, and ecological information. Studies in Computational Intelligence, 1130, 31-45.
Alicea, B., Chakrabarty, R., Dvoretskii, S., Gopiiswaminathan, A.V., Lim, A., and Parent, J.
Continual Developmental Neurosimulation Using Embodied Computational Agents. IOP Conference Series: Materials Science and Engineering, 1321, 012013.
Alicea, B.
Allostasis Machines as Continuous Cognitive Modeling. Studies in Computational Intelligence, 477, 9-18.
Alicea, B.
Book Review: New Directions (and Insights) in Braitenberg Vehicles and Cognitive Science. Artificial Life, 30, 4.
Alicea, B., Bastani, S., Gordon, N.K., Crawford-Young, S., and Gordon, R.
The Molecular Basis of Differentiation Wave Activity in Embryogenesis. BioSystems, 105272.
Alicea, B.
Super-performance: sampling, planning, and ecological information. Studies in Computational Intelligence, 1130, 31-45.
2023
Alicea, B., Pang, A., and Parent, J.
Intelligence Offloading and the Neurosimulation of Developmental Agents. International Workshop on Embodied Intelligence, IOP Conference Series: Materials Science and Engineering, 1292, 012019.
Alicea, B., Gordon, R., and Parent, J.
Embodied cognitive morphogenesis as a route to intelligent systems. Royal Society Interface Focus, 13(3), 20220067.
Alicea, B., Gordon, R., and Parent, J.
The Psychophysical World of the Motile Diatom Bacillaria Paradoxa. Mathematics and Biology of Diatoms, 9, 229-263.
Grover, A., Yadav, V., and Alicea, B.
Flipping the Switch on Local Exploration: Genetic Algorithms with Reversals. Lecture Notes in Networks and Systems, 608, 719–734.
Alicea, B., Pang, A., and Parent, J.
Intelligence Offloading and the Neurosimulation of Developmental Agents. International Workshop on Embodied Intelligence, IOP Conference Series: Materials Science and Engineering, 1292, 012019.
Alicea, B., Gordon, R., and Parent, J.
Embodied cognitive morphogenesis as a route to intelligent systems. Royal Society Interface Focus, 13(3), 20220067.
Alicea, B., Gordon, R., and Parent, J.
The Psychophysical World of the Motile Diatom Bacillaria Paradoxa. Mathematics and Biology of Diatoms, 9, 229-263.
Grover, A., Yadav, V., and Alicea, B.
Flipping the Switch on Local Exploration: Genetic Algorithms with Reversals. Lecture Notes in Networks and Systems, 608, 719–734.
2022
’t Hart, B.M. et.al (156 co-authors)
Neuromatch Academy: a 3-week, online summer school in computational neuroscience. Journal of Open Source Education, 4(44), 118.
Alicea, B. and Parent, J.
Layers, Folds, and Semi-Neuronal Information Processing. Procedia Computer Science, 213, 443-452.
Alicea, B. and Parent, J.
Meta-brain Models: biologically-inspired cognitive agents. International Workshop on Embodied Intelligence, IOP Conference Series: Materials Science and Engineering, 1261, 012019.
Dvoretskii, S., Gong, Z., Gupta, A., Parent, J., and Alicea, B.
Braitenberg Vehicles as Developmental Neurosimulation. Artificial Life, 28(3), 369-395.
Alicea, B., Cialfi, D., Lim, A., and Parent, J.
Gibsonian Information: a new approach to quantitative information. Studies in Computational Intelligence, 1032.
Alicea, B., Gordon, R. and Portegys, T.
Data-theoretical Synthesis of the Early Developmental Process. Neuroinformatics, 20, 7-23.
’t Hart, B.M. et.al (156 co-authors)
Neuromatch Academy: a 3-week, online summer school in computational neuroscience. Journal of Open Source Education, 4(44), 118.
Alicea, B. and Parent, J.
Layers, Folds, and Semi-Neuronal Information Processing. Procedia Computer Science, 213, 443-452.
Alicea, B. and Parent, J.
Meta-brain Models: biologically-inspired cognitive agents. International Workshop on Embodied Intelligence, IOP Conference Series: Materials Science and Engineering, 1261, 012019.
Dvoretskii, S., Gong, Z., Gupta, A., Parent, J., and Alicea, B.
Braitenberg Vehicles as Developmental Neurosimulation. Artificial Life, 28(3), 369-395.
Alicea, B., Cialfi, D., Lim, A., and Parent, J.
Gibsonian Information: a new approach to quantitative information. Studies in Computational Intelligence, 1032.
Alicea, B., Gordon, R. and Portegys, T.
Data-theoretical Synthesis of the Early Developmental Process. Neuroinformatics, 20, 7-23.
2021
Alicea, B. and Yuan, C.
Complex Temporal Biology: towards a unified multi-scale approach to predict the flow of information. Integrative and Comparative Biology, 61(6), 2075-2081.
Kulkarni, H. and Alicea, B.
Sentiment Progression based Searching and Indexing of Literary Textual Artefacts. Lecture Notes in Computer Science, 18201, 264-271.
Jambor, H., Antonietti, A., Alicea, B., Audisio, T.L., Auer, S., Bhardwaj, V., Burgess, S.J., Ferling, I., Gazda, M.A., Hoeppner, L.H., Ilangovan, V., Lo, H., Olson, M., Mohamed, S.Y., Sarabipour, S., Varma, A., Walavalkar, K., Wissink, E.M., and Weissgerber, T.L.
Creating clear and informative image-based figures for scientific publications. PLoS Biology, 19(3), e3001161.
Alicea, B., Cialfi, D., Lim, A., and Parent, J.
Allostasis Machines: a model for understanding internal states and technological environments. Emergent Interaction Workshop, ACM SIGCHI.
Alicea, B., Parent, J., and Singh, U.
Periodicity in the Embryo: emergence of order in space, diffusion of order in time. Biosystems, 204, 104405.
Alicea, B. and Yuan, C.
Complex Temporal Biology: towards a unified multi-scale approach to predict the flow of information. Integrative and Comparative Biology, 61(6), 2075-2081.
Kulkarni, H. and Alicea, B.
Sentiment Progression based Searching and Indexing of Literary Textual Artefacts. Lecture Notes in Computer Science, 18201, 264-271.
Jambor, H., Antonietti, A., Alicea, B., Audisio, T.L., Auer, S., Bhardwaj, V., Burgess, S.J., Ferling, I., Gazda, M.A., Hoeppner, L.H., Ilangovan, V., Lo, H., Olson, M., Mohamed, S.Y., Sarabipour, S., Varma, A., Walavalkar, K., Wissink, E.M., and Weissgerber, T.L.
Creating clear and informative image-based figures for scientific publications. PLoS Biology, 19(3), e3001161.
Alicea, B., Cialfi, D., Lim, A., and Parent, J.
Allostasis Machines: a model for understanding internal states and technological environments. Emergent Interaction Workshop, ACM SIGCHI.
Alicea, B., Parent, J., and Singh, U.
Periodicity in the Embryo: emergence of order in space, diffusion of order in time. Biosystems, 204, 104405.
2020
Alicea, B.
Raising the Connectome: the emergence of neuronal activity and behavior in C. elegans. Frontiers in Cellular Neuroscience, 14, 524791.
Alicea, B.
Virtual Reality for Communication Neuroscience. Handbook of Communication Neuroscience (Chapter 32), K. Floyd and R. Weber eds., Routledge Press.
Alicea, B.
Raising the Connectome: the emergence of neuronal activity and behavior in C. elegans. Frontiers in Cellular Neuroscience, 14, 524791.
Alicea, B.
Virtual Reality for Communication Neuroscience. Handbook of Communication Neuroscience (Chapter 32), K. Floyd and R. Weber eds., Routledge Press.
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. Diatom Gliding Motility (Chapter 10), S.A. Cohn, K.M. Manoylov, and R. Gordon eds., Scrivener Publishing.
Alicea, B., Bohil, C., Biocca, F., and Owen, C.
Targeting in Virtual Workspaces: motor learning consolidates spatial memory for performance clusters. Psyarxiv, doi:10.31234/osf.io/7z9q6.
Kulkarni, H. and Alicea, B.
Cultural association based on machine learning for team formation. arXiv, 1908.00234.
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. Diatom Gliding Motility (Chapter 10), S.A. Cohn, K.M. Manoylov, and R. Gordon eds., Scrivener Publishing.
Alicea, B., Bohil, C., Biocca, F., and Owen, C.
Targeting in Virtual Workspaces: motor learning consolidates spatial memory for performance clusters. Psyarxiv, doi:10.31234/osf.io/7z9q6.
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.
Alicea, B.
An integrative introduction to human augmentation science. arXiv, 1804.10521.
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.
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, 12, 182.
Alicea, B. and Gordon R.
Cell Differentiation Processes as Spatial Networks: identifying four-dimensional structure in embryogenesis. BioSystems, 173, 235-246.
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.
Alicea, B.
An integrative introduction to human augmentation science. arXiv, 1804.10521.
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.
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, 12, 182.
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.
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.
The Long Road to Theoretical Synthesis: Review of “Embryogenesis Explained”. International Journal of Developmental Biology, 61, 113-114.
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.
2016
Alicea, B.
Evolution in Eggs and Phases: experimental selection on fecundity and reproductive timing in Caenorhabditis elegans. Royal Society Open Science, 3, 160496.
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.
Alicea, B.
Evolution in Eggs and Phases: experimental selection on fecundity and reproductive timing in Caenorhabditis elegans. Royal Society Open Science, 3, 160496.
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.
2015
Alicea, B.
Animal-oriented Virtual Environments: illusion, dilation, and discovery. F1000 Research, 3:202.
Alicea, B.
Animal-oriented Virtual Environments: illusion, dilation, and discovery. F1000 Research, 3:202.
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.
Alicea, B.
Modeling Cellular Information Processing Using a Dynamical Approximation of Cellular mRNA. bioRxiv, doi:10.1101/006775.
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.
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.
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
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.
Lagrangian Coherent Structures (LCS) may describe evolvable frontiers in natural populations. arXiv, 1101.6071.
Alicea, B.
Naturally Supervised Learning in Motion and Touch-driven Technologies. arXiv, 1106:1105.
Alicea, B.
The ‘Machinery’ of Biocomplexity: understanding non-optimal architectures in biological systems. arXiv, 1104.3559.
Bohil, C., Alicea, B., and Biocca, F.
Virtual Reality in Neuroscience Research and Therapy. Nature Reviews Neuroscience, 12, 752-762
Alicea, B.
Lagrangian Coherent Structures (LCS) may describe evolvable frontiers in natural populations. arXiv, 1101.6071.
Alicea, B.
Naturally Supervised Learning in Motion and Touch-driven Technologies. arXiv, 1106:1105.
Alicea, B.
The ‘Machinery’ of Biocomplexity: understanding non-optimal architectures in biological systems. arXiv, 1104.3559.
2009
Alicea, B.
Range-based techniques for discovering optimality and analyzing scaling relationships in neuromechanical systems. Nature Precedings, npre.2009. 2845.1.
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.
Stochastic Resonance (SR) can drive adaptive physiological processes. Nature Precedings, npre.2009.3301.1.
Alicea, B.
Range-based techniques for discovering optimality and analyzing scaling relationships in neuromechanical systems. Nature Precedings, npre.2009. 2845.1.
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.
Stochastic Resonance (SR) can drive adaptive physiological processes. Nature Precedings, npre.2009.3301.1.
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]
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.
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.
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.